Query psy15782
Match_columns 129
No_of_seqs 182 out of 1112
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 21:12:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3428|consensus 100.0 8.5E-29 1.8E-33 168.4 9.6 98 1-99 4-101 (109)
2 cd01724 Sm_D1 The eukaryotic S 100.0 5.5E-28 1.2E-32 162.2 10.7 85 1-85 3-87 (90)
3 KOG3172|consensus 99.9 4.1E-25 8.8E-30 150.0 11.5 80 1-87 7-86 (119)
4 cd01721 Sm_D3 The eukaryotic S 99.9 1.9E-24 4.2E-29 138.8 9.5 69 1-69 2-70 (70)
5 cd01733 LSm10 The eukaryotic S 99.9 1.3E-23 2.9E-28 137.5 9.3 68 1-68 11-78 (78)
6 KOG3293|consensus 99.9 9.5E-24 2.1E-28 146.4 7.9 74 2-76 5-79 (134)
7 cd01723 LSm4 The eukaryotic Sm 99.9 5.6E-23 1.2E-27 133.9 8.8 71 1-71 3-74 (76)
8 cd01725 LSm2 The eukaryotic Sm 99.9 1.9E-22 4.2E-27 132.9 9.5 71 1-71 3-75 (81)
9 cd01726 LSm6 The eukaryotic Sm 99.8 6.3E-21 1.4E-25 121.4 8.7 66 1-66 2-67 (67)
10 cd01722 Sm_F The eukaryotic Sm 99.8 2.7E-20 5.8E-25 118.8 8.3 66 1-66 3-68 (68)
11 PRK00737 small nuclear ribonuc 99.8 3E-19 6.5E-24 115.2 8.8 66 1-66 6-71 (72)
12 cd01731 archaeal_Sm1 The archa 99.8 5.7E-19 1.2E-23 112.6 9.0 66 1-66 2-67 (68)
13 smart00651 Sm snRNP Sm protein 99.8 1E-18 2.2E-23 110.4 8.8 66 2-67 1-67 (67)
14 PF01423 LSM: LSM domain ; In 99.8 9.2E-19 2E-23 110.7 8.1 66 2-67 1-67 (67)
15 cd00600 Sm_like The eukaryotic 99.7 1.2E-17 2.5E-22 104.1 8.6 63 4-66 1-63 (63)
16 cd01719 Sm_G The eukaryotic Sm 99.7 1.6E-17 3.4E-22 107.2 9.0 68 2-69 3-70 (72)
17 cd01732 LSm5 The eukaryotic Sm 99.7 1.2E-17 2.7E-22 108.8 8.6 65 2-66 6-73 (76)
18 COG1958 LSM1 Small nuclear rib 99.7 3.9E-17 8.6E-22 106.8 8.4 65 2-66 10-78 (79)
19 KOG3448|consensus 99.7 6.1E-17 1.3E-21 106.7 7.7 69 2-70 5-75 (96)
20 cd01729 LSm7 The eukaryotic Sm 99.7 7E-16 1.5E-20 101.6 8.9 66 4-69 7-80 (81)
21 KOG3482|consensus 99.7 1.6E-16 3.4E-21 101.2 5.3 65 2-66 11-75 (79)
22 cd01730 LSm3 The eukaryotic Sm 99.6 2.4E-15 5.1E-20 99.2 8.4 65 2-66 4-81 (82)
23 cd01720 Sm_D2 The eukaryotic S 99.6 3.1E-15 6.7E-20 99.8 8.3 65 2-66 5-84 (87)
24 cd01718 Sm_E The eukaryotic Sm 99.6 6.1E-15 1.3E-19 96.7 7.8 65 2-66 9-78 (79)
25 cd01728 LSm1 The eukaryotic Sm 99.6 2.1E-14 4.6E-19 93.1 8.8 66 2-67 5-73 (74)
26 cd01717 Sm_B The eukaryotic Sm 99.6 2.1E-14 4.5E-19 94.0 8.4 64 4-67 5-78 (79)
27 KOG1783|consensus 99.5 1E-15 2.2E-20 97.6 0.7 68 2-69 9-76 (77)
28 cd01727 LSm8 The eukaryotic Sm 99.5 6.1E-14 1.3E-18 90.8 8.8 67 3-69 3-73 (74)
29 cd06168 LSm9 The eukaryotic Sm 99.5 2.1E-13 4.5E-18 88.7 8.3 66 2-67 3-74 (75)
30 PTZ00138 small nuclear ribonuc 99.5 5.1E-13 1.1E-17 89.4 8.3 66 2-67 17-87 (89)
31 KOG1780|consensus 99.4 9.1E-13 2E-17 84.3 5.9 65 3-67 8-72 (77)
32 KOG3262|consensus 99.3 2.9E-12 6.4E-17 95.4 6.1 70 3-80 67-142 (215)
33 KOG1775|consensus 99.2 1.6E-11 3.4E-16 79.1 2.7 66 2-67 10-78 (84)
34 KOG3460|consensus 99.1 1.4E-11 2.9E-16 80.6 1.8 69 2-70 8-89 (91)
35 KOG1774|consensus 98.7 2.1E-08 4.5E-13 65.5 4.9 58 11-68 26-86 (88)
36 KOG3168|consensus 98.4 4.5E-07 9.7E-12 66.6 3.9 72 4-75 9-90 (177)
37 KOG1781|consensus 98.3 8.8E-08 1.9E-12 64.6 -0.4 68 4-71 22-97 (108)
38 KOG1784|consensus 98.3 9.1E-07 2E-11 58.9 3.8 74 3-77 4-81 (96)
39 KOG1782|consensus 98.1 5.7E-07 1.2E-11 62.9 -0.4 66 4-69 14-82 (129)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.0 1.8E-05 3.9E-10 51.1 5.8 44 3-46 6-52 (77)
41 KOG0947|consensus 97.4 0.00034 7.3E-09 63.5 6.0 44 34-77 456-499 (1248)
42 cd01716 Hfq Hfq, an abundant, 97.2 0.0016 3.6E-08 40.6 5.6 34 2-35 2-37 (61)
43 PRK00395 hfq RNA-binding prote 97.1 0.0019 4.1E-08 42.3 5.8 33 3-35 11-45 (79)
44 cd01739 LSm11_C The eukaryotic 96.9 0.00086 1.9E-08 42.3 2.8 36 9-44 8-47 (66)
45 PF12701 LSM14: Scd6-like Sm d 96.8 0.0074 1.6E-07 40.9 7.0 65 5-69 4-78 (96)
46 TIGR02383 Hfq RNA chaperone Hf 96.7 0.0035 7.5E-08 39.1 4.3 33 3-35 7-41 (61)
47 COG1923 Hfq Uncharacterized ho 96.4 0.014 2.9E-07 37.9 5.6 32 2-33 10-43 (77)
48 KOG3459|consensus 96.3 0.00078 1.7E-08 46.4 -0.6 58 9-66 36-106 (114)
49 cd01736 LSm14_N LSm14 (also kn 96.1 0.043 9.4E-07 35.5 6.8 58 6-63 3-71 (74)
50 PF11095 Gemin7: Gem-associate 96.0 0.048 1E-06 35.8 6.9 60 2-67 17-78 (80)
51 PRK14091 RNA-binding protein H 95.5 0.036 7.8E-07 40.9 5.2 32 3-34 16-49 (165)
52 PRK14091 RNA-binding protein H 95.5 0.045 9.8E-07 40.4 5.7 33 3-35 96-130 (165)
53 PF10842 DUF2642: Protein of u 93.4 0.45 9.8E-06 30.1 6.0 50 2-65 14-64 (66)
54 KOG1073|consensus 93.2 0.23 5E-06 41.0 5.6 68 4-71 4-82 (361)
55 PF02237 BPL_C: Biotin protein 91.6 0.75 1.6E-05 26.8 5.0 31 8-39 2-32 (48)
56 cd01735 LSm12_N LSm12 belongs 89.1 3.5 7.7E-05 25.6 6.7 30 7-36 4-33 (61)
57 KOG3262|consensus 88.5 1.8 4E-05 32.8 6.0 10 25-34 70-80 (215)
58 PF06372 Gemin6: Gemin6 protei 87.9 3 6.5E-05 30.9 6.8 60 3-69 11-71 (166)
59 PRK14638 hypothetical protein; 87.2 1.2 2.5E-05 32.4 4.2 29 4-32 95-123 (150)
60 PRK02001 hypothetical protein; 86.5 4.6 0.0001 29.4 7.0 29 4-32 85-113 (152)
61 PRK13149 H/ACA RNA-protein com 86.5 1.9 4.1E-05 27.5 4.4 34 13-51 29-62 (73)
62 PRK14639 hypothetical protein; 86.4 1.4 3E-05 31.6 4.2 29 4-32 83-111 (140)
63 PRK14642 hypothetical protein; 83.5 4.7 0.0001 30.7 6.1 29 4-32 95-136 (197)
64 PRK00092 ribosome maturation p 83.0 5.8 0.00013 28.6 6.3 28 4-31 93-124 (154)
65 PF02576 DUF150: Uncharacteris 82.2 3.3 7.1E-05 29.3 4.6 28 4-31 82-113 (141)
66 PRK09618 flgD flagellar basal 81.3 6.2 0.00014 28.5 5.8 25 6-30 89-113 (142)
67 cd01734 YlxS_C YxlS is a Bacil 80.4 3.7 8.1E-05 26.5 4.1 29 4-32 20-52 (83)
68 PRK14644 hypothetical protein; 80.3 3.2 6.9E-05 29.7 4.0 29 4-32 80-112 (136)
69 COG3277 GAR1 RNA-binding prote 80.1 14 0.00031 25.1 6.9 34 12-50 29-62 (98)
70 PRK11625 Rho-binding antitermi 77.6 15 0.00033 24.2 6.3 23 7-29 21-43 (84)
71 PRK14640 hypothetical protein; 77.6 4.4 9.5E-05 29.4 4.1 30 4-33 92-125 (152)
72 COG0779 Uncharacterized protei 77.1 4.8 0.00011 29.4 4.2 30 4-33 94-127 (153)
73 PRK14633 hypothetical protein; 76.6 9.4 0.0002 27.6 5.6 29 4-32 89-121 (150)
74 PRK14636 hypothetical protein; 76.4 7.9 0.00017 28.8 5.3 29 4-32 93-125 (176)
75 PRK10590 ATP-dependent RNA hel 74.8 8.7 0.00019 32.1 5.7 10 59-68 343-352 (456)
76 PF07073 ROF: Modulator of Rho 74.7 3.2 6.9E-05 27.1 2.4 28 5-34 13-40 (80)
77 PRK14647 hypothetical protein; 73.2 10 0.00022 27.6 5.1 29 4-32 94-131 (159)
78 PRK14632 hypothetical protein; 72.3 16 0.00035 27.0 6.0 29 4-32 93-128 (172)
79 PRK14645 hypothetical protein; 72.0 6.6 0.00014 28.6 3.8 28 4-32 97-124 (154)
80 PRK14631 hypothetical protein; 71.1 14 0.00029 27.5 5.4 27 4-30 112-142 (174)
81 PRK14643 hypothetical protein; 70.6 7.7 0.00017 28.6 3.9 30 4-33 99-132 (164)
82 PRK14634 hypothetical protein; 69.4 8.6 0.00019 28.0 4.0 30 4-33 95-128 (155)
83 PF11607 DUF3247: Protein of u 66.9 9 0.00019 25.9 3.3 19 9-27 28-46 (101)
84 PRK14637 hypothetical protein; 65.8 11 0.00025 27.3 4.0 29 4-32 93-122 (151)
85 PRK14646 hypothetical protein; 65.6 11 0.00025 27.3 4.0 29 4-32 95-127 (155)
86 PF12764 Gly-rich_Ago1: Glycin 62.0 14 0.00031 25.2 3.6 6 102-107 17-22 (104)
87 PF04410 Gar1: Gar1/Naf1 RNA b 61.9 7.2 0.00016 28.2 2.3 22 13-35 53-74 (154)
88 PRK14641 hypothetical protein; 59.3 15 0.00032 27.3 3.7 27 4-30 99-129 (173)
89 PRK06792 flgD flagellar basal 58.6 32 0.0007 26.1 5.4 28 6-33 115-142 (190)
90 PF03614 Flag1_repress: Repres 55.2 31 0.00066 25.4 4.6 25 8-32 119-143 (165)
91 PRK06789 flagellar motor switc 53.4 29 0.00063 22.3 3.8 35 4-38 36-70 (74)
92 PRK13325 bifunctional biotin-- 52.8 50 0.0011 29.1 6.4 32 7-38 276-307 (592)
93 PRK11911 flgD flagellar basal 51.7 45 0.00097 24.1 5.0 27 6-32 90-116 (140)
94 PF10618 Tail_tube: Phage tail 49.2 37 0.00081 23.5 4.2 22 4-25 69-90 (119)
95 PRK14630 hypothetical protein; 46.6 35 0.00076 24.4 3.8 29 4-33 92-120 (143)
96 PF03614 Flag1_repress: Repres 44.8 21 0.00045 26.3 2.4 33 9-41 29-61 (165)
97 PF14153 Spore_coat_CotO: Spor 43.5 23 0.0005 26.7 2.5 32 1-32 123-157 (185)
98 PF09923 DUF2155: Uncharacteri 42.5 30 0.00065 23.0 2.7 41 1-47 3-43 (90)
99 PF10961 DUF2763: Protein of u 42.5 62 0.0013 21.5 4.2 10 71-80 34-43 (91)
100 PF11684 DUF3280: Protein of u 41.3 50 0.0011 23.7 3.9 40 20-63 83-125 (140)
101 PRK10898 serine endoprotease; 40.6 1.1E+02 0.0023 25.0 6.2 31 10-40 102-132 (353)
102 COG4568 Rof Transcriptional an 40.0 38 0.00082 22.1 2.8 27 6-34 20-46 (84)
103 PF01052 SpoA: Surface present 40.0 75 0.0016 19.6 4.2 33 8-40 41-73 (77)
104 KOG0921|consensus 39.8 40 0.00086 31.9 3.8 16 23-38 1075-1091(1282)
105 TIGR02603 CxxCH_TIGR02603 puta 39.3 49 0.0011 23.0 3.6 21 11-31 59-79 (133)
106 PRK06955 biotin--protein ligas 37.6 85 0.0019 24.9 5.1 33 6-38 246-278 (300)
107 PF04452 Methyltrans_RNA: RNA 37.6 28 0.00061 26.3 2.3 32 2-33 13-44 (225)
108 smart00333 TUDOR Tudor domain. 36.2 85 0.0018 17.9 5.6 25 8-32 5-29 (57)
109 PRK11886 bifunctional biotin-- 35.6 1.3E+02 0.0028 23.8 5.9 31 7-38 270-300 (319)
110 COG1512 Beta-propeller domains 35.4 63 0.0014 25.8 4.0 23 8-30 133-155 (271)
111 TIGR02038 protease_degS peripl 35.4 1.4E+02 0.003 24.3 6.1 31 10-40 102-132 (351)
112 PTZ00034 40S ribosomal protein 35.4 43 0.00094 23.7 2.7 18 50-70 55-72 (124)
113 PRK06009 flgD flagellar basal 33.6 1.2E+02 0.0027 21.8 4.9 26 6-34 94-119 (140)
114 TIGR00567 3mg DNA-3-methyladen 33.5 74 0.0016 24.1 3.9 30 5-34 15-44 (192)
115 PRK14635 hypothetical protein; 33.5 1.9E+02 0.0041 21.0 6.8 29 4-32 94-127 (162)
116 PRK10139 serine endoprotease; 32.2 1.1E+02 0.0024 25.9 5.2 61 10-71 115-177 (455)
117 PRK06788 flagellar motor switc 32.1 97 0.0021 21.7 4.1 35 5-39 64-98 (119)
118 PRK10942 serine endoprotease; 31.7 90 0.0019 26.6 4.6 31 10-40 136-166 (473)
119 PF06331 Tbf5: Transcription f 31.2 26 0.00056 22.1 0.9 14 20-33 3-16 (68)
120 TIGR00121 birA_ligase birA, bi 31.2 1.9E+02 0.004 22.0 5.9 31 7-38 191-221 (237)
121 cd04479 RPA3 RPA3: A subfamily 29.6 1E+02 0.0022 20.5 3.7 23 2-32 8-30 (101)
122 PF05037 DUF669: Protein of un 29.3 34 0.00074 24.1 1.4 26 2-27 96-122 (141)
123 PRK08158 type III secretion sy 28.2 1.2E+02 0.0025 24.7 4.4 38 4-41 259-296 (303)
124 PF02751 TFIIA_gamma_C: Transc 28.0 1.4E+02 0.003 17.8 4.5 40 17-56 3-46 (52)
125 PF05954 Phage_GPD: Phage late 27.9 89 0.0019 23.7 3.7 26 5-30 24-49 (292)
126 TIGR02037 degP_htrA_DO peripla 27.3 1.5E+02 0.0032 24.6 5.1 31 10-40 82-112 (428)
127 TIGR00999 8a0102 Membrane Fusi 27.1 1.3E+02 0.0027 22.7 4.4 27 8-34 141-167 (265)
128 PRK08330 biotin--protein ligas 27.0 1.6E+02 0.0034 22.4 4.9 33 6-38 185-217 (236)
129 PRK06461 single-stranded DNA-b 27.0 2.2E+02 0.0047 19.7 5.9 7 71-77 103-109 (129)
130 PF02245 Pur_DNA_glyco: Methyl 26.8 90 0.0019 23.4 3.4 30 4-34 13-42 (184)
131 KOG4401|consensus 26.5 65 0.0014 24.3 2.5 44 8-53 10-53 (184)
132 PF13437 HlyD_3: HlyD family s 25.5 1.6E+02 0.0034 18.9 4.1 24 8-31 53-78 (105)
133 PF09465 LBR_tudor: Lamin-B re 25.5 1.6E+02 0.0034 17.9 3.6 27 8-34 8-35 (55)
134 PF02736 Myosin_N: Myosin N-te 24.9 66 0.0014 17.9 1.9 17 6-22 20-36 (42)
135 COG0340 BirA Biotin-(acetyl-Co 24.4 1.9E+02 0.0041 22.4 4.9 33 7-39 188-220 (238)
136 PRK13829 rimM 16S rRNA-process 24.3 2.8E+02 0.006 20.0 6.9 26 4-33 91-116 (162)
137 TIGR03344 VI_effect_Hcp1 type 24.2 1.3E+02 0.0028 22.0 3.7 43 29-71 106-157 (166)
138 PRK10708 hypothetical protein; 23.6 98 0.0021 19.0 2.5 26 8-33 3-28 (62)
139 TIGR00046 RNA methyltransferas 22.4 95 0.0021 23.8 2.9 30 3-32 29-58 (240)
140 PRK05698 fliN flagellar motor 22.4 1.7E+02 0.0036 21.5 4.0 34 6-39 110-143 (155)
141 cd05694 S1_Rrp5_repeat_hs2_sc2 22.1 95 0.0021 19.3 2.4 17 16-32 2-18 (74)
142 PF11717 Tudor-knot: RNA bindi 21.8 1.8E+02 0.0038 17.0 3.4 26 8-33 3-28 (55)
143 PTZ00275 biotin-acetyl-CoA-car 21.8 2.5E+02 0.0053 22.2 5.2 31 7-38 235-265 (285)
144 PF13861 FLgD_tudor: FlgD Tudo 21.5 1.6E+02 0.0036 17.4 3.3 25 6-30 9-35 (61)
145 PRK11634 ATP-dependent RNA hel 21.3 1.3E+02 0.0029 26.6 3.9 36 94-129 579-615 (629)
146 PRK08916 flagellar motor switc 20.3 2.5E+02 0.0053 19.5 4.3 31 7-37 77-107 (116)
147 cd05790 S1_Rrp40 S1_Rrp40: Rrp 20.1 1.8E+02 0.0038 19.1 3.4 27 13-39 47-73 (86)
148 PF10781 DSRB: Dextransucrase 20.0 1.1E+02 0.0025 18.8 2.3 26 8-33 3-28 (62)
No 1
>KOG3428|consensus
Probab=99.96 E-value=8.5e-29 Score=168.42 Aligned_cols=98 Identities=67% Similarity=1.022 Sum_probs=86.7
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD 80 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~ 80 (129)
|+||++|.+++|+|||||+++++|+|.++|.+||++|.+|+++.+. +|++++.++|+||+|+||++||++++|++|+++
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Llvd~ 82 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLLVDD 82 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceeeeeh
Confidence 6899999999999999999999999999999999999999999876 999999999999999999999999999999999
Q ss_pred CCccCCCCCCCCCCCCCCC
Q psy15782 81 APRSKGKRDSRRGGGAGGA 99 (129)
Q Consensus 81 ~~~~k~~~~~~~g~g~g~g 99 (129)
+|+.+.+...+.++++++|
T Consensus 83 ~~~~~~~~~~~~~rgrgrg 101 (109)
T KOG3428|consen 83 APRLHLRKNEKVGRGRGRG 101 (109)
T ss_pred hhhhhhhcccccccccccc
Confidence 8877655443333444333
No 2
>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=99.95 E-value=5.5e-28 Score=162.22 Aligned_cols=85 Identities=69% Similarity=1.115 Sum_probs=80.2
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD 80 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~ 80 (129)
++||+++.|++|+||||||++|+|+|.+||.|||++|+||+++.+++.+..+++++|||++|+||++||.++++++|.++
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~~ 82 (90)
T cd01724 3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVDS 82 (90)
T ss_pred hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhhc
Confidence 57999999999999999999999999999999999999999998888899999999999999999999999999999887
Q ss_pred CCccC
Q psy15782 81 APRSK 85 (129)
Q Consensus 81 ~~~~k 85 (129)
++.++
T Consensus 83 ~~~~~ 87 (90)
T cd01724 83 TPKPK 87 (90)
T ss_pred CCccc
Confidence 66554
No 3
>KOG3172|consensus
Probab=99.93 E-value=4.1e-25 Score=150.03 Aligned_cols=80 Identities=29% Similarity=0.522 Sum_probs=73.0
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCccccccCCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLLIDD 80 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L~~~ 80 (129)
|.+|....++-|++|+++|++|+|+|.++|++||++|.|+++|..++...+++++||||+.|+|+++||.| ++
T Consensus 7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmL-------Kn 79 (119)
T KOG3172|consen 7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDML-------KN 79 (119)
T ss_pred eeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHh-------hc
Confidence 46788888999999999999999999999999999999999999999999999999999999999999987 46
Q ss_pred CCccCCC
Q psy15782 81 APRSKGK 87 (129)
Q Consensus 81 ~~~~k~~ 87 (129)
+|.+|+.
T Consensus 80 APmFkk~ 86 (119)
T KOG3172|consen 80 APMFKKG 86 (119)
T ss_pred Ccccccc
Confidence 6665533
No 4
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=1.9e-24 Score=138.79 Aligned_cols=69 Identities=33% Similarity=0.611 Sum_probs=66.2
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
++||++++|++|+||||||++|+|+|.+||.|||++|+||+++..+++...++++||||++|+||++||
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 479999999999999999999999999999999999999999888888899999999999999999997
No 5
>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=99.90 E-value=1.3e-23 Score=137.55 Aligned_cols=68 Identities=35% Similarity=0.552 Sum_probs=65.3
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILP 68 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~p 68 (129)
+.||+.+.|++|+|||||+.+|+|+|.+||.+||++|+||+++..++.+..+++++|||++|+||++|
T Consensus 11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 46999999999999999999999999999999999999999998888888999999999999999998
No 6
>KOG3293|consensus
Probab=99.90 E-value=9.5e-24 Score=146.42 Aligned_cols=74 Identities=27% Similarity=0.501 Sum_probs=67.8
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc-eecceEEEecCeEEEEEcCCCCccccc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYILPDSLPLETL 76 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~pd~l~l~~~ 76 (129)
.+|....++++.|||||+++|.|.|++||.|||++|++|++++++++. +.+.+|+|||++|+|+.+||++ +|.+
T Consensus 5 sLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i-id~v 79 (134)
T KOG3293|consen 5 SLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI-IDKV 79 (134)
T ss_pred hHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH-HHHH
Confidence 578888999999999999999999999999999999999999998764 7899999999999999999995 4444
No 7
>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=99.89 E-value=5.6e-23 Score=133.89 Aligned_cols=71 Identities=31% Similarity=0.519 Sum_probs=66.3
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc-eecceEEEecCeEEEEEcCCCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYILPDSL 71 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~pd~l 71 (129)
++||+++.+++|+|||||+++|+|+|.+||.|||++|+||+++..+++. ..++++||||++|+||++||++
T Consensus 3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred hHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 4799999999999999999999999999999999999999999777765 5689999999999999999985
No 8
>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=99.88 E-value=1.9e-22 Score=132.91 Aligned_cols=71 Identities=31% Similarity=0.486 Sum_probs=64.5
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc--ceecceEEEecCeEEEEEcCCCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE--PTTLDSISLRGNNIRYYILPDSL 71 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~--~~~l~~~~IrGn~Ir~Ii~pd~l 71 (129)
+.||+++.|++|+||||||++|+|+|.+||.|||++|+||+++..+.. ...+++++|||++|+||++||.+
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence 369999999999999999999999999999999999999998865543 35679999999999999999984
No 9
>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=99.85 E-value=6.3e-21 Score=121.38 Aligned_cols=66 Identities=26% Similarity=0.407 Sum_probs=62.0
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
.+||+++++++|+|+|+|+++|+|+|.+||.|||++|+||+++...+++..++.++|||++|+||.
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 379999999999999999999999999999999999999999877777889999999999999973
No 10
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.83 E-value=2.7e-20 Score=118.85 Aligned_cols=66 Identities=32% Similarity=0.468 Sum_probs=61.1
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
++||+++++++|+|+|+||.+|.|+|.+||.|||++|+||+++....++..++.++|||++|+||.
T Consensus 3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 478999999999999999999999999999999999999998866666788999999999999983
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.80 E-value=3e-19 Score=115.20 Aligned_cols=66 Identities=27% Similarity=0.487 Sum_probs=60.8
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
++||.++++++|+|+|+||++|+|+|.+||.|||++|+||+++...+....++.++|||++|.+|.
T Consensus 6 ~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred HHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 368999999999999999999999999999999999999999876656678999999999999985
No 12
>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=99.79 E-value=5.7e-19 Score=112.56 Aligned_cols=66 Identities=23% Similarity=0.418 Sum_probs=62.1
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
++||+++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..+.+...++.++|||++|.||.
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 368999999999999999999999999999999999999999887777889999999999999985
No 13
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.79 E-value=1e-18 Score=110.37 Aligned_cols=66 Identities=45% Similarity=0.649 Sum_probs=62.1
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-CcceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-KEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
.||.++++++|+|+|+|++++.|+|.+||.+||++|+||+++..+ .++..++.++|||++|+||+.
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 489999999999999999999999999999999999999999877 678899999999999999874
No 14
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.78 E-value=9.2e-19 Score=110.68 Aligned_cols=66 Identities=44% Similarity=0.603 Sum_probs=62.6
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-cceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-EPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
.||+++++++|+|+|+||.+|.|+|.+||.+||++|+||+++.... +...++.++|||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4899999999999999999999999999999999999999998877 78899999999999999974
No 15
>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=99.75 E-value=1.2e-17 Score=104.14 Aligned_cols=63 Identities=33% Similarity=0.490 Sum_probs=59.9
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
|+++++++|+|+|+|+++|.|+|.+||.+||+.|+|++++.++.++..++.++|||++|++|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 678999999999999999999999999999999999999988888899999999999999984
No 16
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.74 E-value=1.6e-17 Score=107.23 Aligned_cols=68 Identities=24% Similarity=0.345 Sum_probs=62.5
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
.+|.++++++|.|+|+++.+|.|+|.+||.|||++|+||+++....+...++.++|||++|.+|..-|
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 47899999999999999999999999999999999999999876667788999999999999988654
No 17
>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=99.74 E-value=1.2e-17 Score=108.81 Aligned_cols=65 Identities=31% Similarity=0.400 Sum_probs=59.4
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEe---cCCcceecceEEEecCeEEEEE
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTV---KGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~---~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
.||+++++++|+|+|+++++|.|+|.+||.|||++|+||+++. ..++..+++.++|||++|.+|+
T Consensus 6 ~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 6 ELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred HHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 6899999999999999999999999999999999999998886 3334578999999999999987
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.72 E-value=3.9e-17 Score=106.85 Aligned_cols=65 Identities=34% Similarity=0.475 Sum_probs=57.2
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec-CCcc--e-ecceEEEecCeEEEEE
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEP--T-TLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~--~-~l~~~~IrGn~Ir~Ii 66 (129)
.||.++++++|.|+|+|+++|.|+|.+||.|||++|+||+++.. +++. . ..+.++|||++|.+|.
T Consensus 10 ~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 10 SFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred HHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence 68999999999999999999999999999999999999999874 3232 3 3449999999999986
No 19
>KOG3448|consensus
Probab=99.70 E-value=6.1e-17 Score=106.72 Aligned_cols=69 Identities=32% Similarity=0.535 Sum_probs=64.6
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcc--eecceEEEecCeEEEEEcCCC
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP--TTLDSISLRGNNIRYYILPDS 70 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~--~~l~~~~IrGn~Ir~Ii~pd~ 70 (129)
+|++.++++.|+|||||+..+.|+|.++|+|+|++|.|+.+++.++-| .....|||||+.|+||.+|..
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence 588999999999999999999999999999999999999999887776 567899999999999999977
No 20
>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=99.66 E-value=7e-16 Score=101.60 Aligned_cols=66 Identities=20% Similarity=0.347 Sum_probs=58.8
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC--------cceecceEEEecCeEEEEEcCC
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK--------EPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~--------~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
|.++++++|.|.|+++++|.|+|.+||.|||++|+||++..... +...++.++|||++|.+|...+
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 77899999999999999999999999999999999999886532 3567899999999999987654
No 21
>KOG3482|consensus
Probab=99.66 E-value=1.6e-16 Score=101.24 Aligned_cols=65 Identities=32% Similarity=0.448 Sum_probs=61.6
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEE
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
.||+.|+|++|.|.||.|.+|.|+|.++|.+||+.|.++++.........+.+++||.|||.||.
T Consensus 11 pFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 11 PFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred HHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence 59999999999999999999999999999999999999999877777889999999999999985
No 22
>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=99.62 E-value=2.4e-15 Score=99.21 Aligned_cols=65 Identities=17% Similarity=0.301 Sum_probs=57.6
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-------------cceecceEEEecCeEEEEE
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-------------EPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-------------~~~~l~~~~IrGn~Ir~Ii 66 (129)
.||.+.++++|.|.|+++++|.|+|.+||.|||++|+||++..... ....++.++|||++|.+|.
T Consensus 4 ~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 4 DLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 6889999999999999999999999999999999999999886431 1347899999999999875
No 23
>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=99.61 E-value=3.1e-15 Score=99.77 Aligned_cols=65 Identities=20% Similarity=0.306 Sum_probs=56.5
Q ss_pred hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc-------------ceecceEEEecCeEEEEE
Q psy15782 2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE-------------PTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~-------------~~~l~~~~IrGn~Ir~Ii 66 (129)
.||.+++ +++|.|.|+++.+|.|+|.+||.|||+.|+||+++.+... ...++.+||||++|.+|.
T Consensus 5 ~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is 84 (87)
T cd01720 5 SLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVL 84 (87)
T ss_pred HHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEe
Confidence 5788885 8999999999999999999999999999999998764422 236899999999999975
No 24
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.59 E-value=6.1e-15 Score=96.68 Aligned_cols=65 Identities=28% Similarity=0.367 Sum_probs=57.0
Q ss_pred hhhhhcCCC--eEEEEEc--CCcEEEEEEEEecccccceEeeEEEEec-CCcceecceEEEecCeEEEEE
Q psy15782 2 NFLMKLSHE--TVTIELK--NGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 2 ~~L~~l~~~--~V~VeLk--ng~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~~~l~~~~IrGn~Ir~Ii 66 (129)
.+|++++.+ +|.|+|+ ++.+|.|+|.+||.|||++|+|+++... ..+...++.++|||+||.+|+
T Consensus 9 ~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 9 NLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred HHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 467888888 6888887 8999999999999999999999998875 445678999999999999976
No 25
>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=99.57 E-value=2.1e-14 Score=93.09 Aligned_cols=66 Identities=17% Similarity=0.175 Sum_probs=57.6
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC---cceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK---EPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~---~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
..|.++++++|.|.|+++++|.|+|.+||.|||+.|+||++....+ ....++.++|||++|.+|.+
T Consensus 5 ~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 5 ASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 4688899999999999999999999999999999999998775432 24678899999999998753
No 26
>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=99.56 E-value=2.1e-14 Score=94.01 Aligned_cols=64 Identities=28% Similarity=0.367 Sum_probs=56.8
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC----------CcceecceEEEecCeEEEEEc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG----------KEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~----------~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
|.++++++|.|.|+++.+|.|+|.+||.|||++|+||+++... .++..++.++|||++|.+|.+
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 6789999999999999999999999999999999999987532 234678999999999999864
No 27
>KOG1783|consensus
Probab=99.54 E-value=1e-15 Score=97.62 Aligned_cols=68 Identities=28% Similarity=0.425 Sum_probs=64.1
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
+||.+.+|++|.|+|.++..|+|+|.++|.+||+.|+.+++....+.+..+...|||||+|.||...+
T Consensus 9 ~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 9 EFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred HHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence 69999999999999999999999999999999999999998888888899999999999999998754
No 28
>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=99.54 E-value=6.1e-14 Score=90.77 Aligned_cols=67 Identities=28% Similarity=0.303 Sum_probs=58.8
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC---C-cceecceEEEecCeEEEEEcCC
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG---K-EPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~---~-~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
-|.++++++|.|.|+++..|.|+|.+||.|||+.|++|++.... + +...++.+++||++|.+|..-|
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 47889999999999999999999999999999999999887532 1 3567899999999999988654
No 29
>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=99.49 E-value=2.1e-13 Score=88.67 Aligned_cols=66 Identities=21% Similarity=0.249 Sum_probs=59.5
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC------CcceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG------KEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~------~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
+-|.++++++|.|.|+||.+|.|+|.++|.+||+.|+||++.... .+...++.++|+|++|..+..
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 468899999999999999999999999999999999999998654 345789999999999998864
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.45 E-value=5.1e-13 Score=89.40 Aligned_cols=66 Identities=27% Similarity=0.380 Sum_probs=54.4
Q ss_pred hhhhhcCCC--eEEEEEcC--CcEEEEEEEEecccccceEeeEEEEecC-CcceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHE--TVTIELKN--GTQVHGTIQGVDVAMNTHLKTVKMTVKG-KEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~--~V~VeLkn--g~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
.+|.+++.+ +|.|+|.+ +.+|.|+|.+||.|||++|+|++++..+ .+...++.++||||||.+|..
T Consensus 17 ~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 17 NQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred HHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 456666554 58888877 4899999999999999999999988653 345789999999999999864
No 31
>KOG1780|consensus
Probab=99.39 E-value=9.1e-13 Score=84.34 Aligned_cols=65 Identities=23% Similarity=0.341 Sum_probs=61.0
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEc
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
-|.|+.++++.+.|..+..+.|.|.+||.|||++|+++++...+++...+...+||||+|..+-.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEee
Confidence 48899999999999999999999999999999999999999999889999999999999987654
No 32
>KOG3262|consensus
Probab=99.32 E-value=2.9e-12 Score=95.44 Aligned_cols=70 Identities=26% Similarity=0.457 Sum_probs=57.1
Q ss_pred hhhhcCCCeE-----EEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecceEEEecCeEEEEEcCCC-Cccccc
Q psy15782 3 FLMKLSHETV-----TIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDS-LPLETL 76 (129)
Q Consensus 3 ~L~~l~~~~V-----~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~-l~l~~~ 76 (129)
++|++.+++| .|+|+|.++| |+|++|...||- ++++++..+.+...++.. ..+++|.||+ |+++.|
T Consensus 67 ~Vck~~~~kIPyfNAPIylenk~qI-GKVDEIfG~i~d----~~fsIK~~dgv~assfk~---g~k~fi~p~KllPl~RF 138 (215)
T KOG3262|consen 67 LVCKLTNKKIPYFNAPIYLENKEQI-GKVDEIFGPIND----VHFSIKPSDGVQASSFKP---GDKLFIDPDKLLPLDRF 138 (215)
T ss_pred eEEeeccccCCCCCCceeecchhhh-cchhhhcccccc----cEEEEecCCCceeecccC---CCeEEecccccCcHhhc
Confidence 5667777776 8999999999 999999999995 667777777776666554 4788899999 999999
Q ss_pred cCCC
Q psy15782 77 LIDD 80 (129)
Q Consensus 77 L~~~ 80 (129)
|+.+
T Consensus 139 LP~p 142 (215)
T KOG3262|consen 139 LPQP 142 (215)
T ss_pred CCCC
Confidence 9754
No 33
>KOG1775|consensus
Probab=99.17 E-value=1.6e-11 Score=79.07 Aligned_cols=66 Identities=29% Similarity=0.333 Sum_probs=58.0
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec--C-CcceecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK--G-KEPTTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~--~-~~~~~l~~~~IrGn~Ir~Ii~ 67 (129)
+++.|++|.+|.|.+|+.+++.|+|.+||+|.|+.|+||+++.. + +...+++.+++.||+|..++.
T Consensus 10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP 78 (84)
T KOG1775|consen 10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP 78 (84)
T ss_pred HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence 57889999999999999999999999999999999999976632 2 345789999999999998654
No 34
>KOG3460|consensus
Probab=99.15 E-value=1.4e-11 Score=80.60 Aligned_cols=69 Identities=23% Similarity=0.352 Sum_probs=58.7
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc-------------ceecceEEEecCeEEEEEcC
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE-------------PTTLDSISLRGNNIRYYILP 68 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~-------------~~~l~~~~IrGn~Ir~Ii~p 68 (129)
.||.-.+.+.|-|+|+++.++.|+|.+||+|+|+.|.||+++.+.-+ ....+.+|+||++|.+|..|
T Consensus 8 dllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp 87 (91)
T KOG3460|consen 8 DLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP 87 (91)
T ss_pred HHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence 57777899999999999999999999999999999999987754211 24577999999999999887
Q ss_pred CC
Q psy15782 69 DS 70 (129)
Q Consensus 69 d~ 70 (129)
-.
T Consensus 88 ~~ 89 (91)
T KOG3460|consen 88 LR 89 (91)
T ss_pred cc
Confidence 54
No 35
>KOG1774|consensus
Probab=98.74 E-value=2.1e-08 Score=65.47 Aligned_cols=58 Identities=31% Similarity=0.367 Sum_probs=49.3
Q ss_pred eEEEEEcC--CcEEEEEEEEecccccceEeeEEEEec-CCcceecceEEEecCeEEEEEcC
Q psy15782 11 TVTIELKN--GTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILP 68 (129)
Q Consensus 11 ~V~VeLkn--g~~~~G~L~~~D~~mNl~Lkdv~~~~~-~~~~~~l~~~~IrGn~Ir~Ii~p 68 (129)
.|.|+|.. +..++|.+.+||+|||+++++++++.. .+...+++.++++|+||..|...
T Consensus 26 ~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 26 RVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred ceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeec
Confidence 58888887 689999999999999999999987754 34445899999999999988653
No 36
>KOG3168|consensus
Probab=98.35 E-value=4.5e-07 Score=66.58 Aligned_cols=72 Identities=22% Similarity=0.327 Sum_probs=59.5
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEec---------C-CcceecceEEEecCeEEEEEcCCCCcc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK---------G-KEPTTLDSISLRGNNIRYYILPDSLPL 73 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~---------~-~~~~~l~~~~IrGn~Ir~Ii~pd~l~l 73 (129)
|..++|..+.|.|.|++++.|++..||.|||+.|.||++.-. + .+...+..+++||.+|......+....
T Consensus 9 ml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~ 88 (177)
T KOG3168|consen 9 MLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPP 88 (177)
T ss_pred HHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCC
Confidence 556789999999999999999999999999999998875421 1 234678999999999999988877554
Q ss_pred cc
Q psy15782 74 ET 75 (129)
Q Consensus 74 ~~ 75 (129)
++
T Consensus 89 s~ 90 (177)
T KOG3168|consen 89 SD 90 (177)
T ss_pred cc
Confidence 43
No 37
>KOG1781|consensus
Probab=98.32 E-value=8.8e-08 Score=64.56 Aligned_cols=68 Identities=19% Similarity=0.321 Sum_probs=58.0
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecC-C-------cceecceEEEecCeEEEEEcCCCC
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG-K-------EPTTLDSISLRGNNIRYYILPDSL 71 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~-~-------~~~~l~~~~IrGn~Ir~Ii~pd~l 71 (129)
|.++++++|.|.+..|.++.|+|.+||+.||++|+|+.+...+ . +...++.+.+||..+..|...|-.
T Consensus 22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~ 97 (108)
T KOG1781|consen 22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS 97 (108)
T ss_pred HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence 5678999999999999999999999999999999999765432 1 236789999999999988887764
No 38
>KOG1784|consensus
Probab=98.29 E-value=9.1e-07 Score=58.95 Aligned_cols=74 Identities=22% Similarity=0.332 Sum_probs=62.5
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEe----cCCcceecceEEEecCeEEEEEcCCCCcccccc
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTV----KGKEPTTLDSISLRGNNIRYYILPDSLPLETLL 77 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~----~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L 77 (129)
-|..++++.|.|-..+|+.+.|.|.+||...|+.++++.+-. ...+...++.++|||.|+-.|-.-|+ .+|+.|
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE-e~d~~l 81 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE-ELDSRL 81 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch-hhhhhh
Confidence 367889999999999999999999999999999999985432 23456789999999999999988887 466666
No 39
>KOG1782|consensus
Probab=98.09 E-value=5.7e-07 Score=62.88 Aligned_cols=66 Identities=18% Similarity=0.224 Sum_probs=53.9
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCc---ceecceEEEecCeEEEEEcCC
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE---PTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~---~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
|.+.+.+++.|-|++|..+.|.|.|||+|-|+.|.++++-+--++ ..+.+.|+|||.||..+-.-|
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 456688999999999999999999999999999999875332222 256788999999999986544
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.02 E-value=1.8e-05 Score=51.09 Aligned_cols=44 Identities=25% Similarity=0.372 Sum_probs=35.2
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEecc---cccceEeeEEEEecC
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDV---AMNTHLKTVKMTVKG 46 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~---~mNl~Lkdv~~~~~~ 46 (129)
++..++|++|.|.++||.+|+|.+.+++. -+.+.|+-+..+...
T Consensus 6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~ 52 (77)
T PF14438_consen 6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS 52 (77)
T ss_dssp HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence 56789999999999999999999999998 899999998876543
No 41
>KOG0947|consensus
Probab=97.40 E-value=0.00034 Score=63.54 Aligned_cols=44 Identities=18% Similarity=0.171 Sum_probs=39.3
Q ss_pred cceEeeEEEEecCCcceecceEEEecCeEEEEEcCCCCcccccc
Q psy15782 34 NTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPDSLPLETLL 77 (129)
Q Consensus 34 Nl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd~l~l~~~L 77 (129)
=++.+++++|++.++|++|++|++-+.+...|+....+++..-+
T Consensus 456 RtK~K~IyViST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~ 499 (1248)
T KOG0947|consen 456 RTKQKTIYVISTSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGI 499 (1248)
T ss_pred hccCceEEEEecCCCccceEEEEEeccceehhhcccchhhhhcc
Confidence 47889999999999999999999999999999999998875544
No 42
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=97.16 E-value=0.0016 Score=40.60 Aligned_cols=34 Identities=35% Similarity=0.389 Sum_probs=28.3
Q ss_pred hhhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782 2 NFLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT 35 (129)
Q Consensus 2 ~~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl 35 (129)
.||..+- ..+|+|+|.||-.+.|++.+||.|+=+
T Consensus 2 ~fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl 37 (61)
T cd01716 2 QFLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVL 37 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE
Confidence 3677664 457999999999999999999999843
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.12 E-value=0.0019 Score=42.27 Aligned_cols=33 Identities=36% Similarity=0.469 Sum_probs=27.7
Q ss_pred hhhhc--CCCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782 3 FLMKL--SHETVTIELKNGTQVHGTIQGVDVAMNT 35 (129)
Q Consensus 3 ~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~mNl 35 (129)
||..+ ...+|+|+|.||-.+.|+|.+||.|+=+
T Consensus 11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVl 45 (79)
T PRK00395 11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVL 45 (79)
T ss_pred HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEE
Confidence 56655 3557999999999999999999999843
No 44
>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=96.94 E-value=0.00086 Score=42.28 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=28.5
Q ss_pred CCeEEEEEcC--C--cEEEEEEEEecccccceEeeEEEEe
Q psy15782 9 HETVTIELKN--G--TQVHGTIQGVDVAMNTHLKTVKMTV 44 (129)
Q Consensus 9 ~~~V~VeLkn--g--~~~~G~L~~~D~~mNl~Lkdv~~~~ 44 (129)
...|.|.++. + -.++|.|++||.|||+.|.||.++.
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y 47 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY 47 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence 3457776665 2 4677999999999999999998764
No 45
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.85 E-value=0.0074 Score=40.89 Aligned_cols=65 Identities=17% Similarity=0.229 Sum_probs=53.9
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCc---------ceecceEEEecCeEEEEEcCC
Q psy15782 5 MKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKE---------PTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 5 ~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~---------~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
..++|++|.+.-+++..|+|+|..+|. .-.+.|++|...-+.++ ...++.+..+|+.|+-+.+-+
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e 78 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIE 78 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEc
Confidence 467999999999999999999999995 67899999988766554 245788889999999776644
No 46
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=96.71 E-value=0.0035 Score=39.14 Aligned_cols=33 Identities=36% Similarity=0.430 Sum_probs=27.6
Q ss_pred hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782 3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT 35 (129)
Q Consensus 3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl 35 (129)
||..+- ..+|+|+|.||..+.|++.+||.|+=+
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVl 41 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVL 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEE
Confidence 566553 557999999999999999999999843
No 47
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.40 E-value=0.014 Score=37.93 Aligned_cols=32 Identities=34% Similarity=0.463 Sum_probs=27.3
Q ss_pred hhhhhc--CCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 2 NFLMKL--SHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 2 ~~L~~l--~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
.||..+ ...+|+|+|-||-..+|.+.+||.|.
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 366655 45689999999999999999999987
No 48
>KOG3459|consensus
Probab=96.28 E-value=0.00078 Score=46.43 Aligned_cols=58 Identities=21% Similarity=0.316 Sum_probs=47.2
Q ss_pred CCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC-------c------ceecceEEEecCeEEEEE
Q psy15782 9 HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK-------E------PTTLDSISLRGNNIRYYI 66 (129)
Q Consensus 9 ~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~-------~------~~~l~~~~IrGn~Ir~Ii 66 (129)
+.+|.|-++|...+.|.+.+||-|.|++|+++.+..+.. . ...+..+||||+++..+.
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 567999999999999999999999999999997654321 1 134678999999988765
No 49
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.11 E-value=0.043 Score=35.48 Aligned_cols=58 Identities=19% Similarity=0.312 Sum_probs=45.0
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcc----------eecceEEEecCeEE
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEP----------TTLDSISLRGNNIR 63 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~----------~~l~~~~IrGn~Ir 63 (129)
.++|++|.+--|.+..|.|+|.++|. ---+.|+||...-+.+++ ..++.+..||+.|+
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 57899999999999999999999995 446789999877665543 33556666666664
No 50
>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=96.04 E-value=0.048 Score=35.79 Aligned_cols=60 Identities=17% Similarity=0.261 Sum_probs=45.2
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcc-eecceEEEecCeEEEEEc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEP-TTLDSISLRGNNIRYYIL 67 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~-~~l~~~~IrGn~Ir~Ii~ 67 (129)
++|.++.+++|.+.|.+.+++.|+...+|. ..|+..+|-. .| -..++-.+|.+.|..+..
T Consensus 17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~------TPlGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ------TPLGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE------TTTTEEEEEEEEGGGEEEEEE
T ss_pred HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC------CCcccChhheeecCCEEEEEe
Confidence 567788999999999999999999999994 5577666542 33 134778899999988765
No 51
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.52 E-value=0.036 Score=40.95 Aligned_cols=32 Identities=31% Similarity=0.356 Sum_probs=26.8
Q ss_pred hhhhcC--CCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
||..+- ..+|+|+|.||-.++|+|.+||.|.=
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftV 49 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSI 49 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEE
Confidence 566654 44699999999999999999999873
No 52
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.51 E-value=0.045 Score=40.44 Aligned_cols=33 Identities=33% Similarity=0.435 Sum_probs=27.4
Q ss_pred hhhhcC--CCeEEEEEcCCcEEEEEEEEecccccc
Q psy15782 3 FLMKLS--HETVTIELKNGTQVHGTIQGVDVAMNT 35 (129)
Q Consensus 3 ~L~~l~--~~~V~VeLkng~~~~G~L~~~D~~mNl 35 (129)
||..+- ..+|+|+|.||-.++|+|.+||.|+=+
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvl 130 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCML 130 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEE
Confidence 566553 457999999999999999999999844
No 53
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=93.43 E-value=0.45 Score=30.08 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=35.5
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcceecceEEEecCeEEEE
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYY 65 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~I 65 (129)
+.|++++|++|.|++-.|+. +|+|.++. +|+=+ + . . -..+|||=..|.+|
T Consensus 14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhIvl--~-----~-~-----~~~~~IR~~~IV~v 64 (66)
T PF10842_consen 14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHIVL--E-----E-N-----GTPFFIRIAQIVWV 64 (66)
T ss_pred HHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEEEE--E-----e-C-----CcEEEEEeeeEEEE
Confidence 56889999999999988877 69999987 34421 1 0 0 24577776666655
No 54
>KOG1073|consensus
Probab=93.23 E-value=0.23 Score=41.03 Aligned_cols=68 Identities=16% Similarity=0.235 Sum_probs=54.9
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEec-ccccceEeeEEEEecCCcc---------e-ecceEEEecCeEEEEEcCCCC
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVD-VAMNTHLKTVKMTVKGKEP---------T-TLDSISLRGNNIRYYILPDSL 71 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D-~~mNl~Lkdv~~~~~~~~~---------~-~l~~~~IrGn~Ir~Ii~pd~l 71 (129)
...++|++|.+.=|++..|+|.|.-+| +---|-|++|...-+.+++ . .++.++.||+.|+-+++-+..
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 346799999999999999999999999 5668889999766554431 2 678999999999977776653
No 55
>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=91.62 E-value=0.75 Score=26.78 Aligned_cols=31 Identities=19% Similarity=0.318 Sum_probs=25.9
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccccceEee
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAMNTHLKT 39 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkd 39 (129)
+|++|+|++ ++..++|+...+|..=.+.++.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 689999999 5666689999999988886654
No 56
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=89.13 E-value=3.5 Score=25.59 Aligned_cols=30 Identities=10% Similarity=0.068 Sum_probs=26.6
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccce
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTH 36 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~ 36 (129)
.+|..|.+++-.+.+++|.|..||...++.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~l 33 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKML 33 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEE
Confidence 468899999999999999999999887653
No 57
>KOG3262|consensus
Probab=88.51 E-value=1.8 Score=32.82 Aligned_cols=10 Identities=10% Similarity=0.119 Sum_probs=5.4
Q ss_pred EEEEec-cccc
Q psy15782 25 TIQGVD-VAMN 34 (129)
Q Consensus 25 ~L~~~D-~~mN 34 (129)
+|.+.| .|.|
T Consensus 70 k~~~~kIPyfN 80 (215)
T KOG3262|consen 70 KLTNKKIPYFN 80 (215)
T ss_pred eeccccCCCCC
Confidence 355555 4555
No 58
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=87.94 E-value=3 Score=30.92 Aligned_cols=60 Identities=10% Similarity=0.121 Sum_probs=37.2
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEecc-cccceEeeEEEEecCCcceecceEEEecCeEEEEEcCC
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDV-AMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRYYILPD 69 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~-~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir~Ii~pd 69 (129)
.+..++++.|.|.+.| +++.|-|..+|. .-|++|-+... +++ ...-+|-|-.|+.|..-+
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~sv~~I~ghaVk~vevl~ 71 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---RSVKVIMGHAVKSVEVLS 71 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----EEEEEE-GGGEEEEEEEE
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---eeEEEEEccceEEEEEcc
Confidence 3567899999999999 999999999995 55765553321 221 123556677777665443
No 59
>PRK14638 hypothetical protein; Provisional
Probab=87.18 E-value=1.2 Score=32.36 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=26.0
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
+.+.+|++|.|.|++.+.+.|+|.++|..
T Consensus 95 f~r~~G~~v~V~~~~~k~~~G~L~~~~~~ 123 (150)
T PRK14638 95 YVRFTGKLAKIVTKDGKTFIGRIESFVDG 123 (150)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence 45678999999999999999999999964
No 60
>PRK02001 hypothetical protein; Validated
Probab=86.49 E-value=4.6 Score=29.42 Aligned_cols=29 Identities=21% Similarity=0.336 Sum_probs=26.2
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
+.+.+|+.|.|.|.++..+.|+|.++|+.
T Consensus 85 f~r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 85 YKKNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 45678999999999999999999999975
No 61
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=86.46 E-value=1.9 Score=27.54 Aligned_cols=34 Identities=15% Similarity=0.099 Sum_probs=26.0
Q ss_pred EEEEcCCcEEEEEEEEecccccceEeeEEEEecCCccee
Q psy15782 13 TIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTT 51 (129)
Q Consensus 13 ~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~ 51 (129)
.|.++|.+.+ |+|.++..+.|- .|++.+..+...
T Consensus 29 ~V~~~~~~~I-GkV~dIfGPV~~----pY~~Vk~~~~~~ 62 (73)
T PRK13149 29 VVYDKKLKKI-GKVVDVFGPVKE----PYVLVKPDKKDP 62 (73)
T ss_pred EeECCCCCEe-EEEEEEECCCCC----cEEEEEeCCCCC
Confidence 6788999999 999999999985 566555444433
No 62
>PRK14639 hypothetical protein; Provisional
Probab=86.36 E-value=1.4 Score=31.60 Aligned_cols=29 Identities=28% Similarity=0.288 Sum_probs=26.1
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
+.+.+|++|.|.|.+...+.|+|.++|..
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~ 111 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE 111 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence 45778999999999999999999999984
No 63
>PRK14642 hypothetical protein; Provisional
Probab=83.47 E-value=4.7 Score=30.72 Aligned_cols=29 Identities=24% Similarity=0.486 Sum_probs=25.2
Q ss_pred hhhcCCCeEEEEEc-------------CCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELK-------------NGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk-------------ng~~~~G~L~~~D~~ 32 (129)
+.+.+|+.|.|.|+ +.+.++|+|.++|..
T Consensus 95 f~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 95 FERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 35678999999998 679999999999974
No 64
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=82.98 E-value=5.8 Score=28.62 Aligned_cols=28 Identities=18% Similarity=0.349 Sum_probs=24.1
Q ss_pred hhhcCCCeEEEEE----cCCcEEEEEEEEecc
Q psy15782 4 LMKLSHETVTIEL----KNGTQVHGTIQGVDV 31 (129)
Q Consensus 4 L~~l~~~~V~VeL----kng~~~~G~L~~~D~ 31 (129)
+.+.+|+.|.|.| .+...+.|+|.++|.
T Consensus 93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 4567899999997 467899999999998
No 65
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=82.18 E-value=3.3 Score=29.34 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=21.6
Q ss_pred hhhcCCCeEEEEEc----CCcEEEEEEEEecc
Q psy15782 4 LMKLSHETVTIELK----NGTQVHGTIQGVDV 31 (129)
Q Consensus 4 L~~l~~~~V~VeLk----ng~~~~G~L~~~D~ 31 (129)
+.+.+|+.|.|.|+ +...+.|+|.+++.
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 45678999999994 45789999999998
No 66
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=81.31 E-value=6.2 Score=28.53 Aligned_cols=25 Identities=32% Similarity=0.421 Sum_probs=23.4
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEec
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVD 30 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D 30 (129)
.|+|++|.+++.++..+.|++.+|.
T Consensus 89 slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 89 ELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 5899999999999999999999997
No 67
>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=80.43 E-value=3.7 Score=26.50 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=24.1
Q ss_pred hhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELK---NG-TQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk---ng-~~~~G~L~~~D~~ 32 (129)
+.+.+|+.|.|+|+ ++ +.+.|.|.++|+.
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 35678999999997 55 6899999999983
No 68
>PRK14644 hypothetical protein; Provisional
Probab=80.29 E-value=3.2 Score=29.65 Aligned_cols=29 Identities=14% Similarity=0.200 Sum_probs=25.3
Q ss_pred hhhcCCCeEEEEEcCC----cEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNG----TQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng----~~~~G~L~~~D~~ 32 (129)
+.+.+|+.|.|.|++. ..+.|+|.++|+.
T Consensus 80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~ 112 (136)
T PRK14644 80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE 112 (136)
T ss_pred HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC
Confidence 4567899999999886 9999999999973
No 69
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=80.10 E-value=14 Score=25.07 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=26.9
Q ss_pred EEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcce
Q psy15782 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPT 50 (129)
Q Consensus 12 V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~ 50 (129)
-.|.+++...+ |+|..|..++|- .|++.+..+..
T Consensus 29 ~~V~~~~~k~I-G~V~dVfGPv~~----PY~~Vkp~~~~ 62 (98)
T COG3277 29 APVYDANLKRI-GKVVDVFGPVDE----PYILVKPDDRD 62 (98)
T ss_pred CeeEecCCCEE-EEEEEEEccCCC----CEEEEeccccc
Confidence 37888999999 999999999984 77776664433
No 70
>PRK11625 Rho-binding antiterminator; Provisional
Probab=77.63 E-value=15 Score=24.18 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=19.0
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEe
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGV 29 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~ 29 (129)
+-+-+|.++|+||+++.|+....
T Consensus 21 ~~~~~l~l~l~dGe~~~g~A~D~ 43 (84)
T PRK11625 21 QHHLMLTLELKDGEVLQAKASDL 43 (84)
T ss_pred hcCCeEEEEECCCCEEEEEEEee
Confidence 45778999999999999987443
No 71
>PRK14640 hypothetical protein; Provisional
Probab=77.56 E-value=4.4 Score=29.37 Aligned_cols=30 Identities=23% Similarity=0.371 Sum_probs=25.2
Q ss_pred hhhcCCCeEEEEE----cCCcEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIEL----KNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeL----kng~~~~G~L~~~D~~m 33 (129)
+.+.+|+.|.|.| .+.+.+.|+|.++|+..
T Consensus 92 f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~ 125 (152)
T PRK14640 92 FEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDM 125 (152)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEEeCCE
Confidence 4567899999999 46799999999999743
No 72
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.06 E-value=4.8 Score=29.42 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=26.4
Q ss_pred hhhcCCCeEEEEE----cCCcEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIEL----KNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeL----kng~~~~G~L~~~D~~m 33 (129)
+...+|++|.|+| .+.+.+.|+|.++|..+
T Consensus 94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3467899999999 77899999999999876
No 73
>PRK14633 hypothetical protein; Provisional
Probab=76.62 E-value=9.4 Score=27.59 Aligned_cols=29 Identities=17% Similarity=0.119 Sum_probs=24.5
Q ss_pred hhhcCCCeEEEEEc----CCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELK----NGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk----ng~~~~G~L~~~D~~ 32 (129)
+.+.+|++|.|.|+ +...+.|+|.++++.
T Consensus 89 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~ 121 (150)
T PRK14633 89 AQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN 121 (150)
T ss_pred HHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC
Confidence 45678999999984 569999999999875
No 74
>PRK14636 hypothetical protein; Provisional
Probab=76.43 E-value=7.9 Score=28.82 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=24.2
Q ss_pred hhhcCCCeEEEEEc---CC-cEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELK---NG-TQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk---ng-~~~~G~L~~~D~~ 32 (129)
+...+|++|.|+|+ ++ +.+.|+|.++|..
T Consensus 93 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~ 125 (176)
T PRK14636 93 FADWAGHEARIALSEPLDGRKQFRGELKGIDGD 125 (176)
T ss_pred HHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence 35678999999997 44 7999999999873
No 75
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=74.85 E-value=8.7 Score=32.12 Aligned_cols=10 Identities=10% Similarity=0.292 Sum_probs=4.2
Q ss_pred cCeEEEEEcC
Q psy15782 59 GNNIRYYILP 68 (129)
Q Consensus 59 Gn~Ir~Ii~p 68 (129)
|..|.++...
T Consensus 343 G~ai~l~~~~ 352 (456)
T PRK10590 343 GEALSLVCVD 352 (456)
T ss_pred eeEEEEecHH
Confidence 3344444433
No 76
>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=74.68 E-value=3.2 Score=27.11 Aligned_cols=28 Identities=29% Similarity=0.477 Sum_probs=16.0
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 5 MKLSHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 5 ~~l~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
..+-+.+|.++|+||+.+.|+ ..|-..|
T Consensus 13 AC~~~~~v~L~l~dG~~~~g~--A~dt~~~ 40 (80)
T PF07073_consen 13 ACMYRYPVKLTLKDGEQIEGK--ALDTRTN 40 (80)
T ss_dssp HHTTTT-EEEE-TTT--EEES--S-EEE--
T ss_pred HHhcCCeEEEEEeCCCEEEEE--EEEEEEe
Confidence 346678999999999999997 3444444
No 77
>PRK14647 hypothetical protein; Provisional
Probab=73.18 E-value=10 Score=27.62 Aligned_cols=29 Identities=10% Similarity=0.194 Sum_probs=24.2
Q ss_pred hhhcCCCeEEEEEc---------CCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELK---------NGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk---------ng~~~~G~L~~~D~~ 32 (129)
+.+.+|++|.|.|+ +.+.+.|+|.++|..
T Consensus 94 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 94 YERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred HHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 45678999999995 358999999999963
No 78
>PRK14632 hypothetical protein; Provisional
Probab=72.32 E-value=16 Score=27.03 Aligned_cols=29 Identities=10% Similarity=0.235 Sum_probs=24.6
Q ss_pred hhhcCCCeEEEEEcC-------CcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKN-------GTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkn-------g~~~~G~L~~~D~~ 32 (129)
+.+.+|+.|.|.|++ .+.+.|+|.++|+.
T Consensus 93 f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~ 128 (172)
T PRK14632 93 MSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD 128 (172)
T ss_pred HHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC
Confidence 456789999999986 57999999999864
No 79
>PRK14645 hypothetical protein; Provisional
Probab=71.95 E-value=6.6 Score=28.61 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=23.8
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
+.+.+|++|.|.+ ++..+.|+|.++|+.
T Consensus 97 f~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 97 FERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 4567899999976 789999999999975
No 80
>PRK14631 hypothetical protein; Provisional
Probab=71.15 E-value=14 Score=27.54 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=23.3
Q ss_pred hhhcCCCeEEEEEc----CCcEEEEEEEEec
Q psy15782 4 LMKLSHETVTIELK----NGTQVHGTIQGVD 30 (129)
Q Consensus 4 L~~l~~~~V~VeLk----ng~~~~G~L~~~D 30 (129)
+...+|+.|.|.|+ +.+.++|+|.++|
T Consensus 112 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 112 LQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 45678999999996 4599999999998
No 81
>PRK14643 hypothetical protein; Provisional
Probab=70.60 E-value=7.7 Score=28.58 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=24.9
Q ss_pred hhhcCCCeEEEEEcC----CcEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIELKN----GTQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeLkn----g~~~~G~L~~~D~~m 33 (129)
+...+|++|.|.|++ ...+.|+|.++|...
T Consensus 99 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 99 LVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT 132 (164)
T ss_pred HHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence 346789999999976 599999999999643
No 82
>PRK14634 hypothetical protein; Provisional
Probab=69.37 E-value=8.6 Score=27.97 Aligned_cols=30 Identities=7% Similarity=0.152 Sum_probs=24.5
Q ss_pred hhhcCCCeEEEEEcCC----cEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIELKNG----TQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeLkng----~~~~G~L~~~D~~m 33 (129)
+.+.+|++|.|+|++. ..+.|+|.++|+..
T Consensus 95 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~ 128 (155)
T PRK14634 95 FQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH 128 (155)
T ss_pred HHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE
Confidence 3567899999999742 79999999999743
No 83
>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=66.92 E-value=9 Score=25.94 Aligned_cols=19 Identities=37% Similarity=0.732 Sum_probs=15.1
Q ss_pred CCeEEEEEcCCcEEEEEEE
Q psy15782 9 HETVTIELKNGTQVHGTIQ 27 (129)
Q Consensus 9 ~~~V~VeLkng~~~~G~L~ 27 (129)
...|.++|+||+.+.|+|.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 3479999999999999874
No 84
>PRK14637 hypothetical protein; Provisional
Probab=65.78 E-value=11 Score=27.27 Aligned_cols=29 Identities=28% Similarity=0.225 Sum_probs=23.0
Q ss_pred hhhcCCCeEEEEEcCCcEE-EEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKNGTQV-HGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~-~G~L~~~D~~ 32 (129)
+...+|++|.|.|.+...+ +|+|.++|+.
T Consensus 93 f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~ 122 (151)
T PRK14637 93 FSIFVGETVKVWFECTGQWQVGTIAEADET 122 (151)
T ss_pred HHHhCCCEEEEEECCCCcEEEEEEEEEeCC
Confidence 4567899999999544555 7999999974
No 85
>PRK14646 hypothetical protein; Provisional
Probab=65.64 E-value=11 Score=27.34 Aligned_cols=29 Identities=14% Similarity=0.141 Sum_probs=23.9
Q ss_pred hhhcCCCeEEEEEcC----CcEEEEEEEEeccc
Q psy15782 4 LMKLSHETVTIELKN----GTQVHGTIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLkn----g~~~~G~L~~~D~~ 32 (129)
+...+|++|.|+|++ ...+.|+|.++|+.
T Consensus 95 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~ 127 (155)
T PRK14646 95 FKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD 127 (155)
T ss_pred HHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC
Confidence 356789999999965 37889999999985
No 86
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=61.99 E-value=14 Score=25.24 Aligned_cols=6 Identities=67% Similarity=1.354 Sum_probs=2.6
Q ss_pred CCCCCC
Q psy15782 102 RGGRGG 107 (129)
Q Consensus 102 rgg~gg 107 (129)
+||+++
T Consensus 17 qgG~~~ 22 (104)
T PF12764_consen 17 QGGRPG 22 (104)
T ss_pred cCCCCC
Confidence 444433
No 87
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. This entry represents Gar1 and Naf1. Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex being replaced by GAR1 to yield mature H/ACA snoRNPs complex. Naf1 reveals a striking structural homology with the core domain of archaeal Gar1 [].; GO: 0030515 snoRNA binding, 0031120 snRNA pseudouridine synthesis, 0042254 ribosome biogenesis; PDB: 2EY4_C 3MQK_C 2RFK_C 2HVY_B 3HAY_B 3U28_C 3UAI_C 2EQN_A 2V3M_F.
Probab=61.93 E-value=7.2 Score=28.17 Aligned_cols=22 Identities=18% Similarity=0.380 Sum_probs=19.4
Q ss_pred EEEEcCCcEEEEEEEEecccccc
Q psy15782 13 TIELKNGTQVHGTIQGVDVAMNT 35 (129)
Q Consensus 13 ~VeLkng~~~~G~L~~~D~~mNl 35 (129)
.|.|.|.+.+ |+|.++....|-
T Consensus 53 ~v~~edr~~i-G~V~eiFGpV~~ 74 (154)
T PF04410_consen 53 VVCLEDRTKI-GKVDEIFGPVNN 74 (154)
T ss_dssp EEEETTSBEE-EEEEEEESESSS
T ss_pred EEECCCCCEe-EEEeeEeCCCCc
Confidence 6778998887 999999999985
No 88
>PRK14641 hypothetical protein; Provisional
Probab=59.32 E-value=15 Score=27.34 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=22.7
Q ss_pred hhhcCCCeEEEEEcC----CcEEEEEEEEec
Q psy15782 4 LMKLSHETVTIELKN----GTQVHGTIQGVD 30 (129)
Q Consensus 4 L~~l~~~~V~VeLkn----g~~~~G~L~~~D 30 (129)
+.+.+|+.|.|.|++ ...+.|+|.++|
T Consensus 99 f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 456789999999976 468999999996
No 89
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=58.64 E-value=32 Score=26.09 Aligned_cols=28 Identities=29% Similarity=0.321 Sum_probs=23.6
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
.|+|+.|.+.-.++..+.|++.++.-.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~~~ 142 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRLAE 142 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEEcc
Confidence 5799999988888999999999987443
No 90
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=55.19 E-value=31 Score=25.42 Aligned_cols=25 Identities=16% Similarity=0.517 Sum_probs=22.3
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
.++.|.|+|.+|.+++|+-.++|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 5788999999999999999998854
No 91
>PRK06789 flagellar motor switch protein; Validated
Probab=53.36 E-value=29 Score=22.29 Aligned_cols=35 Identities=23% Similarity=0.211 Sum_probs=24.7
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
|.++.+++|.|.+++-..-+|.|..+|+.+=+.+.
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIt 70 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIV 70 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEE
Confidence 45667777788877777777888888876654443
No 92
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=52.80 E-value=50 Score=29.07 Aligned_cols=32 Identities=28% Similarity=0.281 Sum_probs=26.4
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
+.|++|.|...++.+++|++..+|..=.+.++
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 57899998766677799999999988777665
No 93
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=51.66 E-value=45 Score=24.06 Aligned_cols=27 Identities=15% Similarity=0.254 Sum_probs=23.5
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
.|+|++|+..+.++..+.|++.+|...
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~~ 116 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQT 116 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEEc
Confidence 589999998888999999999988754
No 94
>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=49.15 E-value=37 Score=23.54 Aligned_cols=22 Identities=32% Similarity=0.400 Sum_probs=18.2
Q ss_pred hhhcCCCeEEEEEcCCcEEEEE
Q psy15782 4 LMKLSHETVTIELKNGTQVHGT 25 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~ 25 (129)
|....+-+|++||.||.+|...
T Consensus 69 i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 69 INDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred HhCCcccEEEEEecCCcEEEec
Confidence 5677888999999999999443
No 95
>PRK14630 hypothetical protein; Provisional
Probab=46.56 E-value=35 Score=24.44 Aligned_cols=29 Identities=14% Similarity=0.166 Sum_probs=22.9
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+.+.+|++|.|.|.... ..|+|.++|+..
T Consensus 92 f~r~~G~~v~V~l~~~~-~~G~L~~~~d~~ 120 (143)
T PRK14630 92 FKIFEGKKIKLMLDNDF-EEGFILEAKADS 120 (143)
T ss_pred HHHhCCCEEEEEEcCcc-eEEEEEEEeCCE
Confidence 35678999999997654 479999998743
No 96
>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=44.84 E-value=21 Score=26.26 Aligned_cols=33 Identities=18% Similarity=0.094 Sum_probs=28.5
Q ss_pred CCeEEEEEcCCcEEEEEEEEecccccceEeeEE
Q psy15782 9 HETVTIELKNGTQVHGTIQGVDVAMNTHLKTVK 41 (129)
Q Consensus 9 ~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~ 41 (129)
.-+|.|.+.|+.++.+.+..++..-|..|..+.
T Consensus 29 ~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 29 DIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred CCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 457999999999999999999999998766544
No 97
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=43.55 E-value=23 Score=26.68 Aligned_cols=32 Identities=25% Similarity=0.532 Sum_probs=23.5
Q ss_pred ChhhhhcCCC--eEEEEEcC-CcEEEEEEEEeccc
Q psy15782 1 MNFLMKLSHE--TVTIELKN-GTQVHGTIQGVDVA 32 (129)
Q Consensus 1 ~~~L~~l~~~--~V~VeLkn-g~~~~G~L~~~D~~ 32 (129)
|.||..+-++ +|.+++.. +.+|.|.|.++|.-
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 4688888776 46555553 57888999999964
No 98
>PF09923 DUF2155: Uncharacterized protein conserved in bacteria (DUF2155); InterPro: IPR019225 This entry contains various hypothetical prokaryotic proteins that have no known function.
Probab=42.52 E-value=30 Score=22.98 Aligned_cols=41 Identities=15% Similarity=0.170 Sum_probs=29.2
Q ss_pred ChhhhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCC
Q psy15782 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGK 47 (129)
Q Consensus 1 ~~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~ 47 (129)
++.|.|+.++...++++.|+.++ | ..+-+.++.|+......
T Consensus 3 l~~LDKitg~~~~~~v~~G~~~~-----~-g~L~i~~~~C~~r~p~~ 43 (90)
T PF09923_consen 3 LRGLDKITGRVTDFEVPVGETVQ-----F-GNLTITLRACVSRPPTE 43 (90)
T ss_pred EEEEecccCeEEEEEEcCCCEEE-----E-ccEEEEhhheecCCCCC
Confidence 46789999999999999997762 2 45667777776544433
No 99
>PF10961 DUF2763: Protein of unknown function (DUF2763); InterPro: IPR024491 This entry represents an eukaryotic family of selenoproteins. It includes SelK, which seems to play an important role in protecting cells from endoplasmic reticulum stress-induced apoptosis [] and SelG, which may be involved in regulating the redox state of the cell [].
Probab=42.48 E-value=62 Score=21.50 Aligned_cols=10 Identities=40% Similarity=0.487 Sum_probs=5.6
Q ss_pred CccccccCCC
Q psy15782 71 LPLETLLIDD 80 (129)
Q Consensus 71 l~l~~~L~~~ 80 (129)
++..++|..+
T Consensus 34 lFF~Tl~~p~ 43 (91)
T PF10961_consen 34 LFFQTLFSPD 43 (91)
T ss_pred HHHHHHhCCC
Confidence 4557777433
No 100
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=41.32 E-value=50 Score=23.68 Aligned_cols=40 Identities=25% Similarity=0.344 Sum_probs=29.8
Q ss_pred cEEEEEEEEec---ccccceEeeEEEEecCCcceecceEEEecCeEE
Q psy15782 20 TQVHGTIQGVD---VAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIR 63 (129)
Q Consensus 20 ~~~~G~L~~~D---~~mNl~Lkdv~~~~~~~~~~~l~~~~IrGn~Ir 63 (129)
-.+.|.+..+- -+||+++.|+ ..++.+....+-||||+..
T Consensus 83 ~~lvG~VqKvS~Lil~~~~~v~Dv----~tg~~v~~~~~diRgntD~ 125 (140)
T PF11684_consen 83 YVLVGEVQKVSNLILNMNVYVRDV----ETGKVVRGRSVDIRGNTDE 125 (140)
T ss_pred EEEEEEEechhhhheeeeEEEEEC----CCCCEEeeeeeeEecCcHH
Confidence 45567776665 4888888887 4577888888999998753
No 101
>PRK10898 serine endoprotease; Provisional
Probab=40.60 E-value=1.1e+02 Score=25.01 Aligned_cols=31 Identities=13% Similarity=0.350 Sum_probs=26.8
Q ss_pred CeEEEEEcCCcEEEEEEEEecccccceEeeE
Q psy15782 10 ETVTIELKNGTQVHGTIQGVDVAMNTHLKTV 40 (129)
Q Consensus 10 ~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv 40 (129)
..|.|.+.++..|..+|..+|..+++-+=.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 4689999999999999999999999865544
No 102
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=40.03 E-value=38 Score=22.14 Aligned_cols=27 Identities=30% Similarity=0.447 Sum_probs=19.7
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
.+-.-.++.+||+|.+++|+- -|-..|
T Consensus 20 Cl~hl~l~L~lkdGev~~a~A--~d~~~r 46 (84)
T COG4568 20 CLHHLPLTLELKDGEVLQAKA--SDLQRR 46 (84)
T ss_pred HhhhceEEEEEcCCeEEEEEe--hhhhhh
Confidence 345668999999999998874 344444
No 103
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=39.97 E-value=75 Score=19.61 Aligned_cols=33 Identities=12% Similarity=0.298 Sum_probs=26.0
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccccceEeeE
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAMNTHLKTV 40 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv 40 (129)
.++.|.|...+-..+.|.+..++..+=+.+.+.
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~ 73 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITEL 73 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 457788888888899999999998776665554
No 104
>KOG0921|consensus
Probab=39.79 E-value=40 Score=31.86 Aligned_cols=16 Identities=25% Similarity=0.339 Sum_probs=13.2
Q ss_pred EEE-EEEecccccceEe
Q psy15782 23 HGT-IQGVDVAMNTHLK 38 (129)
Q Consensus 23 ~G~-L~~~D~~mNl~Lk 38 (129)
-|. |+-||+|+++.++
T Consensus 1075 dgq~IV~VDdWIklqIs 1091 (1282)
T KOG0921|consen 1075 DGQGIVRVDDWIKLQIS 1091 (1282)
T ss_pred cCcceEEeeceeeEecc
Confidence 467 8899999998776
No 105
>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=39.30 E-value=49 Score=22.97 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=18.1
Q ss_pred eEEEEEcCCcEEEEEEEEecc
Q psy15782 11 TVTIELKNGTQVHGTIQGVDV 31 (129)
Q Consensus 11 ~V~VeLkng~~~~G~L~~~D~ 31 (129)
.+.|.|+||+++.|.|.+=|.
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~ 79 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA 79 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC
Confidence 479999999999999988553
No 106
>PRK06955 biotin--protein ligase; Provisional
Probab=37.65 E-value=85 Score=24.95 Aligned_cols=33 Identities=15% Similarity=0.196 Sum_probs=26.5
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
.+.+++|+|...++..+.|++..+|..=.+.++
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 357999999766677789999999987776554
No 107
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=37.59 E-value=28 Score=26.33 Aligned_cols=32 Identities=9% Similarity=0.124 Sum_probs=24.5
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+.|..-.|..|.|..-+|..|.++|.+++...
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~ 44 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKS 44 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSE
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcE
Confidence 34556679999999999999999999999654
No 108
>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=36.23 E-value=85 Score=17.87 Aligned_cols=25 Identities=20% Similarity=0.217 Sum_probs=21.4
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
.|+.|.+...++.-|++++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5777888877899999999999975
No 109
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=35.63 E-value=1.3e+02 Score=23.83 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=25.4
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
+.|++|+|...+ ..+.|++..+|..=.+.++
T Consensus 270 ~~g~~v~~~~~~-~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLIIGD-KEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEeCC-cEEEEEEEEECCCceEEEE
Confidence 579999998754 5788999999988877664
No 110
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=35.44 E-value=63 Score=25.77 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=12.0
Q ss_pred CCCeEEEEEcCCcEEEEEEEEec
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVD 30 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D 30 (129)
+-++|.-+++++..+.|....+|
T Consensus 133 Ir~~i~P~fr~gny~~gi~~~id 155 (271)
T COG1512 133 IRETIAPAFRDGNYAGGLEAGID 155 (271)
T ss_pred HHhhhCcccccCcHHHHHHHHHH
Confidence 33455666666665544444444
No 111
>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=35.44 E-value=1.4e+02 Score=24.25 Aligned_cols=31 Identities=13% Similarity=0.393 Sum_probs=26.5
Q ss_pred CeEEEEEcCCcEEEEEEEEecccccceEeeE
Q psy15782 10 ETVTIELKNGTQVHGTIQGVDVAMNTHLKTV 40 (129)
Q Consensus 10 ~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv 40 (129)
.++.|.+.++..+.++|..+|...++-+=.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 3578999999999999999999999866544
No 112
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=35.37 E-value=43 Score=23.70 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=11.9
Q ss_pred eecceEEEecCeEEEEEcCCC
Q psy15782 50 TTLDSISLRGNNIRYYILPDS 70 (129)
Q Consensus 50 ~~l~~~~IrGn~Ir~Ii~pd~ 70 (129)
..-+.+.|+ =.|+.|.|+
T Consensus 55 ~Vke~f~Wr---hyYw~LT~e 72 (124)
T PTZ00034 55 LVKEQFAWQ---HYYYYLTDE 72 (124)
T ss_pred ceEEEEeeE---EEEEEEchH
Confidence 344677887 666676665
No 113
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=33.60 E-value=1.2e+02 Score=21.79 Aligned_cols=26 Identities=31% Similarity=0.451 Sum_probs=19.4
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
.|+|++|++ .++ .+.|++.+|.-..+
T Consensus 94 slIGk~V~~--~~~-~~~G~V~sV~~~~~ 119 (140)
T PRK06009 94 GLIGRTVTS--ADG-SITGVVKSVTVYSD 119 (140)
T ss_pred HhcCCEEEe--cCC-cEEEEEEEEEEeCC
Confidence 478999975 445 57899999985554
No 114
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=33.48 E-value=74 Score=24.10 Aligned_cols=30 Identities=27% Similarity=0.385 Sum_probs=25.9
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 5 MKLSHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 5 ~~l~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
..|+|+.+..++.++..+.|.|++++.|+-
T Consensus 15 ~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 15 PRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 468999998888888877899999999873
No 115
>PRK14635 hypothetical protein; Provisional
Probab=33.47 E-value=1.9e+02 Score=21.01 Aligned_cols=29 Identities=10% Similarity=0.133 Sum_probs=22.6
Q ss_pred hhhcCCCeEEEEEc--CCcEEEE---EEEEeccc
Q psy15782 4 LMKLSHETVTIELK--NGTQVHG---TIQGVDVA 32 (129)
Q Consensus 4 L~~l~~~~V~VeLk--ng~~~~G---~L~~~D~~ 32 (129)
+....|+.|.|.+. ++..+.| +|.++|+.
T Consensus 94 ~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~ 127 (162)
T PRK14635 94 LDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD 127 (162)
T ss_pred HHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC
Confidence 45678999988886 4577777 99999864
No 116
>PRK10139 serine endoprotease; Provisional
Probab=32.16 E-value=1.1e+02 Score=25.94 Aligned_cols=61 Identities=15% Similarity=0.171 Sum_probs=38.4
Q ss_pred CeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecc--eEEEecCeEEEEEcCCCC
Q psy15782 10 ETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLD--SISLRGNNIRYYILPDSL 71 (129)
Q Consensus 10 ~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~--~~~IrGn~Ir~Ii~pd~l 71 (129)
.+|.|.|.|+++|..+|..+|...++-+=.+... .+-.+..+. .-.--|..+..|-.|..+
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~-~~l~~~~lg~s~~~~~G~~V~aiG~P~g~ 177 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP-SKLTQIAIADSDKLRVGDFAVAVGNPFGL 177 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC-CCCceeEecCccccCCCCEEEEEecCCCC
Confidence 4689999999999999999999998855444210 011122221 112236666667776553
No 117
>PRK06788 flagellar motor switch protein; Validated
Probab=32.06 E-value=97 Score=21.66 Aligned_cols=35 Identities=17% Similarity=0.031 Sum_probs=20.6
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEecccccceEee
Q psy15782 5 MKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKT 39 (129)
Q Consensus 5 ~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkd 39 (129)
.+..+..|.|.+.+-..++|.+..++..+=+.+.+
T Consensus 64 dk~~~dpv~v~Vng~~~f~G~~Gv~~~~~AVrIte 98 (119)
T PRK06788 64 EKNLGHKVDVYLSNMKVGIGEAIVMDEKFGIIISE 98 (119)
T ss_pred CCcCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 34455566666666666666666666655544443
No 118
>PRK10942 serine endoprotease; Provisional
Probab=31.70 E-value=90 Score=26.60 Aligned_cols=31 Identities=16% Similarity=0.380 Sum_probs=26.7
Q ss_pred CeEEEEEcCCcEEEEEEEEecccccceEeeE
Q psy15782 10 ETVTIELKNGTQVHGTIQGVDVAMNTHLKTV 40 (129)
Q Consensus 10 ~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv 40 (129)
..|.|.|.|+++|..++...|...++.+=.+
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999998866544
No 119
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=31.22 E-value=26 Score=22.15 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=10.7
Q ss_pred cEEEEEEEEecccc
Q psy15782 20 TQVHGTIQGVDVAM 33 (129)
Q Consensus 20 ~~~~G~L~~~D~~m 33 (129)
..++|.|.+||..|
T Consensus 3 ~a~kGvLv~CDpa~ 16 (68)
T PF06331_consen 3 NAIKGVLVECDPAI 16 (68)
T ss_dssp EEEEEEEEES-HHH
T ss_pred ceeeeEEEEcCHHH
Confidence 35789999999876
No 120
>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=31.19 E-value=1.9e+02 Score=21.96 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=25.1
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
+.+++|+|...+ .++.|++..+|..=.+.++
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 569999998755 5688999999987777664
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=29.61 E-value=1e+02 Score=20.49 Aligned_cols=23 Identities=30% Similarity=0.420 Sum_probs=15.5
Q ss_pred hhhhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
.+|.++++++|++- |++.++|..
T Consensus 8 ~~L~~f~gk~V~iv--------GkV~~~~~~ 30 (101)
T cd04479 8 AMLSQFVGKTVRIV--------GKVEKVDGD 30 (101)
T ss_pred HHHHhhCCCEEEEE--------EEEEEecCC
Confidence 36788899998654 555555543
No 122
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.32 E-value=34 Score=24.13 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=20.3
Q ss_pred hhhhhcCCCeEEEEEcCC-cEEEEEEE
Q psy15782 2 NFLMKLSHETVTIELKNG-TQVHGTIQ 27 (129)
Q Consensus 2 ~~L~~l~~~~V~VeLkng-~~~~G~L~ 27 (129)
.|+..|++++|.|+++.. ..+.|+..
T Consensus 96 ~~~~~l~gk~l~V~v~~~~~e~nGk~y 122 (141)
T PF05037_consen 96 QFLNQLLGKPLRVTVKWEENEYNGKTY 122 (141)
T ss_pred HHHHHHcCCeeEEEecccccCCCCcEe
Confidence 367788999999999987 77767543
No 123
>PRK08158 type III secretion system protein SpaO; Validated
Probab=28.18 E-value=1.2e+02 Score=24.74 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=30.4
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccccceEeeEE
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVK 41 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~ 41 (129)
|.+..++.|.|..++-..-+|.|+.+|+.+=+.+.++.
T Consensus 259 L~~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i~ 296 (303)
T PRK08158 259 LPTNAELNVEIRANGALLGNGELVQMDDTLGVEIHEWL 296 (303)
T ss_pred CCCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEEe
Confidence 34557888999998889999999999988877666654
No 124
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=27.97 E-value=1.4e+02 Score=17.83 Aligned_cols=40 Identities=23% Similarity=0.360 Sum_probs=24.9
Q ss_pred cCCcEEEEEEEE---ecccccceEeeEEEEe-cCCcceecceEE
Q psy15782 17 KNGTQVHGTIQG---VDVAMNTHLKTVKMTV-KGKEPTTLDSIS 56 (129)
Q Consensus 17 kng~~~~G~L~~---~D~~mNl~Lkdv~~~~-~~~~~~~l~~~~ 56 (129)
++...+.|+|.. ||+-.-..|+|+.+.. ...+....+.+-
T Consensus 3 k~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkvK 46 (52)
T PF02751_consen 3 KNKLSFKGHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKVK 46 (52)
T ss_dssp --EEEEEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEEE
T ss_pred ceeEEEEEeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeEE
Confidence 455677788875 6777778899998876 333444444433
No 125
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=27.94 E-value=89 Score=23.67 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=22.4
Q ss_pred hhcCCCeEEEEEcCCcEEEEEEEEec
Q psy15782 5 MKLSHETVTIELKNGTQVHGTIQGVD 30 (129)
Q Consensus 5 ~~l~~~~V~VeLkng~~~~G~L~~~D 30 (129)
..++|++|.|.|.....++|.|.+++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 45899999999998899999999995
No 126
>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=27.32 E-value=1.5e+02 Score=24.62 Aligned_cols=31 Identities=16% Similarity=0.415 Sum_probs=26.7
Q ss_pred CeEEEEEcCCcEEEEEEEEecccccceEeeE
Q psy15782 10 ETVTIELKNGTQVHGTIQGVDVAMNTHLKTV 40 (129)
Q Consensus 10 ~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv 40 (129)
..+.|.+.++..|..+|..+|..+++.+=.+
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 3678999999999999999999999866554
No 127
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=27.13 E-value=1.3e+02 Score=22.66 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=23.3
Q ss_pred CCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
.|.+|.|++.++..+.|+|..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 477899999888899999999997664
No 128
>PRK08330 biotin--protein ligase; Provisional
Probab=26.96 E-value=1.6e+02 Score=22.39 Aligned_cols=33 Identities=18% Similarity=0.113 Sum_probs=24.1
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
.+.+++|+|...+...+.|++..+|..=.+.++
T Consensus 185 ~~~g~~v~~~~~~~~~~~G~~~gI~~~G~L~v~ 217 (236)
T PRK08330 185 MILGKRVKIIGDGEILVEGIAEDIDEFGALILR 217 (236)
T ss_pred HhcCCeEEEEECCcEEEEEEEEEECCCCEEEEE
Confidence 367999999764433347999999987766554
No 129
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=26.96 E-value=2.2e+02 Score=19.70 Aligned_cols=7 Identities=14% Similarity=0.311 Sum_probs=3.1
Q ss_pred Ccccccc
Q psy15782 71 LPLETLL 77 (129)
Q Consensus 71 l~l~~~L 77 (129)
++...+|
T Consensus 103 v~~~~~i 109 (129)
T PRK06461 103 VPEAEEI 109 (129)
T ss_pred cCCCCcc
Confidence 4444444
No 130
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=26.77 E-value=90 Score=23.42 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=21.8
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEeccccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMN 34 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~mN 34 (129)
=..|+|+.+..++.++. +.|.|++++.|+-
T Consensus 13 A~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 13 ARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 35789999999999988 6699999987764
No 131
>KOG4401|consensus
Probab=26.47 E-value=65 Score=24.31 Aligned_cols=44 Identities=11% Similarity=0.150 Sum_probs=32.8
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccccceEeeEEEEecCCcceecc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLD 53 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkdv~~~~~~~~~~~l~ 53 (129)
++-.|.|...++....|.|.+||-.-++..-++. ..++.|.+..
T Consensus 10 vg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~--~s~~~P~~~~ 53 (184)
T KOG4401|consen 10 VGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP--SSNGKPNHAK 53 (184)
T ss_pred EEEEEEecccccceeeeEEEEEEcccCeeEeccc--ccCCCCccch
Confidence 3556788899999999999999988887666665 3445555443
No 132
>PF13437 HlyD_3: HlyD family secretion protein
Probab=25.48 E-value=1.6e+02 Score=18.85 Aligned_cols=24 Identities=21% Similarity=0.504 Sum_probs=20.0
Q ss_pred CCCeEEEEEcCC--cEEEEEEEEecc
Q psy15782 8 SHETVTIELKNG--TQVHGTIQGVDV 31 (129)
Q Consensus 8 ~~~~V~VeLkng--~~~~G~L~~~D~ 31 (129)
.|..|+|.+.++ ..+.|+|.+++.
T Consensus 53 ~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 53 PGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred CCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 578899998854 688999999987
No 133
>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=25.45 E-value=1.6e+02 Score=17.91 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=19.2
Q ss_pred CCCeEEEEEcCCcEE-EEEEEEeccccc
Q psy15782 8 SHETVTIELKNGTQV-HGTIQGVDVAMN 34 (129)
Q Consensus 8 ~~~~V~VeLkng~~~-~G~L~~~D~~mN 34 (129)
.|+.|.+.--+...| .+++.++|..--
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~~~ 35 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSKSD 35 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETTTT
T ss_pred CCCEEEEECCCCCcEEEEEEEEecccCc
Confidence 688899988887555 999999997543
No 134
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=24.91 E-value=66 Score=17.92 Aligned_cols=17 Identities=24% Similarity=0.474 Sum_probs=13.2
Q ss_pred hcCCCeEEEEEcCCcEE
Q psy15782 6 KLSHETVTIELKNGTQV 22 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~ 22 (129)
+..+.+|+|++.+|++.
T Consensus 20 ~~~g~~vtV~~~~G~~~ 36 (42)
T PF02736_consen 20 EEEGDKVTVKTEDGKEV 36 (42)
T ss_dssp EEESSEEEEEETTTEEE
T ss_pred EEcCCEEEEEECCCCEE
Confidence 45677899999998765
No 135
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=24.43 E-value=1.9e+02 Score=22.39 Aligned_cols=33 Identities=24% Similarity=0.281 Sum_probs=28.8
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceEee
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLKT 39 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkd 39 (129)
.+|++|++.+.++..+.|+...+|..-.+.++.
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~ 220 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLET 220 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEe
Confidence 479999999999999988999999988776654
No 136
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional
Probab=24.32 E-value=2.8e+02 Score=19.98 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=18.8
Q ss_pred hhhcCCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 4 L~~l~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+..|+|-+|. .++..+ |+|.+++.+-
T Consensus 91 ~~dLiG~~V~---~~g~~l-G~V~~v~~~g 116 (162)
T PRK13829 91 YHELRGLPVY---VDGEPL-GEVVDVEDAG 116 (162)
T ss_pred ehhccCeEEE---ECCEee-EEEEEEecCC
Confidence 4456777775 577666 9999998754
No 137
>TIGR03344 VI_effect_Hcp1 type VI secretion system effector, Hcp1 family. This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens.
Probab=24.22 E-value=1.3e+02 Score=21.96 Aligned_cols=43 Identities=12% Similarity=0.127 Sum_probs=28.6
Q ss_pred ecccccceEeeEEEEecC---------CcceecceEEEecCeEEEEEcCCCC
Q psy15782 29 VDVAMNTHLKTVKMTVKG---------KEPTTLDSISLRGNNIRYYILPDSL 71 (129)
Q Consensus 29 ~D~~mNl~Lkdv~~~~~~---------~~~~~l~~~~IrGn~Ir~Ii~pd~l 71 (129)
-..||.+.|+||.++.-. ....+.|.+.+.-..|.+-+.+...
T Consensus 106 ~~~y~~itL~~a~Issi~~~~~~~~~~~~~~~~E~vs~~y~~I~~~y~~~~~ 157 (166)
T TIGR03344 106 QELYYTIKLEGALIVDIKPYMPHCLDPNNAQPLEDVSFRYRKITWTHHIAGT 157 (166)
T ss_pred EEEEEEEEEeeEEEEEEEcccCcccCCCCCCceEEEEEEeeEEEEEEECCCe
Confidence 346889999988876422 2234667888877777777765543
No 138
>PRK10708 hypothetical protein; Provisional
Probab=23.56 E-value=98 Score=19.04 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=21.8
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+|-.|+|++..+..-.|+|..+..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 46789999999988889999888764
No 139
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=22.43 E-value=95 Score=23.77 Aligned_cols=30 Identities=13% Similarity=0.112 Sum_probs=24.4
Q ss_pred hhhhcCCCeEEEEEcCCcEEEEEEEEeccc
Q psy15782 3 FLMKLSHETVTIELKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 3 ~L~~l~~~~V~VeLkng~~~~G~L~~~D~~ 32 (129)
.|..-.|..|.|..-++..|.++|..++..
T Consensus 29 VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~ 58 (240)
T TIGR00046 29 VLRLKKGDKLKLLDGDGFIYHCEIKKISKK 58 (240)
T ss_pred cccCCCCCEEEEEeCCCCEEEEEEEEEcCC
Confidence 455567888988888899999999998854
No 140
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=22.37 E-value=1.7e+02 Score=21.45 Aligned_cols=34 Identities=18% Similarity=0.307 Sum_probs=19.9
Q ss_pred hcCCCeEEEEEcCCcEEEEEEEEecccccceEee
Q psy15782 6 KLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKT 39 (129)
Q Consensus 6 ~l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lkd 39 (129)
+..++.|.|...+-..++|.+.-++..+=+.+.+
T Consensus 110 k~~~epv~V~VnG~~~f~Ge~Gvvn~k~AVrIte 143 (155)
T PRK05698 110 RLAGEPLDVLVNGTLIAHGEVVVVNEKFGIRLTD 143 (155)
T ss_pred CCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEE
Confidence 4445556666666666666666666655554444
No 141
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.11 E-value=95 Score=19.30 Aligned_cols=17 Identities=24% Similarity=0.423 Sum_probs=14.3
Q ss_pred EcCCcEEEEEEEEeccc
Q psy15782 16 LKNGTQVHGTIQGVDVA 32 (129)
Q Consensus 16 Lkng~~~~G~L~~~D~~ 32 (129)
|+.|..++|++.++.+|
T Consensus 2 l~~G~~v~g~V~si~d~ 18 (74)
T cd05694 2 LVEGMVLSGCVSSVEDH 18 (74)
T ss_pred CCCCCEEEEEEEEEeCC
Confidence 67788999999999864
No 142
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=21.82 E-value=1.8e+02 Score=16.99 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=21.3
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+|++|.++-++++.+..+|..+..--
T Consensus 3 vG~~v~~~~~~~~~y~A~I~~~r~~~ 28 (55)
T PF11717_consen 3 VGEKVLCKYKDGQWYEAKILDIREKN 28 (55)
T ss_dssp TTEEEEEEETTTEEEEEEEEEEEECT
T ss_pred cCCEEEEEECCCcEEEEEEEEEEecC
Confidence 57888888888999999998887633
No 143
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=21.76 E-value=2.5e+02 Score=22.23 Aligned_cols=31 Identities=19% Similarity=0.210 Sum_probs=24.4
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceEe
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHLK 38 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~Lk 38 (129)
+.++.|.|.. ++..+.|++..+|..=.+.++
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~ 265 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLL 265 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEE
Confidence 4789999876 457889999999987666554
No 144
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=21.54 E-value=1.6e+02 Score=17.43 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=14.8
Q ss_pred hcCCCeEEEE--EcCCcEEEEEEEEec
Q psy15782 6 KLSHETVTIE--LKNGTQVHGTIQGVD 30 (129)
Q Consensus 6 ~l~~~~V~Ve--Lkng~~~~G~L~~~D 30 (129)
.|+|++|.+. ..--....|++.+++
T Consensus 9 ~lIGk~V~~~~~~~~~~~~~g~V~sV~ 35 (61)
T PF13861_consen 9 SLIGKEVLVPKSVAATTLVSGRVESVT 35 (61)
T ss_dssp CTTTSEEEEEEEEEE-EEEEEEEEEEE
T ss_pred HhcCCEEEECCcEeeeeEEEEEEEEEE
Confidence 4789999986 222344445555554
No 145
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=21.28 E-value=1.3e+02 Score=26.58 Aligned_cols=36 Identities=36% Similarity=0.532 Sum_probs=0.0
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy15782 94 GGAGGARGRG-GRGGRGGGRGGRGRGGPRGRGGPPRR 129 (129)
Q Consensus 94 ~g~g~g~grg-g~gg~~~~~~~~~~~~~~g~g~~~~~ 129 (129)
+|..++++|+ +++++.++++++.+++..++.....|
T Consensus 579 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 615 (629)
T PRK11634 579 GGERREGGRNFSGERREGGRGDGRRFSGERREGRAPR 615 (629)
T ss_pred CCCCCCCCcCCCCCCCCCCccccccCcCcCCCCCCCC
No 146
>PRK08916 flagellar motor switch protein; Reviewed
Probab=20.27 E-value=2.5e+02 Score=19.53 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=16.8
Q ss_pred cCCCeEEEEEcCCcEEEEEEEEecccccceE
Q psy15782 7 LSHETVTIELKNGTQVHGTIQGVDVAMNTHL 37 (129)
Q Consensus 7 l~~~~V~VeLkng~~~~G~L~~~D~~mNl~L 37 (129)
..++.|.|...+-..++|.+.-++..+=+.+
T Consensus 77 ~~~e~V~I~Vng~~~~~Gelg~~~~rlAVrI 107 (116)
T PRK08916 77 KVGEAIDIYVNNRLVARGEVVLVEDRLGVTM 107 (116)
T ss_pred CCCCCEEEEECCEEEEEEEEEEECCEEEEEE
Confidence 3445555655555666666666555444433
No 147
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit 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=20.10 E-value=1.8e+02 Score=19.05 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=21.8
Q ss_pred EEEEcCCcEEEEEEEEecccccceEee
Q psy15782 13 TIELKNGTQVHGTIQGVDVAMNTHLKT 39 (129)
Q Consensus 13 ~VeLkng~~~~G~L~~~D~~mNl~Lkd 39 (129)
.=.|+.|..+...|.++|..|...|+-
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~~~eLtc 73 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDMEPELSC 73 (86)
T ss_pred cccCCCCCEEEEEEEecCCCCCeEEEE
Confidence 456788888889999999999876663
No 148
>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=20.04 E-value=1.1e+02 Score=18.76 Aligned_cols=26 Identities=23% Similarity=0.366 Sum_probs=21.6
Q ss_pred CCCeEEEEEcCCcEEEEEEEEecccc
Q psy15782 8 SHETVTIELKNGTQVHGTIQGVDVAM 33 (129)
Q Consensus 8 ~~~~V~VeLkng~~~~G~L~~~D~~m 33 (129)
+|-.|+|++..+..-.|+|..+..|-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 46679999999988889999888764
Done!