Query 033737
Match_columns 112
No_of_seqs 109 out of 1089
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 05:43:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033737.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033737hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.9 5.9E-23 1.3E-27 136.9 9.4 74 38-111 2-75 (81)
2 cd01717 Sm_B The eukaryotic Sm 99.9 1.7E-21 3.7E-26 128.7 9.1 71 41-111 3-75 (79)
3 cd01728 LSm1 The eukaryotic Sm 99.9 5.2E-21 1.1E-25 125.9 9.6 68 39-111 3-70 (74)
4 cd01719 Sm_G The eukaryotic Sm 99.8 7E-21 1.5E-25 124.4 8.5 64 40-111 2-65 (72)
5 cd06168 LSm9 The eukaryotic Sm 99.8 1.5E-20 3.3E-25 123.9 9.7 69 41-111 3-71 (75)
6 cd01730 LSm3 The eukaryotic Sm 99.8 9.5E-21 2.1E-25 126.1 8.7 71 41-111 3-79 (82)
7 PRK00737 small nuclear ribonuc 99.8 1.2E-20 2.5E-25 123.0 8.5 64 40-111 6-69 (72)
8 cd01727 LSm8 The eukaryotic Sm 99.8 1.4E-20 3.1E-25 123.0 8.8 66 41-110 2-67 (74)
9 cd01732 LSm5 The eukaryotic Sm 99.8 5E-20 1.1E-24 121.7 9.2 66 41-111 6-71 (76)
10 cd01731 archaeal_Sm1 The archa 99.8 4.5E-20 9.7E-25 118.6 8.4 62 41-110 3-64 (68)
11 cd01720 Sm_D2 The eukaryotic S 99.8 4.4E-19 9.6E-24 120.0 8.5 69 43-111 7-82 (87)
12 cd01726 LSm6 The eukaryotic Sm 99.8 5.3E-19 1.1E-23 113.5 8.4 61 42-110 4-64 (67)
13 cd01722 Sm_F The eukaryotic Sm 99.8 5.6E-19 1.2E-23 113.8 7.4 63 41-111 4-66 (68)
14 KOG1781 Small Nuclear ribonucl 99.8 2E-20 4.4E-25 129.0 0.0 84 28-111 7-90 (108)
15 smart00651 Sm snRNP Sm protein 99.8 1.6E-18 3.4E-23 109.8 8.4 63 42-111 2-64 (67)
16 PF01423 LSM: LSM domain ; In 99.8 1.9E-18 4.2E-23 109.5 8.3 63 42-111 2-64 (67)
17 KOG1780 Small Nuclear ribonucl 99.8 8.7E-19 1.9E-23 115.3 5.7 63 41-111 7-69 (77)
18 cd01718 Sm_E The eukaryotic Sm 99.8 5.5E-18 1.2E-22 113.0 8.5 64 40-110 8-75 (79)
19 cd00600 Sm_like The eukaryotic 99.7 1.4E-17 3E-22 104.0 8.2 60 43-110 1-60 (63)
20 COG1958 LSM1 Small nuclear rib 99.7 2.3E-17 4.9E-22 108.7 8.8 68 39-110 8-75 (79)
21 PTZ00138 small nuclear ribonuc 99.7 2.8E-16 6.1E-21 106.9 8.5 63 42-111 18-84 (89)
22 cd01721 Sm_D3 The eukaryotic S 99.6 7.6E-16 1.7E-20 99.8 7.9 61 42-110 4-64 (70)
23 cd01723 LSm4 The eukaryotic Sm 99.6 9.2E-16 2E-20 100.8 7.8 62 42-110 5-66 (76)
24 cd01724 Sm_D1 The eukaryotic S 99.6 2.5E-15 5.5E-20 102.0 8.0 62 41-110 4-65 (90)
25 KOG3482 Small nuclear ribonucl 99.6 1.2E-15 2.6E-20 100.3 5.4 62 41-110 11-72 (79)
26 cd01733 LSm10 The eukaryotic S 99.6 5.3E-15 1.1E-19 98.1 7.9 62 41-110 12-73 (78)
27 KOG3168 U1 snRNP component [Tr 99.6 2.2E-16 4.7E-21 117.8 0.4 72 40-111 6-79 (177)
28 cd01725 LSm2 The eukaryotic Sm 99.6 1.4E-14 3.1E-19 96.4 7.8 64 41-110 4-67 (81)
29 KOG3460 Small nuclear ribonucl 99.5 1.6E-14 3.5E-19 97.2 1.9 72 39-110 5-82 (91)
30 KOG1783 Small nuclear ribonucl 99.5 1.1E-14 2.5E-19 95.6 0.6 70 33-110 1-70 (77)
31 KOG1782 Small Nuclear ribonucl 99.4 2.6E-14 5.7E-19 101.9 -0.1 67 40-111 11-77 (129)
32 KOG1784 Small Nuclear ribonucl 99.4 2.5E-13 5.5E-18 92.6 4.2 65 41-109 3-67 (96)
33 KOG1775 U6 snRNA-associated Sm 99.3 1.1E-12 2.3E-17 87.1 3.6 68 38-110 6-74 (84)
34 KOG1774 Small nuclear ribonucl 99.2 1.2E-11 2.5E-16 83.1 3.4 62 42-110 16-81 (88)
35 KOG3459 Small nuclear ribonucl 98.7 1.8E-09 3.9E-14 75.9 0.1 86 25-110 13-103 (114)
36 KOG3448 Predicted snRNP core p 98.7 5.9E-08 1.3E-12 66.2 7.1 63 41-109 5-67 (96)
37 KOG3293 Small nuclear ribonucl 98.4 3.9E-07 8.5E-12 65.4 5.3 60 43-109 7-66 (134)
38 KOG3428 Small nuclear ribonucl 98.2 1E-05 2.2E-10 56.9 7.1 61 40-109 4-64 (109)
39 cd01739 LSm11_C The eukaryotic 98.0 5.6E-06 1.2E-10 53.6 2.8 37 49-85 9-49 (66)
40 PF14438 SM-ATX: Ataxin 2 SM d 97.9 3.5E-05 7.7E-10 50.0 5.2 67 43-110 7-76 (77)
41 KOG3172 Small nuclear ribonucl 97.7 0.00017 3.7E-09 50.9 6.7 59 43-109 10-68 (119)
42 PF02237 BPL_C: Biotin protein 96.5 0.015 3.2E-07 34.7 6.0 35 46-81 1-35 (48)
43 PF12701 LSM14: Scd6-like Sm d 96.1 0.032 7E-07 38.4 6.6 66 44-109 4-71 (96)
44 cd01716 Hfq Hfq, an abundant, 95.7 0.024 5.1E-07 36.2 4.2 32 47-78 10-41 (61)
45 TIGR02383 Hfq RNA chaperone Hf 95.5 0.028 6E-07 35.9 4.1 32 47-78 14-45 (61)
46 cd01736 LSm14_N LSm14 (also kn 95.1 0.22 4.8E-06 32.9 7.4 65 45-109 3-70 (74)
47 PRK00395 hfq RNA-binding prote 95.0 0.046 9.9E-07 36.6 4.1 33 47-79 18-50 (79)
48 PRK14638 hypothetical protein; 94.8 0.083 1.8E-06 38.7 5.5 38 39-77 91-128 (150)
49 PF06372 Gemin6: Gemin6 protei 94.8 0.054 1.2E-06 40.7 4.5 43 38-81 7-50 (166)
50 PRK14639 hypothetical protein; 94.4 0.12 2.6E-06 37.5 5.4 37 39-76 79-115 (140)
51 PRK14091 RNA-binding protein H 94.2 0.23 5E-06 37.4 6.6 73 4-79 59-135 (165)
52 PRK02001 hypothetical protein; 94.1 0.15 3.2E-06 37.7 5.4 37 39-76 81-117 (152)
53 cd01735 LSm12_N LSm12 belongs 94.1 0.15 3.3E-06 32.5 4.7 36 46-81 4-39 (61)
54 PRK14091 RNA-binding protein H 93.9 0.13 2.8E-06 38.7 4.9 49 31-79 3-55 (165)
55 PRK14644 hypothetical protein; 93.3 0.34 7.3E-06 35.1 6.1 41 36-77 73-117 (136)
56 cd01734 YlxS_C YxlS is a Bacil 92.4 0.52 1.1E-05 30.9 5.5 37 39-76 16-56 (83)
57 PRK14633 hypothetical protein; 91.5 0.62 1.3E-05 34.1 5.6 37 39-76 85-125 (150)
58 PRK14640 hypothetical protein; 91.2 0.7 1.5E-05 33.8 5.6 38 39-77 88-129 (152)
59 PF02576 DUF150: Uncharacteris 91.0 0.66 1.4E-05 33.1 5.2 36 40-76 79-118 (141)
60 PRK14642 hypothetical protein; 90.9 0.7 1.5E-05 35.6 5.5 37 39-76 91-140 (197)
61 COG1923 Hfq Uncharacterized ho 90.7 0.51 1.1E-05 31.5 4.0 31 47-77 18-48 (77)
62 PRK14645 hypothetical protein; 90.6 0.76 1.7E-05 33.9 5.3 35 40-76 94-128 (154)
63 PRK14636 hypothetical protein; 90.2 0.87 1.9E-05 34.3 5.5 37 39-76 89-129 (176)
64 PRK00092 ribosome maturation p 90.1 1 2.2E-05 32.8 5.6 31 40-70 90-124 (154)
65 COG0779 Uncharacterized protei 90.0 1.3 2.8E-05 32.9 6.1 33 40-72 91-127 (153)
66 PRK14634 hypothetical protein; 89.8 1.1 2.3E-05 33.0 5.5 37 39-76 91-131 (155)
67 PRK14643 hypothetical protein; 89.4 1.1 2.4E-05 33.3 5.5 32 40-71 96-131 (164)
68 PRK14632 hypothetical protein; 89.4 1.1 2.5E-05 33.5 5.5 37 40-77 90-133 (172)
69 PRK14646 hypothetical protein; 89.2 1.3 2.7E-05 32.7 5.5 37 39-76 91-131 (155)
70 PRK14647 hypothetical protein; 88.1 1.6 3.5E-05 32.1 5.5 32 39-70 90-130 (159)
71 PRK14631 hypothetical protein; 87.8 1.6 3.4E-05 32.9 5.3 31 39-69 108-142 (174)
72 PRK14637 hypothetical protein; 86.1 2.2 4.7E-05 31.3 5.2 38 39-77 89-127 (151)
73 PRK14641 hypothetical protein; 85.9 2.2 4.7E-05 32.2 5.2 30 40-69 96-129 (173)
74 PF11095 Gemin7: Gem-associate 84.9 2.6 5.7E-05 28.2 4.7 57 41-110 17-74 (80)
75 PRK06955 biotin--protein ligas 84.7 4 8.7E-05 32.6 6.6 33 46-78 247-279 (300)
76 PF10842 DUF2642: Protein of u 82.7 2.9 6.4E-05 26.9 4.1 38 39-78 12-49 (66)
77 PRK11886 bifunctional biotin-- 80.3 8.1 0.00018 30.7 6.8 31 46-77 270-300 (319)
78 PRK14630 hypothetical protein; 78.0 6.5 0.00014 28.5 5.1 36 39-76 88-123 (143)
79 PRK08330 biotin--protein ligas 76.3 12 0.00027 28.5 6.5 33 45-78 185-218 (236)
80 PRK13325 bifunctional biotin-- 75.8 10 0.00022 33.4 6.6 33 46-78 276-308 (592)
81 TIGR00121 birA_ligase birA, bi 75.5 17 0.00036 27.8 7.0 31 46-77 191-221 (237)
82 PF03614 Flag1_repress: Repres 75.4 3.2 6.9E-05 31.2 2.9 25 47-71 119-143 (165)
83 PF03614 Flag1_repress: Repres 75.2 6.7 0.00014 29.5 4.5 36 45-80 26-61 (165)
84 PRK14635 hypothetical protein; 72.8 11 0.00024 27.7 5.3 37 39-76 90-131 (162)
85 KOG1073 Uncharacterized mRNA-a 71.3 14 0.00031 31.0 6.0 65 44-109 5-73 (361)
86 COG0340 BirA Biotin-(acetyl-Co 70.6 20 0.00044 28.0 6.5 36 45-80 187-222 (238)
87 PTZ00275 biotin-acetyl-CoA-car 68.0 12 0.00026 29.8 4.8 32 46-78 235-266 (285)
88 PRK10898 serine endoprotease; 66.7 12 0.00026 30.6 4.7 32 49-80 102-133 (353)
89 PF14563 DUF4444: Domain of un 65.4 8.5 0.00018 22.9 2.6 22 61-82 10-31 (42)
90 TIGR02038 protease_degS peripl 64.6 13 0.00029 30.2 4.6 32 49-80 102-133 (351)
91 KOG3382 NADH:ubiquinone oxidor 63.7 3.8 8.3E-05 30.2 1.2 24 56-79 40-63 (151)
92 PF11607 DUF3247: Protein of u 62.0 12 0.00025 26.1 3.2 18 49-66 29-46 (101)
93 PRK10942 serine endoprotease; 61.5 15 0.00034 31.2 4.6 31 49-79 136-166 (473)
94 PRK10139 serine endoprotease; 61.2 16 0.00036 30.9 4.7 32 49-80 115-146 (455)
95 PF03122 Herpes_MCP: Herpes vi 59.9 3 6.4E-05 40.3 0.0 55 51-111 250-304 (1354)
96 PRK09618 flgD flagellar basal 56.3 48 0.001 24.3 5.9 43 42-84 86-131 (142)
97 PF05071 NDUFA12: NADH ubiquin 55.8 5.2 0.00011 27.5 0.7 17 63-79 1-17 (105)
98 TIGR02037 degP_htrA_DO peripla 52.9 27 0.00058 28.9 4.6 32 49-80 82-113 (428)
99 PF07073 ROF: Modulator of Rho 46.9 20 0.00044 23.7 2.4 24 41-64 10-33 (80)
100 PRK08477 biotin--protein ligas 45.0 74 0.0016 24.4 5.6 35 46-81 173-207 (211)
101 PF06257 DUF1021: Protein of u 39.1 31 0.00067 22.8 2.3 28 41-68 10-41 (76)
102 PRK06630 hypothetical protein; 37.6 18 0.0004 25.1 1.1 19 61-79 11-29 (99)
103 PF01887 SAM_adeno_trans: S-ad 36.4 52 0.0011 26.0 3.7 22 60-81 169-190 (258)
104 TIGR03170 flgA_cterm flagella 36.3 46 0.001 22.5 3.0 23 45-67 93-116 (122)
105 KOG3493 Ubiquitin-like protein 33.2 33 0.00072 22.4 1.7 18 43-60 6-23 (73)
106 cd04454 S1_Rrp4_like S1_Rrp4_l 32.8 1.3E+02 0.0027 18.8 4.7 24 55-78 51-74 (82)
107 TIGR02603 CxxCH_TIGR02603 puta 32.6 68 0.0015 22.4 3.4 21 50-70 59-79 (133)
108 smart00166 UBX Domain present 31.5 47 0.001 21.0 2.3 22 49-70 5-26 (80)
109 PRK11911 flgD flagellar basal 30.9 94 0.002 22.8 4.0 27 44-70 89-115 (140)
110 PLN03095 NADH:ubiquinone oxido 30.3 29 0.00063 24.7 1.2 19 62-80 9-27 (115)
111 COG4466 Veg Uncharacterized pr 30.2 53 0.0011 22.0 2.3 21 41-61 12-32 (80)
112 PF10618 Tail_tube: Phage tail 30.0 99 0.0022 21.6 3.9 32 33-64 59-90 (119)
113 PLN02732 Probable NADH dehydro 28.9 43 0.00093 25.1 1.9 19 62-80 48-66 (159)
114 PF14485 DUF4431: Domain of un 28.7 55 0.0012 19.5 2.1 16 39-54 10-25 (48)
115 smart00333 TUDOR Tudor domain. 28.7 1.2E+02 0.0026 17.3 4.1 25 47-71 5-29 (57)
116 PRK07018 flgA flagellar basal 28.4 66 0.0014 24.8 3.0 22 46-67 205-227 (235)
117 cd01772 SAKS1_UBX SAKS1-like U 27.7 47 0.001 21.2 1.8 25 46-70 2-26 (79)
118 PF00789 UBX: UBX domain; Int 27.6 69 0.0015 20.0 2.5 22 49-70 7-28 (82)
119 COG0265 DegQ Trypsin-like seri 27.4 1.2E+02 0.0025 24.3 4.3 33 48-80 95-127 (347)
120 cd01767 UBX UBX (ubiquitin reg 26.9 70 0.0015 20.0 2.5 22 49-70 3-24 (77)
121 cd04479 RPA3 RPA3: A subfamily 25.8 1.6E+02 0.0035 19.6 4.3 15 40-54 7-21 (101)
122 KOG4401 Uncharacterized conser 25.6 94 0.002 23.9 3.3 35 46-80 9-43 (184)
123 PRK10708 hypothetical protein; 24.8 83 0.0018 20.0 2.4 36 47-82 3-40 (62)
124 PF09465 LBR_tudor: Lamin-B re 24.8 1.4E+02 0.0031 18.6 3.5 25 47-71 8-33 (55)
125 PRK08183 NADH dehydrogenase; V 24.1 42 0.00091 24.4 1.1 19 62-80 25-43 (133)
126 PRK11625 Rho-binding antitermi 22.2 2.1E+02 0.0045 19.1 4.1 38 42-85 17-54 (84)
127 PF05954 Phage_GPD: Phage late 21.8 1.2E+02 0.0027 22.7 3.4 29 41-69 21-49 (292)
128 TIGR03361 VI_Rhs_Vgr type VI s 20.7 1.7E+02 0.0037 24.7 4.3 30 40-69 39-72 (513)
129 PTZ00276 biotin/lipoate protei 20.7 1.5E+02 0.0033 22.9 3.7 32 47-78 197-231 (245)
130 PF10781 DSRB: Dextransucrase 20.7 1E+02 0.0022 19.6 2.2 26 47-72 3-28 (62)
131 PRK06792 flgD flagellar basal 20.5 1.6E+02 0.0034 22.7 3.7 27 43-69 113-139 (190)
No 1
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=5.9e-23 Score=136.89 Aligned_cols=74 Identities=64% Similarity=0.992 Sum_probs=63.6
Q ss_pred CChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 38 ~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
..+++|.++++++|+|+|+|||+++|+|.|||+||||+|++|+|+...++++.....+.+.+|+++|||++|+.
T Consensus 2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~ 75 (81)
T cd01729 2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVL 75 (81)
T ss_pred cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEE
Confidence 45788999999999999999999999999999999999999999987643322222467899999999999973
No 2
>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=99.86 E-value=1.7e-21 Score=128.68 Aligned_cols=71 Identities=25% Similarity=0.440 Sum_probs=61.0
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
+.|.+|++++|+|+|+|||.+.|+|.|||+||||+|++|+|++....+. .....++|.+|+++|||++||.
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~ 75 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVS 75 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEE
Confidence 4689999999999999999999999999999999999999998754321 1122468899999999999984
No 3
>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=99.85 E-value=5.2e-21 Score=125.86 Aligned_cols=68 Identities=31% Similarity=0.375 Sum_probs=60.5
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
+.++|+++++|+|.|+|+|||.+.|+|.|||+|||++|++|.|+...++. ..++.+|+++|||++|+.
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~-----~~~~~lG~~viRG~~V~~ 70 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDK-----YGDIPRGIFIIRGENVVL 70 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCc-----cceeEeeEEEEECCEEEE
Confidence 47789999999999999999999999999999999999999999865321 246889999999999974
No 4
>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=99.85 E-value=7e-21 Score=124.41 Aligned_cols=64 Identities=36% Similarity=0.647 Sum_probs=58.2
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.++|+++++|+|+|+|++|+.++|+|.|||+||||+|++|.|+... .+.+.+|.++|||++|+.
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~--------~~~~~lg~v~IRG~~I~~ 65 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG--------GEKNNIGMVVIRGNSIVM 65 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC--------CceeEeceEEECCCEEEE
Confidence 4689999999999999999999999999999999999999999742 257899999999999973
No 5
>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=99.84 E-value=1.5e-20 Score=123.93 Aligned_cols=69 Identities=23% Similarity=0.360 Sum_probs=61.2
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
..|++|++++|+|+|+|||.|.|+|.|||+||||+|++|.|++....+. ...+.|.+|+++|||++|+.
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~--~~~~~r~lGlv~IrG~~Iv~ 71 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF--SPTEPRVLGLVMIPGHHIVS 71 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc--CCccEEEeeeEEEeCCeEEE
Confidence 5789999999999999999999999999999999999999999765432 22478999999999999974
No 6
>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=99.84 E-value=9.5e-21 Score=126.12 Aligned_cols=71 Identities=28% Similarity=0.418 Sum_probs=59.6
Q ss_pred hh-HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCceec
Q 033737 41 LD-LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~-L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv~ 111 (112)
++ |+..++++|.|+|+|||.++|+|.|||+||||+|+||+|++...+++. ......|.+|+++||||+||.
T Consensus 3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~ 79 (82)
T cd01730 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVIL 79 (82)
T ss_pred hHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEE
Confidence 44 577799999999999999999999999999999999999987643321 112367899999999999984
No 7
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.84 E-value=1.2e-20 Score=123.00 Aligned_cols=64 Identities=38% Similarity=0.521 Sum_probs=57.1
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
...|.++++++|+|+|+||+.|+|+|.|||+|||++|+||.|...+ +..+.+|.++|||++|+.
T Consensus 6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~lg~v~iRG~~V~~ 69 (72)
T PRK00737 6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG--------EVVRKLGKVVIRGDNVVY 69 (72)
T ss_pred HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC--------CeEeEcCcEEEeCCEEEE
Confidence 4458999999999999999999999999999999999999997532 256889999999999973
No 8
>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=99.84 E-value=1.4e-20 Score=123.05 Aligned_cols=66 Identities=35% Similarity=0.473 Sum_probs=58.7
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
+.|++|++++|+|+++|||.++|+|.|||+|||++|++|.|+....+.+ ...+.+|+++|||++|+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~----~~~~~lG~~~iRG~~I~ 67 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEG----VEQVVLGLYIIRGDNIA 67 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCC----ceeeEeceEEECCCEEE
Confidence 5799999999999999999999999999999999999999997643321 35778999999999997
No 9
>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=99.83 E-value=5e-20 Score=121.69 Aligned_cols=66 Identities=18% Similarity=0.323 Sum_probs=57.5
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.-|+++++++|+|+++|||.++|+|.|||+|||++|++|.|++..++. .+.+.+|.++|||++|+.
T Consensus 6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-----~~~~~lg~v~iRG~nV~~ 71 (76)
T cd01732 6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-----RKITKLDQILLNGNNICM 71 (76)
T ss_pred HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-----ceeeEcCeEEEeCCeEEE
Confidence 346899999999999999999999999999999999999999853221 256889999999999973
No 10
>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=99.82 E-value=4.5e-20 Score=118.62 Aligned_cols=62 Identities=39% Similarity=0.508 Sum_probs=56.7
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|++++|++|+|+|+||+.|.|+|.|||+||||+|++|+|++.+. +.+.+|.++|||++|+
T Consensus 3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~--------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE--------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred HHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC--------eEeEcCcEEEeCCEEE
Confidence 4588999999999999999999999999999999999999987542 5788999999999997
No 11
>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=99.79 E-value=4.4e-19 Score=120.02 Aligned_cols=69 Identities=19% Similarity=0.312 Sum_probs=57.3
Q ss_pred HHhhc--CCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCceec
Q 033737 43 LAKFV--DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 43 L~~~i--~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv~ 111 (112)
|...+ +++|.|+|++|+.+.|+|.|||+||||+|+||+|++...+++. ......+.+|.++||||+||.
T Consensus 7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 46665 8999999999999999999999999999999999987643221 112357789999999999983
No 12
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=5.3e-19 Score=113.54 Aligned_cols=61 Identities=21% Similarity=0.302 Sum_probs=55.4
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
.|++++|++|+|+|++|++|+|+|.|||+|||++|++|+|.... .+.+.+|.++|||++|+
T Consensus 4 ~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~--------~~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 4 FLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG--------QLKNKYGDAFIRGNNVL 64 (67)
T ss_pred HHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC--------ceeeEeCCEEEECCEEE
Confidence 47899999999999999999999999999999999999987542 25778999999999986
No 13
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.78 E-value=5.6e-19 Score=113.81 Aligned_cols=63 Identities=30% Similarity=0.382 Sum_probs=56.1
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
..|++++|++|+|.|+||++|.|+|.|||+|||++|++|.|+... ...+.+|.++|||++|+.
T Consensus 4 ~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~--------~~~~~lg~~~IRG~~I~~ 66 (68)
T cd01722 4 PFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG--------KSTGNLGEVLIRCNNVLY 66 (68)
T ss_pred HHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC--------ccccCcCcEEEECCEEEE
Confidence 458899999999999999999999999999999999999998542 246779999999999873
No 14
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.78 E-value=2e-20 Score=128.98 Aligned_cols=84 Identities=55% Similarity=0.848 Sum_probs=76.0
Q ss_pred ccccccCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCC
Q 033737 28 LKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCD 107 (112)
Q Consensus 28 ~~~~~ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd 107 (112)
++.-.+++++.+.++|.+|++|+|+|++.+||+..|+|.|||+.|||||++++||..+++++.....+.|.+|++++||.
T Consensus 7 ~~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGT 86 (108)
T KOG1781|consen 7 QRKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGT 86 (108)
T ss_pred ccccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEccc
Confidence 34445678889999999999999999999999999999999999999999999999998888776677899999999999
Q ss_pred ceec
Q 033737 108 ACVT 111 (112)
Q Consensus 108 ~iv~ 111 (112)
.+|.
T Consensus 87 alvl 90 (108)
T KOG1781|consen 87 ALVL 90 (108)
T ss_pred EEEE
Confidence 8873
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.78 E-value=1.6e-18 Score=109.76 Aligned_cols=63 Identities=41% Similarity=0.639 Sum_probs=57.7
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.|++++|++|+|.|+||+.+.|+|.|||+|||++|++|.|+.... .+.+.+|.++|||++|+.
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------~~~~~~~~~~IrG~~I~~ 64 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------EKKRKLGLVFIRGNNIVY 64 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------cEEeEeCCEEEcCCEEEE
Confidence 588999999999999999999999999999999999999998652 268899999999999973
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=99.77 E-value=1.9e-18 Score=109.51 Aligned_cols=63 Identities=35% Similarity=0.518 Sum_probs=58.0
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.|++++|++|+|.|+||+.++|+|.+||+|||++|++|.|+..... +.+.+|.++|||++|+.
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------~~~~~~~~~irG~~I~~ 64 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------EKRSLGLVFIRGSNIRY 64 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------EEEEEEEEEEEGGGEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------cEeECcEEEEECCEEEE
Confidence 5889999999999999999999999999999999999999987531 68899999999999974
No 17
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.76 E-value=8.7e-19 Score=115.30 Aligned_cols=63 Identities=41% Similarity=0.701 Sum_probs=58.0
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
++|++|++|++.++|+.||...|+|+|||.|||+||++++|...+ ..+..+|.++|||++||.
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~--------~~~~~ig~~vIrgnsiv~ 69 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD--------GDKNNIGMVVIRGNSIVM 69 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc--------CCcceeeeEEEeccEEEE
Confidence 399999999999999999999999999999999999999998664 256789999999999984
No 18
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.75 E-value=5.5e-18 Score=112.98 Aligned_cols=64 Identities=28% Similarity=0.394 Sum_probs=54.7
Q ss_pred hhhHHhhcCC--eEEEEEc--CCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 40 VLDLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 40 ~~~L~~~i~k--~V~V~L~--dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
...+.+|+++ +|.|+++ +|+.++|+|.|||+||||+|+||+|+.... .+.+.+|+++||||+|+
T Consensus 8 ~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~-------~~~~~lG~iliRGnnV~ 75 (79)
T cd01718 8 INLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT-------KTRKPLGRILLKGDNIT 75 (79)
T ss_pred HHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCC-------ceEeEcCcEEEeCCEEE
Confidence 3447899998 6677766 999999999999999999999999997531 25788999999999997
No 19
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.74 E-value=1.4e-17 Score=103.98 Aligned_cols=60 Identities=37% Similarity=0.581 Sum_probs=55.4
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
|++++|++|+|.|+||+.+.|+|.|||+|||++|++|.|+... ...+.+|.++|||++|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------~~~~~~~~~~irG~~I~ 60 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------GKKRVLGLVLIRGDNVR 60 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------CcEEECCeEEEECCEEE
Confidence 5678999999999999999999999999999999999999765 25789999999999986
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.73 E-value=2.3e-17 Score=108.75 Aligned_cols=68 Identities=37% Similarity=0.483 Sum_probs=55.6
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
....|+++++++|.|+|++|+++.|+|.|||+|||++|++|.|+...... . ...+..|.++|||++|+
T Consensus 8 ~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~-~---~~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGE-K---NVRRLGGEVLIRGDNIV 75 (79)
T ss_pred cHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCc-c---ccceeccEEEEECCcEE
Confidence 35568999999999999999999999999999999999999999851110 0 12344449999999986
No 21
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.67 E-value=2.8e-16 Score=106.88 Aligned_cols=63 Identities=27% Similarity=0.443 Sum_probs=52.5
Q ss_pred hHHhhcCC--eEEEEEcC--CeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 42 DLAKFVDK--GVQVKLTG--GRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 42 ~L~~~i~k--~V~V~L~d--gr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.+.+++.. +|.|++.| +++++|+|.|||+||||+|+||+|++.+. ++.+.+|+++||||+|+.
T Consensus 18 ~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-------~~~~~lG~ilIRGnnV~~ 84 (89)
T PTZ00138 18 QIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-------NTRKDLGRILLKGDNITL 84 (89)
T ss_pred HHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-------ceeeEcCeEEEcCCEEEE
Confidence 36778776 66777767 59999999999999999999999987532 257899999999999973
No 22
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.65 E-value=7.6e-16 Score=99.84 Aligned_cols=61 Identities=21% Similarity=0.133 Sum_probs=53.5
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
-|.+..|++|.|.|+||.+|.|+|.++|+|||++|++|.+...+. +...+|.++|||++|.
T Consensus 4 ~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g--------~~~~~~~v~IRG~nI~ 64 (70)
T cd01721 4 LLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG--------RVSQLEQVYIRGSKIR 64 (70)
T ss_pred HHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCC--------cEeEcCcEEEeCCEEE
Confidence 468889999999999999999999999999999999998754331 3567899999999985
No 23
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.64 E-value=9.2e-16 Score=100.80 Aligned_cols=62 Identities=19% Similarity=0.187 Sum_probs=53.7
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
-|+++.|++|.|.|++|+.+.|+|.+||+|||++|++|.|...+. +....+|.++|||++|.
T Consensus 5 ~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g-------~~~~~~~~v~IRG~~I~ 66 (76)
T cd01723 5 LLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDG-------DKFWKMPECYIRGNTIK 66 (76)
T ss_pred HHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCC-------cEeeeCCcEEEeCCEEE
Confidence 368899999999999999999999999999999999999874332 13456799999999986
No 24
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.61 E-value=2.5e-15 Score=102.04 Aligned_cols=62 Identities=23% Similarity=0.264 Sum_probs=55.7
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|+++.|++|+|.|++|..|+|+|.++|.|||++|+||.++..+ .....+|.++|||++|.
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~--------~~~~~~~~v~IRG~nI~ 65 (90)
T cd01724 4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG--------RNPVPLDTLSIRGNNIR 65 (90)
T ss_pred HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC--------CceeEcceEEEeCCEEE
Confidence 457899999999999999999999999999999999999988543 24678999999999985
No 25
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.60 E-value=1.2e-15 Score=100.33 Aligned_cols=62 Identities=34% Similarity=0.407 Sum_probs=56.9
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
+.|+.+.||+|.|+|++|.+|+|+|.+.|.||||.|.+|+|++.. .....+|.++||.++|-
T Consensus 11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG--------~~~g~lGEilIRCNNvl 72 (79)
T KOG3482|consen 11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG--------VSTGNLGEILIRCNNVL 72 (79)
T ss_pred HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc--------cccccceeEEEEeccEE
Confidence 358999999999999999999999999999999999999999876 35778999999999974
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.60 E-value=5.3e-15 Score=98.06 Aligned_cols=62 Identities=23% Similarity=0.216 Sum_probs=54.3
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|+...|+.|.|.|+||..|.|+|.++|+|||++|+||.+...+ .....+|.++|||++|.
T Consensus 12 ~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~--------~~~~~~~~v~IRG~nI~ 73 (78)
T cd01733 12 ILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN--------GKQVQVEEIMVTGRNIR 73 (78)
T ss_pred HHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC--------CceeECCcEEEECCEEE
Confidence 346889999999999999999999999999999999999876433 23557999999999986
No 27
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.58 E-value=2.2e-16 Score=117.78 Aligned_cols=72 Identities=25% Similarity=0.446 Sum_probs=64.0
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC--CccccceEeeeeEEEeCCceec
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
...|.+++|++++|.++|||.++|.+.+||+|||++|.+|+|++..+.+. ..+++++|-+|++++||++||.
T Consensus 6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs 79 (177)
T KOG3168|consen 6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVS 79 (177)
T ss_pred hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEE
Confidence 45688999999999999999999999999999999999999998875443 2346799999999999999984
No 28
>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=99.56 E-value=1.4e-14 Score=96.40 Aligned_cols=64 Identities=20% Similarity=0.108 Sum_probs=53.8
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|+++.|++|+|.|++|..|.|+|.++|.|||++|++|.+...+.. .....+|.++|||++|.
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~------~~~~~~~~v~IRG~~I~ 67 (81)
T cd01725 4 SFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY------PHMLSVKNCFIRGSVVR 67 (81)
T ss_pred HHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc------ccccccCeEEEECCEEE
Confidence 34788999999999999999999999999999999999987643221 12456799999999985
No 29
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.47 E-value=1.6e-14 Score=97.20 Aligned_cols=72 Identities=28% Similarity=0.374 Sum_probs=59.5
Q ss_pred ChhhHH-hhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCC-----ccccceEeeeeEEEeCCcee
Q 033737 39 TVLDLA-KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPL-----KTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 39 ~~~~L~-~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~-----~~~~~~r~lGlvvIRGd~iv 110 (112)
.|++|. -+++.+|.|+++++|.+.|+|.|||+|.||+|.+++|.+..-+... ..+..+|.+.++++|||+|+
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi 82 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI 82 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence 466754 4599999999999999999999999999999999999987533211 12357889999999999986
No 30
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.46 E-value=1.1e-14 Score=95.65 Aligned_cols=70 Identities=23% Similarity=0.252 Sum_probs=61.1
Q ss_pred cCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 33 ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
||.+......|++.+|++|.|+|.+|-.|.|+|.+.|.|||+.|+.+.|+... +.++++|.++|||++|-
T Consensus 1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng--------ql~n~ygdaFirGnnVl 70 (77)
T KOG1783|consen 1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG--------QLKNKYGDAFIRGNNVL 70 (77)
T ss_pred CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcC--------cccccccceeeccccEE
Confidence 55444445568999999999999999999999999999999999999999754 36788999999999874
No 31
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.41 E-value=2.6e-14 Score=101.93 Aligned_cols=67 Identities=28% Similarity=0.389 Sum_probs=59.9
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
+.+|.+++++++.|.|+|||.+.|.|++||||.|++|+.|+|++...+. .-.+..|..+|||+|||-
T Consensus 11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-----Y~di~~glfiIRGENVvl 77 (129)
T KOG1782|consen 11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-----YCDIPRGLFIIRGENVVL 77 (129)
T ss_pred hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-----ecccCceEEEEecCcEEE
Confidence 4568999999999999999999999999999999999999999986432 466778999999999983
No 32
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.40 E-value=2.5e-13 Score=92.63 Aligned_cols=65 Identities=29% Similarity=0.430 Sum_probs=58.1
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i 109 (112)
+.|+.|++++|.|...|||.+.|.|.||||-.||+|+++-|++..... ..++..+|+.+|||+|+
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~----gv~q~~lGlyiirgeNv 67 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE----GVEQIVLGLYIIRGENV 67 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc----chhheeeEEEEEecCcc
Confidence 468999999999999999999999999999999999999999875332 24678899999999986
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.33 E-value=1.1e-12 Score=87.15 Aligned_cols=68 Identities=21% Similarity=0.369 Sum_probs=57.9
Q ss_pred CChhhH-HhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 38 ETVLDL-AKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 38 ~~~~~L-~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|++| .+.+|.+++|.++++|++.|+|.|||.|.|++|+|+.||-..... ....+++.+++.|++|-
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-----r~~tk~~~iLLnGNni~ 74 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-----RRMTKLDQILLNGNNIT 74 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-----ceeeeeeeeeecCCcEE
Confidence 446665 588999999999999999999999999999999999999765432 35668999999999873
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.20 E-value=1.2e-11 Score=83.08 Aligned_cols=62 Identities=31% Similarity=0.455 Sum_probs=49.7
Q ss_pred hHHhhcCC--eEEEEEc--CCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 42 DLAKFVDK--GVQVKLT--GGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 42 ~L~~~i~k--~V~V~L~--dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
.+-+|+.. +|.|+|. -|..++|.++|||+|||+||++|+|.....+ ..+.+|.++++||+|-
T Consensus 16 ~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~-------~rk~lGRilLKGDnIt 81 (88)
T KOG1774|consen 16 LIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK-------SRKELGRILLKGDNIT 81 (88)
T ss_pred HHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc-------CCCccccEEEcCCcEE
Confidence 34677775 5556664 4899999999999999999999999866432 3458999999999984
No 35
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.74 E-value=1.8e-09 Score=75.94 Aligned_cols=86 Identities=16% Similarity=0.217 Sum_probs=67.5
Q ss_pred cccccccccCCCCCChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCC---C--ccccceEee
Q 033737 25 LGFLKSLKMSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDP---L--KTTDQTRQL 99 (112)
Q Consensus 25 ~~~~~~~~ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~---~--~~~~~~r~l 99 (112)
..-.+..+|..+|.+...-..--...|.|.++|++.+-|++.|||.|.|++|+++.|.+....++ . ......|.+
T Consensus 13 ~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~i 92 (114)
T KOG3459|consen 13 LEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFI 92 (114)
T ss_pred cccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhh
Confidence 45566777777776655555456678999999999999999999999999999999998764332 1 112458999
Q ss_pred eeEEEeCCcee
Q 033737 100 GLIGNCCDACV 110 (112)
Q Consensus 100 GlvvIRGd~iv 110 (112)
|.++||||+|+
T Consensus 93 sK~flRGdsvI 103 (114)
T KOG3459|consen 93 SKMFLRGDSVI 103 (114)
T ss_pred heeeecCCeEE
Confidence 99999999986
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.72 E-value=5.9e-08 Score=66.19 Aligned_cols=63 Identities=24% Similarity=0.152 Sum_probs=50.8
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i 109 (112)
...+.++|++|.|.|+++..|.|+|.+.|+|.|+-|.|..-...++ . ..-..+-.++|||..|
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~k---y---Phm~Sv~ncfIRGSvv 67 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDK---Y---PHMLSVKNCFIRGSVV 67 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCccc---C---CCeeeeeeEEEeccEE
Confidence 3467889999999999999999999999999999999976553321 1 2345567899999875
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.44 E-value=3.9e-07 Score=65.45 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=52.0
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i 109 (112)
|+..-+.++.|.|++|.+|.|.|+..|.+|||.|.+++++..+.+ .--.+..+.|||.+|
T Consensus 7 L~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd-------kf~r~pEcYirGttI 66 (134)
T KOG3293|consen 7 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD-------KFFRMPECYIRGTTI 66 (134)
T ss_pred HHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC-------ceeecceeEEeccee
Confidence 455678999999999999999999999999999999999877643 345578999999987
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.16 E-value=1e-05 Score=56.88 Aligned_cols=61 Identities=21% Similarity=0.280 Sum_probs=51.5
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i 109 (112)
...|+++.+.+++|.|++|..+.|++.+.|.+||..|.++.-.... ++..+-.+.|||++|
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~---------~pv~l~~lsirgnni 64 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG---------EPVRLDTLSIRGNNI 64 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC---------CceeEEEEEeecceE
Confidence 3467889999999999999999999999999999999987765432 345677888999987
No 39
>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=97.98 E-value=5.6e-06 Score=53.58 Aligned_cols=37 Identities=27% Similarity=0.425 Sum_probs=30.5
Q ss_pred CeEEEEEcC--C--eEEEEEEEeecCccceeecceEEEeec
Q 033737 49 KGVQVKLTG--G--RQVTGTLKGYDQLLNLVLDEAVEFLRD 85 (112)
Q Consensus 49 k~V~V~L~d--g--r~i~G~L~~fD~~mNlvL~~a~E~~~~ 85 (112)
.+|+|.++. | -.++|.|.|||+|+||+|.|+.|....
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 577777653 2 378999999999999999999998765
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.87 E-value=3.5e-05 Score=50.03 Aligned_cols=67 Identities=15% Similarity=0.173 Sum_probs=41.1
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEeecC---ccceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQ---LLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~---~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
+..++|++|.|+++||..|+|.|.+++. -+.++|.-|........++ ...........++|+++.||
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-SDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------EEEEEEE-GGGEEE-----
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-CCccCCCCCceEEEeccccC
Confidence 5678999999999999999999999988 8899998888765432211 11123445567788888776
No 41
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=97.70 E-value=0.00017 Score=50.92 Aligned_cols=59 Identities=20% Similarity=0.128 Sum_probs=49.6
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCce
Q 033737 43 LAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~i 109 (112)
|.+.-|.-|++.+..|..|.|+|.-.|..||++|+|..-...+. ....+-.++|||+.|
T Consensus 10 LhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg--------~vs~le~V~IRGS~I 68 (119)
T KOG3172|consen 10 LHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG--------RVSQLEQVFIRGSKI 68 (119)
T ss_pred eecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCC--------cceeeeeEEEecCeE
Confidence 34456778999999999999999999999999999998876543 455678999999976
No 42
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.52 E-value=0.015 Score=34.72 Aligned_cols=35 Identities=20% Similarity=0.300 Sum_probs=30.4
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E 81 (112)
++|++|++.+ ++..++|+..++|....|+++....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 4799999999 6677799999999999999977555
No 43
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.08 E-value=0.032 Score=38.38 Aligned_cols=66 Identities=9% Similarity=0.065 Sum_probs=47.3
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEeecC-ccceeecceEEEeecCCC-CCccccceEeeeeEEEeCCce
Q 033737 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLNLVLDEAVEFLRDADD-PLKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 44 ~~~i~k~V~V~L~dgr~i~G~L~~fD~-~mNlvL~~a~E~~~~~~~-~~~~~~~~r~lGlvvIRGd~i 109 (112)
.+|+|++|.+..+++-+|+|+|...|. ...|.|.++.-+-..... +...-....-...++.||..|
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDI 71 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDI 71 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEcccc
Confidence 358999999999999999999999996 589999998776543211 110001233467888888765
No 44
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.66 E-value=0.024 Score=36.21 Aligned_cols=32 Identities=22% Similarity=0.408 Sum_probs=27.6
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
-..+|.|.|.+|-.++|.+.|||+|+=++-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 34689999999999999999999998776555
No 45
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.54 E-value=0.028 Score=35.92 Aligned_cols=32 Identities=25% Similarity=0.380 Sum_probs=27.4
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
-..+|+|.|.+|-.+.|.+.|||+|+=++-.+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 34689999999999999999999998776544
No 46
>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=95.05 E-value=0.22 Score=32.93 Aligned_cols=65 Identities=8% Similarity=0.057 Sum_probs=47.6
Q ss_pred hhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCC--CccccceEeeeeEEEeCCce
Q 033737 45 KFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDP--LKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 45 ~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~--~~~~~~~r~lGlvvIRGd~i 109 (112)
+|+|+++.+.-+.+-+|+|+|..+|.. .-+.|.++.-+-...... .+.-....-+..++.||..|
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDI 70 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDI 70 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcc
Confidence 589999999999999999999999966 567799987665432211 10112344567899999876
No 47
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.02 E-value=0.046 Score=36.61 Aligned_cols=33 Identities=18% Similarity=0.406 Sum_probs=28.1
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a 79 (112)
-..+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 446899999999999999999999987766554
No 48
>PRK14638 hypothetical protein; Provisional
Probab=94.82 E-value=0.083 Score=38.72 Aligned_cols=38 Identities=13% Similarity=0.310 Sum_probs=32.0
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~ 77 (112)
.+.++.+++|++|+|++.+++.++|+|.++|.- ++.|.
T Consensus 91 ~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 91 GPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 366789999999999999999999999999863 44443
No 49
>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=94.80 E-value=0.054 Score=40.74 Aligned_cols=43 Identities=26% Similarity=0.394 Sum_probs=32.8
Q ss_pred CChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEE
Q 033737 38 ETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVE 81 (112)
Q Consensus 38 ~~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E 81 (112)
.+|.....|++|.|+|++.| +++.|-+..+|.- .|+||-+-.|
T Consensus 7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 45788999999999999999 9999999999966 6898885444
No 50
>PRK14639 hypothetical protein; Provisional
Probab=94.42 E-value=0.12 Score=37.46 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=31.9
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL 76 (112)
.+.+..+++|++|+|++.+++.+.|+|.++|.- ++.|
T Consensus 79 ~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 79 KIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred CHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 366789999999999999999999999999883 4444
No 51
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.17 E-value=0.23 Score=37.41 Aligned_cols=73 Identities=21% Similarity=0.269 Sum_probs=47.2
Q ss_pred eEEEeeEEEEEEecccccccccccccccccCCCCCChhh--HHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737 4 FVEINAVSFFIVCRSARVSFNLGFLKSLKMSGRKETVLD--LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ms~~~~~~~~--L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a 79 (112)
.+==||.|=+.-.+..- +... .+...++++.....+ |+.+.. .+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus 59 LIYKHAISTI~p~~~i~--~~~~-~~~~~~~~~~~nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 59 LVYKHAISTIMPAHPLD--LSRF-SKSLDANKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred EEEeeeeeeecccCCcc--hhhh-cchhhhcccccccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 34447777666555542 2222 244445544455444 555533 4888999999999999999999986666554
No 52
>PRK02001 hypothetical protein; Validated
Probab=94.12 E-value=0.15 Score=37.68 Aligned_cols=37 Identities=22% Similarity=0.396 Sum_probs=31.7
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL 76 (112)
.+.+..+++|+.|+|++.+++.++|+|.++|.- ++.|
T Consensus 81 ~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 356789999999999999999999999999864 4444
No 53
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.06 E-value=0.15 Score=32.46 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=30.3
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E 81 (112)
.+|..|++++-.|.+|+|.+.+||.-.++++=.|.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999887776554433
No 54
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.92 E-value=0.13 Score=38.72 Aligned_cols=49 Identities=18% Similarity=0.313 Sum_probs=36.3
Q ss_pred cccCCCCCChhh--HHhhcC--CeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737 31 LKMSGRKETVLD--LAKFVD--KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 31 ~~ms~~~~~~~~--L~~~i~--k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a 79 (112)
-.|++++....+ |+.+.. .+|.|.|.+|-.++|.+.+||+|.=|+-.+.
T Consensus 3 ~~m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 3 ANMAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred ccccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 357766666555 555543 4788899999999999999999986665453
No 55
>PRK14644 hypothetical protein; Provisional
Probab=93.33 E-value=0.34 Score=35.08 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=32.5
Q ss_pred CCCChhhHHhhcCCeEEEEEcCC----eEEEEEEEeecCccceeec
Q 033737 36 RKETVLDLAKFVDKGVQVKLTGG----RQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 36 ~~~~~~~L~~~i~k~V~V~L~dg----r~i~G~L~~fD~~mNlvL~ 77 (112)
+|....++.+++|+.|.|+|++. +.++|.|.++|.. ++.|.
T Consensus 73 RpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 73 MDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred CCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 33444578999999999999877 9999999999873 45553
No 56
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=92.42 E-value=0.52 Score=30.88 Aligned_cols=37 Identities=38% Similarity=0.502 Sum_probs=30.0
Q ss_pred ChhhHHhhcCCeEEEEEc---CC-eEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~---dg-r~i~G~L~~fD~~mNlvL 76 (112)
.+.++.+++|+.|.|+++ +| +.+.|.|.++|.- ++.|
T Consensus 16 ~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 16 KEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 356789999999999997 55 6899999999874 3444
No 57
>PRK14633 hypothetical protein; Provisional
Probab=91.53 E-value=0.62 Score=34.07 Aligned_cols=37 Identities=16% Similarity=0.281 Sum_probs=30.2
Q ss_pred ChhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL 76 (112)
.+.++.+++|++|.|++ .+++.++|+|.++|.. ++.|
T Consensus 85 ~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 85 NIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 35678999999999998 4679999999999874 4444
No 58
>PRK14640 hypothetical protein; Provisional
Probab=91.17 E-value=0.7 Score=33.82 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=30.8
Q ss_pred ChhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceeec
Q 033737 39 TVLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL~ 77 (112)
.+.++.+++|++|.|++ .+++.++|+|.++|.. ++.|.
T Consensus 88 ~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 88 KVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 36678999999999999 5679999999999874 44443
No 59
>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=91.04 E-value=0.66 Score=33.09 Aligned_cols=36 Identities=31% Similarity=0.556 Sum_probs=27.1
Q ss_pred hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCccceee
Q 033737 40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~mNlvL 76 (112)
..++.+++|++|.|++ .+.+.+.|+|.++|. -.++|
T Consensus 79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 5578999999999999 455789999999998 34444
No 60
>PRK14642 hypothetical protein; Provisional
Probab=90.91 E-value=0.7 Score=35.62 Aligned_cols=37 Identities=16% Similarity=0.327 Sum_probs=30.7
Q ss_pred ChhhHHhhcCCeEEEEEc-------------CCeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLT-------------GGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~-------------dgr~i~G~L~~fD~~mNlvL 76 (112)
...++.+++|+.|.|+|+ +.+.++|+|.++|.. ++.|
T Consensus 91 ~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 91 HEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 366789999999999998 679999999999874 4434
No 61
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=90.73 E-value=0.51 Score=31.46 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=25.9
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~ 77 (112)
-..+|.|-|.||-.+.|.+.|||+|.=|+=.
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~ 48 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFVVLLKN 48 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEEEEEEc
Confidence 3458999999999999999999999754433
No 62
>PRK14645 hypothetical protein; Provisional
Probab=90.56 E-value=0.76 Score=33.89 Aligned_cols=35 Identities=17% Similarity=0.295 Sum_probs=29.0
Q ss_pred hhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737 40 VLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL 76 (112)
+.++.+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus 94 ~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 94 ARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 5678999999999986 789999999999874 3444
No 63
>PRK14636 hypothetical protein; Provisional
Probab=90.21 E-value=0.87 Score=34.28 Aligned_cols=37 Identities=27% Similarity=0.499 Sum_probs=30.0
Q ss_pred ChhhHHhhcCCeEEEEEc---CC-eEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLT---GG-RQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~---dg-r~i~G~L~~fD~~mNlvL 76 (112)
.+.++.+++|++|.|+++ +| +.++|+|.++|.- ++.|
T Consensus 89 ~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 89 RPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 366789999999999997 55 6999999999873 4444
No 64
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=90.10 E-value=1 Score=32.81 Aligned_cols=31 Identities=32% Similarity=0.594 Sum_probs=27.9
Q ss_pred hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecC
Q 033737 40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQ 70 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~ 70 (112)
+.++.+++|+.|+|++ .+++.++|+|.++|.
T Consensus 90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 5679999999999997 578899999999987
No 65
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.04 E-value=1.3 Score=32.89 Aligned_cols=33 Identities=27% Similarity=0.477 Sum_probs=30.1
Q ss_pred hhhHHhhcCCeEEEEE----cCCeEEEEEEEeecCcc
Q 033737 40 VLDLAKFVDKGVQVKL----TGGRQVTGTLKGYDQLL 72 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L----~dgr~i~G~L~~fD~~m 72 (112)
..+..+++|+.|.|+| .+++.++|+|.++|.-.
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 5568999999999999 88999999999999876
No 66
>PRK14634 hypothetical protein; Provisional
Probab=89.77 E-value=1.1 Score=33.02 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=29.5
Q ss_pred ChhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~mNlvL 76 (112)
.+.+..+++|++|+|++.+ .+.++|+|.++|.- ++.|
T Consensus 91 ~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 91 SDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 3667899999999999863 37899999999864 3444
No 67
>PRK14643 hypothetical protein; Provisional
Probab=89.45 E-value=1.1 Score=33.32 Aligned_cols=32 Identities=22% Similarity=0.298 Sum_probs=28.0
Q ss_pred hhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCc
Q 033737 40 VLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQL 71 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~ 71 (112)
..++.+++|++|.|++.+ .+.++|+|.++|.-
T Consensus 96 ~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 96 QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 667899999999999865 68999999999865
No 68
>PRK14632 hypothetical protein; Provisional
Probab=89.39 E-value=1.1 Score=33.47 Aligned_cols=37 Identities=19% Similarity=0.380 Sum_probs=30.1
Q ss_pred hhhHHhhcCCeEEEEEcC-------CeEEEEEEEeecCccceeec
Q 033737 40 VLDLAKFVDKGVQVKLTG-------GRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~d-------gr~i~G~L~~fD~~mNlvL~ 77 (112)
..++.+++|+.|.|++.+ .+.+.|+|.++|.- ++.|.
T Consensus 90 ~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 90 AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 567899999999999975 57999999999853 44443
No 69
>PRK14646 hypothetical protein; Provisional
Probab=89.15 E-value=1.3 Score=32.65 Aligned_cols=37 Identities=22% Similarity=0.202 Sum_probs=29.6
Q ss_pred ChhhHHhhcCCeEEEEEcC----CeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLTG----GRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD~~mNlvL 76 (112)
...++.+++|++|.|+|++ -+.++|+|.++|.- .+.|
T Consensus 91 ~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 91 SERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 3567899999999999854 37789999999874 4554
No 70
>PRK14647 hypothetical protein; Provisional
Probab=88.07 E-value=1.6 Score=32.09 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=27.5
Q ss_pred ChhhHHhhcCCeEEEEEc---------CCeEEEEEEEeecC
Q 033737 39 TVLDLAKFVDKGVQVKLT---------GGRQVTGTLKGYDQ 70 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~---------dgr~i~G~L~~fD~ 70 (112)
.+.++.+++|++|.|+++ +.+.++|+|.++|.
T Consensus 90 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 90 KEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 356789999999999995 35899999999986
No 71
>PRK14631 hypothetical protein; Provisional
Probab=87.77 E-value=1.6 Score=32.87 Aligned_cols=31 Identities=19% Similarity=0.375 Sum_probs=27.4
Q ss_pred ChhhHHhhcCCeEEEEEc----CCeEEEEEEEeec
Q 033737 39 TVLDLAKFVDKGVQVKLT----GGRQVTGTLKGYD 69 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~----dgr~i~G~L~~fD 69 (112)
...++.+++|+.|.|++. +.+.++|+|.++|
T Consensus 108 ~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 108 QLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 366799999999999995 5599999999998
No 72
>PRK14637 hypothetical protein; Provisional
Probab=86.06 E-value=2.2 Score=31.34 Aligned_cols=38 Identities=29% Similarity=0.349 Sum_probs=28.8
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEE-EEEEEeecCccceeec
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLD 77 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i-~G~L~~fD~~mNlvL~ 77 (112)
.+.++.+++|++|.|++.+.+.+ +|+|.++|.- ++.|.
T Consensus 89 ~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 89 NAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 36678999999999999544455 7999999874 44443
No 73
>PRK14641 hypothetical protein; Provisional
Probab=85.87 E-value=2.2 Score=32.16 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=26.3
Q ss_pred hhhHHhhcCCeEEEEEcC----CeEEEEEEEeec
Q 033737 40 VLDLAKFVDKGVQVKLTG----GRQVTGTLKGYD 69 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~d----gr~i~G~L~~fD 69 (112)
..+..+++|+.|.|++.+ .+.++|+|.++|
T Consensus 96 ~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 96 PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 567899999999999965 568999999996
No 74
>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=84.88 E-value=2.6 Score=28.16 Aligned_cols=57 Identities=16% Similarity=0.093 Sum_probs=40.0
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeecCc-cceeecceEEEeecCCCCCccccceEeeeeEEEeCCcee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYDQL-LNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACV 110 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~-mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv 110 (112)
..|....|++|.+.|.++.+..|++.|+|.. .|+..++-. . .-......++|...|+
T Consensus 17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T------------PlGv~~eAlLR~~DVi 74 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T------------PLGVQPEALLRCSDVI 74 (80)
T ss_dssp HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T------------TTTEEEEEEEEGGGEE
T ss_pred HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C------------CcccChhheeecCCEE
Confidence 3467778999999999999999999999966 577666522 1 1122467788887776
No 75
>PRK06955 biotin--protein ligase; Provisional
Probab=84.71 E-value=4 Score=32.59 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=28.9
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
++|++|++...+++.+.|++.|+|....|+++.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 588999997767788999999999999999853
No 76
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=82.70 E-value=2.9 Score=26.94 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=28.4
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
.-..|++++|++|.|.+..|.. .|+|.+.... .++|+.
T Consensus 12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~ 49 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEE 49 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEe
Confidence 3456899999999999977765 9999998532 234443
No 77
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=80.27 E-value=8.1 Score=30.72 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=27.0
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~ 77 (112)
++|++|++... +..++|++.|+|....|++.
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence 58899999874 45799999999999999995
No 78
>PRK14630 hypothetical protein; Provisional
Probab=77.97 E-value=6.5 Score=28.54 Aligned_cols=36 Identities=11% Similarity=0.161 Sum_probs=27.9
Q ss_pred ChhhHHhhcCCeEEEEEcCCeEEEEEEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL 76 (112)
.+.+..+++|++|.|++... ..+|+|.++|. .++.|
T Consensus 88 ~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 88 SDREFKIFEGKKIKLMLDND-FEEGFILEAKA-DSFIF 123 (143)
T ss_pred CHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeC-CEEEE
Confidence 35678999999999999654 45999999987 34444
No 79
>PRK08330 biotin--protein ligase; Provisional
Probab=76.32 E-value=12 Score=28.55 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=27.3
Q ss_pred hhcCCeEEEEEcCCeEE-EEEEEeecCccceeecc
Q 033737 45 KFVDKGVQVKLTGGRQV-TGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 45 ~~i~k~V~V~L~dgr~i-~G~L~~fD~~mNlvL~~ 78 (112)
.++|++|++.. ++..+ .|+..|+|....|++..
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 36899999975 56665 79999999999999974
No 80
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=75.83 E-value=10 Score=33.44 Aligned_cols=33 Identities=30% Similarity=0.248 Sum_probs=28.8
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
++|++|++...+++.+.|+..|+|....|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 578999987677778999999999999999963
No 81
>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=75.53 E-value=17 Score=27.78 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=26.9
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeec
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLD 77 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~ 77 (112)
++|++|.+...+ ..+.|+..|+|....|+++
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 579999998654 5699999999999999996
No 82
>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=75.44 E-value=3.2 Score=31.17 Aligned_cols=25 Identities=24% Similarity=0.512 Sum_probs=22.9
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCc
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~ 71 (112)
-|+.|+|.+.|||.|+|+=.|.|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 6789999999999999999999864
No 83
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=75.24 E-value=6.7 Score=29.48 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=32.1
Q ss_pred hhcCCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 45 ~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
++-+-+|+|.+.||+.|.|.+.||++--|.+|..+.
T Consensus 26 r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 26 RFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred HhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 445679999999999999999999999999988764
No 84
>PRK14635 hypothetical protein; Provisional
Probab=72.80 E-value=11 Score=27.72 Aligned_cols=37 Identities=19% Similarity=0.151 Sum_probs=28.9
Q ss_pred ChhhHHhhcCCeEEEEEc--CCeEEEE---EEEeecCccceee
Q 033737 39 TVLDLAKFVDKGVQVKLT--GGRQVTG---TLKGYDQLLNLVL 76 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~L~--dgr~i~G---~L~~fD~~mNlvL 76 (112)
.+.++.++.|+.|.|++. ++..+.| +|.++|.- ++.|
T Consensus 90 ~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 90 LPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 366799999999999875 4678887 99999864 4444
No 85
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=71.26 E-value=14 Score=31.03 Aligned_cols=65 Identities=12% Similarity=0.061 Sum_probs=46.7
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEeec-CccceeecceEEEeecC-CCC--CccccceEeeeeEEEeCCce
Q 033737 44 AKFVDKGVQVKLTGGRQVTGTLKGYD-QLLNLVLDEAVEFLRDA-DDP--LKTTDQTRQLGLIGNCCDAC 109 (112)
Q Consensus 44 ~~~i~k~V~V~L~dgr~i~G~L~~fD-~~mNlvL~~a~E~~~~~-~~~--~~~~~~~r~lGlvvIRGd~i 109 (112)
-.|||++|.++-+..-+|+|+|.-+| +.-=|-|.++.-+-... +++ .+....+ -+--|+.||..|
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~k-Vy~YIlFRGSDI 73 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDK-VYDYILFRGSDI 73 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCcc-ceeeEEecCccc
Confidence 35899999999999999999999999 56788888864443322 111 2221222 567899999876
No 86
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=70.56 E-value=20 Score=27.96 Aligned_cols=36 Identities=31% Similarity=0.355 Sum_probs=32.4
Q ss_pred hhcCCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 45 KFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 45 ~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
..+|++|++...++....|+..++|....|+|+...
T Consensus 187 ~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~~ 222 (238)
T COG0340 187 LSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETDD 222 (238)
T ss_pred ccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeCC
Confidence 348999999999999999999999999999998863
No 87
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=67.95 E-value=12 Score=29.81 Aligned_cols=32 Identities=25% Similarity=0.305 Sum_probs=27.4
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecc
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
++|++|.+.. ++..+.|++.|+|....|+|..
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 3789999874 6788999999999999999864
No 88
>PRK10898 serine endoprotease; Provisional
Probab=66.71 E-value=12 Score=30.61 Aligned_cols=32 Identities=28% Similarity=0.352 Sum_probs=28.0
Q ss_pred CeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
..+.|++.||+.+.++++++|...+|-|=...
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57899999999999999999999988766553
No 89
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=65.40 E-value=8.5 Score=22.87 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=15.0
Q ss_pred EEEEEEeecCccceeecceEEE
Q 033737 61 VTGTLKGYDQLLNLVLDEAVEF 82 (112)
Q Consensus 61 i~G~L~~fD~~mNlvL~~a~E~ 82 (112)
..|++.|.|+...|+|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999987654
No 90
>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=64.60 E-value=13 Score=30.17 Aligned_cols=32 Identities=28% Similarity=0.399 Sum_probs=28.0
Q ss_pred CeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
..+.|++.||+.+.++++++|...+|.|=...
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 36899999999999999999999998876554
No 91
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=63.68 E-value=3.8 Score=30.20 Aligned_cols=24 Identities=25% Similarity=0.307 Sum_probs=18.8
Q ss_pred cCCeEEEEEEEeecCccceeecce
Q 033737 56 TGGRQVTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 56 ~dgr~i~G~L~~fD~~mNlvL~~a 79 (112)
+.+-.=+|+|+|.|+|.|=--++-
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred hcccccceeeeeecccccchhccc
Confidence 344556799999999999877765
No 92
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=61.99 E-value=12 Score=26.08 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=14.6
Q ss_pred CeEEEEEcCCeEEEEEEE
Q 033737 49 KGVQVKLTGGRQVTGTLK 66 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~ 66 (112)
.+|.+.|+||+.+.|++.
T Consensus 29 ~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 29 ERVELELDDGSMLRGTVA 46 (101)
T ss_dssp -EEEEEETTS-EEEEEEC
T ss_pred ceEEEEEcCCCeeeeeec
Confidence 489999999999999974
No 93
>PRK10942 serine endoprotease; Provisional
Probab=61.46 E-value=15 Score=31.24 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=27.5
Q ss_pred CeEEEEEcCCeEEEEEEEeecCccceeecce
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a 79 (112)
..+.|++.||+.+.++++++|...+|-|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999998877654
No 94
>PRK10139 serine endoprotease; Provisional
Probab=61.19 E-value=16 Score=30.94 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=28.2
Q ss_pred CeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
.++.|++.||+.+.++++|+|....|-+=...
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 58999999999999999999999988775543
No 95
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=59.87 E-value=3 Score=40.25 Aligned_cols=55 Identities=16% Similarity=0.164 Sum_probs=0.0
Q ss_pred EEEEEcCCeEEEEEEEeecCccceeecceEEEeecCCCCCccccceEeeeeEEEeCCceec
Q 033737 51 VQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRDADDPLKTTDQTRQLGLIGNCCDACVT 111 (112)
Q Consensus 51 V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~~~~~~~~~~~~r~lGlvvIRGd~iv~ 111 (112)
.+=...+|+.+.|.|+..|.-|+.+|.---+..+.. ..-+..+|.++|+|+|.||
T Consensus 250 ~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~~------v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 250 STYTTSSGRPVDGVLVTTANVMQKLLNLLGQISDTS------VSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -------------------------------------------------------------
T ss_pred ceeecCCCCEeceEEeccHHHHHHHHHHHhhhccce------eecchhheeeeecCccHHH
Confidence 333468999999999999988887776655522211 1356789999999999998
No 96
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=56.26 E-value=48 Score=24.30 Aligned_cols=43 Identities=26% Similarity=0.330 Sum_probs=31.8
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecC-ccc--eeecceEEEee
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQ-LLN--LVLDEAVEFLR 84 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~-~mN--lvL~~a~E~~~ 84 (112)
....++||.|.+...+|..+.|++.++.- ... +++.+..++.-
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~~~~g~~~~~~v~G~~~~l 131 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNGTWIVA 131 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEEEcCCcEEEEEECCEEEec
Confidence 45689999999999999999999999862 222 34556555543
No 97
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=55.85 E-value=5.2 Score=27.49 Aligned_cols=17 Identities=35% Similarity=0.483 Sum_probs=15.2
Q ss_pred EEEEeecCccceeecce
Q 033737 63 GTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 63 G~L~~fD~~mNlvL~~a 79 (112)
|+|+|.|.|.|.--+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999987776
No 98
>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=52.92 E-value=27 Score=28.93 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=28.2
Q ss_pred CeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
.++.|++.||+.+.+++.++|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47899999999999999999999998876654
No 99
>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=46.87 E-value=20 Score=23.71 Aligned_cols=24 Identities=25% Similarity=0.484 Sum_probs=16.1
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEE
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGT 64 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~ 64 (112)
.++.=..+.+|+++|+||..++|+
T Consensus 10 iEiAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 10 IEIACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHHHTTTT-EEEE-TTT--EEES
T ss_pred HHHHHhcCCeEEEEEeCCCEEEEE
Confidence 345556788999999999999997
No 100
>PRK08477 biotin--protein ligase; Provisional
Probab=45.02 E-value=74 Score=24.37 Aligned_cols=35 Identities=9% Similarity=-0.025 Sum_probs=29.5
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecceEE
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVE 81 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E 81 (112)
.+++.|++. .+++.++|+..+.|...-|++.--.-
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 488999986 57899999999999999998876443
No 101
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=39.07 E-value=31 Score=22.76 Aligned_cols=28 Identities=32% Similarity=0.456 Sum_probs=21.2
Q ss_pred hhHHhhcCCeEEEEEcCCeE----EEEEEEee
Q 033737 41 LDLAKFVDKGVQVKLTGGRQ----VTGTLKGY 68 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~----i~G~L~~f 68 (112)
.+|.+++|++|.++.+.||. -+|+|...
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 35889999999999999974 67888764
No 102
>PRK06630 hypothetical protein; Provisional
Probab=37.57 E-value=18 Score=25.14 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=16.5
Q ss_pred EEEEEEeecCccceeecce
Q 033737 61 VTGTLKGYDQLLNLVLDEA 79 (112)
Q Consensus 61 i~G~L~~fD~~mNlvL~~a 79 (112)
..|+|+|-|+|.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999888774
No 103
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=36.40 E-value=52 Score=26.02 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=19.2
Q ss_pred EEEEEEEeecCccceeecceEE
Q 033737 60 QVTGTLKGYDQLLNLVLDEAVE 81 (112)
Q Consensus 60 ~i~G~L~~fD~~mNlvL~~a~E 81 (112)
.++|.+.-+|.|.|++++=..+
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~~ 190 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISRE 190 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEHH
T ss_pred eEEEEEEEECccCCeeeCCCHH
Confidence 8999999999999999875443
No 104
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=36.28 E-value=46 Score=22.50 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=18.4
Q ss_pred hhcCCeEEEE-EcCCeEEEEEEEe
Q 033737 45 KFVDKGVQVK-LTGGRQVTGTLKG 67 (112)
Q Consensus 45 ~~i~k~V~V~-L~dgr~i~G~L~~ 67 (112)
-.+|..|+|+ +..|+.+.|+..+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 3578888888 7888888888765
No 105
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=33.18 E-value=33 Score=22.44 Aligned_cols=18 Identities=28% Similarity=0.265 Sum_probs=14.4
Q ss_pred HHhhcCCeEEEEEcCCeE
Q 033737 43 LAKFVDKGVQVKLTGGRQ 60 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~ 60 (112)
++..+||+|||+.+...+
T Consensus 6 ~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 6 LNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhcCceEEEEeCCccc
Confidence 678899999999765544
No 106
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=32.77 E-value=1.3e+02 Score=18.78 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=18.9
Q ss_pred EcCCeEEEEEEEeecCccceeecc
Q 033737 55 LTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 55 L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
++-|..+.+.+..+|+-+.+.|+-
T Consensus 51 ~~~GD~i~~~V~~~~~~~~i~LS~ 74 (82)
T cd04454 51 LQPGDLILAKVISLGDDMNVLLTT 74 (82)
T ss_pred CCCCCEEEEEEEEeCCCCCEEEEE
Confidence 677889999999998766777654
No 107
>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=32.61 E-value=68 Score=22.39 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=18.1
Q ss_pred eEEEEEcCCeEEEEEEEeecC
Q 033737 50 GVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 50 ~V~V~L~dgr~i~G~L~~fD~ 70 (112)
...|.++||+.+.|.+..=|.
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~ 79 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA 79 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC
Confidence 478999999999999998553
No 108
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=31.55 E-value=47 Score=21.00 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=19.3
Q ss_pred CeEEEEEcCCeEEEEEEEeecC
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~ 70 (112)
.+|.|++-||..+++++..-|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCc
Confidence 5899999999999999987664
No 109
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=30.90 E-value=94 Score=22.76 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=23.4
Q ss_pred HhhcCCeEEEEEcCCeEEEEEEEeecC
Q 033737 44 AKFVDKGVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 44 ~~~i~k~V~V~L~dgr~i~G~L~~fD~ 70 (112)
..++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 478999999888999999999997753
No 110
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=30.34 E-value=29 Score=24.67 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=16.2
Q ss_pred EEEEEeecCccceeecceE
Q 033737 62 TGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 62 ~G~L~~fD~~mNlvL~~a~ 80 (112)
.|+|+|.|++.|---++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6999999999998887643
No 111
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.23 E-value=53 Score=22.03 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=17.8
Q ss_pred hhHHhhcCCeEEEEEcCCeEE
Q 033737 41 LDLAKFVDKGVQVKLTGGRQV 61 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i 61 (112)
.++..++|++|.+++++||.=
T Consensus 12 ~~i~ah~G~~v~lk~ngGRKk 32 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRKK 32 (80)
T ss_pred HHHHhccCcEEEEEecCCcee
Confidence 357788999999999999863
No 112
>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=30.05 E-value=99 Score=21.61 Aligned_cols=32 Identities=19% Similarity=0.262 Sum_probs=26.4
Q ss_pred cCCCCCChhhHHhhcCCeEEEEEcCCeEEEEE
Q 033737 33 MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGT 64 (112)
Q Consensus 33 ms~~~~~~~~L~~~i~k~V~V~L~dgr~i~G~ 64 (112)
...+..+..+|...-+-.|...+.+|+.|.+.
T Consensus 59 ~~~~~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 59 RDTKDTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred EcCCCCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 33555667888999999999999999999875
No 113
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=28.86 E-value=43 Score=25.11 Aligned_cols=19 Identities=26% Similarity=0.207 Sum_probs=16.3
Q ss_pred EEEEEeecCccceeecceE
Q 033737 62 TGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 62 ~G~L~~fD~~mNlvL~~a~ 80 (112)
.|+|+|-|+|.|---++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999998887763
No 114
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=28.73 E-value=55 Score=19.54 Aligned_cols=16 Identities=25% Similarity=0.229 Sum_probs=12.8
Q ss_pred ChhhHHhhcCCeEEEE
Q 033737 39 TVLDLAKFVDKGVQVK 54 (112)
Q Consensus 39 ~~~~L~~~i~k~V~V~ 54 (112)
....+++++||+|+|.
T Consensus 10 ~~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 10 DYSYLKSLLGKRVSVT 25 (48)
T ss_pred hhHHHHHhcCCeEEEE
Confidence 3556778999999987
No 115
>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=28.65 E-value=1.2e+02 Score=17.33 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=20.8
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCc
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQL 71 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~ 71 (112)
.|..+.+...||+.+.|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777778999999999999864
No 116
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.43 E-value=66 Score=24.76 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=19.1
Q ss_pred hcCCeEEEE-EcCCeEEEEEEEe
Q 033737 46 FVDKGVQVK-LTGGRQVTGTLKG 67 (112)
Q Consensus 46 ~i~k~V~V~-L~dgr~i~G~L~~ 67 (112)
.+|..|+|+ +..|+.+.|+..+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 578899999 8999999998876
No 117
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=27.71 E-value=47 Score=21.23 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=20.4
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecC
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~ 70 (112)
|-..+|.|+|-||..+++++-.-|.
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~t 26 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKAREQ 26 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCCh
Confidence 3456899999999999999886553
No 118
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=27.56 E-value=69 Score=20.03 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.8
Q ss_pred CeEEEEEcCCeEEEEEEEeecC
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~ 70 (112)
.+|.|++-||..++.++..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 4789999999999999987664
No 119
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.43 E-value=1.2e+02 Score=24.29 Aligned_cols=33 Identities=27% Similarity=0.426 Sum_probs=26.5
Q ss_pred CCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 48 DKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 48 ~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
..++.+.+.||+.+.+.+.|.|...-+.+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 468888899999999999999988766554433
No 120
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=26.88 E-value=70 Score=19.98 Aligned_cols=22 Identities=14% Similarity=0.445 Sum_probs=18.7
Q ss_pred CeEEEEEcCCeEEEEEEEeecC
Q 033737 49 KGVQVKLTGGRQVTGTLKGYDQ 70 (112)
Q Consensus 49 k~V~V~L~dgr~i~G~L~~fD~ 70 (112)
.+|+|++-||..+++++..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4789999999999999876664
No 121
>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=25.82 E-value=1.6e+02 Score=19.65 Aligned_cols=15 Identities=33% Similarity=0.401 Sum_probs=11.9
Q ss_pred hhhHHhhcCCeEEEE
Q 033737 40 VLDLAKFVDKGVQVK 54 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~ 54 (112)
...|.+|.|++|++.
T Consensus 7 ~~~L~~f~gk~V~iv 21 (101)
T cd04479 7 GAMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHHhhCCCEEEEE
Confidence 345899999999875
No 122
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.64 E-value=94 Score=23.90 Aligned_cols=35 Identities=11% Similarity=0.111 Sum_probs=30.9
Q ss_pred hcCCeEEEEEcCCeEEEEEEEeecCccceeecceE
Q 033737 46 FVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 46 ~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~ 80 (112)
-+|..|++..-++...+|.+.+||--.+...-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 36788999999999999999999988888777776
No 123
>PRK10708 hypothetical protein; Provisional
Probab=24.85 E-value=83 Score=20.00 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=27.1
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCcc--ceeecceEEE
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLL--NLVLDEAVEF 82 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~m--NlvL~~a~E~ 82 (112)
++.+|.|++..|-.=+|++.+...|. -+.|-.-.+|
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~EG~MyLvaL~dY 40 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFSEGTMYLVSLEDY 40 (62)
T ss_pred cccEEEEecCCCccccceEEEEeeccCcEEEEEEcCcC
Confidence 56799999999999999999998773 3444443343
No 124
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=24.85 E-value=1.4e+02 Score=18.56 Aligned_cols=25 Identities=24% Similarity=0.379 Sum_probs=18.1
Q ss_pred cCCeEEEEEcCC-eEEEEEEEeecCc
Q 033737 47 VDKGVQVKLTGG-RQVTGTLKGYDQL 71 (112)
Q Consensus 47 i~k~V~V~L~dg-r~i~G~L~~fD~~ 71 (112)
.|..|.++--++ ..|.|++.+||.-
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred CCCEEEEECCCCCcEEEEEEEEeccc
Confidence 788999998765 5569999999953
No 125
>PRK08183 NADH dehydrogenase; Validated
Probab=24.12 E-value=42 Score=24.37 Aligned_cols=19 Identities=21% Similarity=0.195 Sum_probs=16.0
Q ss_pred EEEEEeecCccceeecceE
Q 033737 62 TGTLKGYDQLLNLVLDEAV 80 (112)
Q Consensus 62 ~G~L~~fD~~mNlvL~~a~ 80 (112)
.|+|+|-|++.|---++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999998876543
No 126
>PRK11625 Rho-binding antiterminator; Provisional
Probab=22.20 E-value=2.1e+02 Score=19.13 Aligned_cols=38 Identities=21% Similarity=0.220 Sum_probs=25.6
Q ss_pred hHHhhcCCeEEEEEcCCeEEEEEEEeecCccceeecceEEEeec
Q 033737 42 DLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLRD 85 (112)
Q Consensus 42 ~L~~~i~k~V~V~L~dgr~i~G~L~~fD~~mNlvL~~a~E~~~~ 85 (112)
++.=.-+.++.+.|+||..++|+- .|-+ ..+-.|+...
T Consensus 17 ElAC~~~~~l~l~l~dGe~~~g~A--~D~~----~~~k~EyL~l 54 (84)
T PRK11625 17 ELACQHHLMLTLELKDGEVLQAKA--SDLV----SRKNVEYLVV 54 (84)
T ss_pred HHHHhcCCeEEEEECCCCEEEEEE--Eeee----cCCceEEEEE
Confidence 444446789999999999999986 3433 2344555443
No 127
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=21.77 E-value=1.2e+02 Score=22.67 Aligned_cols=29 Identities=28% Similarity=0.489 Sum_probs=23.2
Q ss_pred hhHHhhcCCeEEEEEcCCeEEEEEEEeec
Q 033737 41 LDLAKFVDKGVQVKLTGGRQVTGTLKGYD 69 (112)
Q Consensus 41 ~~L~~~i~k~V~V~L~dgr~i~G~L~~fD 69 (112)
.++..++|++|.|.+...+.+.|.+..++
T Consensus 21 ~~~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 21 LDLKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp S-CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred CChhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 34455899999999998899999998885
No 128
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=20.73 E-value=1.7e+02 Score=24.74 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=24.7
Q ss_pred hhhHHhhcCCeEEEEEc--CC--eEEEEEEEeec
Q 033737 40 VLDLAKFVDKGVQVKLT--GG--RQVTGTLKGYD 69 (112)
Q Consensus 40 ~~~L~~~i~k~V~V~L~--dg--r~i~G~L~~fD 69 (112)
..++.+++|+++.|.+. +| |.+.|.+..+.
T Consensus 39 ~l~~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 39 DIDLEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred CCCHHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 35688899999999985 33 77999999885
No 129
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=20.70 E-value=1.5e+02 Score=22.87 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=24.0
Q ss_pred cCCeEEEE---EcCCeEEEEEEEeecCccceeecc
Q 033737 47 VDKGVQVK---LTGGRQVTGTLKGYDQLLNLVLDE 78 (112)
Q Consensus 47 i~k~V~V~---L~dgr~i~G~L~~fD~~mNlvL~~ 78 (112)
+++.+.+. ..++..+.|+..|+|....|+++.
T Consensus 197 ~~~~~~~~~~~~~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 197 MDKSLKLHKRTPTGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred HhhhhccCeEEEcCCcEEEEEEEEECCCCeEEEEE
Confidence 35554332 246778899999999999999975
No 130
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=20.66 E-value=1e+02 Score=19.57 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=22.8
Q ss_pred cCCeEEEEEcCCeEEEEEEEeecCcc
Q 033737 47 VDKGVQVKLTGGRQVTGTLKGYDQLL 72 (112)
Q Consensus 47 i~k~V~V~L~dgr~i~G~L~~fD~~m 72 (112)
++.+|.|++..|-.=.|++.+...|.
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 56789999999999999999998873
No 131
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=20.53 E-value=1.6e+02 Score=22.74 Aligned_cols=27 Identities=33% Similarity=0.367 Sum_probs=23.4
Q ss_pred HHhhcCCeEEEEEcCCeEEEEEEEeec
Q 033737 43 LAKFVDKGVQVKLTGGRQVTGTLKGYD 69 (112)
Q Consensus 43 L~~~i~k~V~V~L~dgr~i~G~L~~fD 69 (112)
-..|+||.|.+.-.+|..+.|++.+..
T Consensus 113 a~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 113 GMKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 357899999998889999999998775
Done!