Query 034890
Match_columns 80
No_of_seqs 123 out of 1104
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 07:24:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034890.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034890hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01719 Sm_G The eukaryotic Sm 99.9 3.1E-24 6.6E-29 126.1 10.0 69 7-75 2-71 (72)
2 PRK00737 small nuclear ribonuc 99.9 1.6E-24 3.4E-29 127.1 8.7 69 1-71 1-71 (72)
3 cd01729 LSm7 The eukaryotic Sm 99.9 4.7E-24 1E-28 127.8 9.1 70 5-74 2-80 (81)
4 cd01731 archaeal_Sm1 The archa 99.9 5.6E-24 1.2E-28 123.3 8.5 66 7-72 1-68 (68)
5 cd01726 LSm6 The eukaryotic Sm 99.9 1E-23 2.2E-28 122.0 8.2 65 7-71 1-67 (67)
6 cd01730 LSm3 The eukaryotic Sm 99.9 3.4E-23 7.3E-28 124.1 8.2 67 6-72 1-82 (82)
7 cd01732 LSm5 The eukaryotic Sm 99.9 5.7E-23 1.2E-27 121.9 8.8 67 6-72 3-74 (76)
8 cd01721 Sm_D3 The eukaryotic S 99.9 7.9E-23 1.7E-27 119.4 9.1 68 7-74 1-70 (70)
9 cd01717 Sm_B The eukaryotic Sm 99.9 1.6E-22 3.4E-27 120.3 9.5 65 8-72 3-78 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.9 6.3E-23 1.4E-27 119.1 7.2 65 7-71 2-68 (68)
11 cd01727 LSm8 The eukaryotic Sm 99.9 4.1E-22 9E-27 117.3 9.2 68 8-75 2-74 (74)
12 cd01723 LSm4 The eukaryotic Sm 99.9 2.3E-22 5E-27 119.0 8.1 70 7-76 2-74 (76)
13 PF01423 LSM: LSM domain ; In 99.9 4.6E-22 9.9E-27 114.2 9.0 64 9-72 2-67 (67)
14 smart00651 Sm snRNP Sm protein 99.9 6.4E-22 1.4E-26 113.5 9.0 64 9-72 2-67 (67)
15 cd01720 Sm_D2 The eukaryotic S 99.9 5.6E-22 1.2E-26 120.3 8.2 68 6-73 2-86 (87)
16 cd01724 Sm_D1 The eukaryotic S 99.9 2.5E-21 5.3E-26 118.1 9.4 69 9-77 5-74 (90)
17 cd06168 LSm9 The eukaryotic Sm 99.9 3.5E-21 7.5E-26 114.0 9.5 65 8-72 3-74 (75)
18 KOG1780 Small Nuclear ribonucl 99.9 1.1E-21 2.3E-26 115.0 6.7 75 1-76 1-76 (77)
19 cd01728 LSm1 The eukaryotic Sm 99.9 3.1E-21 6.6E-26 114.0 8.8 65 8-72 5-73 (74)
20 COG1958 LSM1 Small nuclear rib 99.9 6.5E-21 1.4E-25 113.2 9.1 67 6-72 7-79 (79)
21 cd00600 Sm_like The eukaryotic 99.9 8.9E-21 1.9E-25 107.3 8.8 62 10-71 1-63 (63)
22 cd01718 Sm_E The eukaryotic Sm 99.8 5.9E-21 1.3E-25 114.0 8.0 67 6-72 6-79 (79)
23 cd01733 LSm10 The eukaryotic S 99.8 1.5E-20 3.3E-25 111.9 8.9 64 10-73 14-78 (78)
24 cd01725 LSm2 The eukaryotic Sm 99.8 2.5E-20 5.4E-25 111.6 8.1 67 10-76 6-75 (81)
25 PTZ00138 small nuclear ribonuc 99.8 5E-19 1.1E-23 107.8 8.7 68 6-73 14-88 (89)
26 KOG1783 Small nuclear ribonucl 99.8 8.2E-20 1.8E-24 106.8 1.1 73 1-73 1-75 (77)
27 KOG3482 Small nuclear ribonucl 99.7 2.5E-17 5.4E-22 96.4 6.5 66 9-74 12-78 (79)
28 KOG3460 Small nuclear ribonucl 99.7 1.9E-18 4E-23 103.4 1.3 73 3-75 2-89 (91)
29 KOG1781 Small Nuclear ribonucl 99.7 1.8E-18 3.9E-23 106.2 -1.8 70 6-75 18-96 (108)
30 KOG3293 Small nuclear ribonucl 99.6 2.1E-15 4.6E-20 95.9 5.1 71 6-76 2-75 (134)
31 KOG1784 Small Nuclear ribonucl 99.6 2.6E-15 5.6E-20 91.2 4.6 70 9-78 4-78 (96)
32 KOG3168 U1 snRNP component [Tr 99.6 4.2E-16 9E-21 103.6 0.7 73 6-78 5-88 (177)
33 KOG3448 Predicted snRNP core p 99.5 4.5E-14 9.7E-19 85.4 6.0 67 10-76 7-76 (96)
34 KOG1775 U6 snRNA-associated Sm 99.5 2.8E-14 6.1E-19 84.2 2.7 70 3-72 4-78 (84)
35 KOG1782 Small Nuclear ribonucl 99.4 2.1E-14 4.6E-19 91.2 0.0 69 10-78 14-86 (129)
36 KOG1774 Small nuclear ribonucl 99.4 1.5E-13 3.4E-18 82.0 3.5 69 6-74 12-87 (88)
37 KOG3172 Small nuclear ribonucl 99.3 8.7E-12 1.9E-16 77.9 7.8 74 5-78 4-79 (119)
38 KOG3428 Small nuclear ribonucl 99.3 1.2E-11 2.7E-16 77.2 8.1 68 9-76 6-73 (109)
39 KOG3459 Small nuclear ribonucl 98.8 9.9E-10 2.1E-14 68.8 -0.0 69 5-73 23-108 (114)
40 cd01739 LSm11_C The eukaryotic 98.7 2.3E-08 4.9E-13 57.6 3.0 37 15-51 8-48 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 98.2 4.9E-06 1.1E-10 48.7 5.8 59 10-68 7-76 (77)
42 PF12701 LSM14: Scd6-like Sm d 97.9 9.2E-05 2E-09 45.6 6.8 66 11-76 4-80 (96)
43 PF06372 Gemin6: Gemin6 protei 97.4 0.00044 9.5E-09 46.4 5.1 64 6-75 8-72 (166)
44 cd01736 LSm14_N LSm14 (also kn 97.0 0.0075 1.6E-07 35.6 6.8 59 11-69 2-72 (74)
45 PF02237 BPL_C: Biotin protein 96.8 0.0049 1.1E-07 33.0 4.9 34 13-47 1-34 (48)
46 PF11095 Gemin7: Gem-associate 96.8 0.012 2.5E-07 35.3 6.7 60 10-73 19-79 (80)
47 cd01735 LSm12_N LSm12 belongs 96.6 0.015 3.2E-07 33.1 6.0 36 13-48 4-39 (61)
48 PRK00395 hfq RNA-binding prote 96.5 0.0062 1.3E-07 36.4 4.3 31 15-45 19-49 (79)
49 cd01716 Hfq Hfq, an abundant, 96.4 0.0084 1.8E-07 34.2 4.0 32 14-45 10-41 (61)
50 TIGR02383 Hfq RNA chaperone Hf 96.3 0.0095 2.1E-07 34.0 4.0 31 15-45 15-45 (61)
51 PF10842 DUF2642: Protein of u 96.2 0.033 7.1E-07 32.2 6.1 50 10-71 16-65 (66)
52 PRK14638 hypothetical protein; 96.0 0.01 2.2E-07 39.0 3.8 35 9-44 94-128 (150)
53 PRK14639 hypothetical protein; 95.6 0.019 4.2E-07 37.3 3.7 35 9-44 82-116 (140)
54 PRK02001 hypothetical protein; 95.6 0.02 4.4E-07 37.8 3.7 35 9-44 84-118 (152)
55 COG1923 Hfq Uncharacterized ho 95.2 0.038 8.3E-07 32.8 3.6 25 15-39 19-43 (77)
56 cd01734 YlxS_C YxlS is a Bacil 94.6 0.064 1.4E-06 31.7 3.6 35 9-44 19-57 (83)
57 PRK14640 hypothetical protein; 94.5 0.093 2E-06 34.5 4.5 35 9-44 91-129 (152)
58 PRK14091 RNA-binding protein H 94.4 0.11 2.4E-06 34.9 4.7 32 15-46 24-55 (165)
59 PRK14644 hypothetical protein; 94.1 0.16 3.4E-06 32.9 5.0 35 9-44 79-117 (136)
60 PRK14633 hypothetical protein; 93.8 0.11 2.4E-06 34.1 3.8 35 9-44 88-126 (150)
61 PRK14642 hypothetical protein; 93.7 0.11 2.4E-06 35.8 3.8 34 9-43 94-140 (197)
62 PRK00092 ribosome maturation p 93.5 0.14 3.1E-06 33.5 4.0 35 8-43 91-129 (154)
63 KOG1073 Uncharacterized mRNA-a 93.4 0.35 7.5E-06 36.2 6.3 65 11-75 5-81 (361)
64 PRK14645 hypothetical protein; 93.4 0.12 2.7E-06 34.1 3.5 34 9-44 96-129 (154)
65 PF02576 DUF150: Uncharacteris 93.3 0.12 2.7E-06 33.1 3.3 34 9-43 81-118 (141)
66 PRK14636 hypothetical protein; 93.0 0.16 3.4E-06 34.3 3.6 35 9-44 92-130 (176)
67 PRK14632 hypothetical protein; 92.9 0.17 3.7E-06 33.9 3.7 35 9-44 92-133 (172)
68 COG0779 Uncharacterized protei 92.9 0.27 5.9E-06 32.6 4.5 34 10-44 94-131 (153)
69 PRK14634 hypothetical protein; 92.7 0.2 4.3E-06 33.1 3.7 35 9-44 94-132 (155)
70 PRK14091 RNA-binding protein H 92.6 0.23 5.1E-06 33.4 4.0 31 15-45 104-134 (165)
71 PRK14643 hypothetical protein; 92.3 0.29 6.4E-06 32.6 4.2 30 9-38 98-131 (164)
72 PRK14647 hypothetical protein; 92.2 0.25 5.4E-06 32.7 3.7 34 9-43 93-135 (159)
73 PRK14646 hypothetical protein; 91.9 0.28 6E-06 32.4 3.7 35 9-44 94-132 (155)
74 PRK14631 hypothetical protein; 91.4 0.32 7E-06 32.7 3.7 34 9-43 111-150 (174)
75 PRK14637 hypothetical protein; 91.2 0.33 7.1E-06 32.0 3.5 35 9-44 92-127 (151)
76 PRK06955 biotin--protein ligas 90.7 2.2 4.8E-05 30.6 7.6 33 13-45 247-279 (300)
77 PRK11886 bifunctional biotin-- 90.6 1.8 3.9E-05 31.0 7.1 47 13-64 270-317 (319)
78 PRK14641 hypothetical protein; 90.1 0.44 9.5E-06 32.1 3.4 28 9-36 98-129 (173)
79 PF03614 Flag1_repress: Repres 89.3 0.67 1.5E-05 31.0 3.7 34 14-47 28-61 (165)
80 PF14563 DUF4444: Domain of un 88.0 0.6 1.3E-05 24.7 2.3 21 28-48 10-30 (42)
81 PRK14635 hypothetical protein; 87.5 1.3 2.8E-05 29.3 4.2 36 8-44 92-132 (162)
82 PRK13325 bifunctional biotin-- 87.1 4.2 9E-05 32.1 7.4 33 13-45 276-308 (592)
83 PF03614 Flag1_repress: Repres 87.0 0.76 1.6E-05 30.7 2.8 32 14-45 119-151 (165)
84 TIGR00121 birA_ligase birA, bi 86.9 4.6 0.0001 27.8 6.9 31 13-44 191-221 (237)
85 PRK08330 biotin--protein ligas 86.0 4.3 9.4E-05 27.9 6.4 33 13-46 186-219 (236)
86 PRK14630 hypothetical protein; 83.9 1.7 3.7E-05 28.3 3.4 34 9-44 91-124 (143)
87 PTZ00275 biotin-acetyl-CoA-car 82.0 4.2 9.1E-05 29.1 5.0 31 14-45 236-266 (285)
88 PRK10139 serine endoprotease; 81.6 8.7 0.00019 29.3 6.9 59 16-74 115-175 (455)
89 PF11607 DUF3247: Protein of u 79.7 3.3 7.2E-05 25.6 3.3 19 15-33 28-46 (101)
90 PRK10898 serine endoprotease; 78.9 5.9 0.00013 29.1 5.1 32 16-47 102-133 (353)
91 PRK10942 serine endoprotease; 78.4 14 0.0003 28.3 7.1 32 16-47 136-167 (473)
92 PRK09618 flgD flagellar basal 77.5 11 0.00023 24.8 5.5 27 10-36 87-113 (142)
93 TIGR02038 protease_degS peripl 77.5 6.3 0.00014 28.8 4.9 33 16-48 102-134 (351)
94 COG0340 BirA Biotin-(acetyl-Co 76.7 7.6 0.00016 27.2 4.9 35 12-46 187-221 (238)
95 TIGR02037 degP_htrA_DO peripla 70.9 28 0.0006 26.0 7.0 32 16-47 82-113 (428)
96 TIGR02603 CxxCH_TIGR02603 puta 68.3 13 0.00028 23.5 4.1 29 17-46 59-87 (133)
97 PF07073 ROF: Modulator of Rho 65.6 5.5 0.00012 23.6 1.9 50 13-74 15-70 (80)
98 PRK08477 biotin--protein ligas 63.1 33 0.00071 23.6 5.6 34 13-47 173-206 (211)
99 KOG3382 NADH:ubiquinone oxidor 61.8 4.8 0.0001 26.5 1.2 27 23-49 40-66 (151)
100 PRK06789 flagellar motor switc 56.7 26 0.00057 20.5 3.7 40 6-45 32-71 (74)
101 PRK11911 flgD flagellar basal 55.6 28 0.0006 22.8 4.0 26 11-36 89-114 (140)
102 KOG4401 Uncharacterized conser 55.4 19 0.00041 24.7 3.3 41 8-48 4-44 (184)
103 PF05071 NDUFA12: NADH ubiquin 53.8 8.7 0.00019 23.6 1.4 17 30-46 1-17 (105)
104 COG1886 FliN Flagellar motor s 52.9 33 0.00071 22.0 4.0 39 6-44 96-134 (136)
105 TIGR03170 flgA_cterm flagella 51.7 22 0.00048 21.7 3.0 22 13-34 94-116 (122)
106 PF09465 LBR_tudor: Lamin-B re 50.7 39 0.00084 18.8 3.5 25 14-38 8-33 (55)
107 cd01737 LSm16_N LSm16 belongs 49.9 47 0.001 18.8 4.5 55 11-67 2-58 (62)
108 PRK11625 Rho-binding antitermi 49.3 25 0.00055 21.0 2.9 51 14-73 22-74 (84)
109 PF05954 Phage_GPD: Phage late 48.3 38 0.00081 23.1 4.0 29 8-36 21-49 (292)
110 PF01887 SAM_adeno_trans: S-ad 44.7 35 0.00077 24.2 3.5 18 27-44 169-186 (258)
111 COG2451 Ribosomal protein L35A 44.4 41 0.00089 20.8 3.3 36 5-40 36-72 (100)
112 PRK07018 flgA flagellar basal 44.3 30 0.00064 24.0 3.0 22 13-34 205-227 (235)
113 PF11931 DUF3449: Domain of un 43.9 7.6 0.00017 26.8 0.0 33 7-40 89-123 (196)
114 smart00166 UBX Domain present 43.8 25 0.00053 20.0 2.2 22 15-36 4-25 (80)
115 PRK06630 hypothetical protein; 43.3 14 0.0003 23.0 1.1 20 28-47 11-30 (99)
116 PRK06792 flgD flagellar basal 43.3 50 0.0011 22.8 3.9 26 11-36 114-139 (190)
117 cd01772 SAKS1_UBX SAKS1-like U 42.9 22 0.00047 20.5 1.8 23 14-36 3-25 (79)
118 PF11743 DUF3301: Protein of u 40.9 81 0.0018 19.0 4.4 37 38-74 57-96 (97)
119 COG0265 DegQ Trypsin-like seri 40.9 69 0.0015 23.0 4.6 33 15-47 95-127 (347)
120 PF07024 ImpE: ImpE protein; 39.4 51 0.0011 21.1 3.3 29 6-34 42-70 (123)
121 cd01767 UBX UBX (ubiquitin reg 39.1 35 0.00075 19.2 2.3 21 16-36 3-23 (77)
122 KOG3493 Ubiquitin-like protein 38.8 27 0.00059 20.3 1.8 19 10-28 6-24 (73)
123 PF06257 DUF1021: Protein of u 38.6 34 0.00073 20.1 2.2 27 9-35 11-41 (76)
124 smart00333 TUDOR Tudor domain. 37.6 62 0.0013 16.7 4.3 25 14-38 5-29 (57)
125 PF00789 UBX: UBX domain; Int 37.5 43 0.00093 18.9 2.5 21 16-36 7-27 (82)
126 TIGR03361 VI_Rhs_Vgr type VI s 37.2 74 0.0016 24.2 4.4 29 8-36 40-72 (513)
127 PLN02732 Probable NADH dehydro 36.1 33 0.00071 23.0 2.1 19 29-47 48-66 (159)
128 PLN03095 NADH:ubiquinone oxido 36.0 23 0.0005 22.5 1.3 20 29-48 9-28 (115)
129 PF10618 Tail_tube: Phage tail 34.7 58 0.0013 20.4 3.0 22 10-31 69-90 (119)
130 PRK12617 flgA flagellar basal 34.6 55 0.0012 22.7 3.1 22 13-34 184-206 (214)
131 COG4466 Veg Uncharacterized pr 33.8 45 0.00097 19.9 2.2 24 10-33 14-41 (80)
132 PRK06005 flgA flagellar basal 33.8 60 0.0013 21.3 3.1 22 13-34 129-151 (160)
133 PF07202 Tcp10_C: T-complex pr 32.9 83 0.0018 21.3 3.7 33 12-44 141-177 (179)
134 PTZ00276 biotin/lipoate protei 32.6 70 0.0015 22.2 3.4 23 23-45 209-231 (245)
135 TIGR00999 8a0102 Membrane Fusi 32.1 1.1E+02 0.0025 20.5 4.4 27 14-40 141-167 (265)
136 PF14485 DUF4431: Domain of un 30.5 30 0.00065 18.4 1.0 14 8-21 12-25 (48)
137 PF10246 MRP-S35: Mitochondria 30.4 35 0.00076 21.3 1.4 34 14-48 63-96 (104)
138 cd06920 NEAT NEAr Transport do 30.2 76 0.0016 19.1 2.9 41 4-44 15-56 (117)
139 PRK08515 flgA flagellar basal 30.1 90 0.002 21.5 3.6 22 13-34 194-215 (222)
140 PRK10708 hypothetical protein; 29.9 72 0.0016 18.0 2.5 26 14-39 3-28 (62)
141 PF14153 Spore_coat_CotO: Spor 29.8 72 0.0016 21.7 3.0 47 17-72 135-182 (185)
142 PRK12618 flgA flagellar basal 29.5 82 0.0018 20.3 3.1 22 13-34 110-132 (141)
143 PRK08183 NADH dehydrogenase; V 28.4 33 0.00072 22.2 1.1 19 29-47 25-43 (133)
144 cd01770 p47_UBX p47-like ubiqu 28.3 63 0.0014 18.6 2.2 21 16-36 5-25 (79)
145 PRK06804 flgA flagellar basal 28.0 81 0.0018 22.5 3.1 22 13-34 231-253 (261)
146 COG1363 FrvX Cellulase M and r 27.9 77 0.0017 23.7 3.1 25 10-34 92-116 (355)
147 COG5316 Uncharacterized conser 27.9 1.7E+02 0.0036 22.6 4.8 39 10-49 77-115 (421)
148 COG4568 Rof Transcriptional an 27.4 92 0.002 18.6 2.8 19 14-32 22-40 (84)
149 PF12945 YcgR_2: Flagellar pro 26.4 1.3E+02 0.0027 16.7 4.4 33 14-46 3-39 (87)
150 PF10781 DSRB: Dextransucrase 25.1 87 0.0019 17.6 2.3 26 14-39 3-28 (62)
151 PRK04337 50S ribosomal protein 24.9 1.7E+02 0.0036 17.7 4.8 33 10-42 35-67 (87)
152 TIGR00008 infA translation ini 24.4 1.4E+02 0.003 17.1 3.1 22 13-34 15-36 (68)
153 PF13144 SAF_2: SAF-like 24.3 1.3E+02 0.0029 19.7 3.5 22 13-34 168-190 (196)
154 PF01052 SpoA: Surface present 24.3 1.4E+02 0.003 16.5 4.0 37 10-46 37-73 (77)
155 PF04528 Adeno_E4_34: Adenovir 23.2 1.4E+02 0.003 19.7 3.3 22 51-72 30-51 (148)
156 PF07076 DUF1344: Protein of u 23.2 98 0.0021 17.5 2.3 23 27-49 4-27 (61)
157 PF08863 YolD: YolD-like prote 22.9 1.6E+02 0.0034 16.7 4.7 31 15-45 42-75 (92)
158 PRK08158 type III secretion sy 22.8 1.5E+02 0.0033 21.8 3.7 39 8-46 257-295 (303)
159 PRK12442 translation initiatio 22.7 1.6E+02 0.0034 17.8 3.2 22 13-34 17-38 (87)
160 smart00725 NEAT NEAr Transport 22.2 1.1E+02 0.0024 19.1 2.7 32 5-36 17-49 (123)
161 PF03122 Herpes_MCP: Herpes vi 22.1 30 0.00064 30.3 0.0 53 18-70 250-305 (1354)
162 PRK05163 rpsL 30S ribosomal pr 22.1 1.3E+02 0.0028 19.4 3.0 30 7-36 42-71 (124)
163 PRK09961 exoaminopeptidase; Pr 22.0 1.2E+02 0.0026 22.2 3.1 23 11-33 90-112 (344)
164 PF05031 NEAT: Iron Transport- 22.0 1E+02 0.0022 18.9 2.4 25 5-29 22-46 (124)
165 PF05343 Peptidase_M42: M42 gl 21.8 1.2E+02 0.0027 21.7 3.1 24 11-35 49-72 (292)
166 PF09883 DUF2110: Uncharacteri 21.5 81 0.0018 22.3 2.0 18 25-42 75-92 (225)
167 PF02707 MOSP_N: Major Outer S 21.2 70 0.0015 22.3 1.7 17 26-42 30-46 (204)
168 COG0048 RpsL Ribosomal protein 20.4 1.4E+02 0.0031 19.3 2.9 28 7-34 48-75 (129)
169 cd00319 Ribosomal_S12_like Rib 20.3 1.4E+02 0.0031 18.3 2.7 28 7-34 27-54 (95)
170 COG1912 Uncharacterized conser 20.1 1.7E+02 0.0036 21.3 3.5 23 22-44 168-190 (268)
171 PRK09864 putative peptidase; P 20.1 1.5E+02 0.0032 22.1 3.3 25 10-34 88-112 (356)
172 PRK12786 flgA flagellar basal 20.0 1.4E+02 0.003 22.1 3.1 22 13-34 287-309 (338)
No 1
>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=99.92 E-value=3.1e-24 Score=126.10 Aligned_cols=69 Identities=74% Similarity=1.169 Sum_probs=64.1
Q ss_pred CCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCC
Q 034890 7 PPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEP 75 (80)
Q Consensus 7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~ 75 (80)
+++|.++++++|.|+|++|++++|+|.+||+|||++|+||.|+. +...+.+|.++|||++|++|++.|+
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence 56799999999999999999999999999999999999999985 4467789999999999999998875
No 2
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.92 E-value=1.6e-24 Score=127.15 Aligned_cols=69 Identities=39% Similarity=0.691 Sum_probs=62.8
Q ss_pred CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034890 1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE 71 (80)
Q Consensus 1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~ 71 (80)
|+ ..|+. |.++++++|.|+|+||+.|+|+|.+||+|||++|+||.|.. ++..+.+|.++|||++|++|.
T Consensus 1 ~~--~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 1 MA--QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred CC--cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 56 46887 89999999999999999999999999999999999999986 445678999999999999986
No 3
>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=99.91 E-value=4.7e-24 Score=127.76 Aligned_cols=70 Identities=41% Similarity=0.758 Sum_probs=63.3
Q ss_pred CCCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC---------ceeeeecEEEEcCCcEEEEEecC
Q 034890 5 GQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG---------NEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 5 ~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~---------~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
..+++|.++++++|+|.|++||+|.|+|.+||+||||+|++|.|+.. ...+.+|.++|||++|++|.+.+
T Consensus 2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 35788999999999999999999999999999999999999999752 24678999999999999998765
No 4
>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=99.91 E-value=5.6e-24 Score=123.32 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=60.3
Q ss_pred CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEe
Q 034890 7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
|++ |+++++++|.|+|++|+.|+|+|.+||+|||++|+||.|.+ +...+.+|.++|||++|++|++
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence 555 89999999999999999999999999999999999999985 4466789999999999999964
No 5
>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=99.90 E-value=1e-23 Score=122.04 Aligned_cols=65 Identities=34% Similarity=0.553 Sum_probs=59.4
Q ss_pred CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034890 7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE 71 (80)
Q Consensus 7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~ 71 (80)
|++ |++++|++|+|+|++|++|+|+|.+||+|||++|+||+|.. ++..+.+|.++|||++|++|+
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 566 89999999999999999999999999999999999999875 456678999999999999984
No 6
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=3.4e-23 Score=124.10 Aligned_cols=67 Identities=30% Similarity=0.614 Sum_probs=59.8
Q ss_pred CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--------------eeeeecEEEEcCCcEEEE
Q 034890 6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--------------EKNDIGMVVIRGNSVVTV 70 (80)
Q Consensus 6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--------------~~~~~g~v~IrG~~I~~I 70 (80)
.|++ |+.+++++|.|++++||.+.|+|.|||+||||+|+||+|.+.. ..|.+|.+||||++|++|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 4777 6888999999999999999999999999999999999998621 367899999999999998
Q ss_pred Ee
Q 034890 71 EA 72 (80)
Q Consensus 71 ~~ 72 (80)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 63
No 7
>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=99.89 E-value=5.7e-23 Score=121.87 Aligned_cols=67 Identities=24% Similarity=0.602 Sum_probs=61.1
Q ss_pred CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----CceeeeecEEEEcCCcEEEEEe
Q 034890 6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----GNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
.|++ |+++++++|.|++++|+++.|+|.|||+|||++|+||.|.+ +++.+.+|.++|||++|.+|++
T Consensus 3 ~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 3 LPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred ChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 4777 79999999999999999999999999999999999999975 3356789999999999999985
No 8
>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=99.89 E-value=7.9e-23 Score=119.39 Aligned_cols=68 Identities=16% Similarity=0.233 Sum_probs=61.6
Q ss_pred CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034890 7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
|++ |+++.|++|.|+|+||.+|+|+|.++|+|||++|+||.+.. +++...++.+||||++|.||..||
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 555 78999999999999999999999999999999999998764 445667899999999999999987
No 9
>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=99.89 E-value=1.6e-22 Score=120.35 Aligned_cols=65 Identities=29% Similarity=0.628 Sum_probs=59.3
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-----------ceeeeecEEEEcCCcEEEEEe
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-----------NEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-----------~~~~~~g~v~IrG~~I~~I~~ 72 (80)
..|.++++++|.|+++|||.+.|+|.|||+||||+|+||.|++. .+.+.+|+++|||++|++|+.
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 56999999999999999999999999999999999999999751 245789999999999999975
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=99.89 E-value=6.3e-23 Score=119.10 Aligned_cols=65 Identities=34% Similarity=0.490 Sum_probs=59.0
Q ss_pred CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEE
Q 034890 7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVE 71 (80)
Q Consensus 7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~ 71 (80)
|.. |++++|++|.|+|+||++|+|+|.+||+|||++|+||+|.. +.....+|.++|||++|++|.
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 555 89999999999999999999999999999999999999875 445678999999999999983
No 11
>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=99.88 E-value=4.1e-22 Score=117.32 Aligned_cols=68 Identities=35% Similarity=0.670 Sum_probs=61.6
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----CceeeeecEEEEcCCcEEEEEecCC
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----GNEKNDIGMVVIRGNSVVTVEALEP 75 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----~~~~~~~g~v~IrG~~I~~I~~~d~ 75 (80)
+.|.++++++|+|.+++|+.+.|+|.+||+|||++|++|.|.. +...+.+|.+++||++|++|++.|+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 5689999999999999999999999999999999999999974 2246689999999999999998774
No 12
>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=99.88 E-value=2.3e-22 Score=119.01 Aligned_cols=70 Identities=20% Similarity=0.365 Sum_probs=63.0
Q ss_pred CCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCCc
Q 034890 7 PPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 7 p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
|+. |+++.|++|.|+|++|++++|+|.+||+|||++|+||.+.. ++....++.+||||++|.+|+.+|.+
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 677 79999999999999999999999999999999999999874 44456689999999999999998864
No 13
>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=99.88 E-value=4.6e-22 Score=114.19 Aligned_cols=64 Identities=39% Similarity=0.655 Sum_probs=59.7
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--eeeeecEEEEcCCcEEEEEe
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--EKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--~~~~~g~v~IrG~~I~~I~~ 72 (80)
+|++++|++|+|+|+||++++|+|.+||+|||++|+||.+.... +.++++.+||||++|++|++
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 48899999999999999999999999999999999999998643 78899999999999999975
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.88 E-value=6.4e-22 Score=113.47 Aligned_cols=64 Identities=42% Similarity=0.702 Sum_probs=59.6
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--ceeeeecEEEEcCCcEEEEEe
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--NEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--~~~~~~g~v~IrG~~I~~I~~ 72 (80)
+|++++|++|+|+|+||+.++|+|.+||+|||++|+||.|.+. .+.+.++.+||||++|++|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 5899999999999999999999999999999999999999863 567899999999999999974
No 15
>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=99.87 E-value=5.6e-22 Score=120.30 Aligned_cols=68 Identities=25% Similarity=0.453 Sum_probs=59.5
Q ss_pred CCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc--------------eeeeecEEEEcCCcEE
Q 034890 6 QPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN--------------EKNDIGMVVIRGNSVV 68 (80)
Q Consensus 6 ~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--------------~~~~~g~v~IrG~~I~ 68 (80)
.|+. |.+++ +++|.|+|++|+.+.|+|.|||+||||+|+||+|.+.. +.+++|.+||||++|+
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 5777 67886 89999999999999999999999999999999997521 2457899999999999
Q ss_pred EEEec
Q 034890 69 TVEAL 73 (80)
Q Consensus 69 ~I~~~ 73 (80)
+|+.-
T Consensus 82 ~Is~~ 86 (87)
T cd01720 82 LVLRN 86 (87)
T ss_pred EEecC
Confidence 99753
No 16
>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=99.86 E-value=2.5e-21 Score=118.05 Aligned_cols=69 Identities=23% Similarity=0.341 Sum_probs=63.4
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCcc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVS 77 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~ 77 (80)
.|+++.|++|+|+|++|..|+|+|.++|.|||++|+||++.. ++....++.++|||++|.||+.||.+.
T Consensus 5 fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 5 FLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred HHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence 378999999999999999999999999999999999999875 456678999999999999999999864
No 17
>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=99.86 E-value=3.5e-21 Score=114.00 Aligned_cols=65 Identities=23% Similarity=0.492 Sum_probs=59.8
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-------ceeeeecEEEEcCCcEEEEEe
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-------NEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-------~~~~~~g~v~IrG~~I~~I~~ 72 (80)
..|.++++++|+|+|+|||.|.|+|.|||++||++|+||.|+.. .+.|.+|+++|||++|++|+.
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 35899999999999999999999999999999999999999851 457899999999999999974
No 18
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.86 E-value=1.1e-21 Score=114.97 Aligned_cols=75 Identities=68% Similarity=1.087 Sum_probs=69.0
Q ss_pred CCCCCCCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-ceeeeecEEEEcCCcEEEEEecCCc
Q 034890 1 MSRSGQPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-NEKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 1 M~~~~~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-~~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
|++++.| +|.+|++|++.++|..||.++|.|.+||.|||+||+++.|..+ +.+..+|.++|||++|+.+.+.|.+
T Consensus 1 Msksg~P-eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~~ 76 (77)
T KOG1780|consen 1 MSKSGHP-ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALERV 76 (77)
T ss_pred CCcccCc-hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecccc
Confidence 8999998 9999999999999999999999999999999999999999864 3456799999999999999988764
No 19
>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=99.86 E-value=3.1e-21 Score=113.96 Aligned_cols=65 Identities=40% Similarity=0.645 Sum_probs=58.5
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--Cc--eeeeecEEEEcCCcEEEEEe
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GN--EKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~--~~~~~g~v~IrG~~I~~I~~ 72 (80)
+.|.++++++|.|.+++|++|.|+|.+||+|||++|+||.|.. +. ..+.+|.++|||++|++|+.
T Consensus 5 ~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 5 ASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred HHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 4599999999999999999999999999999999999998864 21 35789999999999999975
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=6.5e-21 Score=113.25 Aligned_cols=67 Identities=42% Similarity=0.737 Sum_probs=57.8
Q ss_pred CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec---Cce-eeeec-EEEEcCCcEEEEEe
Q 034890 6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN---GNE-KNDIG-MVVIRGNSVVTVEA 72 (80)
Q Consensus 6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~---~~~-~~~~g-~v~IrG~~I~~I~~ 72 (80)
.|.. |.++++++|.|+|++|++|+|+|.|||+|||++|+||.|.. +.. .+.++ .++|||++|++|..
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 3555 89999999999999999999999999999999999999975 333 24455 99999999999863
No 21
>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=99.85 E-value=8.9e-21 Score=107.33 Aligned_cols=62 Identities=37% Similarity=0.668 Sum_probs=57.4
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC-ceeeeecEEEEcCCcEEEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG-NEKNDIGMVVIRGNSVVTVE 71 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~-~~~~~~g~v~IrG~~I~~I~ 71 (80)
|++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+.+. ...+.++.+||||++|++|.
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 678999999999999999999999999999999999999863 56788999999999999984
No 22
>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=99.85 E-value=5.9e-21 Score=114.02 Aligned_cols=67 Identities=28% Similarity=0.662 Sum_probs=59.2
Q ss_pred CCCc-hhhhcCC--EEEEEEc--CCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEe
Q 034890 6 QPPD-LKKYMDK--KLQIKLN--ANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 6 ~p~~-L~~~~~k--~V~V~l~--~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
.|.+ |.+++++ +|.|+++ +|++++|+|.|||+|||++|+||+|+. +.+.+.+|.++|||++|++|++
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 4777 8899988 7888877 899999999999999999999999985 3566789999999999999873
No 23
>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=99.84 E-value=1.5e-20 Score=111.92 Aligned_cols=64 Identities=16% Similarity=0.374 Sum_probs=58.9
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEec
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEAL 73 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~ 73 (80)
|+++.|++|.|+|+||.+|+|+|.++|++||++|+||++.. ++....++.+||||++|.||+.|
T Consensus 14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 78899999999999999999999999999999999999875 44555799999999999999876
No 24
>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=99.83 E-value=2.5e-20 Score=111.58 Aligned_cols=67 Identities=24% Similarity=0.358 Sum_probs=59.6
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc---eeeeecEEEEcCCcEEEEEecCCc
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN---EKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~---~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
|+++.|++|.|+|++|..|+|+|.++|+|||++|+||++.... ....++.++|||++|.+|+.||.+
T Consensus 6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence 7899999999999999999999999999999999999877532 234578999999999999999864
No 25
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.80 E-value=5e-19 Score=107.76 Aligned_cols=68 Identities=32% Similarity=0.664 Sum_probs=57.3
Q ss_pred CCCc-hhhhcCC--EEEEEEcC--CeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEec
Q 034890 6 QPPD-LKKYMDK--KLQIKLNA--NRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEAL 73 (80)
Q Consensus 6 ~p~~-L~~~~~k--~V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~ 73 (80)
.|.+ +.+++.+ +|.|++.+ +++++|+|.|||+|||++|+||+|.. +...+.+|.++|||++|++|++.
T Consensus 14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcC
Confidence 4555 6778755 68888877 59999999999999999999999985 34567899999999999999864
No 26
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.77 E-value=8.2e-20 Score=106.77 Aligned_cols=73 Identities=34% Similarity=0.521 Sum_probs=67.0
Q ss_pred CCCCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEec
Q 034890 1 MSRSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEAL 73 (80)
Q Consensus 1 M~~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~ 73 (80)
||..+.|.+ |.+++||+|.|+|.+|-.|+|+|.++|.|||+-|+.++|.. |..++++|..||||++|.+|+..
T Consensus 1 ~s~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 1 MSEGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred CCcccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEec
Confidence 777777877 89999999999999999999999999999999999999975 66788999999999999999865
No 27
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.72 E-value=2.5e-17 Score=96.35 Aligned_cols=66 Identities=29% Similarity=0.423 Sum_probs=60.4
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecC
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
+|+.+.|++|.|+|+-|.+|+|+|++.|+|||+.|.+|+|.. |.....+|.++||.+||.+|.-.+
T Consensus 12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred HHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecCC
Confidence 488999999999999999999999999999999999999964 666778999999999999997644
No 28
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.71 E-value=1.9e-18 Score=103.42 Aligned_cols=73 Identities=29% Similarity=0.498 Sum_probs=62.7
Q ss_pred CCCCCCchh-hhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----C----------ceeeeecEEEEcCCcE
Q 034890 3 RSGQPPDLK-KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----G----------NEKNDIGMVVIRGNSV 67 (80)
Q Consensus 3 ~~~~p~~L~-~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~----------~~~~~~g~v~IrG~~I 67 (80)
+...|++|- =.++.+|.|+++++|+++|+|.|||+|.|++|.|++|.. + ..+|.+..+|+||++|
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence 345789854 559999999999999999999999999999999998864 1 2357899999999999
Q ss_pred EEEEecCC
Q 034890 68 VTVEALEP 75 (80)
Q Consensus 68 ~~I~~~d~ 75 (80)
.+|++|-.
T Consensus 82 ilvspp~~ 89 (91)
T KOG3460|consen 82 ILVSPPLR 89 (91)
T ss_pred EEEcCccc
Confidence 99998754
No 29
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.68 E-value=1.8e-18 Score=106.22 Aligned_cols=70 Identities=40% Similarity=0.717 Sum_probs=63.4
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec---------CceeeeecEEEEcCCcEEEEEecCC
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN---------GNEKNDIGMVVIRGNSVVTVEALEP 75 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~---------~~~~~~~g~v~IrG~~I~~I~~~d~ 75 (80)
+.++|.+|++++|+|++..||+.+|+|.|||+.||+||+|+.|+- +.+.|++|++++||..+++|++.|.
T Consensus 18 silDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG 96 (108)
T KOG1781|consen 18 SILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADG 96 (108)
T ss_pred HHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcc
Confidence 446799999999999999999999999999999999999999863 2345899999999999999999875
No 30
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.59 E-value=2.1e-15 Score=95.93 Aligned_cols=71 Identities=20% Similarity=0.337 Sum_probs=64.4
Q ss_pred CCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecCCc
Q 034890 6 QPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 6 ~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
.|+. |....++++.|+|+||..|.|.|+.+|.+|||.|.++.++. +.+...++.++|||++|.|+.++|++
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i 75 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI 75 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH
Confidence 4777 67778999999999999999999999999999999999874 56777899999999999999999864
No 31
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.58 E-value=2.6e-15 Score=91.16 Aligned_cols=70 Identities=36% Similarity=0.656 Sum_probs=63.3
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----CceeeeecEEEEcCCcEEEEEecCCccC
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----GNEKNDIGMVVIRGNSVVTVEALEPVSK 78 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----~~~~~~~g~v~IrG~~I~~I~~~d~~~~ 78 (80)
.|..|++++|.|.+.|||.+.|.|.|||+..|++|+++.|+. +.....+|..+|||+||..|...|+.+.
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d 78 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD 78 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence 489999999999999999999999999999999999999874 4455679999999999999999987543
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.57 E-value=4.2e-16 Score=103.58 Aligned_cols=73 Identities=26% Similarity=0.620 Sum_probs=64.7
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-----------CceeeeecEEEEcCCcEEEEEecC
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-----------GNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-----------~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
.+..|.++++.+++|.++|||.|.|+|.+||+|||++|.+|+|.. ++++|-+|++++||++|++.+..+
T Consensus 5 ~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 5 KSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred chhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 456789999999999999999999999999999999999999864 346788999999999999999877
Q ss_pred CccC
Q 034890 75 PVSK 78 (80)
Q Consensus 75 ~~~~ 78 (80)
.-..
T Consensus 85 ppp~ 88 (177)
T KOG3168|consen 85 PPPP 88 (177)
T ss_pred CCCC
Confidence 5443
No 33
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.51 E-value=4.5e-14 Score=85.44 Aligned_cols=67 Identities=24% Similarity=0.381 Sum_probs=58.4
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCcee---eeecEEEEcCCcEEEEEecCCc
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEK---NDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~---~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
+..++|++|.|+|+|+-.+.|+|.++|+|+|+.|.|....+.++. .....+||||+.|.||..+...
T Consensus 7 Fkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~ 76 (96)
T KOG3448|consen 7 FKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA 76 (96)
T ss_pred HHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH
Confidence 577899999999999999999999999999999999987764332 3567899999999999987653
No 34
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.47 E-value=2.8e-14 Score=84.25 Aligned_cols=70 Identities=26% Similarity=0.572 Sum_probs=60.5
Q ss_pred CCCCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec----CceeeeecEEEEcCCcEEEEEe
Q 034890 3 RSGQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN----GNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 3 ~~~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~----~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
..-.|++ ..+++|.+|.|.+++.+++.|+|.+||.|.|++|+|+.|+. +....+++.+++.|++|....+
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP 78 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP 78 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence 3446778 57899999999999999999999999999999999999974 3344579999999999987755
No 35
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.42 E-value=2.1e-14 Score=91.22 Aligned_cols=69 Identities=39% Similarity=0.676 Sum_probs=61.0
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--Cce--eeeecEEEEcCCcEEEEEecCCccC
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNE--KNDIGMVVIRGNSVVTVEALEPVSK 78 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~--~~~~g~v~IrG~~I~~I~~~d~~~~ 78 (80)
|.+++++++.|-|+|||.+.|.|.+||+|.|++|.+|.|+. ++. ....|..+|||+||+.+...|..+.
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE 86 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE 86 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence 88999999999999999999999999999999999999874 432 2456899999999999999887654
No 36
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.42 E-value=1.5e-13 Score=81.97 Aligned_cols=69 Identities=28% Similarity=0.639 Sum_probs=55.7
Q ss_pred CCCc-hhhhcC--CEEEEEEcC--CeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEecC
Q 034890 6 QPPD-LKKYMD--KKLQIKLNA--NRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 6 ~p~~-L~~~~~--k~V~V~l~~--g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
.|.+ +-+|+. .+|.|+|.+ |-.++|+++|||+|||+||++|+|.. ....+.+|.++++|+||..|...+
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeecC
Confidence 4555 456664 478888866 88999999999999999999999975 223348999999999999998754
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.34 E-value=8.7e-12 Score=77.90 Aligned_cols=74 Identities=15% Similarity=0.229 Sum_probs=65.7
Q ss_pred CCCCc-hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec-CceeeeecEEEEcCCcEEEEEecCCccC
Q 034890 5 GQPPD-LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN-GNEKNDIGMVVIRGNSVVTVEALEPVSK 78 (80)
Q Consensus 5 ~~p~~-L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~-~~~~~~~g~v~IrG~~I~~I~~~d~~~~ 78 (80)
+-|.+ |.+..|.-|++++..|..|+|+|.-.|.+||+.|+|..-+. ++....+..+||||+.|.++-.||-+|.
T Consensus 4 gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKn 79 (119)
T KOG3172|consen 4 GVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKN 79 (119)
T ss_pred ccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhc
Confidence 45777 78999999999999999999999999999999999998764 4566678999999999999999997653
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.33 E-value=1.2e-11 Score=77.16 Aligned_cols=68 Identities=22% Similarity=0.324 Sum_probs=61.7
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCCc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
.|+++.+.++.|+|++|...+|++.+.|.+||..|.++.-...+++.++..++|||++|.|+..||..
T Consensus 6 ~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~~pv~l~~lsirgnniRy~~lpD~l 73 (109)
T KOG3428|consen 6 FLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKGEPVRLDTLSIRGNNIRYYILPDSL 73 (109)
T ss_pred HHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCCCceeEEEEEeecceEEEEEccCCc
Confidence 47889999999999999999999999999999999999877544566788999999999999999974
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.78 E-value=9.9e-10 Score=68.80 Aligned_cols=69 Identities=25% Similarity=0.408 Sum_probs=56.6
Q ss_pred CCCCc-hhhhc--CCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecC--------c------eeeeecEEEEcCCcE
Q 034890 5 GQPPD-LKKYM--DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG--------N------EKNDIGMVVIRGNSV 67 (80)
Q Consensus 5 ~~p~~-L~~~~--~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~--------~------~~~~~g~v~IrG~~I 67 (80)
..|+. +.+.. ..+|.|.++|++.+-|+..|||.|.|++|+|+.|.|. . ..|.+|.+||||++|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 35666 44443 5689999999999999999999999999999999772 1 257899999999999
Q ss_pred EEEEec
Q 034890 68 VTVEAL 73 (80)
Q Consensus 68 ~~I~~~ 73 (80)
+.+.-.
T Consensus 103 I~v~r~ 108 (114)
T KOG3459|consen 103 ILVLRN 108 (114)
T ss_pred EEEEec
Confidence 988743
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=98.66 E-value=2.3e-08 Score=57.62 Aligned_cols=37 Identities=19% Similarity=0.389 Sum_probs=31.1
Q ss_pred CCEEEEEEcC----CeEEEEEEEEECCCCceEEcceEEecC
Q 034890 15 DKKLQIKLNA----NRMIVGTLRGFDQFMNLVIDNTVEVNG 51 (80)
Q Consensus 15 ~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~~~~e~~~ 51 (80)
+.+|+|.++. +-.++|.|.|||+|+||+|.|++|.+.
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 3678888865 457899999999999999999999763
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.24 E-value=4.9e-06 Score=48.72 Aligned_cols=59 Identities=12% Similarity=0.252 Sum_probs=39.0
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECC---CCceEEcceEEecCc--------eeeeecEEEEcCCcEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQ---FMNLVIDNTVEVNGN--------EKNDIGMVVIRGNSVV 68 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~---~~NlvL~~~~e~~~~--------~~~~~g~v~IrG~~I~ 68 (80)
+..++|++|.|+++||..|+|.|.+++. .+.++|+-+...... .......++|+++.|+
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 4678999999999999999999999998 899999998876421 1123456777776664
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.88 E-value=9.2e-05 Score=45.62 Aligned_cols=66 Identities=17% Similarity=0.337 Sum_probs=53.8
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc----------eeeeecEEEEcCCcEEEEEecCCc
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN----------EKNDIGMVVIRGNSVVTVEALEPV 76 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~----------~~~~~g~v~IrG~~I~~I~~~d~~ 76 (80)
.+|+|++|.+..+.+-.|+|+|..+| +...+.|+|+..+..+ ...-+..+..||+.|.-+...+..
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~ 80 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPP 80 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCC
Confidence 46899999999999999999999999 5899999999875311 112468999999999999876653
No 43
>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=97.39 E-value=0.00044 Score=46.42 Aligned_cols=64 Identities=28% Similarity=0.416 Sum_probs=47.3
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEecCC
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALEP 75 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d~ 75 (80)
.|+.+..|++|.|.|.+.| +++.|.|..+| -..|+||-+-.|. + . ...-+|-|-+|..|...++
T Consensus 8 ~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~-~--~--~sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 8 SPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED-G--K--RSVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp -HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT-S-----EEEEEE-GGGEEEEEEEE-
T ss_pred CHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC-C--c--eeEEEEEccceEEEEEccC
Confidence 5788999999999999999 99999999999 6789999876552 2 1 2368899999999987664
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=96.97 E-value=0.0075 Score=35.61 Aligned_cols=59 Identities=14% Similarity=0.266 Sum_probs=46.0
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc-----------eeeeecEEEEcCCcEEE
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN-----------EKNDIGMVVIRGNSVVT 69 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~-----------~~~~~g~v~IrG~~I~~ 69 (80)
.+++|+++.+..+.+-.|+|+|..+| +..-+.|.|+..+..+ ...-+..+..||+.|.-
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 6677889998765311 11235678888888753
No 45
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.82 E-value=0.0049 Score=33.01 Aligned_cols=34 Identities=15% Similarity=0.276 Sum_probs=29.6
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
.+|++|++.+ ++..++|+..++|++..|+++...
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence 3789999999 667779999999999999997653
No 46
>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=96.79 E-value=0.012 Score=35.28 Aligned_cols=60 Identities=17% Similarity=0.234 Sum_probs=45.3
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCceeeeecEEEEcCCcEEEEEec
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEAL 73 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~ 73 (80)
|..+.|++|.+.|.++....|++.++| ...|+..+|-.--.| ..+...+|.+.|++++..
T Consensus 19 l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlG----v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 19 LLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLG----VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTT----EEEEEEEEGGGEEEEEE-
T ss_pred HHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcc----cChhheeecCCEEEEEec
Confidence 556679999999999999999999999 667777766543223 257899999999998764
No 47
>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=96.60 E-value=0.015 Score=33.11 Aligned_cols=36 Identities=11% Similarity=0.162 Sum_probs=30.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e 48 (80)
.+|..|++++..|..++|.+.+||...+++.-.+.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999888887665544
No 48
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.53 E-value=0.0062 Score=36.37 Aligned_cols=31 Identities=23% Similarity=0.384 Sum_probs=27.4
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
..+|.|.|.||-.+.|.+.+||+|.=++-.+
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 5689999999999999999999998666555
No 49
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.37 E-value=0.0084 Score=34.17 Aligned_cols=32 Identities=22% Similarity=0.336 Sum_probs=27.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
-..+|.|.|.||-.++|.+.+||+|.=++-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 35689999999999999999999998665444
No 50
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=96.29 E-value=0.0095 Score=33.96 Aligned_cols=31 Identities=19% Similarity=0.321 Sum_probs=26.9
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
..+|.|.|.||-.+.|.+.+||+|.=++-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 5689999999999999999999998666544
No 51
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=96.24 E-value=0.033 Score=32.19 Aligned_cols=50 Identities=16% Similarity=0.233 Sum_probs=38.9
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVE 71 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~ 71 (80)
|++++|++|.|.+..|.. +|+|.+.-.. .++|+.. -...|||=.+|++|.
T Consensus 16 lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~----------~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 16 LQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN----------GTPFFIRIAQIVWVM 65 (66)
T ss_pred HHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC----------CcEEEEEeeeEEEEc
Confidence 889999999999987766 9999998744 3455432 137899999999885
No 52
>PRK14638 hypothetical protein; Provisional
Probab=96.04 E-value=0.01 Score=39.02 Aligned_cols=35 Identities=17% Similarity=0.357 Sum_probs=30.0
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus 94 ~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 94 DYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 477889999999999999999999999964 45554
No 53
>PRK14639 hypothetical protein; Provisional
Probab=95.63 E-value=0.019 Score=37.33 Aligned_cols=35 Identities=17% Similarity=0.340 Sum_probs=30.2
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus 82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 477889999999999999999999999984 55553
No 54
>PRK02001 hypothetical protein; Validated
Probab=95.57 E-value=0.02 Score=37.80 Aligned_cols=35 Identities=20% Similarity=0.451 Sum_probs=30.2
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++.+++.++|+|.++|.. ++.|.
T Consensus 84 ~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 84 QYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 477889999999999999999999999975 55553
No 55
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.18 E-value=0.038 Score=32.77 Aligned_cols=25 Identities=24% Similarity=0.389 Sum_probs=23.5
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCC
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFM 39 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~ 39 (80)
..+|.|-|.||-.+.|.+.+||+|.
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 6689999999999999999999986
No 56
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=94.57 E-value=0.064 Score=31.65 Aligned_cols=35 Identities=26% Similarity=0.472 Sum_probs=28.3
Q ss_pred chhhhcCCEEEEEEc---CC-eEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLN---AN-RMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~~NlvL~ 44 (80)
++..++|+.|.|+++ +| +.++|.|.++|.. ++.|.
T Consensus 19 ~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 19 DFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 477889999999997 55 6899999999985 45553
No 57
>PRK14640 hypothetical protein; Provisional
Probab=94.46 E-value=0.093 Score=34.48 Aligned_cols=35 Identities=17% Similarity=0.413 Sum_probs=28.9
Q ss_pred chhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++ .+++.++|+|.++|.. ++.|.
T Consensus 91 ~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 91 QFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 47788999999999 5679999999999874 55554
No 58
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.36 E-value=0.11 Score=34.87 Aligned_cols=32 Identities=19% Similarity=0.259 Sum_probs=27.1
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 46 (80)
..+|.|.|.+|-.++|++.+||+|.=+.-.+.
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 45899999999999999999999976665453
No 59
>PRK14644 hypothetical protein; Provisional
Probab=94.13 E-value=0.16 Score=32.94 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=29.6
Q ss_pred chhhhcCCEEEEEEcCC----eEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNAN----RMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g----~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++++. +.++|+|.++|.. ++.|.
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 37788999999999886 9999999999974 56664
No 60
>PRK14633 hypothetical protein; Provisional
Probab=93.84 E-value=0.11 Score=34.12 Aligned_cols=35 Identities=9% Similarity=0.209 Sum_probs=28.6
Q ss_pred chhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++ .+++.++|+|.++|+. ++.|.
T Consensus 88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 47788999999999 4679999999999874 55553
No 61
>PRK14642 hypothetical protein; Provisional
Probab=93.68 E-value=0.11 Score=35.77 Aligned_cols=34 Identities=21% Similarity=0.370 Sum_probs=28.7
Q ss_pred chhhhcCCEEEEEEc-------------CCeEEEEEEEEECCCCceEE
Q 034890 9 DLKKYMDKKLQIKLN-------------ANRMIVGTLRGFDQFMNLVI 43 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~-------------~g~~~~G~L~~~D~~~NlvL 43 (80)
++.+++|+.|.|+|+ +.+.|+|+|.++|.. ++.|
T Consensus 94 df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 94 DFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 467889999999998 679999999999974 5555
No 62
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=93.51 E-value=0.14 Score=33.45 Aligned_cols=35 Identities=17% Similarity=0.500 Sum_probs=28.3
Q ss_pred CchhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEE
Q 034890 8 PDLKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVI 43 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL 43 (80)
.++.+++|+.|.|++ .+++.++|+|.++|... +.|
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~-i~l 129 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGET-VTL 129 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCE-EEE
Confidence 347888999999997 56799999999999742 444
No 63
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.42 E-value=0.35 Score=36.16 Aligned_cols=65 Identities=14% Similarity=0.212 Sum_probs=52.1
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcceEEecCc-----------eeeeecEEEEcCCcEEEEEecCC
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDNTVEVNGN-----------EKNDIGMVVIRGNSVVTVEALEP 75 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~~~e~~~~-----------~~~~~g~v~IrG~~I~~I~~~d~ 75 (80)
..|||+.|.+.-+....|+|+|.-+| +..-|-|.++.-+..+ ...-+.-++.||+.|.-+...+.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 46899999999999999999999999 8899999998543210 01146789999999997776554
No 64
>PRK14645 hypothetical protein; Provisional
Probab=93.40 E-value=0.12 Score=34.13 Aligned_cols=34 Identities=9% Similarity=0.288 Sum_probs=27.8
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++ +++.++|+|.++|.. .+.|.
T Consensus 96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEEE
Confidence 46788999999986 789999999999874 45553
No 65
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=93.27 E-value=0.12 Score=33.15 Aligned_cols=34 Identities=21% Similarity=0.558 Sum_probs=25.6
Q ss_pred chhhhcCCEEEEEEc----CCeEEEEEEEEECCCCceEE
Q 034890 9 DLKKYMDKKLQIKLN----ANRMIVGTLRGFDQFMNLVI 43 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~----~g~~~~G~L~~~D~~~NlvL 43 (80)
++..++|+.|.|+++ +.+.++|+|.++|. -.++|
T Consensus 81 ~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 81 DFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 477889999999994 45799999999998 45555
No 66
>PRK14636 hypothetical protein; Provisional
Probab=92.99 E-value=0.16 Score=34.30 Aligned_cols=35 Identities=23% Similarity=0.455 Sum_probs=28.3
Q ss_pred chhhhcCCEEEEEEc---CC-eEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLN---AN-RMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~---~g-~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|+++ +| +.++|+|.++|.. ++.|.
T Consensus 92 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 92 DFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 477889999999997 55 7999999999874 45553
No 67
>PRK14632 hypothetical protein; Provisional
Probab=92.90 E-value=0.17 Score=33.93 Aligned_cols=35 Identities=17% Similarity=0.402 Sum_probs=28.7
Q ss_pred chhhhcCCEEEEEEcC-------CeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNA-------NRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~-------g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++.+ .+.++|+|.++|.. ++.|.
T Consensus 92 ~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 92 QMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 4778899999999975 58999999999863 55554
No 68
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.86 E-value=0.27 Score=32.60 Aligned_cols=34 Identities=15% Similarity=0.459 Sum_probs=29.3
Q ss_pred hhhhcCCEEEEEE----cCCeEEEEEEEEECCCCceEEc
Q 034890 10 LKKYMDKKLQIKL----NANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 10 L~~~~~k~V~V~l----~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
+..++|+.|.|+| .+++.++|+|.++|+.. +++.
T Consensus 94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 6778999999999 78999999999999887 4443
No 69
>PRK14634 hypothetical protein; Provisional
Probab=92.70 E-value=0.2 Score=33.08 Aligned_cols=35 Identities=14% Similarity=0.256 Sum_probs=28.0
Q ss_pred chhhhcCCEEEEEEcC----CeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|+.|.|++.+ .+.|+|+|.++|.. ++.|.
T Consensus 94 ~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 94 DFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred HHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 4778899999999964 38999999999974 45553
No 70
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=92.62 E-value=0.23 Score=33.36 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=27.1
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
..+|.|.|.||-.++|.+.+||+|.=+.-.+
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 5689999999999999999999998666555
No 71
>PRK14643 hypothetical protein; Provisional
Probab=92.27 E-value=0.29 Score=32.63 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=26.1
Q ss_pred chhhhcCCEEEEEEcC----CeEEEEEEEEECCC
Q 034890 9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQF 38 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~ 38 (80)
++..++|+.|.|++.. .+.++|+|.++|..
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 4778899999999965 69999999999965
No 72
>PRK14647 hypothetical protein; Provisional
Probab=92.18 E-value=0.25 Score=32.66 Aligned_cols=34 Identities=18% Similarity=0.436 Sum_probs=27.3
Q ss_pred chhhhcCCEEEEEEc---------CCeEEEEEEEEECCCCceEE
Q 034890 9 DLKKYMDKKLQIKLN---------ANRMIVGTLRGFDQFMNLVI 43 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~---------~g~~~~G~L~~~D~~~NlvL 43 (80)
++.+++|+.|.|+++ +.+.++|+|.++|.. .+.|
T Consensus 93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~-~v~l 135 (159)
T PRK14647 93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG-VVTI 135 (159)
T ss_pred HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC-EEEE
Confidence 477889999999995 359999999999863 4444
No 73
>PRK14646 hypothetical protein; Provisional
Probab=91.90 E-value=0.28 Score=32.38 Aligned_cols=35 Identities=23% Similarity=0.346 Sum_probs=28.1
Q ss_pred chhhhcCCEEEEEEcC----CeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D~~~NlvL~ 44 (80)
++..++|+.|.|+|.+ -+.++|+|.++|.. ++.|.
T Consensus 94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 4778899999999954 37889999999985 55553
No 74
>PRK14631 hypothetical protein; Provisional
Probab=91.43 E-value=0.32 Score=32.75 Aligned_cols=34 Identities=18% Similarity=0.408 Sum_probs=27.6
Q ss_pred chhhhcCCEEEEEEc----CCeEEEEEEEEEC--CCCceEE
Q 034890 9 DLKKYMDKKLQIKLN----ANRMIVGTLRGFD--QFMNLVI 43 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~----~g~~~~G~L~~~D--~~~NlvL 43 (80)
++.+++|+.|.|++. +.+.++|+|.++| . .++.|
T Consensus 111 df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 111 QLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 477889999999995 4699999999998 4 35554
No 75
>PRK14637 hypothetical protein; Provisional
Probab=91.24 E-value=0.33 Score=31.98 Aligned_cols=35 Identities=17% Similarity=0.363 Sum_probs=27.1
Q ss_pred chhhhcCCEEEEEEcCCeEE-EEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMI-VGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~-~G~L~~~D~~~NlvL~ 44 (80)
++..++|+.|.|++.+...+ +|+|.++|.. ++.|.
T Consensus 92 ~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 92 EFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 47788999999999544555 7999999875 55554
No 76
>PRK06955 biotin--protein ligase; Provisional
Probab=90.67 E-value=2.2 Score=30.63 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=28.8
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
++|++|+|...+++.++|++.++|....|+++.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 478999997667788999999999999999963
No 77
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=90.64 E-value=1.8 Score=31.01 Aligned_cols=47 Identities=19% Similarity=0.512 Sum_probs=33.8
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCc-eeeeecEEEEcC
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGN-EKNDIGMVVIRG 64 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~-~~~~~g~v~IrG 64 (80)
++|++|.+... +..++|++.++|....|+++. .+. +.-..|.+.+|.
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~----~g~~~~~~~gev~~~~ 317 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLED----DGVEKPFNGGEISLRS 317 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEe----CCcEEEEEEeEEEEec
Confidence 47999999874 467999999999999999962 122 222346666554
No 78
>PRK14641 hypothetical protein; Provisional
Probab=90.13 E-value=0.44 Score=32.13 Aligned_cols=28 Identities=11% Similarity=0.305 Sum_probs=24.0
Q ss_pred chhhhcCCEEEEEEcC----CeEEEEEEEEEC
Q 034890 9 DLKKYMDKKLQIKLNA----NRMIVGTLRGFD 36 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~----g~~~~G~L~~~D 36 (80)
++.+++|+.|.|++.+ .+.++|+|.++|
T Consensus 98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 3678899999999965 568999999995
No 79
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=89.33 E-value=0.67 Score=30.95 Aligned_cols=34 Identities=12% Similarity=0.137 Sum_probs=30.9
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
-+-+|+|.+.||..+.|.+.+|+.--|.+|.-+.
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 4668999999999999999999999999998664
No 80
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=88.01 E-value=0.6 Score=24.65 Aligned_cols=21 Identities=19% Similarity=0.455 Sum_probs=14.5
Q ss_pred EEEEEEEECCCCceEEcceEE
Q 034890 28 IVGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 28 ~~G~L~~~D~~~NlvL~~~~e 48 (80)
.+|++.++|+.+.+.|++...
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 689999999999999998654
No 81
>PRK14635 hypothetical protein; Provisional
Probab=87.49 E-value=1.3 Score=29.33 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=27.9
Q ss_pred CchhhhcCCEEEEEEc--CCeEEEE---EEEEECCCCceEEc
Q 034890 8 PDLKKYMDKKLQIKLN--ANRMIVG---TLRGFDQFMNLVID 44 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~--~g~~~~G---~L~~~D~~~NlvL~ 44 (80)
.++..+.|+.|.|++. ++..+.| +|.++|.. ++.|.
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 3478889999999885 4678888 99999874 55553
No 82
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=87.07 E-value=4.2 Score=32.13 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=28.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
++|++|.+...+++.++|+..++|....|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 479999987677778999999999999999964
No 83
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=87.03 E-value=0.76 Score=30.71 Aligned_cols=32 Identities=22% Similarity=0.401 Sum_probs=25.4
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEC-CCCceEEcc
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFD-QFMNLVIDN 45 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D-~~~NlvL~~ 45 (80)
.|+.|+|.+.|||+++|.-.|.| ...-+.+.|
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnacqVgl~~~~ 151 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNACQVGLILPN 151 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceEEEEEEcCC
Confidence 48899999999999999999988 334444443
No 84
>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=86.90 E-value=4.6 Score=27.78 Aligned_cols=31 Identities=19% Similarity=0.360 Sum_probs=27.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++|++|.+...+ ..++|++.++|....|+++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 469999998754 5699999999999999997
No 85
>PRK08330 biotin--protein ligase; Provisional
Probab=86.00 E-value=4.3 Score=27.93 Aligned_cols=33 Identities=18% Similarity=0.358 Sum_probs=27.2
Q ss_pred hcCCEEEEEEcCCeEE-EEEEEEECCCCceEEcce
Q 034890 13 YMDKKLQIKLNANRMI-VGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~-~G~L~~~D~~~NlvL~~~ 46 (80)
++|++|.+.. ++..+ +|++.++|....|+++..
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 5799999976 55554 799999999999999753
No 86
>PRK14630 hypothetical protein; Provisional
Probab=83.90 E-value=1.7 Score=28.30 Aligned_cols=34 Identities=15% Similarity=0.299 Sum_probs=26.2
Q ss_pred chhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 9 DLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
++.+++|++|.|++.. ...+|+|.++|. -++.|.
T Consensus 91 df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l~ 124 (143)
T PRK14630 91 EFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIFK 124 (143)
T ss_pred HHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEEE
Confidence 4678899999999965 445999999987 345553
No 87
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=81.96 E-value=4.2 Score=29.08 Aligned_cols=31 Identities=35% Similarity=0.439 Sum_probs=27.3
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
+|+.|.|.. ++..+.|++.++|....|+++.
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 689999875 5688999999999999999974
No 88
>PRK10139 serine endoprotease; Provisional
Probab=81.65 E-value=8.7 Score=29.25 Aligned_cols=59 Identities=20% Similarity=0.169 Sum_probs=39.4
Q ss_pred CEEEEEEcCCeEEEEEEEEECCCCceEEcceEEecCceeeeec--EEEEcCCcEEEEEecC
Q 034890 16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIG--MVVIRGNSVVTVEALE 74 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g--~v~IrG~~I~~I~~~d 74 (80)
..+.|++.||+.+.+++.++|....|-+-.......-..-.++ .-+-.|+.|..|..|-
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~~~l~~~~lg~s~~~~~G~~V~aiG~P~ 175 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNPF 175 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCCCCCceeEecCccccCCCCEEEEEecCC
Confidence 5799999999999999999999999988776431111111222 1233466666666553
No 89
>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=79.70 E-value=3.3 Score=25.59 Aligned_cols=19 Identities=21% Similarity=0.625 Sum_probs=15.2
Q ss_pred CCEEEEEEcCCeEEEEEEE
Q 034890 15 DKKLQIKLNANRMIVGTLR 33 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~ 33 (80)
..+|.++|+||+.+.|++.
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 3589999999999999974
No 90
>PRK10898 serine endoprotease; Provisional
Probab=78.92 E-value=5.9 Score=29.08 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=28.9
Q ss_pred CEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
..+.|.+.||+.+.+++.++|...+|-+-...
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 57999999999999999999999999877764
No 91
>PRK10942 serine endoprotease; Provisional
Probab=78.39 E-value=14 Score=28.30 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=28.4
Q ss_pred CEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
..+.|.+.||+.+.+++.++|...++-|-...
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki~ 167 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQ 167 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999999877654
No 92
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=77.51 E-value=11 Score=24.78 Aligned_cols=27 Identities=11% Similarity=0.304 Sum_probs=24.2
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEEC
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
...++||.|.+...+|..++|++.++.
T Consensus 87 a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 87 YSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 357899999999999999999999986
No 93
>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=77.48 E-value=6.3 Score=28.82 Aligned_cols=33 Identities=18% Similarity=0.286 Sum_probs=29.3
Q ss_pred CEEEEEEcCCeEEEEEEEEECCCCceEEcceEE
Q 034890 16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e 48 (80)
..+.|.+.||+.+.+++.++|...++-|-.+..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~~ 134 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIEG 134 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEecC
Confidence 468999999999999999999999998877653
No 94
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=76.74 E-value=7.6 Score=27.24 Aligned_cols=35 Identities=17% Similarity=0.363 Sum_probs=31.8
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034890 12 KYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 12 ~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 46 (80)
..+|++|+++..++....|+..++|....++++..
T Consensus 187 ~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 187 LSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred ccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 34799999999999999999999999999999875
No 95
>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=70.90 E-value=28 Score=25.96 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=28.8
Q ss_pred CEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 16 KKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
..+.|.+.||+.+.+++.++|...++-|-...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999999887765
No 96
>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=68.28 E-value=13 Score=23.45 Aligned_cols=29 Identities=10% Similarity=0.235 Sum_probs=22.2
Q ss_pred EEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034890 17 KLQIKLNANRMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 17 ~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 46 (80)
...|.++||+.++|.+..=| ...+.|.++
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~-~~~~~l~~~ 87 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET-ADGVTVKMP 87 (133)
T ss_pred cEEEEECCCCEEEEEEEecC-CCeEEEEcC
Confidence 48999999999999998844 445555554
No 97
>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=65.65 E-value=5.5 Score=23.63 Aligned_cols=50 Identities=24% Similarity=0.355 Sum_probs=24.7
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCc------eEEcceEEecCceeeeecEEEEcCCcEEEEEecC
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMN------LVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~N------lvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
.-+.+|.++|+||..++|+ +.|=..| |+|+. + -+...||=+.|..+++..
T Consensus 15 ~~~~~v~L~l~dG~~~~g~--A~dt~~~~~k~E~L~l~~-----~-----~~~~~i~Ld~I~~~~al~ 70 (80)
T PF07073_consen 15 MYRYPVKLTLKDGEQIEGK--ALDTRTNAKKEECLVLEQ-----D-----GGEQEIRLDQIASMSALT 70 (80)
T ss_dssp TTTT-EEEE-TTT--EEES--S-EEE---SSS-EEEEEE-----T-----TEEEEESTT--SEEE---
T ss_pred hcCCeEEEEEeCCCEEEEE--EEEEEEecCceEEEEEec-----C-----CcEEEEEhhheeeeeecC
Confidence 3577999999999999997 3332222 22221 1 235678888888887543
No 98
>PRK08477 biotin--protein ligase; Provisional
Probab=63.06 E-value=33 Score=23.60 Aligned_cols=34 Identities=6% Similarity=0.011 Sum_probs=28.7
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
.+++.|+|. .+++.++|+..++|+..-|++..-.
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 478999987 4689999999999999999887543
No 99
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=61.82 E-value=4.8 Score=26.45 Aligned_cols=27 Identities=30% Similarity=0.389 Sum_probs=20.6
Q ss_pred cCCeEEEEEEEEECCCCceEEcceEEe
Q 034890 23 NANRMIVGTLRGFDQFMNLVIDNTVEV 49 (80)
Q Consensus 23 ~~g~~~~G~L~~~D~~~NlvL~~~~e~ 49 (80)
+....=.|+|+|.|+|.|=-.+|-.-.
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~~f 66 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENNDYF 66 (151)
T ss_pred hcccccceeeeeecccccchhccccee
Confidence 344455799999999999888876543
No 100
>PRK06789 flagellar motor switch protein; Validated
Probab=56.71 E-value=26 Score=20.48 Aligned_cols=40 Identities=13% Similarity=0.114 Sum_probs=32.0
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcc
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
+...|.+..+.+|.|.+++-..-+|.+...|..+-+-+.+
T Consensus 32 svi~Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 32 TLYRLENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred CEEEeCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 3445788889999999988888899999999877666654
No 101
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=55.58 E-value=28 Score=22.81 Aligned_cols=26 Identities=12% Similarity=0.244 Sum_probs=22.6
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEEC
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
..++||.|.....+|..++|++.++.
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEE
Confidence 36899999988899999999999765
No 102
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.37 E-value=19 Score=24.67 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=34.1
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEE
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e 48 (80)
....-.+|..|.|...++....|.+.+||-.-+...-++..
T Consensus 4 ~s~~vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~~ 44 (184)
T KOG4401|consen 4 ASATVAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTPS 44 (184)
T ss_pred CcceeEEEEEEEecccccceeeeEEEEEEcccCeeEecccc
Confidence 33445578899999999999999999999888887777763
No 103
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=53.79 E-value=8.7 Score=23.61 Aligned_cols=17 Identities=47% Similarity=0.626 Sum_probs=15.8
Q ss_pred EEEEEECCCCceEEcce
Q 034890 30 GTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 30 G~L~~~D~~~NlvL~~~ 46 (80)
|+|+|.|.+.|.-.++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999999887
No 104
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=52.89 E-value=33 Score=22.01 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=28.9
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEc
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
+...|.+..+.+|.|.+++-..-+|.++.+|..+=+.++
T Consensus 96 svi~Ld~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIt 134 (136)
T COG1886 96 SVIELDKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRIT 134 (136)
T ss_pred CEEEcCCcCCCceEEEECCEEEEEEeEEEECCeEEEEEE
Confidence 334567777888888887777778888888887766554
No 105
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=51.69 E-value=22 Score=21.67 Aligned_cols=22 Identities=18% Similarity=0.613 Sum_probs=18.7
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
.+|..|+|. +..|+.+.|+..+
T Consensus 94 ~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 94 AVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 478899999 7889999998875
No 106
>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=50.74 E-value=39 Score=18.77 Aligned_cols=25 Identities=8% Similarity=0.293 Sum_probs=18.3
Q ss_pred cCCEEEEEEcCCeE-EEEEEEEECCC
Q 034890 14 MDKKLQIKLNANRM-IVGTLRGFDQF 38 (80)
Q Consensus 14 ~~k~V~V~l~~g~~-~~G~L~~~D~~ 38 (80)
.|+.|.++--++.. |.|++.+||.-
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred CCCEEEEECCCCCcEEEEEEEEeccc
Confidence 68899999877655 59999999964
No 107
>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=49.90 E-value=47 Score=18.85 Aligned_cols=55 Identities=13% Similarity=0.201 Sum_probs=37.5
Q ss_pred hhhcCCEEEEEEcCC-eEEEEEEEEECCCC-ceEEcceEEecCceeeeecEEEEcCCcE
Q 034890 11 KKYMDKKLQIKLNAN-RMIVGTLRGFDQFM-NLVIDNTVEVNGNEKNDIGMVVIRGNSV 67 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g-~~~~G~L~~~D~~~-NlvL~~~~e~~~~~~~~~g~v~IrG~~I 67 (80)
++|+|+-|.|...+. -.|.|.+..+|+.. -++|+++.. ++-+...+.+..|...|
T Consensus 2 ~dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~--ngik~~~~EVt~~~~DI 58 (62)
T cd01737 2 QDWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFH--NGVKCLVPEVTFRAGDI 58 (62)
T ss_pred CcccceEEEEecCCceEEEEEEEEEeCccceEEEEeeccc--CCccccCceEEEEEcch
Confidence 468999999999876 78999999999653 577776543 22222345565555444
No 108
>PRK11625 Rho-binding antiterminator; Provisional
Probab=49.35 E-value=25 Score=21.01 Aligned_cols=51 Identities=12% Similarity=0.090 Sum_probs=30.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEec--CceeeeecEEEEcCCcEEEEEec
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVN--GNEKNDIGMVVIRGNSVVTVEAL 73 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~--~~~~~~~g~v~IrG~~I~~I~~~ 73 (80)
-+.++.++++||..++|+-. |=+.+ +-.|+- .. .-+.-.||=++|..++-+
T Consensus 22 ~~~~l~l~l~dGe~~~g~A~--D~~~~----~k~EyL~l~~---~g~~~~iRLD~I~s~~~~ 74 (84)
T PRK11625 22 HHLMLTLELKDGEVLQAKAS--DLVSR----KNVEYLVVEA---AGETRELRLDKIASFSHP 74 (84)
T ss_pred cCCeEEEEECCCCEEEEEEE--eeecC----CceEEEEEEc---CCCEEEEEeeeEeeccCc
Confidence 57899999999999999864 32222 222321 00 012456677777777643
No 109
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=48.33 E-value=38 Score=23.08 Aligned_cols=29 Identities=21% Similarity=0.509 Sum_probs=23.8
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEEC
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
..+..++|++|.|.+...+.++|.+..++
T Consensus 21 ~~~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 21 LDLKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp S-CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred CChhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 34577999999999998899999998884
No 110
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=44.66 E-value=35 Score=24.19 Aligned_cols=18 Identities=33% Similarity=0.432 Sum_probs=17.0
Q ss_pred EEEEEEEEECCCCceEEc
Q 034890 27 MIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 27 ~~~G~L~~~D~~~NlvL~ 44 (80)
.+.|.+..+|.|.|+++.
T Consensus 169 ~i~g~Vi~iD~FGNlitn 186 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITN 186 (258)
T ss_dssp EEEEEEEEEETTSEEEEE
T ss_pred eEEEEEEEECccCCeeeC
Confidence 899999999999999985
No 111
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=44.37 E-value=41 Score=20.81 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=26.6
Q ss_pred CCCCchhhhcCCEEEEEEcC-CeEEEEEEEEECCCCc
Q 034890 5 GQPPDLKKYMDKKLQIKLNA-NRMIVGTLRGFDQFMN 40 (80)
Q Consensus 5 ~~p~~L~~~~~k~V~V~l~~-g~~~~G~L~~~D~~~N 40 (80)
++|.+-+.++|+.|.-.-+. |+.+.|++.-.-...-
T Consensus 36 ~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsG 72 (100)
T COG2451 36 DSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSG 72 (100)
T ss_pred CCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcc
Confidence 34556778899987777766 9999999976654443
No 112
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=44.35 E-value=30 Score=23.96 Aligned_cols=22 Identities=9% Similarity=0.546 Sum_probs=19.5
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
.+|..|+|. +..|+++.|+..+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 478999999 9999999999876
No 113
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=43.86 E-value=7.6 Score=26.78 Aligned_cols=33 Identities=18% Similarity=0.349 Sum_probs=0.0
Q ss_pred CCchhhh--cCCEEEEEEcCCeEEEEEEEEECCCCc
Q 034890 7 PPDLKKY--MDKKLQIKLNANRMIVGTLRGFDQFMN 40 (80)
Q Consensus 7 p~~L~~~--~~k~V~V~l~~g~~~~G~L~~~D~~~N 40 (80)
|..|-++ +++...+++-++..|.|+ .+||+|++
T Consensus 89 PyWLYKLhGL~~ey~CEICGN~~Y~Gr-kaFekHF~ 123 (196)
T PF11931_consen 89 PYWLYKLHGLGVEYKCEICGNQSYKGR-KAFEKHFQ 123 (196)
T ss_dssp ------------------------------------
T ss_pred cHHHHHHhCCCCeeeeEeCCCcceecH-HHHHHhcC
Confidence 4457776 678899999999999998 78999986
No 114
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=43.84 E-value=25 Score=20.04 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=18.7
Q ss_pred CCEEEEEEcCCeEEEEEEEEEC
Q 034890 15 DKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D 36 (80)
..+|.|.+-||..+.+++..-|
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCC
Confidence 3589999999999999998744
No 115
>PRK06630 hypothetical protein; Provisional
Probab=43.34 E-value=14 Score=22.96 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=17.3
Q ss_pred EEEEEEEECCCCceEEcceE
Q 034890 28 IVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 28 ~~G~L~~~D~~~NlvL~~~~ 47 (80)
..|+|+|-|++.|---++..
T Consensus 11 r~G~lVG~D~~GNkYYE~~~ 30 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESRN 30 (99)
T ss_pred ccCeEeEEeCCCChhcccCC
Confidence 37999999999999998753
No 116
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=43.29 E-value=50 Score=22.78 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=22.6
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEEC
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
..++||.|.+.-.+|..++|++.+..
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 46799999988889999999998765
No 117
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=42.88 E-value=22 Score=20.46 Aligned_cols=23 Identities=17% Similarity=0.359 Sum_probs=19.1
Q ss_pred cCCEEEEEEcCCeEEEEEEEEEC
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
-..+|.|++-||..+.+++.+-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 45689999999999999988643
No 118
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=40.91 E-value=81 Score=18.98 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=26.6
Q ss_pred CCceEEcceEEe---cCceeeeecEEEEcCCcEEEEEecC
Q 034890 38 FMNLVIDNTVEV---NGNEKNDIGMVVIRGNSVVTVEALE 74 (80)
Q Consensus 38 ~~NlvL~~~~e~---~~~~~~~~g~v~IrG~~I~~I~~~d 74 (80)
..-+.+...... ..+..|+-|.+...|..+..|..|+
T Consensus 57 ~g~~~~~r~y~FEFS~~G~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 57 RGRLRWRRVYQFEFSSDGEDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred CCCeEEEEEEEEEEeCCChhcceEEEEEECCeeeEEEcCC
Confidence 344445555432 2566788999999999999999875
No 119
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=40.87 E-value=69 Score=23.02 Aligned_cols=33 Identities=18% Similarity=0.291 Sum_probs=27.5
Q ss_pred CCEEEEEEcCCeEEEEEEEEECCCCceEEcceE
Q 034890 15 DKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 15 ~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~ 47 (80)
..++.|.+.||+.+.+.+.++|...-+-+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 467889999999999999999987777665554
No 120
>PF07024 ImpE: ImpE protein; InterPro: IPR009211 This entry contains proteins of unknown function that occur in bacteria that interact with and manipulate eukaryotic cells []. Salmonella enterica protein SciE is encoded in the centisome 7 genomic island (SCI) []. Deletion of the entire island affects the ability of bacteria to enter eukaryotic cells []. Therefore, SciE and other SCI proteins may be involved in virulence. Interestingly, another member of this family, Rhizobium leguminosarum protein ImpE, has been reported to be encoded by an avirulence locus involved in temperature-dependent protein secretion []. It is believed that the imp locus is involved in the secretion to the environment of proteins, including periplasmic RbsB protein, that cause blocking of R. leguminosarum infection in plants [].; PDB: 1ZBP_A.
Probab=39.38 E-value=51 Score=21.06 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=22.9
Q ss_pred CCCchhhhcCCEEEEEEcCCeEEEEEEEE
Q 034890 6 QPPDLKKYMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 6 ~p~~L~~~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
.|..|.+++=+++.|.++||.+..|.+=+
T Consensus 42 ~p~~l~DlvWrpa~i~l~dG~~~~~~iP~ 70 (123)
T PF07024_consen 42 PPASLRDLVWRPAEITLRDGGEGEGFIPA 70 (123)
T ss_dssp ---SSGGGTEEEEEEEETTTEEEEEEEE-
T ss_pred CCCCHHHhcccceEEEEeCCCeEEEEEec
Confidence 45568899999999999999999998854
No 121
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=39.07 E-value=35 Score=19.20 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=17.7
Q ss_pred CEEEEEEcCCeEEEEEEEEEC
Q 034890 16 KKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D 36 (80)
.+|.|.+-||..+++++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 478999999999999987644
No 122
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=38.79 E-value=27 Score=20.27 Aligned_cols=19 Identities=32% Similarity=0.537 Sum_probs=15.1
Q ss_pred hhhhcCCEEEEEEcCCeEE
Q 034890 10 LKKYMDKKLQIKLNANRMI 28 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~ 28 (80)
+.+.+||+|+|+......+
T Consensus 6 ~nDrLGKKVRvKCn~dDti 24 (73)
T KOG3493|consen 6 LNDRLGKKVRVKCNTDDTI 24 (73)
T ss_pred hhhhcCceEEEEeCCcccc
Confidence 6788999999998765443
No 123
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=38.59 E-value=34 Score=20.12 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=20.1
Q ss_pred chhhhcCCEEEEEEcCCe----EEEEEEEEE
Q 034890 9 DLKKYMDKKLQIKLNANR----MIVGTLRGF 35 (80)
Q Consensus 9 ~L~~~~~k~V~V~l~~g~----~~~G~L~~~ 35 (80)
.|.+++|++|.++...|| +-+|.|...
T Consensus 11 ~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 11 ELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 378899999999999986 457988764
No 124
>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=37.62 E-value=62 Score=16.69 Aligned_cols=25 Identities=8% Similarity=0.074 Sum_probs=20.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCC
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQF 38 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~ 38 (80)
.|..+.+...+|.-|+|++..++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777777899999999999964
No 125
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=37.47 E-value=43 Score=18.85 Aligned_cols=21 Identities=14% Similarity=0.249 Sum_probs=17.8
Q ss_pred CEEEEEEcCCeEEEEEEEEEC
Q 034890 16 KKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D 36 (80)
.+|.|.+-||..+..++..-|
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~ 27 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSD 27 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTS
T ss_pred EEEEEECCCCCEEEEEECCcc
Confidence 479999999999999988644
No 126
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=37.19 E-value=74 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=24.3
Q ss_pred CchhhhcCCEEEEEEc--CC--eEEEEEEEEEC
Q 034890 8 PDLKKYMDKKLQIKLN--AN--RMIVGTLRGFD 36 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~--~g--~~~~G~L~~~D 36 (80)
+.+.+++|+++.|.+. +| +.+.|.+..+.
T Consensus 40 l~~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 40 IDLEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred CCHHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 5689999999999995 33 77999999886
No 127
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=36.10 E-value=33 Score=22.99 Aligned_cols=19 Identities=32% Similarity=0.267 Sum_probs=17.0
Q ss_pred EEEEEEECCCCceEEcceE
Q 034890 29 VGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 29 ~G~L~~~D~~~NlvL~~~~ 47 (80)
.|+|+|-|++.|---++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999998874
No 128
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=35.99 E-value=23 Score=22.46 Aligned_cols=20 Identities=35% Similarity=0.400 Sum_probs=17.3
Q ss_pred EEEEEEECCCCceEEcceEE
Q 034890 29 VGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 29 ~G~L~~~D~~~NlvL~~~~e 48 (80)
.|+|+|.|.+.|---++..+
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred cceEeEEcCCCCeeeEcCCC
Confidence 69999999999999987643
No 129
>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=34.65 E-value=58 Score=20.40 Aligned_cols=22 Identities=14% Similarity=0.329 Sum_probs=19.3
Q ss_pred hhhhcCCEEEEEEcCCeEEEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGT 31 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~ 31 (80)
|...-+-.|..++.+|+.|.+.
T Consensus 69 i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 69 INDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred HhCCcccEEEEEecCCcEEEec
Confidence 6777889999999999999875
No 130
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.59 E-value=55 Score=22.66 Aligned_cols=22 Identities=9% Similarity=0.353 Sum_probs=18.8
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
..|..|+|+ +..|++++|+..+
T Consensus 184 ~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 184 GENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 368899999 7999999999865
No 131
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.85 E-value=45 Score=19.88 Aligned_cols=24 Identities=21% Similarity=0.385 Sum_probs=19.1
Q ss_pred hhhhcCCEEEEEEcCCeEEE----EEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIV----GTLR 33 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~----G~L~ 33 (80)
+...+|++|.++..+||.=+ |.|.
T Consensus 14 i~ah~G~~v~lk~ngGRKk~~~r~G~L~ 41 (80)
T COG4466 14 IDAHLGERVTLKANGGRKKTIERSGILI 41 (80)
T ss_pred HHhccCcEEEEEecCCceeeehhceEEe
Confidence 67789999999999997643 6554
No 132
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=33.83 E-value=60 Score=21.34 Aligned_cols=22 Identities=9% Similarity=0.350 Sum_probs=18.3
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
..|..|+|. +..|+.++|+..+
T Consensus 129 ~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 129 AAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 468889999 7889999998765
No 133
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=32.87 E-value=83 Score=21.28 Aligned_cols=33 Identities=24% Similarity=0.301 Sum_probs=26.4
Q ss_pred hhcCCEEEEEEcCCeEE----EEEEEEECCCCceEEc
Q 034890 12 KYMDKKLQIKLNANRMI----VGTLRGFDQFMNLVID 44 (80)
Q Consensus 12 ~~~~k~V~V~l~~g~~~----~G~L~~~D~~~NlvL~ 44 (80)
+|.+-.+.+...||+.- .|++..-|+..|++|+
T Consensus 141 eyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d 177 (179)
T PF07202_consen 141 EYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMD 177 (179)
T ss_pred EcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEec
Confidence 45677788888888543 5999999999999986
No 134
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=32.63 E-value=70 Score=22.23 Aligned_cols=23 Identities=9% Similarity=0.096 Sum_probs=20.2
Q ss_pred cCCeEEEEEEEEECCCCceEEcc
Q 034890 23 NANRMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 23 ~~g~~~~G~L~~~D~~~NlvL~~ 45 (80)
.++..++|++.++|+...|+++.
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 46678899999999999999975
No 135
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=32.14 E-value=1.1e+02 Score=20.51 Aligned_cols=27 Identities=11% Similarity=0.098 Sum_probs=22.6
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCc
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMN 40 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~N 40 (80)
.|.++.|.+.+|..+.|++..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 477899999889999999998886543
No 136
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=30.52 E-value=30 Score=18.44 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=11.4
Q ss_pred CchhhhcCCEEEEE
Q 034890 8 PDLKKYMDKKLQIK 21 (80)
Q Consensus 8 ~~L~~~~~k~V~V~ 21 (80)
..+++++||+|+|.
T Consensus 12 ~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 12 SYLKSLLGKRVSVT 25 (48)
T ss_pred HHHHHhcCCeEEEE
Confidence 34778999999986
No 137
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=30.37 E-value=35 Score=21.34 Aligned_cols=34 Identities=9% Similarity=0.165 Sum_probs=29.6
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEE
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVE 48 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e 48 (80)
.|.+|++.|+| -+++.++.|-|.+.-+.-.||.-
T Consensus 63 ~G~rV~lrLkd-lELs~~FLG~~~d~TllEAd~~L 96 (104)
T PF10246_consen 63 RGSRVRLRLKD-LELSAHFLGASKDTTLLEADATL 96 (104)
T ss_pred cCCEEEEEECC-HhhhhhhccCCCCcEEEEeeeEE
Confidence 58899999997 88999999999999888888764
No 138
>cd06920 NEAT NEAr Transport domain, a component of cell surface proteins. NEAr Transporter (NEAT) domain; used by pathogenic bacteria to to scavenge heme-iron from host hemoproteins. The NEAT domain is a component of cell surface proteins (iron regulated surface determinants, or Isd, such as IsdA and IsdC) in various gram-positive bacteria, and may be arranged in tandem repeats.
Probab=30.17 E-value=76 Score=19.07 Aligned_cols=41 Identities=17% Similarity=0.393 Sum_probs=30.7
Q ss_pred CCCCCchhhhcCCEEEEEEcCC-eEEEEEEEEECCCCceEEc
Q 034890 4 SGQPPDLKKYMDKKLQIKLNAN-RMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 4 ~~~p~~L~~~~~k~V~V~l~~g-~~~~G~L~~~D~~~NlvL~ 44 (80)
..++.-...+++++..++.+|| ..++=+|...|-.-|+.+.
T Consensus 15 ~~~~Sma~~y~~~~a~l~vknGk~~~~lt~~~~~~~k~~~i~ 56 (117)
T cd06920 15 TDEPSMANGYLNKPAKLTVKNGKKYVTLTLKNSDWMKNFKVE 56 (117)
T ss_pred CCCcchhHhhhcCceEEEEECCEEEEEEEEccceeeEEEEEE
Confidence 3456668899999999999997 4556666666666677666
No 139
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.06 E-value=90 Score=21.51 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=19.2
Q ss_pred hcCCEEEEEEcCCeEEEEEEEE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
.+|..|+|+-..|+++.|+..+
T Consensus 194 ~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 194 NLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCEEEEEeCCCCEEEEEEec
Confidence 4788999999889999999876
No 140
>PRK10708 hypothetical protein; Provisional
Probab=29.85 E-value=72 Score=17.98 Aligned_cols=26 Identities=12% Similarity=0.346 Sum_probs=21.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCC
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFM 39 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~ 39 (80)
++-+|.|++..|..-.|++.++..+.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 45689999999999999999988654
No 141
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=29.80 E-value=72 Score=21.72 Aligned_cols=47 Identities=9% Similarity=0.141 Sum_probs=28.6
Q ss_pred EEEEEE-cCCeEEEEEEEEECCCCceEEcceEEecCceeeeecEEEEcCCcEEEEEe
Q 034890 17 KLQIKL-NANRMIVGTLRGFDQFMNLVIDNTVEVNGNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 17 ~V~V~l-~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
++.|.+ .++..|+|.+.++|+-. +.+.... ....+-|.=+.|++|+.
T Consensus 135 ~i~C~i~t~~~~Y~G~I~~~~~~~-v~i~~~~--------~~~~~~i~~~~I~sI~~ 182 (185)
T PF14153_consen 135 PIKCEIETKDKSYRGIILSYDEGE-VSIMPFN--------QGEEIEIPIDDITSIKM 182 (185)
T ss_pred CCceEEEeCCceEEEEEEeccCCE-EEEeccC--------CCcceEeehhheeeeee
Confidence 344444 56899999999999752 2222210 12455666677777665
No 142
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.54 E-value=82 Score=20.29 Aligned_cols=22 Identities=9% Similarity=0.336 Sum_probs=17.9
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
..|..|+|+ +..|++++|+..+
T Consensus 110 ~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 110 GVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 368889996 7889999998875
No 143
>PRK08183 NADH dehydrogenase; Validated
Probab=28.40 E-value=33 Score=22.24 Aligned_cols=19 Identities=26% Similarity=0.247 Sum_probs=16.7
Q ss_pred EEEEEEECCCCceEEcceE
Q 034890 29 VGTLRGFDQFMNLVIDNTV 47 (80)
Q Consensus 29 ~G~L~~~D~~~NlvL~~~~ 47 (80)
.|+|+|.|.+.|---++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999999987754
No 144
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=28.35 E-value=63 Score=18.64 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=17.7
Q ss_pred CEEEEEEcCCeEEEEEEEEEC
Q 034890 16 KKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 16 k~V~V~l~~g~~~~G~L~~~D 36 (80)
.+|.|.|-||..++.++..-|
T Consensus 5 t~iqiRlpdG~r~~~rF~~~~ 25 (79)
T cd01770 5 TSIQIRLADGKRLVQKFNSSH 25 (79)
T ss_pred eEEEEECCCCCEEEEEeCCCC
Confidence 579999999999998877544
No 145
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.95 E-value=81 Score=22.50 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=19.0
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
..|..|+|. +..|++++|+..+
T Consensus 231 ~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 231 RKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 468899999 8889999999876
No 146
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=27.87 E-value=77 Score=23.73 Aligned_cols=25 Identities=12% Similarity=0.258 Sum_probs=21.4
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
-+-+.+++|+|...+|..+.|++-.
T Consensus 92 ~~~~~gq~v~i~t~~g~~i~GvIg~ 116 (355)
T COG1363 92 PQVLEGQRVTIHTDKGKKIRGVIGS 116 (355)
T ss_pred hhhccCcEEEEEeCCCcEEeeeEcc
Confidence 3456799999999999999999983
No 147
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=27.87 E-value=1.7e+02 Score=22.63 Aligned_cols=39 Identities=26% Similarity=0.203 Sum_probs=30.6
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcceEEe
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNTVEV 49 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~ 49 (80)
+.+++||.|+- -++|++.+++|.+=|.-.=+-+.+-.|.
T Consensus 77 ~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v 115 (421)
T COG5316 77 VEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEV 115 (421)
T ss_pred HhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEE
Confidence 57889999988 8999999999999887655555554443
No 148
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=27.40 E-value=92 Score=18.62 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=16.3
Q ss_pred cCCEEEEEEcCCeEEEEEE
Q 034890 14 MDKKLQIKLNANRMIVGTL 32 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L 32 (80)
-.-++..+|++|..+.|.-
T Consensus 22 ~hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 22 HHLPLTLELKDGEVLQAKA 40 (84)
T ss_pred hhceEEEEEcCCeEEEEEe
Confidence 4668999999999999964
No 149
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=26.41 E-value=1.3e+02 Score=16.74 Aligned_cols=33 Identities=18% Similarity=0.291 Sum_probs=23.0
Q ss_pred cCCEEEEEEcCC----eEEEEEEEEECCCCceEEcce
Q 034890 14 MDKKLQIKLNAN----RMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 14 ~~k~V~V~l~~g----~~~~G~L~~~D~~~NlvL~~~ 46 (80)
+|.+|.+++.++ ..|.-++.+++..-.+.++=.
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 578889988443 359999999998877777654
No 150
>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=25.10 E-value=87 Score=17.64 Aligned_cols=26 Identities=12% Similarity=0.323 Sum_probs=21.6
Q ss_pred cCCEEEEEEcCCeEEEEEEEEECCCC
Q 034890 14 MDKKLQIKLNANRMIVGTLRGFDQFM 39 (80)
Q Consensus 14 ~~k~V~V~l~~g~~~~G~L~~~D~~~ 39 (80)
++-+|.|++..|..-.|++.++..+.
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 45689999999999999999988654
No 151
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=24.87 E-value=1.7e+02 Score=17.68 Aligned_cols=33 Identities=18% Similarity=0.116 Sum_probs=27.7
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLV 42 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~Nlv 42 (80)
-+-|+||+|.-.-+.|+.+.|++.---.....|
T Consensus 35 a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 35 AAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 456799999999999999999998877666666
No 152
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=24.38 E-value=1.4e+02 Score=17.10 Aligned_cols=22 Identities=9% Similarity=0.360 Sum_probs=17.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
+-+...+|+|.||.++.+.+.|
T Consensus 15 L~~~~f~V~l~ng~~vla~i~G 36 (68)
T TIGR00008 15 LPNAMFRVELENGHEVLAHISG 36 (68)
T ss_pred CCCCEEEEEECCCCEEEEEecC
Confidence 3466888999999888888776
No 153
>PF13144 SAF_2: SAF-like
Probab=24.33 E-value=1.3e+02 Score=19.69 Aligned_cols=22 Identities=14% Similarity=0.404 Sum_probs=18.4
Q ss_pred hcCCEEEEEEcC-CeEEEEEEEE
Q 034890 13 YMDKKLQIKLNA-NRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~l~~-g~~~~G~L~~ 34 (80)
.+|..|+|.-.+ |+.+.|++.+
T Consensus 168 ~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 168 ALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 478899999855 8999999876
No 154
>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=24.32 E-value=1.4e+02 Score=16.54 Aligned_cols=37 Identities=19% Similarity=0.345 Sum_probs=28.6
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 46 (80)
|....+..+.+...+-..++|.+..++++.=+.+.+.
T Consensus 37 l~~~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~ 73 (77)
T PF01052_consen 37 LDKPADEPVELRVNGQPIFRGELGRVNGRLAVRITEL 73 (77)
T ss_dssp ECCESSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE
T ss_pred eCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 4444668899998877899999999998777666654
No 155
>PF04528 Adeno_E4_34: Adenovirus early E4 34 kDa protein conserved region; InterPro: IPR007615 Adenoviruses E4 is essential for DNA replication and late protein synthesis []. The adenovirus, early region 4 open reading frame 3 (E4 ORF3) protein is required for viral DNA replication during the interferon (IFN)-induced antiviral state []. The E4 ORF3 protein reorganises the promyelocytic leukemia (PML) protein nuclear bodies. These normally punctate structures are reorganised by E4 ORF3 into tracks that eventually surround viral replication centres. PML rearrangement is an evolutionarily conserved function of E4 ORF3 []. The product of adenovirus early region 4 (E4), open reading frame 6, is E4 34k. It modulates viral late gene expression, DNA replication, apoptosis, double strand break repair, and transformation through multiple interactions with components in infected and transformed cells [, ]. Conservation of several cysteine and histidine residues among E4 34k sequences suggests the presence of a zinc binding domain, which is important for its function []. This entry is a conserved region found in the Adenovirus E4 34 kDa protein.
Probab=23.23 E-value=1.4e+02 Score=19.73 Aligned_cols=22 Identities=23% Similarity=0.376 Sum_probs=18.6
Q ss_pred CceeeeecEEEEcCCcEEEEEe
Q 034890 51 GNEKNDIGMVVIRGNSVVTVEA 72 (80)
Q Consensus 51 ~~~~~~~g~v~IrG~~I~~I~~ 72 (80)
.++..+.|.+++||-+-.|+..
T Consensus 30 p~ei~YVGSV~~rg~HlIY~ri 51 (148)
T PF04528_consen 30 PKEIMYVGSVFVRGRHLIYFRI 51 (148)
T ss_pred CCeeEEEEEEEECCeEEEEEEe
Confidence 3456789999999999999975
No 156
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=23.21 E-value=98 Score=17.49 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=19.3
Q ss_pred EEEEEEEEEC-CCCceEEcceEEe
Q 034890 27 MIVGTLRGFD-QFMNLVIDNTVEV 49 (80)
Q Consensus 27 ~~~G~L~~~D-~~~NlvL~~~~e~ 49 (80)
..+|++.++| ..+-|.|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 4689999999 7788999997655
No 157
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=22.89 E-value=1.6e+02 Score=16.67 Aligned_cols=31 Identities=13% Similarity=0.263 Sum_probs=23.1
Q ss_pred CCEEEEEEcC-C--eEEEEEEEEECCCCceEEcc
Q 034890 15 DKKLQIKLNA-N--RMIVGTLRGFDQFMNLVIDN 45 (80)
Q Consensus 15 ~k~V~V~l~~-g--~~~~G~L~~~D~~~NlvL~~ 45 (80)
+..|+|+.-+ | ..++|++..+|...+.+.-.
T Consensus 42 ~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~ 75 (92)
T PF08863_consen 42 NQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLK 75 (92)
T ss_pred CCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEE
Confidence 6678888744 4 67789999999777665543
No 158
>PRK08158 type III secretion system protein SpaO; Validated
Probab=22.78 E-value=1.5e+02 Score=21.80 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=28.4
Q ss_pred CchhhhcCCEEEEEEcCCeEEEEEEEEECCCCceEEcce
Q 034890 8 PDLKKYMDKKLQIKLNANRMIVGTLRGFDQFMNLVIDNT 46 (80)
Q Consensus 8 ~~L~~~~~k~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~ 46 (80)
..|.+..+.+|.|...+-..-+|.|+.+|+.+-+-+.+-
T Consensus 257 l~L~~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i 295 (303)
T PRK08158 257 LSLPTNAELNVEIRANGALLGNGELVQMDDTLGVEIHEW 295 (303)
T ss_pred EECCCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 446667788888888777777888888887766666543
No 159
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.66 E-value=1.6e+02 Score=17.84 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=18.3
Q ss_pred hcCCEEEEEEcCCeEEEEEEEE
Q 034890 13 YMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
+-+-..+|+|.||.++.+.+.|
T Consensus 17 Lp~~~frV~LenG~~vla~isG 38 (87)
T PRK12442 17 LPDSRFRVTLENGVEVGAYASG 38 (87)
T ss_pred CCCCEEEEEeCCCCEEEEEecc
Confidence 3467899999999999888877
No 160
>smart00725 NEAT NEAr Transporter domain.
Probab=22.20 E-value=1.1e+02 Score=19.09 Aligned_cols=32 Identities=13% Similarity=0.250 Sum_probs=22.5
Q ss_pred CCCCchhhhcCCEEEEEEcCCeEE-EEEEEEEC
Q 034890 5 GQPPDLKKYMDKKLQIKLNANRMI-VGTLRGFD 36 (80)
Q Consensus 5 ~~p~~L~~~~~k~V~V~l~~g~~~-~G~L~~~D 36 (80)
.++.-...+++++..+..+||..+ +=+|..-|
T Consensus 17 ~~~Sma~~Y~~~pa~l~v~nGk~~v~ltl~~s~ 49 (123)
T smart00725 17 NEESMMDDYLNKPAKLIVKNGKTYVTLTLNNSS 49 (123)
T ss_pred CchhhHHHhhcCceEEEEECCEEEEEEEEcCCc
Confidence 344557889999999999998554 44455544
No 161
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=22.14 E-value=30 Score=30.34 Aligned_cols=53 Identities=19% Similarity=0.254 Sum_probs=0.0
Q ss_pred EEEEEcCCeEEEEEEEEECCCCceEEcceEEecC---ceeeeecEEEEcCCcEEEE
Q 034890 18 LQIKLNANRMIVGTLRGFDQFMNLVIDNTVEVNG---NEKNDIGMVVIRGNSVVTV 70 (80)
Q Consensus 18 V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~---~~~~~~g~v~IrG~~I~~I 70 (80)
.+=...+|+.+.|.|+..|.-++.+|.--....+ .-+-.+|.++|+|+|.|.-
T Consensus 250 ~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~~v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 250 STYTTSSGRPVDGVLVTTANVMQKLLNLLGQISDTSVSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp --------------------------------------------------------
T ss_pred ceeecCCCCEeceEEeccHHHHHHHHHHHhhhccceeecchhheeeeecCccHHHH
Confidence 3344578999999999999888877754433221 1234689999999998753
No 162
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=22.09 E-value=1.3e+02 Score=19.36 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=22.3
Q ss_pred CCchhhhcCCEEEEEEcCCeEEEEEEEEEC
Q 034890 7 PPDLKKYMDKKLQIKLNANRMIVGTLRGFD 36 (80)
Q Consensus 7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~~D 36 (80)
|-.-.+.+-+-++|.|+||++++..+=+.-
T Consensus 42 pKKPNSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 42 PKKPNSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred ccCCCchhheEEEEEeCCCCEEEEEcCCCC
Confidence 334556677889999999999987766543
No 163
>PRK09961 exoaminopeptidase; Provisional
Probab=22.05 E-value=1.2e+02 Score=22.20 Aligned_cols=23 Identities=17% Similarity=0.130 Sum_probs=19.5
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEE
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLR 33 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~ 33 (80)
..+.+++|+|..++|..+.|.+.
T Consensus 90 ~~~~~~~v~i~~~~g~~i~Gvi~ 112 (344)
T PRK09961 90 AARQLQPVRITTREECKIPGLLN 112 (344)
T ss_pred cccCCCEEEEEeCCCCEeeEEEC
Confidence 45678999999999988999994
No 164
>PF05031 NEAT: Iron Transport-associated domain ; InterPro: IPR006635 This domain identifies a small family of protein with no known function which are found exclusively in bacteria.; PDB: 2O1A_A 2E7D_B 3QUG_A 3QUH_B 2Z6F_A 3OVU_B 2H3K_A 3S48_B 3RTL_C 3RUR_A ....
Probab=22.02 E-value=1e+02 Score=18.92 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=18.9
Q ss_pred CCCCchhhhcCCEEEEEEcCCeEEE
Q 034890 5 GQPPDLKKYMDKKLQIKLNANRMIV 29 (80)
Q Consensus 5 ~~p~~L~~~~~k~V~V~l~~g~~~~ 29 (80)
.++.-...++.++..|..+||..+-
T Consensus 22 ~~~Sma~~y~~~~a~l~vk~gk~~v 46 (124)
T PF05031_consen 22 NEPSMANGYLNKPAKLVVKNGKYYV 46 (124)
T ss_dssp SSBHGGGGGB-SSEEEEEETTEEEE
T ss_pred CccchHHhhccCCEEEEEECCEEEE
Confidence 3455578999999999999997663
No 165
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=21.85 E-value=1.2e+02 Score=21.68 Aligned_cols=24 Identities=13% Similarity=0.205 Sum_probs=20.4
Q ss_pred hhhcCCEEEEEEcCCeEEEEEEEEE
Q 034890 11 KKYMDKKLQIKLNANRMIVGTLRGF 35 (80)
Q Consensus 11 ~~~~~k~V~V~l~~g~~~~G~L~~~ 35 (80)
..+.+++|+|..++| .+.|.+-.-
T Consensus 49 ~~l~gq~v~i~~~~g-~i~Gvig~~ 72 (292)
T PF05343_consen 49 RVLPGQRVRIHTRDG-DIPGVIGSK 72 (292)
T ss_dssp GGTTTEEEEEEETTE-EEEEEEEE-
T ss_pred cccCCCEEEEEcCCc-EEEEEEcCC
Confidence 456899999999999 999999665
No 166
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.48 E-value=81 Score=22.31 Aligned_cols=18 Identities=33% Similarity=0.253 Sum_probs=15.3
Q ss_pred CeEEEEEEEEECCCCceE
Q 034890 25 NRMIVGTLRGFDQFMNLV 42 (80)
Q Consensus 25 g~~~~G~L~~~D~~~Nlv 42 (80)
|.+|.|+|.++|+..=.+
T Consensus 75 Ge~y~G~l~s~~~~G~~~ 92 (225)
T PF09883_consen 75 GETYVGTLISWDEDGYGV 92 (225)
T ss_pred CceEEEEEEeecccceEE
Confidence 999999999999776444
No 167
>PF02707 MOSP_N: Major Outer Sheath Protein N-terminal region; InterPro: IPR003857 This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [].
Probab=21.22 E-value=70 Score=22.28 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=14.7
Q ss_pred eEEEEEEEEECCCCceE
Q 034890 26 RMIVGTLRGFDQFMNLV 42 (80)
Q Consensus 26 ~~~~G~L~~~D~~~Nlv 42 (80)
..++++|++|+.||+|=
T Consensus 30 ~s~eAtLh~ygaYltig 46 (204)
T PF02707_consen 30 FSIEATLHCYGAYLTIG 46 (204)
T ss_pred eeEEEEEEEEeeEEEec
Confidence 46899999999999874
No 168
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=20.41 E-value=1.4e+02 Score=19.29 Aligned_cols=28 Identities=14% Similarity=0.313 Sum_probs=21.2
Q ss_pred CCchhhhcCCEEEEEEcCCeEEEEEEEE
Q 034890 7 PPDLKKYMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
|-+=.+.+-|-++|.|.||++++..+=+
T Consensus 48 pKkPNSAlRK~~RVrL~NG~~VtAyiPg 75 (129)
T COG0048 48 PKKPNSALRKVARVRLINGKEVTAYIPG 75 (129)
T ss_pred cCCCChhhheeEEEEeeCCcEEEEEcCC
Confidence 3344567788899999999999876544
No 169
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=20.33 E-value=1.4e+02 Score=18.31 Aligned_cols=28 Identities=14% Similarity=0.316 Sum_probs=21.1
Q ss_pred CCchhhhcCCEEEEEEcCCeEEEEEEEE
Q 034890 7 PPDLKKYMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 7 p~~L~~~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
|-+-.+.+-|-++|.|.||+.++..+=+
T Consensus 27 pKkPNSA~RK~arV~L~ngk~v~ayIPg 54 (95)
T cd00319 27 PKKPNSALRKVAKVRLTSGYEVTAYIPG 54 (95)
T ss_pred ccCCChhhceEEEEEccCCCEEEEECCC
Confidence 4445667778899999999999766554
No 170
>COG1912 Uncharacterized conserved protein [Function unknown]
Probab=20.15 E-value=1.7e+02 Score=21.30 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=19.9
Q ss_pred EcCCeEEEEEEEEECCCCceEEc
Q 034890 22 LNANRMIVGTLRGFDQFMNLVID 44 (80)
Q Consensus 22 l~~g~~~~G~L~~~D~~~NlvL~ 44 (80)
-.++..+.|++.-+|.|.|++..
T Consensus 168 ~~~~~~v~g~V~~iD~FGNv~TN 190 (268)
T COG1912 168 KVEDGGVKGTVIYVDRFGNVITN 190 (268)
T ss_pred eecCCeEEEEEEEECCcCceeec
Confidence 35678899999999999999864
No 171
>PRK09864 putative peptidase; Provisional
Probab=20.14 E-value=1.5e+02 Score=22.09 Aligned_cols=25 Identities=12% Similarity=0.304 Sum_probs=20.2
Q ss_pred hhhhcCCEEEEEEcCCeEEEEEEEE
Q 034890 10 LKKYMDKKLQIKLNANRMIVGTLRG 34 (80)
Q Consensus 10 L~~~~~k~V~V~l~~g~~~~G~L~~ 34 (80)
-..+.+++|+|..++|..+.|.+-.
T Consensus 88 ~~~l~~q~V~i~t~~g~~v~GVig~ 112 (356)
T PRK09864 88 NQSMLNHRVTIRTHKGVKIPGVIGS 112 (356)
T ss_pred ccccCCCEEEEEeCCCCEEEEEEeC
Confidence 3456789999999998778899854
No 172
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.02 E-value=1.4e+02 Score=22.10 Aligned_cols=22 Identities=23% Similarity=0.457 Sum_probs=18.0
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q 034890 13 YMDKKLQIK-LNANRMIVGTLRG 34 (80)
Q Consensus 13 ~~~k~V~V~-l~~g~~~~G~L~~ 34 (80)
.+|..|+|. +..|++++|+..+
T Consensus 287 ~~Gd~IrV~N~~S~kiv~g~V~g 309 (338)
T PRK12786 287 AEGDVVRVLNLQSKRTVTGTVTG 309 (338)
T ss_pred CCCCEEEEEECCCCCEEEEEEec
Confidence 468889996 8889999998876
Done!