Query 033668
Match_columns 114
No_of_seqs 106 out of 1013
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:55:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033668.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033668hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01724 Sm_D1 The eukaryotic S 100.0 2.3E-29 4.9E-34 170.8 11.4 90 2-91 1-90 (90)
2 KOG3428 Small nuclear ribonucl 99.9 2.4E-27 5.2E-32 164.8 9.9 93 1-94 1-93 (109)
3 KOG3293 Small nuclear ribonucl 99.9 1.6E-26 3.6E-31 163.9 8.6 102 1-103 1-103 (134)
4 cd01721 Sm_D3 The eukaryotic S 99.9 1.9E-25 4.2E-30 144.8 9.9 70 3-72 1-70 (70)
5 cd01733 LSm10 The eukaryotic S 99.9 6E-25 1.3E-29 145.5 10.1 70 2-71 9-78 (78)
6 KOG3172 Small nuclear ribonucl 99.9 5.6E-25 1.2E-29 153.1 9.1 87 3-89 6-92 (119)
7 cd01723 LSm4 The eukaryotic Sm 99.9 2.6E-24 5.6E-29 141.4 9.1 73 2-74 1-74 (76)
8 cd01725 LSm2 The eukaryotic Sm 99.9 4.3E-24 9.2E-29 142.1 9.2 76 2-78 1-78 (81)
9 cd01726 LSm6 The eukaryotic Sm 99.9 1.4E-22 3.1E-27 130.0 9.0 67 3-69 1-67 (67)
10 cd01722 Sm_F The eukaryotic Sm 99.9 8.9E-22 1.9E-26 126.8 9.2 67 3-69 2-68 (68)
11 PRK00737 small nuclear ribonuc 99.9 2.8E-21 6E-26 125.8 9.7 68 2-69 4-71 (72)
12 cd01731 archaeal_Sm1 The archa 99.9 4.6E-21 1E-25 123.1 9.3 67 3-69 1-67 (68)
13 cd01732 LSm5 The eukaryotic Sm 99.8 1.1E-20 2.5E-25 124.6 10.0 70 1-70 2-74 (76)
14 KOG3448 Predicted snRNP core p 99.8 2.8E-21 6.1E-26 130.5 6.8 88 1-89 1-90 (96)
15 PF01423 LSM: LSM domain ; In 99.8 1.2E-20 2.6E-25 119.7 8.7 66 5-70 1-67 (67)
16 smart00651 Sm snRNP Sm protein 99.8 1.9E-20 4.1E-25 118.7 9.1 66 5-70 1-67 (67)
17 cd01719 Sm_G The eukaryotic Sm 99.8 9.1E-20 2E-24 119.0 9.5 69 5-73 3-71 (72)
18 cd00600 Sm_like The eukaryotic 99.8 3E-19 6.5E-24 111.6 8.9 63 7-69 1-63 (63)
19 COG1958 LSM1 Small nuclear rib 99.8 3.7E-19 7.9E-24 117.3 9.1 69 2-70 7-79 (79)
20 cd01729 LSm7 The eukaryotic Sm 99.8 3.5E-18 7.6E-23 113.7 9.3 68 5-72 5-80 (81)
21 cd01730 LSm3 The eukaryotic Sm 99.8 6.1E-18 1.3E-22 112.5 8.9 67 3-69 2-81 (82)
22 cd01720 Sm_D2 The eukaryotic S 99.7 1.2E-17 2.6E-22 112.8 9.1 68 3-70 3-85 (87)
23 cd01718 Sm_E The eukaryotic Sm 99.7 5.5E-17 1.2E-21 107.9 8.9 68 2-69 6-78 (79)
24 KOG3482 Small nuclear ribonucl 99.7 2E-17 4.3E-22 108.3 6.4 67 3-69 9-75 (79)
25 cd01717 Sm_B The eukaryotic Sm 99.7 6.3E-17 1.4E-21 106.8 8.7 65 6-70 4-78 (79)
26 cd01728 LSm1 The eukaryotic Sm 99.7 2.7E-16 5.9E-21 103.3 9.6 67 4-70 4-73 (74)
27 cd01727 LSm8 The eukaryotic Sm 99.7 2.5E-16 5.4E-21 102.8 9.1 68 5-72 2-73 (74)
28 cd06168 LSm9 The eukaryotic Sm 99.7 6.5E-16 1.4E-20 101.7 9.2 66 5-70 3-74 (75)
29 KOG1783 Small nuclear ribonucl 99.7 2E-17 4.3E-22 108.2 0.9 70 3-72 7-76 (77)
30 PTZ00138 small nuclear ribonuc 99.6 7.3E-15 1.6E-19 99.7 9.2 66 3-70 19-87 (89)
31 KOG1780 Small Nuclear ribonucl 99.5 1.2E-14 2.5E-19 95.4 6.0 68 5-72 7-74 (77)
32 KOG3460 Small nuclear ribonucl 99.5 1.3E-14 2.8E-19 97.3 1.8 72 3-74 6-90 (91)
33 KOG1775 U6 snRNA-associated Sm 99.4 2.9E-13 6.3E-18 89.5 3.3 69 2-70 7-78 (84)
34 KOG1774 Small nuclear ribonucl 99.2 1.7E-11 3.6E-16 82.0 4.2 67 2-70 16-85 (88)
35 KOG3168 U1 snRNP component [Tr 99.0 1.3E-10 2.8E-15 86.7 1.5 68 7-74 9-86 (177)
36 KOG1781 Small Nuclear ribonucl 99.0 9.8E-11 2.1E-15 80.7 -0.3 70 6-75 21-98 (108)
37 KOG1784 Small Nuclear ribonucl 98.9 2.4E-09 5.2E-14 72.9 5.2 87 5-92 3-93 (96)
38 KOG1782 Small Nuclear ribonucl 98.3 6.4E-08 1.4E-12 69.1 -0.7 66 5-70 12-80 (129)
39 PF14438 SM-ATX: Ataxin 2 SM d 98.2 1.1E-05 2.3E-10 52.5 6.8 47 2-48 2-51 (77)
40 cd01739 LSm11_C The eukaryotic 97.6 6.4E-05 1.4E-09 48.5 3.0 37 12-48 8-48 (66)
41 PF12701 LSM14: Scd6-like Sm d 97.5 0.00071 1.5E-08 46.5 7.1 66 8-73 4-79 (96)
42 KOG3459 Small nuclear ribonucl 97.0 0.00013 2.8E-09 51.4 -0.7 58 12-69 36-106 (114)
43 PF11095 Gemin7: Gem-associate 96.8 0.012 2.5E-07 39.4 7.5 65 2-71 14-79 (80)
44 cd01736 LSm14_N LSm14 (also kn 96.4 0.019 4.1E-07 37.9 6.4 60 8-67 2-72 (74)
45 PF10842 DUF2642: Protein of u 96.3 0.047 1E-06 35.2 7.6 53 3-69 12-65 (66)
46 PTZ00034 40S ribosomal protein 95.7 0.0085 1.8E-07 43.1 2.6 44 67-112 80-123 (124)
47 cd01716 Hfq Hfq, an abundant, 95.1 0.18 3.8E-06 32.1 6.8 32 11-42 10-41 (61)
48 KOG1073 Uncharacterized mRNA-a 95.1 0.054 1.2E-06 45.1 5.6 67 7-73 4-81 (361)
49 PRK00395 hfq RNA-binding prote 94.9 0.18 4E-06 33.6 6.7 55 11-77 18-72 (79)
50 PF02237 BPL_C: Biotin protein 94.9 0.14 3E-06 30.4 5.5 45 11-61 2-48 (48)
51 PF06372 Gemin6: Gemin6 protei 94.6 0.16 3.5E-06 38.1 6.5 63 5-74 10-73 (166)
52 TIGR02383 Hfq RNA chaperone Hf 94.5 0.084 1.8E-06 33.6 4.3 32 11-42 14-45 (61)
53 cd01735 LSm12_N LSm12 belongs 93.6 0.37 8E-06 30.6 5.9 32 10-41 4-35 (61)
54 PRK14638 hypothetical protein; 91.1 0.55 1.2E-05 34.3 5.0 36 4-40 92-127 (150)
55 PF05918 API5: Apoptosis inhib 90.7 0.073 1.6E-06 46.5 0.0 9 66-74 512-520 (556)
56 PRK14639 hypothetical protein; 89.9 0.84 1.8E-05 33.0 4.9 36 4-40 80-115 (140)
57 PRK14091 RNA-binding protein H 89.1 2.5 5.4E-05 31.8 7.0 55 12-78 24-78 (165)
58 PRK02001 hypothetical protein; 89.0 1 2.3E-05 33.1 5.0 31 5-35 83-113 (152)
59 PRK14091 RNA-binding protein H 88.9 2.2 4.7E-05 32.1 6.6 55 11-77 103-157 (165)
60 COG1923 Hfq Uncharacterized ho 88.8 3 6.5E-05 27.7 6.5 28 11-38 18-45 (77)
61 PRK14644 hypothetical protein; 86.8 1.4 3.1E-05 31.8 4.5 35 6-41 79-117 (136)
62 cd01734 YlxS_C YxlS is a Bacil 86.8 2.1 4.5E-05 28.0 4.9 32 4-35 17-52 (83)
63 COG0779 Uncharacterized protei 86.7 2.3 5E-05 31.5 5.6 33 4-36 91-127 (153)
64 PRK14640 hypothetical protein; 84.0 3 6.4E-05 30.5 5.1 31 5-35 90-124 (152)
65 PRK14643 hypothetical protein; 84.0 5 0.00011 29.8 6.3 31 5-35 97-131 (164)
66 PRK14642 hypothetical protein; 83.8 2.7 5.8E-05 32.4 5.0 71 4-75 92-183 (197)
67 PRK14633 hypothetical protein; 82.5 2.9 6.3E-05 30.5 4.5 35 5-40 87-125 (150)
68 PRK14632 hypothetical protein; 82.2 2.8 6E-05 31.3 4.4 35 5-40 91-132 (172)
69 PRK00092 ribosome maturation p 81.8 7.6 0.00017 28.1 6.5 31 5-35 91-125 (154)
70 PRK14645 hypothetical protein; 79.9 4.5 9.8E-05 29.7 4.8 30 5-35 95-124 (154)
71 PF02576 DUF150: Uncharacteris 78.7 2.9 6.3E-05 29.7 3.4 30 5-34 80-113 (141)
72 PRK14647 hypothetical protein; 78.0 5.8 0.00013 29.1 4.9 32 4-35 91-131 (159)
73 PRK14634 hypothetical protein; 78.0 5.9 0.00013 29.1 4.9 31 5-35 93-127 (155)
74 PRK14636 hypothetical protein; 77.8 5.6 0.00012 29.9 4.8 31 5-35 91-125 (176)
75 PRK14646 hypothetical protein; 77.8 4.9 0.00011 29.5 4.4 35 5-40 93-131 (155)
76 PRK14631 hypothetical protein; 73.4 8.6 0.00019 28.8 4.8 30 4-33 109-142 (174)
77 PRK14637 hypothetical protein; 72.8 8.8 0.00019 28.1 4.7 36 4-40 90-126 (151)
78 PRK09618 flgD flagellar basal 72.1 12 0.00027 27.4 5.3 26 8-33 88-113 (142)
79 PF07073 ROF: Modulator of Rho 70.7 4.9 0.00011 26.6 2.7 23 6-28 11-33 (80)
80 PRK14641 hypothetical protein; 70.7 9.7 0.00021 28.6 4.6 30 4-33 96-129 (173)
81 KOG3428 Small nuclear ribonucl 65.7 4.4 9.6E-05 28.6 1.7 20 76-95 80-99 (109)
82 PRK06955 biotin--protein ligas 64.3 45 0.00098 26.6 7.5 34 8-41 245-278 (300)
83 PRK11886 bifunctional biotin-- 63.1 36 0.00078 27.0 6.7 48 9-62 269-317 (319)
84 PRK13325 bifunctional biotin-- 62.9 31 0.00066 30.5 6.8 51 9-64 275-326 (592)
85 PF11607 DUF3247: Protein of u 62.6 11 0.00024 26.1 3.2 19 12-30 28-46 (101)
86 PRK14630 hypothetical protein; 59.8 18 0.00039 26.2 4.1 30 5-35 90-119 (143)
87 PRK14635 hypothetical protein; 59.0 32 0.0007 25.3 5.4 36 4-40 91-131 (162)
88 PF03614 Flag1_repress: Repres 58.7 12 0.00025 28.1 3.0 25 11-35 119-143 (165)
89 KOG3172 Small nuclear ribonucl 58.6 9.4 0.0002 27.0 2.3 13 76-88 72-84 (119)
90 PRK11911 flgD flagellar basal 54.3 30 0.00064 25.3 4.5 26 9-34 90-115 (140)
91 PRK10590 ATP-dependent RNA hel 52.7 17 0.00037 30.3 3.4 11 61-71 342-352 (456)
92 TIGR00121 birA_ligase birA, bi 51.2 61 0.0013 24.7 6.0 33 8-41 189-221 (237)
93 PRK06789 flagellar motor switc 49.8 36 0.00077 22.3 3.9 36 7-42 36-71 (74)
94 PRK08330 biotin--protein ligas 49.4 1.1E+02 0.0024 23.2 7.2 33 9-42 185-218 (236)
95 PRK11625 Rho-binding antitermi 48.1 81 0.0018 21.0 7.3 55 7-71 18-74 (84)
96 KOG2135 Proteins containing th 47.7 10 0.00022 33.1 1.3 24 90-113 339-363 (526)
97 PRK10898 serine endoprotease; 44.7 79 0.0017 25.8 6.1 60 12-73 101-162 (353)
98 KOG3344 40s ribosomal protein 43.5 24 0.00053 26.0 2.6 13 67-79 79-91 (150)
99 KOG0361 Chaperonin complex com 42.4 17 0.00037 31.4 1.8 24 84-107 517-540 (543)
100 smart00333 TUDOR Tudor domain. 41.8 69 0.0015 18.4 4.8 25 11-35 5-29 (57)
101 PRK10139 serine endoprotease; 40.9 60 0.0013 27.5 4.9 62 12-74 114-177 (455)
102 PF14563 DUF4444: Domain of un 40.8 28 0.00061 20.6 2.1 20 25-44 10-29 (42)
103 KOG4401 Uncharacterized conser 39.4 11 0.00024 28.9 0.2 35 10-44 9-43 (184)
104 TIGR02038 protease_degS peripl 39.3 1E+02 0.0023 25.0 6.0 59 13-73 102-162 (351)
105 COG1886 FliN Flagellar motor s 38.5 58 0.0012 23.3 3.9 36 7-42 100-135 (136)
106 PRK10942 serine endoprotease; 38.3 64 0.0014 27.5 4.7 32 12-43 135-166 (473)
107 KOG4501 Transcription coactiva 37.9 20 0.00043 32.1 1.6 20 94-113 661-680 (707)
108 TIGR02603 CxxCH_TIGR02603 puta 37.8 52 0.0011 23.0 3.5 20 14-33 59-78 (133)
109 TIGR02037 degP_htrA_DO peripla 37.4 69 0.0015 26.5 4.7 32 13-44 82-113 (428)
110 PF04452 Methyltrans_RNA: RNA 37.1 1E+02 0.0023 23.2 5.3 40 3-42 11-51 (225)
111 TIGR01080 rplX_A_E ribosomal p 36.6 1.5E+02 0.0033 20.8 5.9 58 11-71 44-102 (114)
112 TIGR00567 3mg DNA-3-methyladen 36.6 64 0.0014 24.7 4.0 34 5-38 12-45 (192)
113 cd01737 LSm16_N LSm16 belongs 36.4 1.1E+02 0.0025 19.4 5.2 55 9-66 3-59 (62)
114 PRK06792 flgD flagellar basal 36.3 56 0.0012 25.1 3.7 26 9-34 115-140 (190)
115 PF03614 Flag1_repress: Repres 35.2 62 0.0014 24.3 3.6 34 11-44 28-61 (165)
116 PTZ00275 biotin-acetyl-CoA-car 35.1 1.2E+02 0.0026 24.0 5.6 33 9-42 234-266 (285)
117 PF11743 DUF3301: Protein of u 35.0 57 0.0012 22.0 3.2 28 45-72 69-96 (97)
118 KOG3293 Small nuclear ribonucl 34.8 51 0.0011 23.9 3.0 8 15-22 43-50 (134)
119 KOG3262 H/ACA small nucleolar 33.1 1.1E+02 0.0025 23.8 4.9 15 3-17 56-70 (215)
120 COG0340 BirA Biotin-(acetyl-Co 31.5 1.4E+02 0.0031 23.2 5.4 36 8-43 186-221 (238)
121 PF05037 DUF669: Protein of un 30.2 38 0.00083 24.0 1.8 27 3-29 94-121 (141)
122 PF11684 DUF3280: Protein of u 30.0 79 0.0017 22.9 3.4 39 22-64 82-123 (140)
123 PF14485 DUF4431: Domain of un 29.9 53 0.0011 19.6 2.1 15 4-18 11-25 (48)
124 KOG3973 Uncharacterized conser 29.1 62 0.0013 27.6 3.1 33 78-111 351-383 (465)
125 PF07076 DUF1344: Protein of u 28.8 62 0.0013 20.5 2.4 23 24-46 4-27 (61)
126 cd04479 RPA3 RPA3: A subfamily 28.5 1.8E+02 0.004 19.4 7.1 70 5-78 8-86 (101)
127 PF10618 Tail_tube: Phage tail 28.5 1.7E+02 0.0036 20.4 4.8 25 4-28 66-90 (119)
128 PF02245 Pur_DNA_glyco: Methyl 27.8 1.2E+02 0.0026 23.0 4.2 33 4-37 10-42 (184)
129 COG4568 Rof Transcriptional an 27.1 93 0.002 20.8 3.1 23 7-29 18-40 (84)
130 PRK10708 hypothetical protein; 26.8 77 0.0017 20.0 2.5 27 11-37 3-29 (62)
131 PF09465 LBR_tudor: Lamin-B re 26.5 1.4E+02 0.003 18.6 3.6 26 10-35 7-33 (55)
132 PF06257 DUF1021: Protein of u 26.1 1.9E+02 0.0042 18.9 4.5 30 4-33 9-42 (76)
133 PF05954 Phage_GPD: Phage late 25.9 1E+02 0.0022 23.1 3.7 27 7-33 23-49 (292)
134 KOG0116 RasGAP SH3 binding pro 25.3 65 0.0014 27.5 2.6 14 65-78 332-345 (419)
135 PF01052 SpoA: Surface present 25.3 1.7E+02 0.0037 18.1 4.0 34 11-44 41-74 (77)
136 PRK08158 type III secretion sy 25.2 1.3E+02 0.0029 24.6 4.3 39 7-45 259-297 (303)
137 TIGR00999 8a0102 Membrane Fusi 24.7 1.5E+02 0.0032 22.1 4.3 27 11-37 141-167 (265)
138 PF10781 DSRB: Dextransucrase 24.4 83 0.0018 19.9 2.3 27 11-37 3-29 (62)
139 COG5316 Uncharacterized conser 24.3 2E+02 0.0042 24.8 5.2 42 4-46 74-115 (421)
140 PF13437 HlyD_3: HlyD family s 23.2 2E+02 0.0042 18.4 4.2 24 11-34 53-78 (105)
141 TIGR00046 RNA methyltransferas 22.3 3.2E+02 0.007 20.8 5.8 39 3-41 26-65 (240)
142 PRK11713 16S ribosomal RNA met 22.0 1.9E+02 0.004 22.0 4.4 32 3-34 24-55 (234)
143 PRK06009 flgD flagellar basal 21.8 2.4E+02 0.0053 20.5 4.7 27 8-37 93-119 (140)
144 COG1363 FrvX Cellulase M and r 21.6 1.1E+02 0.0024 25.5 3.2 77 8-84 93-193 (355)
145 KOG2097 Predicted N6-adenine m 21.1 1.2E+02 0.0026 25.5 3.3 30 79-110 366-395 (397)
146 PRK08477 biotin--protein ligas 21.1 3.3E+02 0.0071 20.8 5.6 37 8-45 171-207 (211)
147 PF09642 YonK: YonK protein; 20.5 1.2E+02 0.0025 19.3 2.4 22 3-24 34-55 (62)
No 1
>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=99.96 E-value=2.3e-29 Score=170.75 Aligned_cols=90 Identities=83% Similarity=1.202 Sum_probs=84.6
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchhhhhh
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLV 81 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~~~l~ 81 (114)
+|++||+++.|+.|+||||||.+|+|+|.+||+|||++|+||+++..+++...++++||||++|+||++||++|++++|.
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~ 80 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLV 80 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhh
Confidence 58999999999999999999999999999999999999999999988888899999999999999999999999999999
Q ss_pred hhCCCCCCCC
Q 033668 82 EETPRVKPKK 91 (114)
Q Consensus 82 ~~~~~~~~~~ 91 (114)
+.++..++||
T Consensus 81 ~~~~~~~~~~ 90 (90)
T cd01724 81 DSTPKPKSKK 90 (90)
T ss_pred hcCCcccCCC
Confidence 9976655553
No 2
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.95 E-value=2.4e-27 Score=164.78 Aligned_cols=93 Identities=72% Similarity=1.093 Sum_probs=90.1
Q ss_pred CchHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchhhhh
Q 033668 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLL 80 (114)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~~~l 80 (114)
|+|+.||+++.+.+|+|||+||+.+.|+|.++|.+||.+|.+++.+..+ ++.+++.++|||++|+|+++||++++++.+
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Ll 79 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLL 79 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceee
Confidence 8999999999999999999999999999999999999999999998775 789999999999999999999999999999
Q ss_pred hhhCCCCCCCCCCC
Q 033668 81 VEETPRVKPKKPTA 94 (114)
Q Consensus 81 ~~~~~~~~~~~~~~ 94 (114)
.+++++++.+++++
T Consensus 80 vd~~~~~~~~~~~~ 93 (109)
T KOG3428|consen 80 VDDAPRLHLRKNEK 93 (109)
T ss_pred eehhhhhhhhcccc
Confidence 99999999999986
No 3
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.94 E-value=1.6e-26 Score=163.91 Aligned_cols=102 Identities=29% Similarity=0.478 Sum_probs=90.7
Q ss_pred CchHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCc-eeecceEEEeeceEEEEecCCCCchhhh
Q 033668 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKN-PVNLDHLSVRGNNIRYYILPDSLNLETL 79 (114)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~-~~~~~~v~IRG~~I~~I~lpd~l~~~~~ 79 (114)
|+++.+|+...++.+.||||||.+|.|.|++||.||||+|++|+++..|+. ++.+++|+|||++|+|+.+||.+ ++.+
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i-id~v 79 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI-IDKV 79 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH-HHHH
Confidence 889999999999999999999999999999999999999999999998875 57999999999999999999998 9999
Q ss_pred hhhhCCCCCCCCCCCCCCCCCCCC
Q 033668 80 LVEETPRVKPKKPTAGRPVGRGRG 103 (114)
Q Consensus 80 l~~~~~~~~~~~~~~~~~~~~~~~ 103 (114)
-++..+..+++|+...+++||++|
T Consensus 80 kee~~~~~~~r~~~r~~~~grG~g 103 (134)
T KOG3293|consen 80 KEECVSNNRNRKQSRDRGRGRGRG 103 (134)
T ss_pred HHHHHHhccchhccccccCCcCCC
Confidence 999888888887444444444333
No 4
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.93 E-value=1.9e-25 Score=144.82 Aligned_cols=70 Identities=31% Similarity=0.626 Sum_probs=67.3
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCC
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd 72 (114)
++.+|++++|+.|+||||||.+|+|+|.+||+|||++|+||+++..+++...++++||||++|+||++||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 4689999999999999999999999999999999999999999988888899999999999999999997
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=99.92 E-value=6e-25 Score=145.55 Aligned_cols=70 Identities=36% Similarity=0.578 Sum_probs=67.5
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecC
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lp 71 (114)
.|++||+++.|+.|+||||||.+|+|+|.+||+|||++|+||+++..++.+.+++++||||++|+||++|
T Consensus 9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 3789999999999999999999999999999999999999999998888888999999999999999998
No 6
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.92 E-value=5.6e-25 Score=153.09 Aligned_cols=87 Identities=23% Similarity=0.471 Sum_probs=80.6
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchhhhhhh
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVE 82 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~~~l~~ 82 (114)
++.+|.+..|+.|++|+++|.+|+|+|+.+|++|||.|+|++.+.+|+...+++.+|||||.|+|+.+||.|..+|.|+.
T Consensus 6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnAPmFkk 85 (119)
T KOG3172|consen 6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNAPMFKK 85 (119)
T ss_pred ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcCccccc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred hCCCCCC
Q 033668 83 ETPRVKP 89 (114)
Q Consensus 83 ~~~~~~~ 89 (114)
...+.-+
T Consensus 86 ~~~~~~g 92 (119)
T KOG3172|consen 86 GKSRSLG 92 (119)
T ss_pred ccCCcCC
Confidence 5544333
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=99.91 E-value=2.6e-24 Score=141.38 Aligned_cols=73 Identities=32% Similarity=0.486 Sum_probs=68.4
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCce-eecceEEEeeceEEEEecCCCC
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNP-VNLDHLSVRGNNIRYYILPDSL 74 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~-~~~~~v~IRG~~I~~I~lpd~l 74 (114)
+++++|+++.|++|+|+||||.+|+|+|.+||+|||++|+||+++..+|++ ..++++||||++|+||++||++
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 478999999999999999999999999999999999999999999888765 5789999999999999999986
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=99.91 E-value=4.3e-24 Score=142.14 Aligned_cols=76 Identities=29% Similarity=0.469 Sum_probs=68.6
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCc--eeecceEEEeeceEEEEecCCCCchhh
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKN--PVNLDHLSVRGNNIRYYILPDSLNLET 78 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~--~~~~~~v~IRG~~I~~I~lpd~l~~~~ 78 (114)
+++.||+++.|+.|+||||||.+|+|+|.+||+|||++|+||+++.+++. ...++++||||++|+||++||++ +++
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~-i~~ 78 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE-VDT 78 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH-cCc
Confidence 47899999999999999999999999999999999999999999876543 45779999999999999999886 544
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=99.88 E-value=1.4e-22 Score=130.03 Aligned_cols=67 Identities=24% Similarity=0.341 Sum_probs=63.1
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
+.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++++..++.+||||++|+||+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 4689999999999999999999999999999999999999999877767889999999999999985
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=99.87 E-value=8.9e-22 Score=126.78 Aligned_cols=67 Identities=33% Similarity=0.429 Sum_probs=62.8
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
++.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++++..++.+||||++|+||+
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 6789999999999999999999999999999999999999999876666789999999999999984
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=2.8e-21 Score=125.82 Aligned_cols=68 Identities=28% Similarity=0.421 Sum_probs=63.8
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
.++.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++.+..++.+||||++|.||+
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 57889999999999999999999999999999999999999999876666779999999999999996
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=99.85 E-value=4.6e-21 Score=123.13 Aligned_cols=67 Identities=24% Similarity=0.342 Sum_probs=63.5
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
++.+|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..++++..++.+||||++|.||+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 4688999999999999999999999999999999999999999887777889999999999999997
No 13
>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=99.85 E-value=1.1e-20 Score=124.56 Aligned_cols=70 Identities=24% Similarity=0.312 Sum_probs=64.7
Q ss_pred CchHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEc---CCCceeecceEEEeeceEEEEec
Q 033668 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL---KGKNPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~---~~g~~~~~~~v~IRG~~I~~I~l 70 (114)
|+++.+|+++++++|+|+|++|++|.|+|.+||+|||++|+||+|.. .+++..+++.+||||++|.+|+.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 78999999999999999999999999999999999999999999976 33456789999999999999983
No 14
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.85 E-value=2.8e-21 Score=130.48 Aligned_cols=88 Identities=30% Similarity=0.498 Sum_probs=79.9
Q ss_pred CchHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCce--eecceEEEeeceEEEEecCCCCchhh
Q 033668 1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNP--VNLDHLSVRGNNIRYYILPDSLNLET 78 (114)
Q Consensus 1 m~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~--~~~~~v~IRG~~I~~I~lpd~l~~~~ 78 (114)
|+|++|+++++|+.|+|||||+..+.|+|.++|+|+|+.|+|+.+++++..+ .++..|||||+.|+||++|... .+.
T Consensus 1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~-vdt 79 (96)
T KOG3448|consen 1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA-VDT 79 (96)
T ss_pred CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH-HHH
Confidence 8999999999999999999999999999999999999999999999876544 6889999999999999999985 677
Q ss_pred hhhhhCCCCCC
Q 033668 79 LLVEETPRVKP 89 (114)
Q Consensus 79 ~l~~~~~~~~~ 89 (114)
.+.++++|.|.
T Consensus 80 qll~da~R~e~ 90 (96)
T KOG3448|consen 80 QLLQDAARREA 90 (96)
T ss_pred HHHHHHHHHHH
Confidence 77788777654
No 15
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.84 E-value=1.2e-20 Score=119.67 Aligned_cols=66 Identities=41% Similarity=0.554 Sum_probs=62.7
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC-ceeecceEEEeeceEEEEec
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g-~~~~~~~v~IRG~~I~~I~l 70 (114)
.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++ +...++.+||||++|++|++
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 4799999999999999999999999999999999999999998876 78899999999999999985
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=1.9e-20 Score=118.65 Aligned_cols=66 Identities=44% Similarity=0.601 Sum_probs=62.1
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCC-CceeecceEEEeeceEEEEec
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG-KNPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~-g~~~~~~~v~IRG~~I~~I~l 70 (114)
.+|++++|++|+|+|+||+++.|+|.+||+|||++|+||+++..+ +++.+++.+||||++|+||++
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 378999999999999999999999999999999999999998876 678899999999999999974
No 17
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=9.1e-20 Score=118.98 Aligned_cols=69 Identities=25% Similarity=0.293 Sum_probs=64.0
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCC
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDS 73 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~ 73 (114)
.+|+++++++|.|+|++|++|.|+|.+||+|||++|+||+++..+.+...++.++|||++|.+|..-|.
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence 579999999999999999999999999999999999999998766677899999999999999997654
No 18
>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=99.80 E-value=3e-19 Score=111.59 Aligned_cols=63 Identities=33% Similarity=0.492 Sum_probs=59.9
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
|++++|++|+|+|+||++|.|+|.+||+|||++|+||+++..+..+..++.+||||++|++|+
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 578899999999999999999999999999999999999988888899999999999999985
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.80 E-value=3.7e-19 Score=117.25 Aligned_cols=69 Identities=33% Similarity=0.426 Sum_probs=60.6
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcC-CCce--eec-ceEEEeeceEEEEec
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK-GKNP--VNL-DHLSVRGNNIRYYIL 70 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~-~g~~--~~~-~~v~IRG~~I~~I~l 70 (114)
.++.+|+++++++|.|+|+||++|.|+|.+||+|||++|+||+++.. ++.. ..+ +.+||||++|.+|..
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 46899999999999999999999999999999999999999999873 3332 344 499999999999963
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=99.77 E-value=3.5e-18 Score=113.73 Aligned_cols=68 Identities=21% Similarity=0.279 Sum_probs=60.7
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCC--------CceeecceEEEeeceEEEEecCC
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG--------KNPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~--------g~~~~~~~v~IRG~~I~~I~lpd 72 (114)
.-|.++++++|.|.|++|++|.|+|.+||+|||++|+||+|...+ .++..++.++|||++|.+|+..+
T Consensus 5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 358899999999999999999999999999999999999997643 24578999999999999998654
No 21
>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=99.75 E-value=6.1e-18 Score=112.49 Aligned_cols=67 Identities=21% Similarity=0.282 Sum_probs=60.1
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCC-------------CceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG-------------KNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~-------------g~~~~~~~v~IRG~~I~~I~ 69 (114)
++.+|+.+++++|.|.|++|++|.|+|.+||.|||++|+||+|.... .....++.+||||++|.+|+
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 56899999999999999999999999999999999999999997532 12458899999999999987
No 22
>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=99.74 E-value=1.2e-17 Score=112.82 Aligned_cols=68 Identities=19% Similarity=0.245 Sum_probs=60.0
Q ss_pred hHHHHHhcC--CCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC-------------ceeecceEEEeeceEEE
Q 033668 3 LVRFLMKLN--NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-------------NPVNLDHLSVRGNNIRY 67 (114)
Q Consensus 3 l~~~L~~l~--gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g-------------~~~~~~~v~IRG~~I~~ 67 (114)
++.+|+.++ +++|.|.|++|++|.|+|.+||.|||++|+||+|+.... +...++.+||||++|.+
T Consensus 3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 678898886 899999999999999999999999999999999975432 13468999999999999
Q ss_pred Eec
Q 033668 68 YIL 70 (114)
Q Consensus 68 I~l 70 (114)
|+.
T Consensus 83 Is~ 85 (87)
T cd01720 83 VLR 85 (87)
T ss_pred Eec
Confidence 874
No 23
>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=99.71 E-value=5.5e-17 Score=107.94 Aligned_cols=68 Identities=22% Similarity=0.298 Sum_probs=59.9
Q ss_pred chHHHHHhcCCC--EEEEEEc--CCeEEEEEEEEecCccceEEccEEEEcC-CCceeecceEEEeeceEEEEe
Q 033668 2 KLVRFLMKLNNE--TVSIELK--NGTIVHGTITGVDISMNTHLKTVKLTLK-GKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 2 ~l~~~L~~l~gk--~V~VeLk--ng~~~~G~L~~~D~~MNi~L~dv~~~~~-~g~~~~~~~v~IRG~~I~~I~ 69 (114)
+++..|.++..+ +|.|+|+ +|.+|.|+|.+||+|||++|+||+|... +.+...++.++|||++|.+|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 467788888888 7888887 8999999999999999999999999864 345678999999999999997
No 24
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.71 E-value=2e-17 Score=108.27 Aligned_cols=67 Identities=31% Similarity=0.399 Sum_probs=62.8
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
+..||+.+.|++|.|+||+|.+|+|+|+++|.|||+.|.++++...+...-++++++||.++|.||.
T Consensus 9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence 4679999999999999999999999999999999999999999877767789999999999999994
No 25
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.71 E-value=6.3e-17 Score=106.75 Aligned_cols=65 Identities=23% Similarity=0.277 Sum_probs=58.1
Q ss_pred HHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCC----------CceeecceEEEeeceEEEEec
Q 033668 6 FLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG----------KNPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~----------g~~~~~~~v~IRG~~I~~I~l 70 (114)
-|.+++|++|.|.|++|++|.|+|.+||.|||++|+||+|+... .++..++.+||||++|.+|++
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 47889999999999999999999999999999999999996532 235689999999999999985
No 26
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=2.7e-16 Score=103.26 Aligned_cols=67 Identities=16% Similarity=0.158 Sum_probs=58.9
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC---ceeecceEEEeeceEEEEec
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK---NPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g---~~~~~~~v~IRG~~I~~I~l 70 (114)
...|.++++++|.|.|++|++|.|+|.+||+|||++|+||.|...++ .+..++.++|||++|.+|..
T Consensus 4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 35688999999999999999999999999999999999998865332 25678999999999999874
No 27
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=2.5e-16 Score=102.85 Aligned_cols=68 Identities=28% Similarity=0.297 Sum_probs=60.0
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcC---CC-ceeecceEEEeeceEEEEecCC
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK---GK-NPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~---~g-~~~~~~~v~IRG~~I~~I~lpd 72 (114)
..|+++++++|.|.|++|+.|.|+|.+||+|||++|++|++... .+ ....++.++|||++|.+|+.-|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 46889999999999999999999999999999999999999643 12 3567999999999999999654
No 28
>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=99.67 E-value=6.5e-16 Score=101.68 Aligned_cols=66 Identities=20% Similarity=0.215 Sum_probs=60.3
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCC------CceeecceEEEeeceEEEEec
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKG------KNPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~------g~~~~~~~v~IRG~~I~~I~l 70 (114)
..|++++|++|.|.|+||+.|.|+|.+||.+||++|+||.|+... .+...++.++|||++|..|++
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 568899999999999999999999999999999999999998643 456799999999999999985
No 29
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.65 E-value=2e-17 Score=108.21 Aligned_cols=70 Identities=26% Similarity=0.341 Sum_probs=64.9
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCC
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd 72 (114)
+-+||++.+|++|.|+|.+|..|+|+|.++|.||||.|+.+++...+..+..++.+||||++|.||+..+
T Consensus 7 ~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 7 PGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence 4689999999999999999999999999999999999999999876667899999999999999998653
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.60 E-value=7.3e-15 Score=99.74 Aligned_cols=66 Identities=24% Similarity=0.389 Sum_probs=54.1
Q ss_pred hHHHHHhcCCCEEEEEEcC--CeEEEEEEEEecCccceEEccEEEEcCC-CceeecceEEEeeceEEEEec
Q 033668 3 LVRFLMKLNNETVSIELKN--GTIVHGTITGVDISMNTHLKTVKLTLKG-KNPVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkn--g~~~~G~L~~~D~~MNi~L~dv~~~~~~-g~~~~~~~v~IRG~~I~~I~l 70 (114)
++.|++. ..+|.|++.+ +++|.|+|.+||+|||++|+||+|+..+ .+...++.++|||++|.+|+.
T Consensus 19 ~~~~~~~--~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 19 IFRFFTE--KTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred HHHHhcC--CcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 3444544 4478888877 4899999999999999999999998643 356789999999999999974
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.55 E-value=1.2e-14 Score=95.44 Aligned_cols=68 Identities=24% Similarity=0.280 Sum_probs=63.8
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCC
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd 72 (114)
..|+++.+|++.|.|..++.+.|+|.+||.|||++|++++|...++.+..++.++|||++|..+..-|
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~ 74 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALE 74 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecc
Confidence 36899999999999999999999999999999999999999999999999999999999999887544
No 32
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.47 E-value=1.3e-14 Score=97.26 Aligned_cols=72 Identities=24% Similarity=0.304 Sum_probs=63.4
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcC--C-----------CceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK--G-----------KNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~--~-----------g~~~~~~~v~IRG~~I~~I~ 69 (114)
++++|+-.++.+|.|+|+++++++|+|.+||+|+|++|.||+++.. + ..+..++.+||||.+|.+|+
T Consensus 6 PldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvs 85 (91)
T KOG3460|consen 6 PLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVS 85 (91)
T ss_pred cHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEc
Confidence 6899999999999999999999999999999999999999988642 1 12467899999999999999
Q ss_pred cCCCC
Q 033668 70 LPDSL 74 (114)
Q Consensus 70 lpd~l 74 (114)
.|-.+
T Consensus 86 pp~~~ 90 (91)
T KOG3460|consen 86 PPLRL 90 (91)
T ss_pred CcccC
Confidence 88654
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.38 E-value=2.9e-13 Score=89.47 Aligned_cols=69 Identities=23% Similarity=0.248 Sum_probs=62.0
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEc--CCCc-eeecceEEEeeceEEEEec
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL--KGKN-PVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~--~~g~-~~~~~~v~IRG~~I~~I~l 70 (114)
++++++.+++|++|.|.+|+++++.|+|.+||+|.|++|+||+++. +++. ..+++++++.|++|..+..
T Consensus 7 lPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP 78 (84)
T KOG1775|consen 7 LPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP 78 (84)
T ss_pred ccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence 5788999999999999999999999999999999999999999964 4444 3689999999999998764
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.20 E-value=1.7e-11 Score=81.98 Aligned_cols=67 Identities=27% Similarity=0.352 Sum_probs=57.0
Q ss_pred chHHHHHhcCCCEEEEEEcC--CeEEEEEEEEecCccceEEccEEEEcCCCc-eeecceEEEeeceEEEEec
Q 033668 2 KLVRFLMKLNNETVSIELKN--GTIVHGTITGVDISMNTHLKTVKLTLKGKN-PVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkn--g~~~~G~L~~~D~~MNi~L~dv~~~~~~g~-~~~~~~v~IRG~~I~~I~l 70 (114)
+++.||+. -.+|.|+|.+ +..++|.+++||+|||++|+||++.+.... ...++.++++|+||..|+-
T Consensus 16 ~Ifr~Lq~--~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 16 LIFRFLQN--RTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred HHHHHHhc--CCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 35778887 4588888887 789999999999999999999999875433 4589999999999999874
No 35
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.99 E-value=1.3e-10 Score=86.72 Aligned_cols=68 Identities=21% Similarity=0.265 Sum_probs=58.7
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcC---------C-CceeecceEEEeeceEEEEecCCCC
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK---------G-KNPVNLDHLSVRGNNIRYYILPDSL 74 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~---------~-g~~~~~~~v~IRG~~I~~I~lpd~l 74 (114)
|-..++++++|.+.||++|.|++.+||.|||++|.||++... + .++.-++.|++||++|...++.+-.
T Consensus 9 ml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 9 MLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred HHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 456789999999999999999999999999999999988631 1 2467899999999999999987664
No 36
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.95 E-value=9.8e-11 Score=80.73 Aligned_cols=70 Identities=19% Similarity=0.251 Sum_probs=62.8
Q ss_pred HHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC--------ceeecceEEEeeceEEEEecCCCCc
Q 033668 6 FLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK--------NPVNLDHLSVRGNNIRYYILPDSLN 75 (114)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g--------~~~~~~~v~IRG~~I~~I~lpd~l~ 75 (114)
-|.+++++.|.|++..|+++.|+|.+||+.||++|+|+.++-+|. +..+++.+.+||..+..|+..|..+
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 477899999999999999999999999999999999999975432 2489999999999999999988876
No 37
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.91 E-value=2.4e-09 Score=72.93 Aligned_cols=87 Identities=23% Similarity=0.350 Sum_probs=74.0
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEc----CCCceeecceEEEeeceEEEEecCCCCchhhhh
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTL----KGKNPVNLDHLSVRGNNIRYYILPDSLNLETLL 80 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~----~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~~~l 80 (114)
.-|..+++++|.|-+.||+.+.|.|.+||+.-|+.|+++-+-. .+-++..++..+|||.||..|..-|+ ..++.|
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE-e~d~~l 81 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE-ELDSRL 81 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch-hhhhhh
Confidence 4588899999999999999999999999999999999997732 12346788999999999999998887 688899
Q ss_pred hhhCCCCCCCCC
Q 033668 81 VEETPRVKPKKP 92 (114)
Q Consensus 81 ~~~~~~~~~~~~ 92 (114)
++.+-|.|+-++
T Consensus 82 d~tkir~epl~~ 93 (96)
T KOG1784|consen 82 DLTKIRAEPLHP 93 (96)
T ss_pred hhhhcccCCCCC
Confidence 888877766543
No 38
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.34 E-value=6.4e-08 Score=69.09 Aligned_cols=66 Identities=18% Similarity=0.246 Sum_probs=55.6
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEE-cCCCc--eeecceEEEeeceEEEEec
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLT-LKGKN--PVNLDHLSVRGNNIRYYIL 70 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~-~~~g~--~~~~~~v~IRG~~I~~I~l 70 (114)
.-|-+.+++++.|-|+||+.+.|.|.+||+|-|++|.+|.+- .-+.. -...+..+|||.||..+..
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEec
Confidence 346778899999999999999999999999999999999883 32322 2567899999999999874
No 39
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.16 E-value=1.1e-05 Score=52.50 Aligned_cols=47 Identities=28% Similarity=0.420 Sum_probs=37.7
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEecC---ccceEEccEEEEcC
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDI---SMNTHLKTVKLTLK 48 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~---~MNi~L~dv~~~~~ 48 (114)
+|+=++..++|+.|.|.++||..|+|.+.+++. -+.++|+-+.....
T Consensus 2 Rl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 2 RLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp --HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred hHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 356688999999999999999999999999998 89999999988754
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.59 E-value=6.4e-05 Score=48.50 Aligned_cols=37 Identities=22% Similarity=0.327 Sum_probs=31.3
Q ss_pred CCEEEEEEcC--C--eEEEEEEEEecCccceEEccEEEEcC
Q 033668 12 NETVSIELKN--G--TIVHGTITGVDISMNTHLKTVKLTLK 48 (114)
Q Consensus 12 gk~V~VeLkn--g--~~~~G~L~~~D~~MNi~L~dv~~~~~ 48 (114)
+.+|.|.++. | -.++|.|.+||.|+|+.|.||.|+..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 5778888775 3 57889999999999999999999764
No 41
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.47 E-value=0.00071 Score=46.50 Aligned_cols=66 Identities=17% Similarity=0.169 Sum_probs=54.8
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecC-ccceEEccEEEEcCCCc---------eeecceEEEeeceEEEEecCCC
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDI-SMNTHLKTVKLTLKGKN---------PVNLDHLSVRGNNIRYYILPDS 73 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~-~MNi~L~dv~~~~~~g~---------~~~~~~v~IRG~~I~~I~lpd~ 73 (114)
..++|+.|.+..+++..|+|+|..+|. .-.|.|++|...-..+. ...++.+..||+-|.-+.+-+.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 367999999999999999999999995 77899999987643331 3468899999999999888654
No 42
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=96.99 E-value=0.00013 Score=51.38 Aligned_cols=58 Identities=21% Similarity=0.281 Sum_probs=48.4
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcC------CCc-------eeecceEEEeeceEEEEe
Q 033668 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLK------GKN-------PVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~------~g~-------~~~~~~v~IRG~~I~~I~ 69 (114)
...|.|-++|...+-|.+.+||-|+|++|+++.+... +|. -..++.+||||++|..+.
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 5689999999999999999999999999999988542 222 245789999999987765
No 43
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.78 E-value=0.012 Score=39.39 Aligned_cols=65 Identities=15% Similarity=0.168 Sum_probs=50.8
Q ss_pred chHHHHHhcCCCEEEEEEcCCeEEEEEEEEec-CccceEEccEEEEcCCCceeecceEEEeeceEEEEecC
Q 033668 2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (114)
Q Consensus 2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lp 71 (114)
+++.+|.++.|+.|.+.|.++.++.|+..++| +-.|+..++-. + += -..++..||.+-|..+++.
T Consensus 14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T-Pl---Gv~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-T-PL---GVQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T-TT---TEEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-C-Cc---ccChhheeecCCEEEEEec
Confidence 46788999999999999999999999999999 66778777754 1 11 2358999999999998864
No 44
>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=96.40 E-value=0.019 Score=37.87 Aligned_cols=60 Identities=17% Similarity=0.161 Sum_probs=46.5
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEec-CccceEEccEEEEcCCCc----------eeecceEEEeeceEEE
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKN----------PVNLDHLSVRGNNIRY 67 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNi~L~dv~~~~~~g~----------~~~~~~v~IRG~~I~~ 67 (114)
..++|++|.+-.+.+..|+|+|.++| +.--+.|+||...-.++. ..-++.+.-||+.|.-
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 36899999999999999999999999 445588999987654332 2345667778877653
No 45
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=96.27 E-value=0.047 Score=35.23 Aligned_cols=53 Identities=17% Similarity=0.262 Sum_probs=40.7
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEec-CccceEEccEEEEcCCCceeecceEEEeeceEEEEe
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYI 69 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~ 69 (114)
++..|++++|++|.|++-.|+. +|+|.++- +|. +|+.. -..+|||=..|.+|.
T Consensus 12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~~-----------~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEEN-----------GTPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEeC-----------CcEEEEEeeeEEEEc
Confidence 4688999999999999977766 99999998 444 33221 136788888888875
No 46
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=95.75 E-value=0.0085 Score=43.05 Aligned_cols=44 Identities=36% Similarity=0.637 Sum_probs=23.9
Q ss_pred EEecCCCCchhhhhhhhCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 033668 67 YYILPDSLNLETLLVEETPRVKPKKPTAGRPVGRGRGRGRGRGRGR 112 (114)
Q Consensus 67 ~I~lpd~l~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (114)
|+++|+++ +.+++...+...+....++..+.+++. +|+|+|.++
T Consensus 80 yL~LP~ei-vP~T~k~~~~~~~~~~~~~~~r~~~~~-~~~gr~~~r 123 (124)
T PTZ00034 80 YLHLPPDV-FPATHKKKSVNFERKTEEEGSRGGRGG-RGRGRGYGR 123 (124)
T ss_pred HhCCCccc-CchhhcccccCccCccccccccCCCCC-CCCCCCCCC
Confidence 68999998 444555555445555555553333322 444444443
No 47
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.10 E-value=0.18 Score=32.09 Aligned_cols=32 Identities=25% Similarity=0.209 Sum_probs=27.6
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEcc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~d 42 (114)
...+|+|-|.||..++|.+.+||.|+=+.-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 36789999999999999999999998666544
No 48
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.07 E-value=0.054 Score=45.10 Aligned_cols=67 Identities=16% Similarity=0.195 Sum_probs=54.8
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEec-CccceEEccEEEEcCCCc-----e-----eecceEEEeeceEEEEecCCC
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKN-----P-----VNLDHLSVRGNNIRYYILPDS 73 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNi~L~dv~~~~~~g~-----~-----~~~~~v~IRG~~I~~I~lpd~ 73 (114)
...++|+.|.+.-|++..|+|+|..+| +.--|-|.+|..+-+++. . .-++.|+-||+.|+-+.+.+.
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 457899999999999999999999999 788899999966543221 1 157889999999998887664
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.89 E-value=0.18 Score=33.62 Aligned_cols=55 Identities=24% Similarity=0.199 Sum_probs=42.8
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchh
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLE 77 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~ 77 (114)
....|+|-|.||..+.|.+.+||.|+=+.-.+-. .-+|-=..|..|.....+++.
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~gk------------qqLIYKHAISTI~p~~~i~~~ 72 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGK------------SQLVYKHAISTVVPARPVSLH 72 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECCc------------EEEEEEeeeEEEecCCccccc
Confidence 4779999999999999999999999866654431 336666778888877776554
No 50
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=94.85 E-value=0.14 Score=30.38 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=33.9
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC--ceeecceEEEe
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK--NPVNLDHLSVR 61 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g--~~~~~~~v~IR 61 (114)
+|+.|+|++ ++..++|+...+|+.=.|.++.. ++ .....+++++|
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~-----~g~~~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE-----DGSIRTISSGDVSLR 48 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET-----TEEEEEESSSEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC-----CCCEEEEEEEEEEeC
Confidence 689999999 66777999999999999888653 22 13455666654
No 51
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=94.57 E-value=0.16 Score=38.11 Aligned_cols=63 Identities=11% Similarity=0.082 Sum_probs=44.0
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEec-CccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCC
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVD-ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSL 74 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D-~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l 74 (114)
..+..+++|.|.|.+.| +++.|.|..+| ..-|++|-+-.+ +++ ...-+|-|.+|..|.+-++-
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~---~sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK---RSVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS----EEEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc---eeEEEEEccceEEEEEccCC
Confidence 35678999999999999 99999999999 667788765442 332 23588999999999886653
No 52
>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=94.54 E-value=0.084 Score=33.59 Aligned_cols=32 Identities=22% Similarity=0.182 Sum_probs=27.7
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEcc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~d 42 (114)
...+|+|-|.||..+.|.+.+||.|+=+.-.+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 36789999999999999999999998666543
No 53
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=93.62 E-value=0.37 Score=30.58 Aligned_cols=32 Identities=13% Similarity=0.065 Sum_probs=28.1
Q ss_pred cCCCEEEEEEcCCeEEEEEEEEecCccceEEc
Q 033668 10 LNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (114)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~ 41 (114)
.+|..|.+++-.|.+++|.+.+||..-++.+-
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIl 35 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLIL 35 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEE
Confidence 47999999999999999999999988776543
No 54
>PRK14638 hypothetical protein; Provisional
Probab=91.12 E-value=0.55 Score=34.35 Aligned_cols=36 Identities=14% Similarity=0.195 Sum_probs=30.1
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEE
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHL 40 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L 40 (114)
..-+...+|+.|.|+++++..++|+|.++|+. ++.|
T Consensus 92 ~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 92 PKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 34577899999999999999999999999964 3444
No 55
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=90.68 E-value=0.073 Score=46.54 Aligned_cols=9 Identities=22% Similarity=0.146 Sum_probs=0.0
Q ss_pred EEEecCCCC
Q 033668 66 RYYILPDSL 74 (114)
Q Consensus 66 ~~I~lpd~l 74 (114)
.-+..|.+.
T Consensus 512 ~~~y~~p~~ 520 (556)
T PF05918_consen 512 QQQYVPPSG 520 (556)
T ss_dssp ---------
T ss_pred ccccCCCCC
Confidence 344444443
No 56
>PRK14639 hypothetical protein; Provisional
Probab=89.86 E-value=0.84 Score=33.02 Aligned_cols=36 Identities=28% Similarity=0.309 Sum_probs=30.4
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEE
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHL 40 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L 40 (114)
..-++..+|+.|.|+|.+...+.|+|.++|+. ++.|
T Consensus 80 ~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 80 IEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 35578899999999999999999999999984 4444
No 57
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=89.09 E-value=2.5 Score=31.82 Aligned_cols=55 Identities=20% Similarity=0.148 Sum_probs=39.5
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchhh
Q 033668 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLET 78 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~~ 78 (114)
...|+|-|.||..++|++.+||.|.=+.-.+.. ..+|-=..|.-|.....+++..
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~gk------------qqLIYKHAISTI~p~~~i~~~~ 78 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQ------------SQLVYKHAISTIMPAHPLDLSR 78 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc------------eEEEEeeeeeeecccCCcchhh
Confidence 678999999999999999999999766544431 3355555666666655554433
No 58
>PRK02001 hypothetical protein; Validated
Probab=88.98 E-value=1 Score=33.12 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=28.2
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (114)
.-+..++|+.|.|.|.++..+.|+|.++|+.
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 4567889999999999999999999999975
No 59
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.93 E-value=2.2 Score=32.15 Aligned_cols=55 Identities=18% Similarity=0.192 Sum_probs=40.6
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecceEEEeeceEEEEecCCCCchh
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLE 77 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lpd~l~~~ 77 (114)
....|+|-|.||..++|.+.+||.|.=+...+.. .-+|-=..|.-|.+...+++.
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gk------------qqLIYKHAISTI~P~~~v~~~ 157 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGY------------VQLVYKHAVSTVQPAGPVDLT 157 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc------------EEEEEEeEEEEEccCCCcccc
Confidence 3678999999999999999999999866554432 335556667777766665443
No 60
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=88.82 E-value=3 Score=27.70 Aligned_cols=28 Identities=25% Similarity=0.273 Sum_probs=25.1
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccce
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNT 38 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi 38 (114)
...+|+|-|.||..+.|.+.+||.|.=+
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 4789999999999999999999999643
No 61
>PRK14644 hypothetical protein; Provisional
Probab=86.82 E-value=1.4 Score=31.76 Aligned_cols=35 Identities=17% Similarity=0.237 Sum_probs=29.1
Q ss_pred HHHhcCCCEEEEEEcCC----eEEEEEEEEecCccceEEc
Q 033668 6 FLMKLNNETVSIELKNG----TIVHGTITGVDISMNTHLK 41 (114)
Q Consensus 6 ~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~MNi~L~ 41 (114)
-+..++|+.|.|+|++. ..++|.|.++|+. ++.|+
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 47788999999999987 9999999999974 34443
No 62
>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=86.78 E-value=2.1 Score=27.96 Aligned_cols=32 Identities=25% Similarity=0.315 Sum_probs=27.1
Q ss_pred HHHHHhcCCCEEEEEEc---CC-eEEEEEEEEecCc
Q 033668 4 VRFLMKLNNETVSIELK---NG-TIVHGTITGVDIS 35 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLk---ng-~~~~G~L~~~D~~ 35 (114)
..-+...+|+.|.|+++ +| ..+.|.|.++|+.
T Consensus 17 ~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 17 EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 34577889999999998 55 6899999999984
No 63
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.70 E-value=2.3 Score=31.46 Aligned_cols=33 Identities=21% Similarity=0.335 Sum_probs=29.5
Q ss_pred HHHHHhcCCCEEEEEE----cCCeEEEEEEEEecCcc
Q 033668 4 VRFLMKLNNETVSIEL----KNGTIVHGTITGVDISM 36 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~M 36 (114)
..-+..++|+.|.|+| .+.+.++|+|..+|+..
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 4567889999999999 67899999999999876
No 64
>PRK14640 hypothetical protein; Provisional
Probab=84.01 E-value=3 Score=30.47 Aligned_cols=31 Identities=19% Similarity=0.233 Sum_probs=26.9
Q ss_pred HHHHhcCCCEEEEEE----cCCeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIEL----KNGTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~ 35 (114)
.-++.++|+.|.|+| .+...++|+|.++|+.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~ 124 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD 124 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 457789999999999 4669999999999974
No 65
>PRK14643 hypothetical protein; Provisional
Probab=83.98 E-value=5 Score=29.82 Aligned_cols=31 Identities=26% Similarity=0.291 Sum_probs=26.6
Q ss_pred HHHHhcCCCEEEEEEcC----CeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELKN----GTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkn----g~~~~G~L~~~D~~ 35 (114)
.-+..++|+.|.|.|++ ...++|+|.++|+.
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 45678899999999976 59999999999964
No 66
>PRK14642 hypothetical protein; Provisional
Probab=83.80 E-value=2.7 Score=32.36 Aligned_cols=71 Identities=18% Similarity=0.250 Sum_probs=43.0
Q ss_pred HHHHHhcCCCEEEEEEc-------------CCeEEEEEEEEecCccceEE--ccEEEEcCC---Cc---eeecceEEEee
Q 033668 4 VRFLMKLNNETVSIELK-------------NGTIVHGTITGVDISMNTHL--KTVKLTLKG---KN---PVNLDHLSVRG 62 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLk-------------ng~~~~G~L~~~D~~MNi~L--~dv~~~~~~---g~---~~~~~~v~IRG 62 (114)
..-+...+|+.|.|+|+ +...++|+|.++|+. ++.| ++.-+-.+. ++ +.....+-+-=
T Consensus 92 ~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~k~g~~~~k~~~~~~~~~~~~~~ 170 (197)
T PRK14642 92 EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPVKPGQRVSKKRVPAPLQALGFTL 170 (197)
T ss_pred HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccCCCccccccccccccceeEEeeh
Confidence 34567889999999998 679999999999974 3333 322111111 11 12223455555
Q ss_pred ceEEEEecCCCCc
Q 033668 63 NNIRYYILPDSLN 75 (114)
Q Consensus 63 ~~I~~I~lpd~l~ 75 (114)
+.|....+-..+|
T Consensus 171 ~eik~a~l~p~~~ 183 (197)
T PRK14642 171 DELREARLAPIVD 183 (197)
T ss_pred hheeeEEEEEEEe
Confidence 6666666554444
No 67
>PRK14633 hypothetical protein; Provisional
Probab=82.46 E-value=2.9 Score=30.49 Aligned_cols=35 Identities=20% Similarity=0.059 Sum_probs=28.3
Q ss_pred HHHHhcCCCEEEEEEc----CCeEEEEEEEEecCccceEE
Q 033668 5 RFLMKLNNETVSIELK----NGTIVHGTITGVDISMNTHL 40 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D~~MNi~L 40 (114)
.-+..++|+.|.|+++ +...++|+|.++|+. ++.|
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 4577899999999994 569999999999975 3444
No 68
>PRK14632 hypothetical protein; Provisional
Probab=82.22 E-value=2.8 Score=31.33 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=28.6
Q ss_pred HHHHhcCCCEEEEEEcC-------CeEEEEEEEEecCccceEE
Q 033668 5 RFLMKLNNETVSIELKN-------GTIVHGTITGVDISMNTHL 40 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkn-------g~~~~G~L~~~D~~MNi~L 40 (114)
.-++.++|+.|.|+|++ ...++|+|.++|+. ++.|
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 45778999999999986 57999999999964 4444
No 69
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=81.83 E-value=7.6 Score=28.13 Aligned_cols=31 Identities=19% Similarity=0.280 Sum_probs=26.7
Q ss_pred HHHHhcCCCEEEEEE----cCCeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIEL----KNGTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeL----kng~~~~G~L~~~D~~ 35 (114)
.-++..+|+.|.|+| .+...++|+|.++|+.
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 457889999999998 4678999999999983
No 70
>PRK14645 hypothetical protein; Provisional
Probab=79.94 E-value=4.5 Score=29.75 Aligned_cols=30 Identities=17% Similarity=0.218 Sum_probs=26.1
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (114)
.-+...+|+.|.|.+ ++..++|+|.++|+.
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 456788999999986 789999999999975
No 71
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=78.68 E-value=2.9 Score=29.70 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=23.8
Q ss_pred HHHHhcCCCEEEEEEc----CCeEEEEEEEEecC
Q 033668 5 RFLMKLNNETVSIELK----NGTIVHGTITGVDI 34 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D~ 34 (114)
.-+...+|+.|.|.++ +...+.|+|.++|+
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 5678899999999995 45799999999998
No 72
>PRK14647 hypothetical protein; Provisional
Probab=78.05 E-value=5.8 Score=29.11 Aligned_cols=32 Identities=9% Similarity=0.073 Sum_probs=26.8
Q ss_pred HHHHHhcCCCEEEEEEcC---------CeEEEEEEEEecCc
Q 033668 4 VRFLMKLNNETVSIELKN---------GTIVHGTITGVDIS 35 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkn---------g~~~~G~L~~~D~~ 35 (114)
..-++..+|+.|.|+|+. ...++|+|.++|+.
T Consensus 91 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 91 EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 356788999999999963 48999999999963
No 73
>PRK14634 hypothetical protein; Provisional
Probab=78.04 E-value=5.9 Score=29.06 Aligned_cols=31 Identities=10% Similarity=0.153 Sum_probs=26.3
Q ss_pred HHHHhcCCCEEEEEEcCC----eEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELKNG----TIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~ 35 (114)
.-++..+|+.|.|+|++. ..++|+|.++|+.
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~ 127 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED 127 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC
Confidence 456788999999999743 7999999999974
No 74
>PRK14636 hypothetical protein; Provisional
Probab=77.81 E-value=5.6 Score=29.88 Aligned_cols=31 Identities=19% Similarity=0.380 Sum_probs=26.6
Q ss_pred HHHHhcCCCEEEEEEc---CC-eEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELK---NG-TIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLk---ng-~~~~G~L~~~D~~ 35 (114)
.-+...+|+.|.|+|+ +| ..++|+|.++|+.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~ 125 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD 125 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence 4567889999999998 55 7999999999873
No 75
>PRK14646 hypothetical protein; Provisional
Probab=77.76 E-value=4.9 Score=29.50 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=27.9
Q ss_pred HHHHhcCCCEEEEEEcCC----eEEEEEEEEecCccceEE
Q 033668 5 RFLMKLNNETVSIELKNG----TIVHGTITGVDISMNTHL 40 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng----~~~~G~L~~~D~~MNi~L 40 (114)
.-++.++|+.|.|+|++. ..++|+|.++|+. ++.|
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 457788999999999753 7889999999975 3444
No 76
>PRK14631 hypothetical protein; Provisional
Probab=73.35 E-value=8.6 Score=28.83 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=25.9
Q ss_pred HHHHHhcCCCEEEEEEc----CCeEEEEEEEEec
Q 033668 4 VRFLMKLNNETVSIELK----NGTIVHGTITGVD 33 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D 33 (114)
..-++.++|+.|.|+|+ +...++|+|.++|
T Consensus 109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34578899999999996 4599999999998
No 77
>PRK14637 hypothetical protein; Provisional
Probab=72.78 E-value=8.8 Score=28.08 Aligned_cols=36 Identities=22% Similarity=0.102 Sum_probs=27.2
Q ss_pred HHHHHhcCCCEEEEEEcCCeEE-EEEEEEecCccceEE
Q 033668 4 VRFLMKLNNETVSIELKNGTIV-HGTITGVDISMNTHL 40 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~-~G~L~~~D~~MNi~L 40 (114)
..-+...+|+.|.|+|.+...+ +|+|.++|+. ++.|
T Consensus 90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 3457788999999999544555 7999999985 3444
No 78
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=72.12 E-value=12 Score=27.36 Aligned_cols=26 Identities=38% Similarity=0.509 Sum_probs=24.0
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEec
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVD 33 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D 33 (114)
.+++|+.|.++..+|..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 47899999999999999999999986
No 79
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=70.72 E-value=4.9 Score=26.62 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=16.4
Q ss_pred HHHhcCCCEEEEEEcCCeEEEEE
Q 033668 6 FLMKLNNETVSIELKNGTIVHGT 28 (114)
Q Consensus 6 ~L~~l~gk~V~VeLkng~~~~G~ 28 (114)
.|..+-+.+|.++|+||..++|+
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEES
T ss_pred HHHHhcCCeEEEEEeCCCEEEEE
Confidence 45667899999999999999997
No 80
>PRK14641 hypothetical protein; Provisional
Probab=70.67 E-value=9.7 Score=28.58 Aligned_cols=30 Identities=13% Similarity=0.179 Sum_probs=25.5
Q ss_pred HHHHHhcCCCEEEEEEcC----CeEEEEEEEEec
Q 033668 4 VRFLMKLNNETVSIELKN----GTIVHGTITGVD 33 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkn----g~~~~G~L~~~D 33 (114)
..-++.++|+.|.|.|++ ...++|+|.++|
T Consensus 96 ~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 96 PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 345788999999999976 468999999995
No 81
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=65.68 E-value=4.4 Score=28.55 Aligned_cols=20 Identities=5% Similarity=-0.052 Sum_probs=8.6
Q ss_pred hhhhhhhhCCCCCCCCCCCC
Q 033668 76 LETLLVEETPRVKPKKPTAG 95 (114)
Q Consensus 76 ~~~~l~~~~~~~~~~~~~~~ 95 (114)
.+++.....-++++-.++++
T Consensus 80 vd~~~~~~~~~~~~~~rgrg 99 (109)
T KOG3428|consen 80 VDDAPRLHLRKNEKVGRGRG 99 (109)
T ss_pred eehhhhhhhhcccccccccc
Confidence 44444444444444333333
No 82
>PRK06955 biotin--protein ligase; Provisional
Probab=64.32 E-value=45 Score=26.57 Aligned_cols=34 Identities=15% Similarity=0.201 Sum_probs=28.9
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecCccceEEc
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~ 41 (114)
....|+.|+|...++.+++|++.++|+.=.|.++
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 3467999999766778899999999998888875
No 83
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=63.06 E-value=36 Score=27.03 Aligned_cols=48 Identities=21% Similarity=0.308 Sum_probs=34.4
Q ss_pred hcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC-ceeecceEEEee
Q 033668 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRG 62 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g-~~~~~~~v~IRG 62 (114)
...|+.|++... +..++|++.++|+.=.+.+.+ .++ +....+++.++.
T Consensus 269 ~~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~-----~g~~~~~~~gev~~~~ 317 (319)
T PRK11886 269 LFLGREVKLIIG-DKEISGIARGIDEQGALLLED-----DGVEKPFNGGEISLRS 317 (319)
T ss_pred cccCCeEEEEeC-CcEEEEEEEEECCCceEEEEe-----CCcEEEEEEeEEEEec
Confidence 467999999874 457999999999999998851 122 234556666543
No 84
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=62.87 E-value=31 Score=30.47 Aligned_cols=51 Identities=25% Similarity=0.339 Sum_probs=36.7
Q ss_pred hcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCC-ceeecceEEEeece
Q 033668 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGK-NPVNLDHLSVRGNN 64 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g-~~~~~~~v~IRG~~ 64 (114)
...|+.|.|...++.+++|+..++|+.=.+.|+.. ++ +....+++.+|..+
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~~-----~g~~~~~sGEVslr~~~ 326 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLETA-----EGKQTVVSGEISLRSDD 326 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEEC-----CCeEEEEEEeEEEeecC
Confidence 47899999976677789999999999999888531 22 23445666665543
No 85
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=62.58 E-value=11 Score=26.09 Aligned_cols=19 Identities=37% Similarity=0.821 Sum_probs=15.2
Q ss_pred CCEEEEEEcCCeEEEEEEE
Q 033668 12 NETVSIELKNGTIVHGTIT 30 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~ 30 (114)
..+|.++|+||+.+.|++.
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 4589999999999999874
No 86
>PRK14630 hypothetical protein; Provisional
Probab=59.84 E-value=18 Score=26.20 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=24.7
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCc
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDIS 35 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~ 35 (114)
.-++..+|+.|.|+|.+.. .+|+|.++|+.
T Consensus 90 ~df~r~~G~~v~V~l~~~~-~~G~L~~~~d~ 119 (143)
T PRK14630 90 REFKIFEGKKIKLMLDNDF-EEGFILEAKAD 119 (143)
T ss_pred HHHHHhCCCEEEEEEcCcc-eEEEEEEEeCC
Confidence 4567899999999996654 59999999874
No 87
>PRK14635 hypothetical protein; Provisional
Probab=58.98 E-value=32 Score=25.26 Aligned_cols=36 Identities=11% Similarity=0.098 Sum_probs=27.3
Q ss_pred HHHHHhcCCCEEEEEEc--CCeEEEE---EEEEecCccceEE
Q 033668 4 VRFLMKLNNETVSIELK--NGTIVHG---TITGVDISMNTHL 40 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLk--ng~~~~G---~L~~~D~~MNi~L 40 (114)
-.-+..++|+.|.|++. ++..+.| +|.++|+. ++.|
T Consensus 91 ~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 91 PEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 34577889999999986 4578887 99999974 3444
No 88
>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=58.66 E-value=12 Score=28.09 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=23.0
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDIS 35 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~ 35 (114)
.|+.|+|-+.||++++|+-.++|+-
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 5999999999999999999999864
No 89
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=58.56 E-value=9.4 Score=27.04 Aligned_cols=13 Identities=15% Similarity=0.299 Sum_probs=7.4
Q ss_pred hhhhhhhhCCCCC
Q 033668 76 LETLLVEETPRVK 88 (114)
Q Consensus 76 ~~~~l~~~~~~~~ 88 (114)
+-|-.++.+|+-+
T Consensus 72 vlPdmLKnAPmFk 84 (119)
T KOG3172|consen 72 VLPDMLKNAPMFK 84 (119)
T ss_pred ECchHhhcCcccc
Confidence 3455556677655
No 90
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=54.28 E-value=30 Score=25.32 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=23.1
Q ss_pred hcCCCEEEEEEcCCeEEEEEEEEecC
Q 033668 9 KLNNETVSIELKNGTIVHGTITGVDI 34 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~ 34 (114)
+++|+.|.....+|..++|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 68999999888999999999998763
No 91
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=52.74 E-value=17 Score=30.26 Aligned_cols=11 Identities=9% Similarity=0.259 Sum_probs=6.2
Q ss_pred eeceEEEEecC
Q 033668 61 RGNNIRYYILP 71 (114)
Q Consensus 61 RG~~I~~I~lp 71 (114)
.|..|.++...
T Consensus 342 ~G~ai~l~~~~ 352 (456)
T PRK10590 342 TGEALSLVCVD 352 (456)
T ss_pred CeeEEEEecHH
Confidence 46666666543
No 92
>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=51.20 E-value=61 Score=24.67 Aligned_cols=33 Identities=21% Similarity=0.200 Sum_probs=27.7
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecCccceEEc
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLK 41 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~ 41 (114)
....|+.|+|...+ .++.|+..++|+.=.+.++
T Consensus 189 ~~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 189 SAHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hhccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 44679999998755 5689999999999999886
No 93
>PRK06789 flagellar motor switch protein; Validated
Probab=49.77 E-value=36 Score=22.28 Aligned_cols=36 Identities=25% Similarity=0.248 Sum_probs=29.8
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEcc
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~d 42 (114)
|.+..+..|.|.+++-..-+|.+..+|+.+-+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 456778888888888889999999999988777655
No 94
>PRK08330 biotin--protein ligase; Provisional
Probab=49.35 E-value=1.1e+02 Score=23.25 Aligned_cols=33 Identities=24% Similarity=0.227 Sum_probs=26.4
Q ss_pred hcCCCEEEEEEcCCeE-EEEEEEEecCccceEEcc
Q 033668 9 KLNNETVSIELKNGTI-VHGTITGVDISMNTHLKT 42 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~-~~G~L~~~D~~MNi~L~d 42 (114)
...|+.|+|.. ++.. +.|+..++|+.=.+.++.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 47899999986 4555 479999999988887763
No 95
>PRK11625 Rho-binding antiterminator; Provisional
Probab=48.12 E-value=81 Score=21.04 Aligned_cols=55 Identities=20% Similarity=0.338 Sum_probs=33.2
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEE--cCCCceeecceEEEeeceEEEEecC
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLT--LKGKNPVNLDHLSVRGNNIRYYILP 71 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~--~~~g~~~~~~~v~IRG~~I~~I~lp 71 (114)
|..+.+..|.++|+||.++.|+.. |-+.+ +.+++. ...| +...||=.+|..++.|
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A~--D~~~~---~k~EyL~l~~~g-----~~~~iRLD~I~s~~~~ 74 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKAS--DLVSR---KNVEYLVVEAAG-----ETRELRLDKIASFSHP 74 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEEE--eeecC---CceEEEEEEcCC-----CEEEEEeeeEeeccCc
Confidence 444578999999999999999874 33333 333332 2222 2445555566655544
No 96
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=47.66 E-value=10 Score=33.11 Aligned_cols=24 Identities=46% Similarity=0.738 Sum_probs=13.4
Q ss_pred CCCCCC-CCCCCCCCCCCCCCCCCC
Q 033668 90 KKPTAG-RPVGRGRGRGRGRGRGRG 113 (114)
Q Consensus 90 ~~~~~~-~~~~~~~~~~~~~~~~~~ 113 (114)
++++|- +++|+-.|||+|++||++
T Consensus 339 ~~Rgel~rgrg~v~grgkg~rrG~g 363 (526)
T KOG2135|consen 339 RGRGELSRGRGAVHGRGKGRRRGRG 363 (526)
T ss_pred cccchhhhhhhhhhccccccccCCC
Confidence 444444 555555566666666654
No 97
>PRK10898 serine endoprotease; Provisional
Probab=44.73 E-value=79 Score=25.78 Aligned_cols=60 Identities=12% Similarity=0.222 Sum_probs=38.9
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeec--ceEEEeeceEEEEecCCC
Q 033668 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNL--DHLSVRGNNIRYYILPDS 73 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~--~~v~IRG~~I~~I~lpd~ 73 (114)
...+.|.+.+|.+|.+++.++|...++-|=.+... +-....+ ....-.|..|..|..|-.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~l~~~~l~~~~~~~~G~~V~aiG~P~g 162 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--NLPVIPINPKRVPHIGDVVLAIGNPYN 162 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--CCCeeeccCcCcCCCCCEEEEEeCCCC
Confidence 35789999999999999999999999876555321 1011111 112335666666666644
No 98
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=43.52 E-value=24 Score=26.05 Aligned_cols=13 Identities=38% Similarity=0.552 Sum_probs=9.2
Q ss_pred EEecCCCCchhhh
Q 033668 67 YYILPDSLNLETL 79 (114)
Q Consensus 67 ~I~lpd~l~~~~~ 79 (114)
|+++|+++-.++.
T Consensus 79 YLhLP~EiVpaTl 91 (150)
T KOG3344|consen 79 YLHLPPEIVPATL 91 (150)
T ss_pred HhcCCcccccchh
Confidence 7899999844443
No 99
>KOG0361 consensus Chaperonin complex component, TCP-1 eta subunit (CCT7) [Posttranslational modification, protein turnover, chaperones]
Probab=42.37 E-value=17 Score=31.40 Aligned_cols=24 Identities=42% Similarity=0.769 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC
Q 033668 84 TPRVKPKKPTAGRPVGRGRGRGRG 107 (114)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~ 107 (114)
.+-+++.|.+...|.+.|+|||||
T Consensus 517 DeTikn~~S~~~~p~~a~rgrg~g 540 (543)
T KOG0361|consen 517 DETIKNPKSQSAPPSAAGRGRGRG 540 (543)
T ss_pred hhhhcCCcccCCCCCccccCCCCC
Confidence 334555554444555544433333
No 100
>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=41.80 E-value=69 Score=18.42 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=21.7
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDIS 35 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~ 35 (114)
.|..+.+...++.-|++++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5778888887899999999999975
No 101
>PRK10139 serine endoprotease; Provisional
Probab=40.93 E-value=60 Score=27.54 Aligned_cols=62 Identities=16% Similarity=0.166 Sum_probs=39.7
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeecc--eEEEeeceEEEEecCCCC
Q 033668 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLD--HLSVRGNNIRYYILPDSL 74 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~~--~v~IRG~~I~~I~lpd~l 74 (114)
...|.|.+.||++|..++.++|....|-+=.+..- .+=....++ .-+--|..|.-|.-|-.+
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~-~~l~~~~lg~s~~~~~G~~V~aiG~P~g~ 177 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP-SKLTQIAIADSDKLRVGDFAVAVGNPFGL 177 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC-CCCceeEecCccccCCCCEEEEEecCCCC
Confidence 45899999999999999999999999776554310 000112221 122346667666666554
No 102
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=40.80 E-value=28 Score=20.57 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=14.0
Q ss_pred EEEEEEEecCccceEEccEE
Q 033668 25 VHGTITGVDISMNTHLKTVK 44 (114)
Q Consensus 25 ~~G~L~~~D~~MNi~L~dv~ 44 (114)
.+|+..++|+.+.+.|.+..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~ 29 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDD 29 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS
T ss_pred cceeEEeeccccceEEEeCC
Confidence 57999999999999998764
No 103
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.39 E-value=11 Score=28.85 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=30.6
Q ss_pred cCCCEEEEEEcCCeEEEEEEEEecCccceEEccEE
Q 033668 10 LNNETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (114)
Q Consensus 10 l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~ 44 (114)
.+|..|.++.-++....|.+.+||-.-+...-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 35788999999999999999999988887777766
No 104
>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=39.28 E-value=1e+02 Score=24.98 Aligned_cols=59 Identities=12% Similarity=0.164 Sum_probs=38.0
Q ss_pred CEEEEEEcCCeEEEEEEEEecCccceEEccEEEEcCCCceeec--ceEEEeeceEEEEecCCC
Q 033668 13 ETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNL--DHLSVRGNNIRYYILPDS 73 (114)
Q Consensus 13 k~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~~~~g~~~~~--~~v~IRG~~I~~I~lpd~ 73 (114)
..+.|.+.||.++.+++.++|...++-|=.+.... -....+ ..-.=.|..|..|..|-.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~~~~--~~~~~l~~s~~~~~G~~V~aiG~P~~ 162 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIEGDN--LPTIPVNLDRPPHVGDVVLAIGNPYN 162 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEecCCC--CceEeccCcCccCCCCEEEEEeCCCC
Confidence 46889999999999999999999998775553211 011111 112233666666666644
No 105
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=38.52 E-value=58 Score=23.25 Aligned_cols=36 Identities=28% Similarity=0.327 Sum_probs=28.8
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEcc
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~d 42 (114)
|.+..|..|.|-+++-..-+|.|+-+|+.+-+.+.+
T Consensus 100 Ld~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 100 LDKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred cCCcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 345667788888877788899999999998887764
No 106
>PRK10942 serine endoprotease; Provisional
Probab=38.29 E-value=64 Score=27.52 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=27.4
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccceEEccE
Q 033668 12 NETVSIELKNGTIVHGTITGVDISMNTHLKTV 43 (114)
Q Consensus 12 gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv 43 (114)
...|.|.+.||++|.++++..|...++-|=.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999999766543
No 107
>KOG4501 consensus Transcription coactivator complex, P100 component [Transcription]
Probab=37.87 E-value=20 Score=32.10 Aligned_cols=20 Identities=60% Similarity=1.190 Sum_probs=14.0
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 033668 94 AGRPVGRGRGRGRGRGRGRG 113 (114)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~ 113 (114)
.+.|+|++|.++-+++||+.
T Consensus 661 ~gsp~g~gqs~~t~r~Rg~k 680 (707)
T KOG4501|consen 661 NGSPVGTGQSNGTGRGRGRK 680 (707)
T ss_pred cCCCCCcccccccccccccc
Confidence 46678888877777666654
No 108
>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=37.82 E-value=52 Score=22.98 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=17.7
Q ss_pred EEEEEEcCCeEEEEEEEEec
Q 033668 14 TVSIELKNGTIVHGTITGVD 33 (114)
Q Consensus 14 ~V~VeLkng~~~~G~L~~~D 33 (114)
.+.|.++||.++.|.+..=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 47899999999999998855
No 109
>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=37.44 E-value=69 Score=26.52 Aligned_cols=32 Identities=13% Similarity=0.363 Sum_probs=27.7
Q ss_pred CEEEEEEcCCeEEEEEEEEecCccceEEccEE
Q 033668 13 ETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (114)
Q Consensus 13 k~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~ 44 (114)
..+.|.+.++.+|.+++..+|...++-|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47889999999999999999999997775543
No 110
>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=37.10 E-value=1e+02 Score=23.21 Aligned_cols=40 Identities=15% Similarity=0.182 Sum_probs=28.8
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccc-eEEcc
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDISMN-THLKT 42 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MN-i~L~d 42 (114)
+...|+.-.|..|.|-..+|..|.++|..++...- +.+..
T Consensus 11 l~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~ 51 (225)
T PF04452_consen 11 LVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRILE 51 (225)
T ss_dssp HHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEE
T ss_pred HHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEee
Confidence 34567778899999999999999999999995543 44443
No 111
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=36.61 E-value=1.5e+02 Score=20.82 Aligned_cols=58 Identities=14% Similarity=0.092 Sum_probs=41.9
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccc-eEEccEEEEcCCCceeecceEEEeeceEEEEecC
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMN-THLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILP 71 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN-i~L~dv~~~~~~g~~~~~~~v~IRG~~I~~I~lp 71 (114)
.|-.|.|.-=...=.+|++..+|..=| +.++.+....++|.. -.+-|.-|+|.++.+.
T Consensus 44 kGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~---~e~pIh~SnV~l~~l~ 102 (114)
T TIGR01080 44 KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTE---VPVPIHPSNVMITKLN 102 (114)
T ss_pred cCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeE---EEeeechHHeEEEecc
Confidence 466777777666667899999996666 888888877766633 3444788888877653
No 112
>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=36.56 E-value=64 Score=24.68 Aligned_cols=34 Identities=24% Similarity=0.311 Sum_probs=29.0
Q ss_pred HHHHhcCCCEEEEEEcCCeEEEEEEEEecCccce
Q 033668 5 RFLMKLNNETVSIELKNGTIVHGTITGVDISMNT 38 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi 38 (114)
.+=+.|+|+.+..++.++....|.|+.+..|+--
T Consensus 12 ~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G~ 45 (192)
T TIGR00567 12 TLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMGP 45 (192)
T ss_pred HHHHHhCCCEEEEECCCCcEEEEEEEEEecccCC
Confidence 4557899999999999898889999999999753
No 113
>cd01737 LSm16_N LSm16 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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=36.37 E-value=1.1e+02 Score=19.39 Aligned_cols=55 Identities=18% Similarity=0.207 Sum_probs=40.2
Q ss_pred hcCCCEEEEEEcCC-eEEEEEEEEecCc-cceEEccEEEEcCCCceeecceEEEeeceEE
Q 033668 9 KLNNETVSIELKNG-TIVHGTITGVDIS-MNTHLKTVKLTLKGKNPVNLDHLSVRGNNIR 66 (114)
Q Consensus 9 ~l~gk~V~VeLkng-~~~~G~L~~~D~~-MNi~L~dv~~~~~~g~~~~~~~v~IRG~~I~ 66 (114)
..+|+.|.|...+. -.|.|.+..+|.. --|+|.+.. .+|-+...+++.++..-|+
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~---~ngik~~~~EVt~~~~DI~ 59 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF---HNGVKCLVPEVTFRAGDIR 59 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc---cCCccccCceEEEEEcchh
Confidence 45789999999987 7999999999954 346665543 3555667778877766554
No 114
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=36.29 E-value=56 Score=25.14 Aligned_cols=26 Identities=23% Similarity=0.282 Sum_probs=22.8
Q ss_pred hcCCCEEEEEEcCCeEEEEEEEEecC
Q 033668 9 KLNNETVSIELKNGTIVHGTITGVDI 34 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~ 34 (114)
+++|+.|.+.-.+|..+.|++.++.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 67999999988899999999998763
No 115
>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=35.16 E-value=62 Score=24.28 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=30.7
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEccEE
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~ 44 (114)
..-.|+|.+.||.++.|.+.+|+.--|.+|.-+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 4678999999999999999999999999987665
No 116
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=35.10 E-value=1.2e+02 Score=24.03 Aligned_cols=33 Identities=15% Similarity=0.215 Sum_probs=27.3
Q ss_pred hcCCCEEEEEEcCCeEEEEEEEEecCccceEEcc
Q 033668 9 KLNNETVSIELKNGTIVHGTITGVDISMNTHLKT 42 (114)
Q Consensus 9 ~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~d 42 (114)
...|+.|.|.. ++.++.|++.++|+.=.++|..
T Consensus 234 ~~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 234 LYKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred ccCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 35799999976 5678999999999988887753
No 117
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=35.03 E-value=57 Score=21.96 Aligned_cols=28 Identities=14% Similarity=0.037 Sum_probs=24.4
Q ss_pred EEcCCCceeecceEEEeeceEEEEecCC
Q 033668 45 LTLKGKNPVNLDHLSVRGNNIRYYILPD 72 (114)
Q Consensus 45 ~~~~~g~~~~~~~v~IRG~~I~~I~lpd 72 (114)
|.+.+|....-+.+...|..+.-|.+|+
T Consensus 69 EFS~~G~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 69 EFSSDGEDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EEeCCChhcceEEEEEECCeeeEEEcCC
Confidence 4557888889999999999999999985
No 118
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=34.80 E-value=51 Score=23.88 Aligned_cols=8 Identities=25% Similarity=0.347 Sum_probs=3.3
Q ss_pred EEEEEcCC
Q 033668 15 VSIELKNG 22 (114)
Q Consensus 15 V~VeLkng 22 (114)
|++..+||
T Consensus 43 Vi~ts~Dg 50 (134)
T KOG3293|consen 43 VICTSEDG 50 (134)
T ss_pred eEEeccCC
Confidence 44444443
No 119
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=33.10 E-value=1.1e+02 Score=23.75 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=10.1
Q ss_pred hHHHHHhcCCCEEEE
Q 033668 3 LVRFLMKLNNETVSI 17 (114)
Q Consensus 3 l~~~L~~l~gk~V~V 17 (114)
|-.||..|.+..|+=
T Consensus 56 lg~flh~Cegd~Vck 70 (215)
T KOG3262|consen 56 LGKFLHMCEGDLVCK 70 (215)
T ss_pred hhhhhhhcCCceEEe
Confidence 456777887777653
No 120
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=31.52 E-value=1.4e+02 Score=23.17 Aligned_cols=36 Identities=25% Similarity=0.249 Sum_probs=32.0
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccE
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTV 43 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv 43 (114)
...+|+.|++...++....|+..++|..-.+.|+..
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 445899999999999999999999999999888765
No 121
>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=30.15 E-value=38 Score=23.98 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=22.4
Q ss_pred hHHHHHhcCCCEEEEEEcCC-eEEEEEE
Q 033668 3 LVRFLMKLNNETVSIELKNG-TIVHGTI 29 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng-~~~~G~L 29 (114)
|-.++..+.|+.|.|.++.. .++.|+.
T Consensus 94 l~~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 94 LEQFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHHHcCCeeEEEecccccCCCCcE
Confidence 45688899999999999988 7777754
No 122
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=29.99 E-value=79 Score=22.88 Aligned_cols=39 Identities=23% Similarity=0.418 Sum_probs=31.2
Q ss_pred CeEEEEEEEEec---CccceEEccEEEEcCCCceeecceEEEeece
Q 033668 22 GTIVHGTITGVD---ISMNTHLKTVKLTLKGKNPVNLDHLSVRGNN 64 (114)
Q Consensus 22 g~~~~G~L~~~D---~~MNi~L~dv~~~~~~g~~~~~~~v~IRG~~ 64 (114)
+..+.|.+..+- -+||+.+.|+. +|+...-..+-|||++
T Consensus 82 d~~lvG~VqKvS~Lil~~~~~v~Dv~----tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 82 DYVLVGEVQKVSNLILNMNVYVRDVE----TGKVVRGRSVDIRGNT 123 (140)
T ss_pred CEEEEEEEechhhhheeeeEEEEECC----CCCEEeeeeeeEecCc
Confidence 456778777776 68999999984 6777888889999986
No 123
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=29.91 E-value=53 Score=19.55 Aligned_cols=15 Identities=27% Similarity=0.390 Sum_probs=12.8
Q ss_pred HHHHHhcCCCEEEEE
Q 033668 4 VRFLMKLNNETVSIE 18 (114)
Q Consensus 4 ~~~L~~l~gk~V~Ve 18 (114)
++.+++++||.|+|.
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 467888999999986
No 124
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=29.14 E-value=62 Score=27.61 Aligned_cols=33 Identities=39% Similarity=0.584 Sum_probs=0.0
Q ss_pred hhhhhhCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 033668 78 TLLVEETPRVKPKKPTAGRPVGRGRGRGRGRGRG 111 (114)
Q Consensus 78 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 (114)
.++++-..|--..+--.+++.||+ |+|+|+|+|
T Consensus 351 ~~~eqgg~Rgg~Gg~~gGrGgGRG-ggG~GGGgg 383 (465)
T KOG3973|consen 351 QVLEQGGSRGGSGGNWGGRGGGRG-GGGRGGGGG 383 (465)
T ss_pred chhhccCCCCCCCCCCCCCCCCCC-CCCCCCCCC
No 125
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=28.83 E-value=62 Score=20.53 Aligned_cols=23 Identities=35% Similarity=0.356 Sum_probs=18.4
Q ss_pred EEEEEEEEec-CccceEEccEEEE
Q 033668 24 IVHGTITGVD-ISMNTHLKTVKLT 46 (114)
Q Consensus 24 ~~~G~L~~~D-~~MNi~L~dv~~~ 46 (114)
..+|++.++| ..+-|.|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 4689999999 6778888886544
No 126
>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=28.54 E-value=1.8e+02 Score=19.36 Aligned_cols=70 Identities=19% Similarity=0.172 Sum_probs=34.2
Q ss_pred HHHHhcCCCEEEEEEc----CCeEEEEEEEEecC-ccceEEccEEEEcCCCceeec----ceEEEeeceEEEEecCCCCc
Q 033668 5 RFLMKLNNETVSIELK----NGTIVHGTITGVDI-SMNTHLKTVKLTLKGKNPVNL----DHLSVRGNNIRYYILPDSLN 75 (114)
Q Consensus 5 ~~L~~l~gk~V~VeLk----ng~~~~G~L~~~D~-~MNi~L~dv~~~~~~g~~~~~----~~v~IRG~~I~~I~lpd~l~ 75 (114)
.+|++++|+.|++--+ ++. .=++.+.|. ..++.|..-.....++-..-. +..-|+... ++.+.+++|
T Consensus 8 ~~L~~f~gk~V~ivGkV~~~~~~--~~~~~~~Dg~~v~v~l~~~~~~~~~~~vEViG~V~~~~~I~~~~--~~~~g~~~D 83 (101)
T cd04479 8 AMLSQFVGKTVRIVGKVEKVDGD--SLTLISSDGVNVTVELNRPLDLPISGYVEVIGKVSPDLTIRVLS--YIDFGDDFD 83 (101)
T ss_pred HHHHhhCCCEEEEEEEEEEecCC--eEEEEcCCCCEEEEEeCCCCCcccCCEEEEEEEECCCCeEEEEE--EEECCCccC
Confidence 5789999999986533 122 234445554 444444432111111100111 223444443 677888777
Q ss_pred hhh
Q 033668 76 LET 78 (114)
Q Consensus 76 ~~~ 78 (114)
++.
T Consensus 84 ~~~ 86 (101)
T cd04479 84 MDL 86 (101)
T ss_pred HHH
Confidence 654
No 127
>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=28.47 E-value=1.7e+02 Score=20.44 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=21.5
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEE
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGT 28 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~ 28 (114)
+..|+...+-.|+.||.||.+|.+.
T Consensus 66 ~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 66 VDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred HHHHhCCcccEEEEEecCCcEEEec
Confidence 4567889999999999999998764
No 128
>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=27.83 E-value=1.2e+02 Score=22.99 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=25.0
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccc
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMN 37 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (114)
..+=+.|+|+.+..++.++. +.|.|+.+..|+-
T Consensus 10 ~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 10 VEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 34557899999999999888 9999999998876
No 129
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=27.12 E-value=93 Score=20.83 Aligned_cols=23 Identities=26% Similarity=0.518 Sum_probs=18.8
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEE
Q 033668 7 LMKLNNETVSIELKNGTIVHGTI 29 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L 29 (114)
|.-+-.-.++.+||+|..+.|+-
T Consensus 18 lACl~hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 18 LACLHHLPLTLELKDGEVLQAKA 40 (84)
T ss_pred HHHhhhceEEEEEcCCeEEEEEe
Confidence 44556778999999999999964
No 130
>PRK10708 hypothetical protein; Provisional
Probab=26.85 E-value=77 Score=20.05 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=23.1
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMN 37 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (114)
++-+|+|++..+..-.|++.++..|--
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~E 29 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFSE 29 (62)
T ss_pred cccEEEEecCCCccccceEEEEeeccC
Confidence 577899999999999999999987643
No 131
>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=26.46 E-value=1.4e+02 Score=18.58 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=18.3
Q ss_pred cCCCEEEEEEcCCeE-EEEEEEEecCc
Q 033668 10 LNNETVSIELKNGTI-VHGTITGVDIS 35 (114)
Q Consensus 10 l~gk~V~VeLkng~~-~~G~L~~~D~~ 35 (114)
..|..|.+.--++.. |.|++.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 358889998888755 49999999964
No 132
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=26.12 E-value=1.9e+02 Score=18.90 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=22.1
Q ss_pred HHHHHhcCCCEEEEEEcCC----eEEEEEEEEec
Q 033668 4 VRFLMKLNNETVSIELKNG----TIVHGTITGVD 33 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng----~~~~G~L~~~D 33 (114)
-..|.+.+|++|.|....| .+-+|+|...=
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~tY 42 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEETY 42 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE-
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEeec
Confidence 4568899999999999998 46789998763
No 133
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=25.86 E-value=1e+02 Score=23.14 Aligned_cols=27 Identities=22% Similarity=0.441 Sum_probs=23.0
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEec
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVD 33 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D 33 (114)
+..++|+.|.|.+.....+.|.+..++
T Consensus 23 ~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 23 LKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 356899999999998899999999884
No 134
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=25.33 E-value=65 Score=27.51 Aligned_cols=14 Identities=0% Similarity=0.207 Sum_probs=5.7
Q ss_pred EEEEecCCCCchhh
Q 033668 65 IRYYILPDSLNLET 78 (114)
Q Consensus 65 I~~I~lpd~l~~~~ 78 (114)
..||.+-+.....+
T Consensus 332 fgFV~f~~~~~~~~ 345 (419)
T KOG0116|consen 332 FGFVEFENAAAVQN 345 (419)
T ss_pred eEEEEEeecchhhh
Confidence 34554444433333
No 135
>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=25.31 E-value=1.7e+02 Score=18.06 Aligned_cols=34 Identities=15% Similarity=0.324 Sum_probs=27.2
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccceEEccEE
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMNTHLKTVK 44 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~ 44 (114)
.+..|.|...+-..+.|.+..+++.+=+.+++..
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 4577888887778999999999998888877654
No 136
>PRK08158 type III secretion system protein SpaO; Validated
Probab=25.18 E-value=1.3e+02 Score=24.57 Aligned_cols=39 Identities=13% Similarity=0.150 Sum_probs=33.1
Q ss_pred HHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEE
Q 033668 7 LMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKL 45 (114)
Q Consensus 7 L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~ 45 (114)
|....+..|.|..++-..-+|.|+.+|+.+-+.+.+...
T Consensus 259 L~~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i~~ 297 (303)
T PRK08158 259 LPTNAELNVEIRANGALLGNGELVQMDDTLGVEIHEWLS 297 (303)
T ss_pred CCCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEEec
Confidence 445678899999988899999999999999998887643
No 137
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=24.68 E-value=1.5e+02 Score=22.12 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=23.7
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMN 37 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (114)
.|..|.|.+.++..+.|++..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 489999999999999999999997654
No 138
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=24.37 E-value=83 Score=19.91 Aligned_cols=27 Identities=22% Similarity=0.308 Sum_probs=23.1
Q ss_pred CCCEEEEEEcCCeEEEEEEEEecCccc
Q 033668 11 NNETVSIELKNGTIVHGTITGVDISMN 37 (114)
Q Consensus 11 ~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (114)
++-+|+|++..+..-.|++.++..|--
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~E 29 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFNE 29 (62)
T ss_pred cccEEEEecCCcccccceEEEEeeccC
Confidence 577899999999999999999987643
No 139
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=24.31 E-value=2e+02 Score=24.80 Aligned_cols=42 Identities=14% Similarity=0.046 Sum_probs=34.1
Q ss_pred HHHHHhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEEE
Q 033668 4 VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLT 46 (114)
Q Consensus 4 ~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~~ 46 (114)
..++.++.||.|+- =|+|.+++++|.+-|.-.-+.+.|-.+.
T Consensus 74 ~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v 115 (421)
T COG5316 74 GKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEV 115 (421)
T ss_pred hhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEE
Confidence 35778899999999 8899999999999998776666665543
No 140
>PF13437 HlyD_3: HlyD family secretion protein
Probab=23.20 E-value=2e+02 Score=18.42 Aligned_cols=24 Identities=17% Similarity=0.495 Sum_probs=21.3
Q ss_pred CCCEEEEEEcCC--eEEEEEEEEecC
Q 033668 11 NNETVSIELKNG--TIVHGTITGVDI 34 (114)
Q Consensus 11 ~gk~V~VeLkng--~~~~G~L~~~D~ 34 (114)
.|..|++.+.++ ..+.|++..++.
T Consensus 53 ~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 53 PGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred CCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 699999999855 699999999998
No 141
>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=22.34 E-value=3.2e+02 Score=20.85 Aligned_cols=39 Identities=23% Similarity=0.286 Sum_probs=30.6
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecCc-cceEEc
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDIS-MNTHLK 41 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~-MNi~L~ 41 (114)
+...|+.-.|..|.|-.-+|..|.++|..++.. ..+.+.
T Consensus 26 l~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~ 65 (240)
T TIGR00046 26 LVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELL 65 (240)
T ss_pred HHHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEE
Confidence 356778888999999888999999999998754 344443
No 142
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=22.00 E-value=1.9e+02 Score=22.05 Aligned_cols=32 Identities=22% Similarity=0.198 Sum_probs=27.9
Q ss_pred hHHHHHhcCCCEEEEEEcCCeEEEEEEEEecC
Q 033668 3 LVRFLMKLNNETVSIELKNGTIVHGTITGVDI 34 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~ 34 (114)
+...|+.-.|..|.|-.-+|..|.++|..+|.
T Consensus 24 l~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~ 55 (234)
T PRK11713 24 LVRVLRLKEGDELRLFDGDGGEYLAEITEIGK 55 (234)
T ss_pred HHhhccCCCCCEEEEEeCCCCEEEEEEEEecC
Confidence 35677888899999998899999999999985
No 143
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=21.78 E-value=2.4e+02 Score=20.53 Aligned_cols=27 Identities=22% Similarity=0.366 Sum_probs=20.0
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecCccc
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDISMN 37 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MN 37 (114)
.+++|+.|.+ .++ .+.|++.++.-+.+
T Consensus 93 ~slIGk~V~~--~~~-~~~G~V~sV~~~~~ 119 (140)
T PRK06009 93 EGLIGRTVTS--ADG-SITGVVKSVTVYSD 119 (140)
T ss_pred HHhcCCEEEe--cCC-cEEEEEEEEEEeCC
Confidence 4689999975 445 68999999874433
No 144
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=21.64 E-value=1.1e+02 Score=25.55 Aligned_cols=77 Identities=13% Similarity=0.078 Sum_probs=45.7
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEec--------------CccceEEccEEEEcC--------CCce--eecceEEEeec
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVD--------------ISMNTHLKTVKLTLK--------GKNP--VNLDHLSVRGN 63 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D--------------~~MNi~L~dv~~~~~--------~g~~--~~~~~v~IRG~ 63 (114)
+.+.|++|+|...+|..|.|++-+.= +++++.++--..... -|.+ ..-....+...
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg~~p~H~~~~~~~~~~~~~~~el~iDiga~skeea~~lGI~vGd~v~~~~~~~~l~~~ 172 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIGSKPPHLLKEEAERKKPPEWDELFIDIGASSKEEAEELGIRVGDFVVFDPRFRELANG 172 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEcccCccccCccccccCCCchhhEEEECCcCCHHHHHhcCCCCCCEEEEcCceEEecCC
Confidence 45789999999999999999998332 344444432221110 1122 22234445557
Q ss_pred eEEEEecCCCCchhhhhhhhC
Q 033668 64 NIRYYILPDSLNLETLLVEET 84 (114)
Q Consensus 64 ~I~~I~lpd~l~~~~~l~~~~ 84 (114)
+|.-=++.|.+-.+.+|+-.+
T Consensus 173 ~i~skalDdR~gva~lle~lk 193 (355)
T COG1363 173 RVVSKALDDRAGVAALLELLK 193 (355)
T ss_pred cEEeeeccchHhHHHHHHHHH
Confidence 777777777776655554433
No 145
>KOG2097 consensus Predicted N6-adenine methylase involved in transcription regulation [Transcription]
Probab=21.14 E-value=1.2e+02 Score=25.48 Aligned_cols=30 Identities=40% Similarity=0.635 Sum_probs=12.8
Q ss_pred hhhhhCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 033668 79 LLVEETPRVKPKKPTAGRPVGRGRGRGRGRGR 110 (114)
Q Consensus 79 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (114)
.++...++.-..|.. ..+|.|+|+.+||||
T Consensus 366 eIElLRPkSP~~ksq--~lrg~grg~~~~~gr 395 (397)
T KOG2097|consen 366 EIELLRPKSPPPKSQ--SLRGAGRGRRTGRGR 395 (397)
T ss_pred hhhhcCCCCCCcccc--ccccCCCCCcCCCCC
Confidence 344444444444444 344444443333333
No 146
>PRK08477 biotin--protein ligase; Provisional
Probab=21.06 E-value=3.3e+02 Score=20.78 Aligned_cols=37 Identities=11% Similarity=0.054 Sum_probs=29.9
Q ss_pred HhcCCCEEEEEEcCCeEEEEEEEEecCccceEEccEEE
Q 033668 8 MKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKL 45 (114)
Q Consensus 8 ~~l~gk~V~VeLkng~~~~G~L~~~D~~MNi~L~dv~~ 45 (114)
.-.+|+.|+|.. ++.+++|+..++|+.=-+.++.-..
T Consensus 171 ~~~~~~~v~v~~-~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 171 EFEKSKSFSFHI-DGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHHcCCEEEEEE-CCEEEEEEEeeECCCCeEEECCEEe
Confidence 446799999974 6799999999999988887766543
No 147
>PF09642 YonK: YonK protein; InterPro: IPR018600 YonK protein is expressed by the bacterial prophage SPbetaC []. It is a 63 residue protein that associates into a homo-octamer in the form of a beta-stranded barrel with four outer helical features at points of the compass. Its function is unknown. ; PDB: 2H4O_C.
Probab=20.48 E-value=1.2e+02 Score=19.28 Aligned_cols=22 Identities=32% Similarity=0.430 Sum_probs=18.5
Q ss_pred hHHHHHhcCCCEEEEEEcCCeE
Q 033668 3 LVRFLMKLNNETVSIELKNGTI 24 (114)
Q Consensus 3 l~~~L~~l~gk~V~VeLkng~~ 24 (114)
|-+.|.++.|+.|.|.++...+
T Consensus 34 l~eil~~F~gk~VsitIkEe~E 55 (62)
T PF09642_consen 34 LNEILSEFNGKNVSITIKEENE 55 (62)
T ss_dssp HHHHHHTTTTSEEEEEEEEEEE
T ss_pred HHHHHHHhCCceEEEEEeeccc
Confidence 5678999999999999987655
Done!