Query psy17024
Match_columns 132
No_of_seqs 187 out of 1119
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 19:50:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17024hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3172|consensus 100.0 1.7E-41 3.6E-46 243.3 9.9 101 1-101 1-102 (119)
2 cd01724 Sm_D1 The eukaryotic S 100.0 1.8E-28 4E-33 171.6 11.6 82 6-87 2-83 (90)
3 cd01721 Sm_D3 The eukaryotic S 100.0 3.4E-28 7.3E-33 162.7 10.1 70 6-75 1-70 (70)
4 cd01723 LSm4 The eukaryotic Sm 99.9 2.6E-26 5.6E-31 155.6 9.9 73 5-77 1-74 (76)
5 cd01733 LSm10 The eukaryotic S 99.9 6.4E-26 1.4E-30 155.0 10.6 71 4-74 8-78 (78)
6 KOG3293|consensus 99.9 4E-26 8.7E-31 167.2 8.0 75 5-79 2-77 (134)
7 cd01725 LSm2 The eukaryotic Sm 99.9 2.1E-25 4.6E-30 153.1 10.2 76 5-80 1-78 (81)
8 cd01726 LSm6 The eukaryotic Sm 99.9 1E-23 2.2E-28 139.6 9.5 67 6-72 1-67 (67)
9 cd01722 Sm_F The eukaryotic Sm 99.9 9.1E-23 2E-27 135.5 9.6 68 5-72 1-68 (68)
10 PRK00737 small nuclear ribonuc 99.9 1.5E-22 3.2E-27 135.9 10.4 71 1-72 1-71 (72)
11 KOG3428|consensus 99.9 1.5E-21 3.2E-26 140.3 10.6 82 7-89 4-85 (109)
12 cd01731 archaeal_Sm1 The archa 99.9 2.1E-21 4.6E-26 128.6 9.8 67 6-72 1-67 (68)
13 smart00651 Sm snRNP Sm protein 99.8 2.6E-20 5.7E-25 121.6 9.5 65 9-73 2-67 (67)
14 PF01423 LSM: LSM domain ; In 99.8 3E-20 6.6E-25 121.5 8.8 66 8-73 1-67 (67)
15 COG1958 LSM1 Small nuclear rib 99.8 1E-19 2.3E-24 123.6 9.8 70 3-72 5-78 (79)
16 cd01732 LSm5 The eukaryotic Sm 99.8 1.5E-19 3.3E-24 123.0 10.0 69 4-72 2-73 (76)
17 cd00600 Sm_like The eukaryotic 99.8 1.8E-19 3.8E-24 116.1 9.0 63 10-72 1-63 (63)
18 cd01719 Sm_G The eukaryotic Sm 99.8 3.5E-18 7.6E-23 115.0 9.1 69 7-75 2-70 (72)
19 cd01730 LSm3 The eukaryotic Sm 99.7 1E-17 2.2E-22 115.0 9.2 68 5-72 1-81 (82)
20 cd01720 Sm_D2 The eukaryotic S 99.7 1.3E-17 2.8E-22 116.3 9.6 68 5-72 2-84 (87)
21 KOG3448|consensus 99.7 2.1E-17 4.5E-22 115.4 7.4 80 6-85 3-84 (96)
22 KOG3482|consensus 99.7 1.6E-17 3.4E-22 112.3 6.0 67 5-72 8-75 (79)
23 cd01718 Sm_E The eukaryotic Sm 99.7 2.8E-16 6.1E-21 107.9 9.2 70 3-72 4-78 (79)
24 cd01729 LSm7 The eukaryotic Sm 99.7 3.8E-16 8.3E-21 107.2 9.5 66 10-75 7-80 (81)
25 cd01717 Sm_B The eukaryotic Sm 99.6 4.1E-15 8.9E-20 101.2 9.1 65 9-73 4-78 (79)
26 cd01728 LSm1 The eukaryotic Sm 99.6 8.6E-15 1.9E-19 99.2 9.7 68 6-73 3-73 (74)
27 KOG1783|consensus 99.6 3E-16 6.5E-21 106.0 1.3 72 3-75 4-76 (77)
28 cd01727 LSm8 The eukaryotic Sm 99.5 4.8E-14 1E-18 94.9 9.3 67 9-75 3-73 (74)
29 cd06168 LSm9 The eukaryotic Sm 99.5 6.4E-14 1.4E-18 95.2 9.4 66 8-73 3-74 (75)
30 PTZ00138 small nuclear ribonuc 99.5 5.1E-14 1.1E-18 98.7 8.7 71 3-73 12-87 (89)
31 KOG3460|consensus 99.5 4.3E-14 9.4E-19 97.8 3.5 75 2-76 2-89 (91)
32 KOG1775|consensus 99.4 2.9E-13 6.2E-18 92.4 3.7 71 2-72 4-77 (84)
33 KOG1780|consensus 99.3 3.6E-12 7.8E-17 86.4 6.3 70 1-72 1-71 (77)
34 KOG3168|consensus 98.7 2.9E-08 6.3E-13 76.6 4.7 83 1-84 1-93 (177)
35 KOG1774|consensus 98.6 4.5E-08 9.7E-13 67.7 4.3 69 4-72 11-84 (88)
36 KOG1781|consensus 98.3 1E-07 2.2E-12 68.1 -0.3 70 9-78 21-98 (108)
37 PF14438 SM-ATX: Ataxin 2 SM d 98.0 1.9E-05 4E-10 53.0 6.2 45 7-51 4-51 (77)
38 KOG1784|consensus 97.9 1.9E-05 4.2E-10 55.7 4.0 77 9-86 4-84 (96)
39 KOG1782|consensus 97.6 1.6E-05 3.4E-10 58.8 0.1 66 10-75 14-82 (129)
40 cd01739 LSm11_C The eukaryotic 97.5 7.7E-05 1.7E-09 49.7 2.8 39 14-52 7-49 (66)
41 PF12701 LSM14: Scd6-like Sm d 97.5 0.00048 1E-08 48.9 6.8 65 12-76 5-79 (96)
42 KOG3459|consensus 97.5 2.6E-05 5.6E-10 56.7 -0.2 68 5-72 24-106 (114)
43 cd01736 LSm14_N LSm14 (also kn 96.4 0.021 4.6E-07 38.9 6.7 59 12-70 3-72 (74)
44 PF11095 Gemin7: Gem-associate 96.3 0.026 5.7E-07 39.0 7.0 64 6-74 15-79 (80)
45 PF02237 BPL_C: Biotin protein 95.7 0.072 1.6E-06 32.7 6.3 31 14-45 2-32 (48)
46 cd01716 Hfq Hfq, an abundant, 95.7 0.036 7.7E-07 36.5 5.1 35 9-43 3-39 (61)
47 PF10842 DUF2642: Protein of u 95.5 0.12 2.5E-06 34.5 7.2 52 7-72 13-65 (66)
48 TIGR02383 Hfq RNA chaperone Hf 95.4 0.05 1.1E-06 35.8 5.1 36 8-43 6-43 (61)
49 KOG1073|consensus 94.6 0.078 1.7E-06 45.7 5.5 66 11-76 5-81 (361)
50 PRK00395 hfq RNA-binding prote 94.4 0.12 2.7E-06 35.6 5.1 54 8-73 10-65 (79)
51 cd01735 LSm12_N LSm12 belongs 94.2 0.3 6.6E-06 32.0 6.5 31 13-43 4-34 (61)
52 PRK14638 hypothetical protein; 90.9 0.49 1.1E-05 35.8 4.7 29 10-38 95-123 (150)
53 PF06372 Gemin6: Gemin6 protei 90.9 1.5 3.3E-05 34.0 7.5 61 9-76 11-72 (166)
54 PRK02001 hypothetical protein; 90.8 0.7 1.5E-05 35.2 5.4 29 10-38 85-113 (152)
55 COG1923 Hfq Uncharacterized ho 90.6 0.53 1.2E-05 32.3 4.2 32 8-39 10-43 (77)
56 KOG3262|consensus 89.4 1.5 3.2E-05 35.1 6.4 58 7-67 57-131 (215)
57 PRK14639 hypothetical protein; 89.3 0.79 1.7E-05 34.3 4.6 34 9-43 82-115 (140)
58 cd01734 YlxS_C YxlS is a Bacil 89.0 1.3 2.8E-05 29.9 5.1 29 10-38 20-52 (83)
59 PRK14644 hypothetical protein; 88.4 0.76 1.7E-05 34.3 4.0 41 3-44 71-117 (136)
60 PRK14091 RNA-binding protein H 87.6 1.4 3.1E-05 34.3 5.1 36 8-43 15-52 (165)
61 PRK14091 RNA-binding protein H 87.2 1.5 3.3E-05 34.0 5.1 36 8-43 95-132 (165)
62 PRK14642 hypothetical protein; 86.8 1.6 3.5E-05 34.7 5.2 36 3-38 85-136 (197)
63 PRK00092 ribosome maturation p 86.5 3.4 7.3E-05 31.0 6.6 30 9-38 92-125 (154)
64 PRK14632 hypothetical protein; 85.4 2.1 4.6E-05 33.0 5.1 33 10-43 93-132 (172)
65 PRK14647 hypothetical protein; 85.2 3.7 8.1E-05 31.1 6.3 30 9-38 93-131 (159)
66 COG0779 Uncharacterized protei 84.7 2.7 5.9E-05 32.1 5.3 30 10-39 94-127 (153)
67 PRK14636 hypothetical protein; 84.2 3.4 7.4E-05 32.1 5.8 30 9-38 92-125 (176)
68 PRK14640 hypothetical protein; 84.1 2.1 4.6E-05 32.3 4.5 30 9-38 91-124 (152)
69 PRK14633 hypothetical protein; 84.0 2.9 6.2E-05 31.5 5.2 34 9-43 88-125 (150)
70 PRK14643 hypothetical protein; 82.9 3.1 6.8E-05 31.9 5.0 30 9-38 98-131 (164)
71 PF02576 DUF150: Uncharacteris 80.5 4.6 0.0001 29.6 5.1 35 3-37 72-113 (141)
72 PRK14645 hypothetical protein; 80.5 3.1 6.7E-05 31.6 4.2 29 9-38 96-124 (154)
73 PRK14631 hypothetical protein; 79.3 8 0.00017 30.0 6.2 29 8-36 110-142 (174)
74 PRK14634 hypothetical protein; 78.9 3.7 8E-05 31.1 4.2 29 10-38 95-127 (155)
75 PRK14637 hypothetical protein; 78.0 6.1 0.00013 29.9 5.1 30 9-38 92-122 (151)
76 PRK14646 hypothetical protein; 75.3 5.5 0.00012 30.2 4.3 34 9-43 94-131 (155)
77 PRK09618 flgD flagellar basal 74.2 13 0.00028 28.2 6.0 26 11-36 88-113 (142)
78 smart00333 TUDOR Tudor domain. 74.1 13 0.00028 22.4 5.0 26 13-38 4-29 (57)
79 PF10618 Tail_tube: Phage tail 73.3 8.2 0.00018 28.1 4.6 29 3-31 62-90 (119)
80 TIGR00567 3mg DNA-3-methyladen 70.7 10 0.00023 30.0 5.0 36 6-41 10-45 (192)
81 PRK14641 hypothetical protein; 68.7 8 0.00017 30.0 3.9 28 9-36 98-129 (173)
82 PRK06955 biotin--protein ligas 68.4 25 0.00055 29.0 7.0 33 13-45 247-279 (300)
83 PF03614 Flag1_repress: Repres 68.0 8.4 0.00018 29.8 3.8 73 7-81 22-101 (165)
84 PF07073 ROF: Modulator of Rho 67.4 5.1 0.00011 27.4 2.3 20 12-31 14-33 (80)
85 PRK14635 hypothetical protein; 66.8 16 0.00035 27.8 5.2 33 10-43 94-131 (162)
86 PRK14630 hypothetical protein; 61.2 16 0.00036 27.3 4.2 28 10-38 92-119 (143)
87 PRK08330 biotin--protein ligas 61.2 43 0.00093 26.4 6.9 32 13-45 186-218 (236)
88 PRK11625 Rho-binding antitermi 60.9 21 0.00045 24.7 4.4 24 13-36 21-44 (84)
89 TIGR02603 CxxCH_TIGR02603 puta 59.6 18 0.0004 26.1 4.2 29 16-45 58-86 (133)
90 PRK11886 bifunctional biotin-- 59.4 39 0.00084 27.7 6.6 31 13-44 270-300 (319)
91 PF11607 DUF3247: Protein of u 59.4 14 0.0003 26.5 3.3 19 15-33 28-46 (101)
92 PF02245 Pur_DNA_glyco: Methyl 59.2 16 0.00035 28.6 4.1 34 6-40 9-42 (184)
93 cd00540 AAG Alkyladenine DNA g 58.8 24 0.00052 27.6 4.9 35 6-41 6-40 (179)
94 PF11684 DUF3280: Protein of u 58.5 18 0.00038 27.2 4.0 40 24-67 81-123 (140)
95 KOG3262|consensus 56.2 25 0.00054 28.2 4.6 14 34-47 62-75 (215)
96 PRK13325 bifunctional biotin-- 55.0 53 0.0011 30.0 7.1 49 13-66 276-325 (592)
97 PRK11911 flgD flagellar basal 52.9 34 0.00074 25.9 4.7 26 12-37 90-115 (140)
98 PRK06789 flagellar motor switc 51.0 28 0.0006 23.6 3.6 35 11-45 37-71 (74)
99 COG5316 Uncharacterized conser 47.3 76 0.0016 28.1 6.6 42 3-45 70-111 (421)
100 TIGR00121 birA_ligase birA, bi 46.5 88 0.0019 24.6 6.5 31 13-44 191-221 (237)
101 COG4568 Rof Transcriptional an 44.8 26 0.00056 24.3 2.7 25 14-40 22-46 (84)
102 TIGR01080 rplX_A_E ribosomal p 44.1 93 0.002 22.6 5.7 57 14-73 44-101 (114)
103 PRK10898 serine endoprotease; 42.2 1.2E+02 0.0026 25.6 6.9 60 15-76 101-162 (353)
104 COG1886 FliN Flagellar motor s 42.1 39 0.00084 25.0 3.6 34 12-45 102-135 (136)
105 PF07593 UnbV_ASPIC: ASPIC and 42.0 87 0.0019 20.1 4.9 47 13-60 2-61 (71)
106 PF13437 HlyD_3: HlyD family s 41.9 58 0.0012 21.7 4.2 34 4-37 41-78 (105)
107 PRK01191 rpl24p 50S ribosomal 40.3 1.2E+02 0.0026 22.4 5.8 57 14-73 48-105 (120)
108 PTZ00194 60S ribosomal protein 39.5 1E+02 0.0022 23.5 5.5 57 14-73 49-106 (143)
109 PF04452 Methyltrans_RNA: RNA 39.3 21 0.00045 28.0 1.8 61 8-68 13-75 (225)
110 PTZ00034 40S ribosomal protein 39.1 19 0.00042 26.8 1.5 17 70-86 80-96 (124)
111 TIGR00999 8a0102 Membrane Fusi 38.5 74 0.0016 24.6 4.8 37 4-40 130-167 (265)
112 PRK04313 30S ribosomal protein 38.3 1.3E+02 0.0029 24.6 6.4 45 30-74 190-236 (237)
113 TIGR02038 protease_degS peripl 38.2 1.5E+02 0.0032 25.0 6.9 32 16-47 102-133 (351)
114 PTZ00275 biotin-acetyl-CoA-car 38.1 81 0.0018 25.9 5.2 32 13-45 235-266 (285)
115 PRK10708 hypothetical protein; 37.9 37 0.0008 22.2 2.5 27 14-40 3-29 (62)
116 PRK06792 flgD flagellar basal 37.6 1.3E+02 0.0027 24.0 5.9 26 12-37 115-140 (190)
117 COG2094 Mpg 3-methyladenine DN 37.2 84 0.0018 25.2 4.9 41 6-49 15-55 (200)
118 PRK10139 serine endoprotease; 37.2 68 0.0015 28.1 4.9 63 15-78 114-178 (455)
119 COG0340 BirA Biotin-(acetyl-Co 36.6 1.7E+02 0.0036 23.6 6.7 34 13-46 188-221 (238)
120 PF14153 Spore_coat_CotO: Spor 36.0 48 0.001 26.1 3.4 38 1-38 117-157 (185)
121 PF14262 DUF4353: Domain of un 36.0 73 0.0016 26.3 4.6 58 13-75 4-69 (264)
122 TIGR02037 degP_htrA_DO peripla 35.1 76 0.0016 27.2 4.8 32 16-47 82-113 (428)
123 PF03614 Flag1_repress: Repres 35.1 1E+02 0.0022 23.9 4.9 35 14-54 119-153 (165)
124 PRK00802 3-methyladenine DNA g 35.1 73 0.0016 25.1 4.3 32 6-41 14-45 (188)
125 PF10781 DSRB: Dextransucrase 33.6 42 0.00092 22.0 2.3 27 14-40 3-29 (62)
126 PF01052 SpoA: Surface present 33.3 1.3E+02 0.0028 19.3 4.7 34 14-47 41-74 (77)
127 cd05694 S1_Rrp5_repeat_hs2_sc2 32.8 41 0.00088 22.0 2.2 52 21-73 1-55 (74)
128 PF02751 TFIIA_gamma_C: Transc 32.7 1.3E+02 0.0029 19.0 5.1 39 23-61 3-45 (52)
129 PF05037 DUF669: Protein of un 32.2 33 0.00072 25.1 1.8 27 7-33 95-122 (141)
130 KOG4401|consensus 32.1 61 0.0013 25.7 3.4 45 13-59 9-53 (184)
131 PRK10942 serine endoprotease; 31.7 91 0.002 27.5 4.8 32 15-46 135-166 (473)
132 COG4907 Predicted membrane pro 31.5 49 0.0011 30.1 3.0 12 121-132 584-595 (595)
133 TIGR03344 VI_effect_Hcp1 type 31.3 1E+02 0.0023 23.3 4.5 69 4-75 76-155 (166)
134 PF12945 YcgR_2: Flagellar pro 30.9 1.4E+02 0.003 19.1 4.6 31 14-44 3-37 (87)
135 PF10246 MRP-S35: Mitochondria 30.5 1.9E+02 0.0042 20.9 5.5 45 25-74 24-73 (104)
136 PF00575 S1: S1 RNA binding do 30.1 52 0.0011 20.5 2.3 53 21-73 1-60 (74)
137 PF11347 DUF3148: Protein of u 29.5 43 0.00093 22.2 1.8 21 65-85 3-26 (63)
138 PF14563 DUF4444: Domain of un 29.1 62 0.0013 19.8 2.3 20 28-47 10-29 (42)
139 PF00560 LRR_1: Leucine Rich R 29.0 34 0.00074 17.1 1.0 19 58-78 2-20 (22)
140 PRK08477 biotin--protein ligas 28.9 2.2E+02 0.0048 22.5 6.1 37 11-48 171-207 (211)
141 PRK14056 phenylalanine 4-monoo 27.5 1.4E+02 0.0031 27.6 5.3 41 12-52 389-433 (578)
142 TIGR00046 RNA methyltransferas 27.1 92 0.002 24.7 3.7 38 7-44 27-65 (240)
143 PRK11713 16S ribosomal RNA met 26.9 98 0.0021 24.4 3.8 31 7-37 25-55 (234)
144 cd01343 PL1_Passenger_AT Perta 26.3 2.2E+02 0.0049 22.8 5.8 51 17-71 74-125 (233)
145 PRK08158 type III secretion sy 26.3 96 0.0021 26.3 3.8 37 12-48 261-297 (303)
146 PLN00036 40S ribosomal protein 25.0 3.7E+02 0.008 22.4 6.9 46 30-76 193-241 (261)
147 PF05954 Phage_GPD: Phage late 24.4 78 0.0017 24.6 2.8 26 11-36 24-49 (292)
148 PF04234 CopC: CopC domain; I 24.0 1E+02 0.0022 21.0 3.0 46 33-78 24-70 (97)
149 COG1363 FrvX Cellulase M and r 23.1 98 0.0021 26.7 3.3 23 11-33 93-115 (355)
150 KOG1596|consensus 22.9 1.1E+02 0.0023 26.0 3.4 42 91-132 7-51 (317)
151 PRK10590 ATP-dependent RNA hel 22.1 85 0.0018 27.0 2.8 11 64-74 342-352 (456)
152 PLN02432 putative pectinestera 21.9 4.8E+02 0.01 21.9 7.7 35 8-43 31-65 (293)
153 PRK06009 flgD flagellar basal 21.7 2.6E+02 0.0056 21.1 5.0 26 12-40 94-119 (140)
154 COG2336 MazE Growth regulator 21.6 1.4E+02 0.0029 20.8 3.2 26 3-28 14-42 (82)
155 PF09465 LBR_tudor: Lamin-B re 21.6 1.9E+02 0.004 18.6 3.6 39 13-55 7-46 (55)
156 PRK06788 flagellar motor switc 21.2 1.7E+02 0.0036 21.5 3.8 34 13-46 66-99 (119)
157 KOG0921|consensus 20.9 1E+02 0.0022 30.6 3.3 36 1-45 1056-1092(1282)
158 PF11634 IPI_T4: Nuclease inhi 20.8 70 0.0015 21.5 1.6 26 13-39 14-39 (76)
159 PF07076 DUF1344: Protein of u 20.1 1E+02 0.0022 20.2 2.2 19 27-45 4-23 (61)
No 1
>KOG3172|consensus
Probab=100.00 E-value=1.7e-41 Score=243.28 Aligned_cols=101 Identities=62% Similarity=1.107 Sum_probs=93.9
Q ss_pred CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccc
Q psy17024 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNA 80 (132)
Q Consensus 1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~a 80 (132)
||+++|++||||++||.|++|+++|++|+|+|+++||+|||+|+|+++|.+||+++++++||||||+|+|++|||+|+||
T Consensus 1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnA 80 (119)
T KOG3172|consen 1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNA 80 (119)
T ss_pred CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCC-CCccCCchhhh
Q psy17024 81 PMFKGKQGNK-AGAAGRGKSGI 101 (132)
Q Consensus 81 p~lk~~~~~~-~~~~~~g~~~~ 101 (132)
||||..+.+. +...+||++++
T Consensus 81 PmFkk~~~~~~g~~~~RG~~~~ 102 (119)
T KOG3172|consen 81 PMFKKGKSRSLGGGPGRGRARR 102 (119)
T ss_pred cccccccCCcCCCCCCcccccc
Confidence 9999766655 55566776643
No 2
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.96 E-value=1.8e-28 Score=171.61 Aligned_cols=82 Identities=26% Similarity=0.526 Sum_probs=78.0
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCccccccccccc
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKG 85 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk~ 85 (132)
|++||++++|++|+||||||++|+|+|.+||+||||+|+||+++..++...+++++||||++|+||+|||+++..++|.+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~ 81 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVD 81 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhh
Confidence 78999999999999999999999999999999999999999999888889999999999999999999999998888876
Q ss_pred cc
Q psy17024 86 KQ 87 (132)
Q Consensus 86 ~~ 87 (132)
..
T Consensus 82 ~~ 83 (90)
T cd01724 82 ST 83 (90)
T ss_pred cC
Confidence 53
No 3
>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=99.95 E-value=3.4e-28 Score=162.72 Aligned_cols=70 Identities=70% Similarity=1.191 Sum_probs=68.6
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd 75 (132)
|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++++..+++++||||++|+||+|||
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 8999999999999999999999999999999999999999999999999899999999999999999998
No 4
>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=99.94 E-value=2.6e-26 Score=155.64 Aligned_cols=73 Identities=36% Similarity=0.679 Sum_probs=69.5
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCccc
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPDML 77 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd~l 77 (132)
+|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++..+|+ ...++++||||++|+||++||++
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 59999999999999999999999999999999999999999999988886 46789999999999999999986
No 5
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.93 E-value=6.4e-26 Score=154.97 Aligned_cols=71 Identities=30% Similarity=0.514 Sum_probs=68.3
Q ss_pred ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecC
Q psy17024 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILP 74 (132)
Q Consensus 4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lP 74 (132)
..+++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.+++...+++++||||++|+||+||
T Consensus 8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 46789999999999999999999999999999999999999999998888888999999999999999998
No 6
>KOG3293|consensus
Probab=99.93 E-value=4e-26 Score=167.22 Aligned_cols=75 Identities=35% Similarity=0.656 Sum_probs=71.7
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCccccc
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPDMLKN 79 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd~l~~ 79 (132)
+||.||+.+.++++.||||||++|.|.|+.||.+||++|++|++|.+||. ++.+++|||||++|+|+.|||.+-+
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHH
Confidence 79999999999999999999999999999999999999999999999985 8899999999999999999998743
No 7
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.93 E-value=2.1e-25 Score=153.10 Aligned_cols=76 Identities=24% Similarity=0.388 Sum_probs=69.3
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecCcccccc
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILPDMLKNA 80 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lPd~l~~a 80 (132)
+|+.||++++|++|+||||||++|+|+|.+||+||||+|+||+++.+++. ...++++||||++|+||++||++-+.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~ 78 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT 78 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence 58999999999999999999999999999999999999999999976653 56789999999999999999987443
No 8
>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=139.59 Aligned_cols=67 Identities=19% Similarity=0.351 Sum_probs=63.4
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
|++||+++++++|+||||||++|+|+|.+||+|||++|+||+++..+++...++++||||++|+||.
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 8999999999999999999999999999999999999999999876666889999999999999984
No 9
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.89 E-value=9.1e-23 Score=135.52 Aligned_cols=68 Identities=18% Similarity=0.339 Sum_probs=63.1
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
.|+++|++++|++|+||||||++|+|+|.++|+|||++|+||+++...++...++++||||++|+||.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 49999999999999999999999999999999999999999998864446789999999999999984
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.89 E-value=1.5e-22 Score=135.92 Aligned_cols=71 Identities=21% Similarity=0.377 Sum_probs=66.1
Q ss_pred CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
|+ ..|+++|+++++++|+|+||||++|+|+|.+||+|||++|+||+++..+.....++.+||||++|.||.
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 66 689999999999999999999999999999999999999999999865555779999999999999985
No 11
>KOG3428|consensus
Probab=99.87 E-value=1.5e-21 Score=140.25 Aligned_cols=82 Identities=24% Similarity=0.450 Sum_probs=76.9
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcccccccccccc
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGK 86 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk~~ 86 (132)
+.||+++.+++|+||||||++++|+|.++|.+||.+|.+|.++.+. ++.+++.++|||++|||+++||.+...+++.+.
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Llvd~ 82 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLLVDD 82 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceeeeeh
Confidence 7899999999999999999999999999999999999999999764 789999999999999999999999999988876
Q ss_pred cCC
Q psy17024 87 QGN 89 (132)
Q Consensus 87 ~~~ 89 (132)
.+.
T Consensus 83 ~~~ 85 (109)
T KOG3428|consen 83 APR 85 (109)
T ss_pred hhh
Confidence 654
No 12
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.86 E-value=2.1e-21 Score=128.59 Aligned_cols=67 Identities=21% Similarity=0.407 Sum_probs=64.0
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
|+++|+++++++|+|+|+||++|+|+|.+||+|||++|+||+++..++....++.+||||++|.||.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 8999999999999999999999999999999999999999999987777889999999999999985
No 13
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.84 E-value=2.6e-20 Score=121.61 Aligned_cols=65 Identities=32% Similarity=0.556 Sum_probs=61.8
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC-CceeecceEEEecCeEEEEec
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-GKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-g~~~~l~~vfIRGs~Ir~I~l 73 (132)
+|+++++++|+|+|+||++|.|+|.++|+|||++|+||+++..+ .+..+++.+||||++|+||++
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 79999999999999999999999999999999999999999877 678999999999999999974
No 14
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.83 E-value=3e-20 Score=121.47 Aligned_cols=66 Identities=35% Similarity=0.652 Sum_probs=62.7
Q ss_pred HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEecCeEEEEec
Q psy17024 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l 73 (132)
.+|++++|++|+|+|+||.+|+|+|.+||+|||++|+||+++..+. +...++.+||||++|+||++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4799999999999999999999999999999999999999998777 78999999999999999975
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.82 E-value=1e-19 Score=123.62 Aligned_cols=70 Identities=26% Similarity=0.434 Sum_probs=62.2
Q ss_pred cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec-CCce---eecceEEEecCeEEEEe
Q psy17024 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR-DGKV---KPMANIYIRGSKIRFLI 72 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~-dg~~---~~l~~vfIRGs~Ir~I~ 72 (132)
...|+++|+++++++|.|+||||++|+|+|.+||+|||++|+||+++.. ++.. ...+.+||||++|.||.
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence 4568999999999999999999999999999999999999999999874 4433 34459999999999986
No 16
>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=99.82 E-value=1.5e-19 Score=122.98 Aligned_cols=69 Identities=25% Similarity=0.393 Sum_probs=63.6
Q ss_pred ccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---cCCceeecceEEEecCeEEEEe
Q psy17024 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---RDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 4 ~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
.+|+++|+++++++|.|+|++|++|.|+|.+||.|||++|+||+++. .+++..+++.+||||++|.+|+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 47999999999999999999999999999999999999999998875 3334678999999999999987
No 17
>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=99.81 E-value=1.8e-19 Score=116.08 Aligned_cols=63 Identities=29% Similarity=0.555 Sum_probs=60.1
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
|++++|++|+|+|+||++|.|+|.++|+|||++|+||+++..+.+..+++.+||||++|+||+
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 578999999999999999999999999999999999999988888999999999999999984
No 18
>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=99.76 E-value=3.5e-18 Score=115.00 Aligned_cols=69 Identities=17% Similarity=0.176 Sum_probs=62.8
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd 75 (132)
-..|+++++++|.|+|++|.+|.|+|.+||+|||++|+||+++..+.....++.++|||++|.+|..-|
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 457899999999999999999999999999999999999999875556789999999999999998644
No 19
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.75 E-value=1e-17 Score=114.97 Aligned_cols=68 Identities=16% Similarity=0.349 Sum_probs=61.1
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC-------------CceeecceEEEecCeEEEE
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-------------GKVKPMANIYIRGSKIRFL 71 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d-------------g~~~~l~~vfIRGs~Ir~I 71 (132)
.|+++|+.+.+++|+|+|++|.+|.|+|.+||.|||++|+||+++... .....++.+||||++|.+|
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 399999999999999999999999999999999999999999997532 1245889999999999997
Q ss_pred e
Q psy17024 72 I 72 (132)
Q Consensus 72 ~ 72 (132)
.
T Consensus 81 ~ 81 (82)
T cd01730 81 S 81 (82)
T ss_pred C
Confidence 5
No 20
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.74 E-value=1.3e-17 Score=116.27 Aligned_cols=68 Identities=16% Similarity=0.355 Sum_probs=60.4
Q ss_pred cHHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC-------------ceeecceEEEecCeEE
Q psy17024 5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-------------KVKPMANIYIRGSKIR 69 (132)
Q Consensus 5 ~Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg-------------~~~~l~~vfIRGs~Ir 69 (132)
-|+++|+++. +++|.|+|+++..|.|+|.+||.|||++|+||+++.... +...++.|||||++|.
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 4999999996 899999999999999999999999999999999975331 1346899999999999
Q ss_pred EEe
Q psy17024 70 FLI 72 (132)
Q Consensus 70 ~I~ 72 (132)
||.
T Consensus 82 ~Is 84 (87)
T cd01720 82 LVL 84 (87)
T ss_pred EEe
Confidence 976
No 21
>KOG3448|consensus
Probab=99.72 E-value=2.1e-17 Score=115.37 Aligned_cols=80 Identities=23% Similarity=0.365 Sum_probs=71.2
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecCccccccccc
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILPDMLKNAPMF 83 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lPd~l~~ap~l 83 (132)
-.+|++.++|+.|+|||||+-.+.|+|.++|+|+|+.|.|+++++++.- -..+..+|||||.||||.+|..-.+...+
T Consensus 3 FysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtqll 82 (96)
T KOG3448|consen 3 FYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQLL 82 (96)
T ss_pred hHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHHH
Confidence 4689999999999999999999999999999999999999999987653 46788999999999999999877666665
Q ss_pred cc
Q psy17024 84 KG 85 (132)
Q Consensus 84 k~ 85 (132)
.+
T Consensus 83 ~d 84 (96)
T KOG3448|consen 83 QD 84 (96)
T ss_pred HH
Confidence 53
No 22
>KOG3482|consensus
Probab=99.71 E-value=1.6e-17 Score=112.25 Aligned_cols=67 Identities=22% Similarity=0.409 Sum_probs=61.9
Q ss_pred cHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEe
Q psy17024 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 5 ~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~ 72 (132)
.|-.||+.+.|++|.|+||.|.+|+|+|+++|.|||++|.++++.. ||. .-++.+++||.+||.||.
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i-dG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI-DGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh-cccccccceeEEEEeccEEEEe
Confidence 5789999999999999999999999999999999999999998864 554 679999999999999994
No 23
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.68 E-value=2.8e-16 Score=107.89 Aligned_cols=70 Identities=17% Similarity=0.265 Sum_probs=62.4
Q ss_pred cccHHHHHHhhCCC--EEEEEEc--CCCEEEEEEEeeCCccceEEeeEEEEec-CCceeecceEEEecCeEEEEe
Q psy17024 3 IGIPIKLLHEAEGH--IITCETT--NGDLFRGKLVEAEDNMNCAMADVTVTFR-DGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~--~V~VELK--nG~~y~G~L~~~D~~MNi~L~dv~~t~~-dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
+..|+++|+.+..+ +|+|.|+ +|.+|.|+|.+||+|||++|+||++... ......++.++|||++|.+|+
T Consensus 4 ~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 4 MVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred ccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 46799999999999 7888887 8999999999999999999999999864 335678999999999999986
No 24
>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=99.68 E-value=3.8e-16 Score=107.22 Aligned_cols=66 Identities=20% Similarity=0.271 Sum_probs=59.0
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC--------ceeecceEEEecCeEEEEecCc
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG--------KVKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg--------~~~~l~~vfIRGs~Ir~I~lPd 75 (132)
|+++++++|.|.|++|.+|.|+|.+||.|||++|+||++...+. ....++.++|||++|.+|...|
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 88999999999999999999999999999999999999976431 3577999999999999987543
No 25
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.61 E-value=4.1e-15 Score=101.19 Aligned_cols=65 Identities=14% Similarity=0.260 Sum_probs=57.5
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC----------CceeecceEEEecCeEEEEec
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD----------GKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d----------g~~~~l~~vfIRGs~Ir~I~l 73 (132)
=|+++++++|.|.|++|..|.|+|.++|.|||++|+||+++..+ .+..+++.+||||++|.+|.+
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 37889999999999999999999999999999999999996421 135689999999999999875
No 26
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.60 E-value=8.6e-15 Score=99.22 Aligned_cols=68 Identities=18% Similarity=0.144 Sum_probs=59.3
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC---ceeecceEEEecCeEEEEec
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG---KVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg---~~~~l~~vfIRGs~Ir~I~l 73 (132)
++.-|.++++++|.|.|++|++|.|+|.+||.|||++|+||.++..++ ....++.++|||++|.++.+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 355688999999999999999999999999999999999998875433 24678999999999999864
No 27
>KOG1783|consensus
Probab=99.59 E-value=3e-16 Score=106.03 Aligned_cols=72 Identities=21% Similarity=0.395 Sum_probs=66.0
Q ss_pred cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEecCc
Q psy17024 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lPd 75 (132)
-..|-+||.+.+|++|.|+|.+|..|+|+|.++|.||||.|+.+++.. ||+ +..+..+||||++|.||...+
T Consensus 4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCcccccccceeeccccEEEEEecc
Confidence 357999999999999999999999999999999999999999998875 665 789999999999999998753
No 28
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.55 E-value=4.8e-14 Score=94.95 Aligned_cols=67 Identities=19% Similarity=0.242 Sum_probs=58.6
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEec---CC-ceeecceEEEecCeEEEEecCc
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR---DG-KVKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~---dg-~~~~l~~vfIRGs~Ir~I~lPd 75 (132)
-|.++++++|.|.|++|..|.|+|.++|.|||++|++|++... ++ ....++.++|||++|.+|..-|
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 4788999999999999999999999999999999999988743 22 3567999999999999988544
No 29
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.54 E-value=6.4e-14 Score=95.16 Aligned_cols=66 Identities=14% Similarity=0.195 Sum_probs=60.1
Q ss_pred HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecC------CceeecceEEEecCeEEEEec
Q psy17024 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD------GKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~d------g~~~~l~~vfIRGs~Ir~I~l 73 (132)
+-|+++++++|.|.|++|..|.|+|.++|.+||+.|+||.++..+ .....++.++|||++|..|.+
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 568899999999999999999999999999999999999998643 347899999999999999875
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.53 E-value=5.1e-14 Score=98.70 Aligned_cols=71 Identities=15% Similarity=0.284 Sum_probs=59.0
Q ss_pred cccHHHHHHhhCCC--EEEEEEcC--CCEEEEEEEeeCCccceEEeeEEEEecCC-ceeecceEEEecCeEEEEec
Q psy17024 3 IGIPIKLLHEAEGH--IITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~--~V~VELKn--G~~y~G~L~~~D~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l 73 (132)
+..|+++|+++... +|.|.|++ +.+|.|+|.+||.|||++|+||+++..++ ....++.++|||++|.+|..
T Consensus 12 ~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 12 MTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred ecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 46799999999665 45555556 58999999999999999999999986433 46789999999999999863
No 31
>KOG3460|consensus
Probab=99.46 E-value=4.3e-14 Score=97.80 Aligned_cols=75 Identities=17% Similarity=0.322 Sum_probs=65.2
Q ss_pred CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe--cCC-----------ceeecceEEEecCeE
Q psy17024 2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDG-----------KVKPMANIYIRGSKI 68 (132)
Q Consensus 2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~--~dg-----------~~~~l~~vfIRGs~I 68 (132)
++..|++||+-+.+..|.|+|+++++++|+|.+||+|+|++|.||.+|- .+. ....++.+||||++|
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 4678999999999999999999999999999999999999999987653 222 146788999999999
Q ss_pred EEEecCcc
Q psy17024 69 RFLILPDM 76 (132)
Q Consensus 69 r~I~lPd~ 76 (132)
.+|.-|-.
T Consensus 82 ilvspp~~ 89 (91)
T KOG3460|consen 82 ILVSPPLR 89 (91)
T ss_pred EEEcCccc
Confidence 99987754
No 32
>KOG1775|consensus
Probab=99.39 E-value=2.9e-13 Score=92.41 Aligned_cols=71 Identities=27% Similarity=0.428 Sum_probs=64.4
Q ss_pred CcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe--cCCc-eeecceEEEecCeEEEEe
Q psy17024 2 SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDGK-VKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 2 s~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~--~dg~-~~~l~~vfIRGs~Ir~I~ 72 (132)
|.-+|++|+.+++|+.|.|-+|++.++.|||++||+|.|++|+||++.. ++++ ..+++++++.|++|..+.
T Consensus 4 ~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLv 77 (84)
T KOG1775|consen 4 STLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLV 77 (84)
T ss_pred hhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEe
Confidence 3568999999999999999999999999999999999999999999863 5554 689999999999998765
No 33
>KOG1780|consensus
Probab=99.33 E-value=3.6e-12 Score=86.44 Aligned_cols=70 Identities=24% Similarity=0.297 Sum_probs=63.9
Q ss_pred CC-cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 1 MS-IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 1 ms-~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
|| .+.| =|+++.++++.++|..+..+.|.|..||.|||++|+++++...++....+..++|||++|..+-
T Consensus 1 Msksg~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~e 71 (77)
T KOG1780|consen 1 MSKSGHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVE 71 (77)
T ss_pred CCcccCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEe
Confidence 54 3477 6899999999999999999999999999999999999999988888899999999999998764
No 34
>KOG3168|consensus
Probab=98.66 E-value=2.9e-08 Score=76.64 Aligned_cols=83 Identities=18% Similarity=0.307 Sum_probs=68.1
Q ss_pred CCcccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---------cCC-ceeecceEEEecCeEEE
Q psy17024 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---------RDG-KVKPMANIYIRGSKIRF 70 (132)
Q Consensus 1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---------~dg-~~~~l~~vfIRGs~Ir~ 70 (132)
|+++-+.++|+. +++.+.|.++++.+|.|++.+||.|||++|.||++.- .|+ +..-|..|.+||.+|..
T Consensus 1 M~~a~sskml~~-iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs 79 (177)
T KOG3168|consen 1 MTVAKSSKMLQH-INYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVS 79 (177)
T ss_pred CCccchhHHHHh-hcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEE
Confidence 788888888865 7899999999999999999999999999999987642 122 25678999999999999
Q ss_pred EecCcccccccccc
Q psy17024 71 LILPDMLKNAPMFK 84 (132)
Q Consensus 71 I~lPd~l~~ap~lk 84 (132)
..+.+-..-++-|.
T Consensus 80 ~tVegppp~s~s~~ 93 (177)
T KOG3168|consen 80 MTVEGPPPPSDSFR 93 (177)
T ss_pred EeccCCCCCccccc
Confidence 99876665554444
No 35
>KOG1774|consensus
Probab=98.62 E-value=4.5e-08 Score=67.73 Aligned_cols=69 Identities=20% Similarity=0.299 Sum_probs=54.1
Q ss_pred ccHHHHHHhhC--CCEEEEEEcC--CCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecCeEEEEe
Q psy17024 4 GIPIKLLHEAE--GHIITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 4 ~~Pl~lL~~~~--g~~V~VELKn--G~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~ 72 (132)
..|+.++..++ -.+|.|=|.. +..+.|.+++||+|||++|++|++.+...+ -..++.++++|++|..|.
T Consensus 11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~ 84 (88)
T KOG1774|consen 11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQ 84 (88)
T ss_pred cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEe
Confidence 45666666553 3456666665 789999999999999999999998764433 348999999999999876
No 36
>KOG1781|consensus
Probab=98.31 E-value=1e-07 Score=68.05 Aligned_cols=70 Identities=19% Similarity=0.207 Sum_probs=60.7
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCC--------ceeecceEEEecCeEEEEecCcccc
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG--------KVKPMANIYIRGSKIRFLILPDMLK 78 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg--------~~~~l~~vfIRGs~Ir~I~lPd~l~ 78 (132)
=|.+.+++.|.|++..|.++.|+|.++|..||++|+|+.+..+|- +..+++.+.+||..+..|.--|-.+
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 367889999999999999999999999999999999998875543 2478999999999999988766554
No 37
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.03 E-value=1.9e-05 Score=52.98 Aligned_cols=45 Identities=18% Similarity=0.337 Sum_probs=36.6
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCC---ccceEEeeEEEEec
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED---NMNCAMADVTVTFR 51 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~---~MNi~L~dv~~t~~ 51 (132)
+-++..++|++|+|.+|||..|+|.|.+++. .+.+.|+.+.....
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 3467889999999999999999999999998 89999999888653
No 38
>KOG1784|consensus
Probab=97.86 E-value=1.9e-05 Score=55.70 Aligned_cols=77 Identities=14% Similarity=0.164 Sum_probs=61.1
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe---cCC-ceeecceEEEecCeEEEEecCcccccccccc
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF---RDG-KVKPMANIYIRGSKIRFLILPDMLKNAPMFK 84 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~---~dg-~~~~l~~vfIRGs~Ir~I~lPd~l~~ap~lk 84 (132)
-|..+.++.|.|-+.+|+.+-|.|.+||..-|+.|+++-+-. ..+ ....++...|||.||..|-.-|+- ..|+++
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe-~d~~ld 82 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEE-LDSRLD 82 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchh-hhhhhh
Confidence 477889999999999999999999999999999999986532 122 356788899999999998875543 334555
Q ss_pred cc
Q psy17024 85 GK 86 (132)
Q Consensus 85 ~~ 86 (132)
..
T Consensus 83 ~t 84 (96)
T KOG1784|consen 83 LT 84 (96)
T ss_pred hh
Confidence 44
No 39
>KOG1782|consensus
Probab=97.59 E-value=1.6e-05 Score=58.84 Aligned_cols=66 Identities=23% Similarity=0.196 Sum_probs=54.9
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEE-ecCCc--eeecceEEEecCeEEEEecCc
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT-FRDGK--VKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t-~~dg~--~~~l~~vfIRGs~Ir~I~lPd 75 (132)
|-+.+.+.+.|-|++|....|.|.+||+|-|++|++|.+- ..+.+ ....+-..|||.||..+-.-|
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 6677899999999999999999999999999999998773 33332 345677899999999987644
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.52 E-value=7.7e-05 Score=49.72 Aligned_cols=39 Identities=26% Similarity=0.306 Sum_probs=32.1
Q ss_pred CCCEEEEEEcC----CCEEEEEEEeeCCccceEEeeEEEEecC
Q psy17024 14 EGHIITCETTN----GDLFRGKLVEAEDNMNCAMADVTVTFRD 52 (132)
Q Consensus 14 ~g~~V~VELKn----G~~y~G~L~~~D~~MNi~L~dv~~t~~d 52 (132)
..++|.|-++. .-.++|.|++||.|||+.|.||+++...
T Consensus 7 er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 7 ERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 45677777765 3478899999999999999999998754
No 41
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.50 E-value=0.00048 Score=48.90 Aligned_cols=65 Identities=18% Similarity=0.206 Sum_probs=54.9
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCc---------eeecceEEEecCeEEEEecCcc
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGK---------VKPMANIYIRGSKIRFLILPDM 76 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lPd~ 76 (132)
.++|+.|.+..|++..|.|+|..+|. .-.|.|+||....-+++ ...++.+..||+.|.-+.+-+.
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 57899999999999999999999996 88999999988654443 3468899999999999887543
No 42
>KOG3459|consensus
Probab=97.46 E-value=2.6e-05 Score=56.68 Aligned_cols=68 Identities=15% Similarity=0.358 Sum_probs=55.3
Q ss_pred cHHHHHHhhC--CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEe----c--CCc-------eeecceEEEecCeEE
Q psy17024 5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF----R--DGK-------VKPMANIYIRGSKIR 69 (132)
Q Consensus 5 ~Pl~lL~~~~--g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~----~--dg~-------~~~l~~vfIRGs~Ir 69 (132)
-|+++|..+. ..+|.|-+.|...+-|.+.++|-|+|++|+|+.+.. . +|+ ...++.+||||++|.
T Consensus 24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI 103 (114)
T KOG3459|consen 24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI 103 (114)
T ss_pred CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence 4788888874 568999999999999999999999999999987743 1 222 346889999999876
Q ss_pred EEe
Q psy17024 70 FLI 72 (132)
Q Consensus 70 ~I~ 72 (132)
.+.
T Consensus 104 ~v~ 106 (114)
T KOG3459|consen 104 LVL 106 (114)
T ss_pred EEE
Confidence 654
No 43
>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=96.35 E-value=0.021 Score=38.91 Aligned_cols=59 Identities=20% Similarity=0.218 Sum_probs=47.2
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCc----------eeecceEEEecCeEEE
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGK----------VKPMANIYIRGSKIRF 70 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~----------~~~l~~vfIRGs~Ir~ 70 (132)
+++|+.|++-.|++..|.|+|.++|. .--+.|+||....-+|+ ..-++.+.-||+.|.-
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 57899999999999999999999995 55788999988765543 2346677778887753
No 44
>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=96.29 E-value=0.026 Score=38.97 Aligned_cols=64 Identities=11% Similarity=0.134 Sum_probs=50.8
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEecC
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILP 74 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lP 74 (132)
-|.+|..+.|++|.+.|....++.|+..++| +-.|+.++|.. .+=| ..++..||.+-|..+.+.
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlG---v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG---VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT---EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc---cChhheeecCCEEEEEec
Confidence 4788999999999999999999999999999 57799998853 3444 347899999999988764
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=95.66 E-value=0.072 Score=32.66 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=28.2
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
.|++|+|++ ++..++|+...+|++=.+.++.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 589999999 7778899999999999999876
No 46
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.66 E-value=0.036 Score=36.46 Aligned_cols=35 Identities=20% Similarity=0.189 Sum_probs=29.0
Q ss_pred HHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 9 LLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 9 lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
||+++ ...+|+|-|.||..++|++.++|+|+=+.-
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~ 39 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLE 39 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEE
Confidence 45554 677999999999999999999999975443
No 47
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=95.49 E-value=0.12 Score=34.52 Aligned_cols=52 Identities=27% Similarity=0.586 Sum_probs=39.5
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCceeecceEEEecCeEEEEe
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 72 (132)
.+.|++++|+.|+|++-.|+. +|+|.++. ||. .|+. ++ ..+|||=.+|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~-----~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NG-----TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CC-----cEEEEEeeeEEEEc
Confidence 678999999999999977766 99999987 454 2221 12 35789888888764
No 48
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.40 E-value=0.05 Score=35.78 Aligned_cols=36 Identities=17% Similarity=0.134 Sum_probs=29.4
Q ss_pred HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
.||.++ ...+|+|-|.||..++|++.++|+|+=+.-
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 345554 678999999999999999999999975543
No 49
>KOG1073|consensus
Probab=94.59 E-value=0.078 Score=45.66 Aligned_cols=66 Identities=23% Similarity=0.295 Sum_probs=54.6
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEEeeC-CccceEEeeEEEEecCCc---------e-eecceEEEecCeEEEEecCcc
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLVEAE-DNMNCAMADVTVTFRDGK---------V-KPMANIYIRGSKIRFLILPDM 76 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~~~D-~~MNi~L~dv~~t~~dg~---------~-~~l~~vfIRGs~Ir~I~lPd~ 76 (132)
...+|+.|.+.-|++..|+|.|..+| +.-=|-|++|.....+++ . .-++.|+-||+.|+-+++-|.
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 35789999999999999999999999 577899999977654442 1 267889999999998887653
No 50
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.40 E-value=0.12 Score=35.62 Aligned_cols=54 Identities=17% Similarity=0.174 Sum_probs=37.9
Q ss_pred HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 73 (132)
.||..+ ...+|+|-|.||..++|++.++|+|+=+... +++ +-+|-=..|..|..
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~-------~gk-----qqLIYKHAISTI~p 65 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRN-------TGK-----SQLVYKHAISTVVP 65 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEE-------CCc-----EEEEEEeeeEEEec
Confidence 345544 6789999999999999999999999755433 332 22455556666654
No 51
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.20 E-value=0.3 Score=32.02 Aligned_cols=31 Identities=16% Similarity=0.324 Sum_probs=27.8
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
++|+.|.+++-.|++++|.|..||..-++.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lI 34 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLI 34 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEE
Confidence 5799999999999999999999998876654
No 52
>PRK14638 hypothetical protein; Provisional
Probab=90.93 E-value=0.49 Score=35.77 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=26.4
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~ 38 (132)
+..++|+.|.|+|+++..++|+|.++|+.
T Consensus 95 f~r~~G~~v~V~~~~~k~~~G~L~~~~~~ 123 (150)
T PRK14638 95 YVRFTGKLAKIVTKDGKTFIGRIESFVDG 123 (150)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC
Confidence 45689999999999999999999999974
No 53
>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=90.93 E-value=1.5 Score=34.01 Aligned_cols=61 Identities=11% Similarity=0.215 Sum_probs=42.4
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCC-ccceEEeeEEEEecCCceeecceEEEecCeEEEEecCcc
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDM 76 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~-~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd~ 76 (132)
.+..++++.|.|.+.+ .+|.|-|..+|. .-|++|-+.. .|++. .--+|-|.+|+.|.+-+.
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~---e~~~~---sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQ---EDGKR---SVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE----TTS-E---EEEEE-GGGEEEEEEEE-
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcc---cCCce---eEEEEEccceEEEEEccC
Confidence 3567899999999999 999999999996 6788886543 24432 347899999999887543
No 54
>PRK02001 hypothetical protein; Validated
Probab=90.80 E-value=0.7 Score=35.20 Aligned_cols=29 Identities=28% Similarity=0.437 Sum_probs=26.5
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~ 38 (132)
+..++|+.|.|.|+++..|.|+|.++|+.
T Consensus 85 f~r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 85 YKKNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 45689999999999999999999999975
No 55
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=90.63 E-value=0.53 Score=32.32 Aligned_cols=32 Identities=19% Similarity=0.200 Sum_probs=27.2
Q ss_pred HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCcc
Q psy17024 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNM 39 (132)
Q Consensus 8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~M 39 (132)
.||..+ ...+|+|-|.||...+|.+.+||.|.
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 345543 78899999999999999999999885
No 56
>KOG3262|consensus
Probab=89.39 E-value=1.5 Score=35.10 Aligned_cols=58 Identities=29% Similarity=0.350 Sum_probs=30.0
Q ss_pred HHHHHhhCCCEEEEEEcC-------------CCEEEEEEEeeCCccceEEeeEEEEecCC----ceeecceEEEecCe
Q psy17024 7 IKLLHEAEGHIITCETTN-------------GDLFRGKLVEAEDNMNCAMADVTVTFRDG----KVKPMANIYIRGSK 67 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKn-------------G~~y~G~L~~~D~~MNi~L~dv~~t~~dg----~~~~l~~vfIRGs~ 67 (132)
-+|||.+++..|+= |.+ +.+..|++.++=.-+|=++- +++..|+ ....-+++||-..+
T Consensus 57 g~flh~Cegd~Vck-~~~~kIPyfNAPIylenk~qIGKVDEIfG~i~d~~f--sIK~~dgv~assfk~g~k~fi~p~K 131 (215)
T KOG3262|consen 57 GKFLHMCEGDLVCK-LTNKKIPYFNAPIYLENKEQIGKVDEIFGPINDVHF--SIKPSDGVQASSFKPGDKLFIDPDK 131 (215)
T ss_pred hhhhhhcCCceEEe-eccccCCCCCCceeecchhhhcchhhhcccccccEE--EEecCCCceeecccCCCeEEecccc
Confidence 36889999887753 222 33445777776444443332 2222222 13344566665554
No 57
>PRK14639 hypothetical protein; Provisional
Probab=89.25 E-value=0.79 Score=34.27 Aligned_cols=34 Identities=24% Similarity=0.513 Sum_probs=28.6
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
=++.++|+.|.|+|++...+.|+|.++|+. ++.|
T Consensus 82 ~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 82 HFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 356789999999999999999999999984 4444
No 58
>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=89.02 E-value=1.3 Score=29.91 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=24.7
Q ss_pred HHhhCCCEEEEEEc---CC-CEEEEEEEeeCCc
Q psy17024 10 LHEAEGHIITCETT---NG-DLFRGKLVEAEDN 38 (132)
Q Consensus 10 L~~~~g~~V~VELK---nG-~~y~G~L~~~D~~ 38 (132)
+..++|+.|.|+|+ ++ ..+.|+|.++|+.
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 45679999999998 55 5899999999984
No 59
>PRK14644 hypothetical protein; Provisional
Probab=88.36 E-value=0.76 Score=34.30 Aligned_cols=41 Identities=20% Similarity=0.377 Sum_probs=31.5
Q ss_pred cccHHHH--HHhhCCCEEEEEEcCC----CEEEEEEEeeCCccceEEe
Q psy17024 3 IGIPIKL--LHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAMA 44 (132)
Q Consensus 3 ~~~Pl~l--L~~~~g~~V~VELKnG----~~y~G~L~~~D~~MNi~L~ 44 (132)
+..||+- +..++|+.|.|+|++. ..+.|+|.++|+. ++.|+
T Consensus 71 ldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 71 FDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred CCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 3445444 6678999999999987 8999999999984 34443
No 60
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=87.56 E-value=1.4 Score=34.25 Aligned_cols=36 Identities=11% Similarity=-0.004 Sum_probs=29.6
Q ss_pred HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
.||.++ ...+|+|-|.||..++|++.+||+|.=+..
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~ 52 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLR 52 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEE
Confidence 466665 577899999999999999999999865443
No 61
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=87.23 E-value=1.5 Score=34.04 Aligned_cols=36 Identities=17% Similarity=0.171 Sum_probs=29.1
Q ss_pred HHHHhh--CCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 8 ~lL~~~--~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
.||..+ ...+|+|-|.||..++|.+.+||+|.=+..
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~ 132 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLE 132 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEE
Confidence 344444 678999999999999999999999975443
No 62
>PRK14642 hypothetical protein; Provisional
Probab=86.78 E-value=1.6 Score=34.68 Aligned_cols=36 Identities=31% Similarity=0.502 Sum_probs=28.4
Q ss_pred cccHHHH---HHhhCCCEEEEEEc-------------CCCEEEEEEEeeCCc
Q psy17024 3 IGIPIKL---LHEAEGHIITCETT-------------NGDLFRGKLVEAEDN 38 (132)
Q Consensus 3 ~~~Pl~l---L~~~~g~~V~VELK-------------nG~~y~G~L~~~D~~ 38 (132)
+..||+- +..++|+.|.|.|+ +...|+|+|.++|+.
T Consensus 85 ldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 85 IDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred CCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 3445443 44579999999999 679999999999984
No 63
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.54 E-value=3.4 Score=31.00 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=25.5
Q ss_pred HHHhhCCCEEEEEE----cCCCEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCET----TNGDLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VEL----KnG~~y~G~L~~~D~~ 38 (132)
=+..++|+.|.|+| .+...++|+|.++|+.
T Consensus 92 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 92 DFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 35678999999998 4577999999999984
No 64
>PRK14632 hypothetical protein; Provisional
Probab=85.37 E-value=2.1 Score=33.04 Aligned_cols=33 Identities=21% Similarity=0.377 Sum_probs=26.9
Q ss_pred HHhhCCCEEEEEEcC-------CCEEEEEEEeeCCccceEE
Q psy17024 10 LHEAEGHIITCETTN-------GDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 10 L~~~~g~~V~VELKn-------G~~y~G~L~~~D~~MNi~L 43 (132)
+..++|+.|.|+|++ ...+.|+|.++|+. ++.|
T Consensus 93 f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 93 MSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 457899999999986 56999999999974 4444
No 65
>PRK14647 hypothetical protein; Provisional
Probab=85.21 E-value=3.7 Score=31.15 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=25.0
Q ss_pred HHHhhCCCEEEEEEcC---------CCEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCETTN---------GDLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VELKn---------G~~y~G~L~~~D~~ 38 (132)
=+..++|+.|.|+|+. ...|.|+|.++|+.
T Consensus 93 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 93 DYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred HHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 3556899999999963 47999999999973
No 66
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.72 E-value=2.7 Score=32.13 Aligned_cols=30 Identities=17% Similarity=0.323 Sum_probs=26.7
Q ss_pred HHhhCCCEEEEEE----cCCCEEEEEEEeeCCcc
Q psy17024 10 LHEAEGHIITCET----TNGDLFRGKLVEAEDNM 39 (132)
Q Consensus 10 L~~~~g~~V~VEL----KnG~~y~G~L~~~D~~M 39 (132)
+..+.|+.|.|+| .+.+.+.|+|.++|..+
T Consensus 94 f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 94 FARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 4557999999999 67899999999999887
No 67
>PRK14636 hypothetical protein; Provisional
Probab=84.19 E-value=3.4 Score=32.10 Aligned_cols=30 Identities=23% Similarity=0.415 Sum_probs=25.3
Q ss_pred HHHhhCCCEEEEEEc---CC-CEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCETT---NG-DLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VELK---nG-~~y~G~L~~~D~~ 38 (132)
=+..++|+.|.|+|+ +| ..++|+|.++|+.
T Consensus 92 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~ 125 (176)
T PRK14636 92 DFADWAGHEARIALSEPLDGRKQFRGELKGIDGD 125 (176)
T ss_pred HHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence 355789999999998 55 6999999999884
No 68
>PRK14640 hypothetical protein; Provisional
Probab=84.14 E-value=2.1 Score=32.30 Aligned_cols=30 Identities=13% Similarity=0.247 Sum_probs=25.6
Q ss_pred HHHhhCCCEEEEEE----cCCCEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCET----TNGDLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VEL----KnG~~y~G~L~~~D~~ 38 (132)
=++.++|+.|.|+| .+...++|+|.++|+.
T Consensus 91 ~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~ 124 (152)
T PRK14640 91 QFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD 124 (152)
T ss_pred HHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 35578999999999 4668999999999985
No 69
>PRK14633 hypothetical protein; Provisional
Probab=83.99 E-value=2.9 Score=31.55 Aligned_cols=34 Identities=24% Similarity=0.299 Sum_probs=27.0
Q ss_pred HHHhhCCCEEEEEEc----CCCEEEEEEEeeCCccceEE
Q psy17024 9 LLHEAEGHIITCETT----NGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 9 lL~~~~g~~V~VELK----nG~~y~G~L~~~D~~MNi~L 43 (132)
=+..++|+.|.|+|+ +...++|+|.++|+. ++.|
T Consensus 88 ~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 88 QAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 345689999999995 568999999999985 4444
No 70
>PRK14643 hypothetical protein; Provisional
Probab=82.86 E-value=3.1 Score=31.94 Aligned_cols=30 Identities=20% Similarity=0.164 Sum_probs=25.7
Q ss_pred HHHhhCCCEEEEEEcC----CCEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCETTN----GDLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VELKn----G~~y~G~L~~~D~~ 38 (132)
=+..++|+.|.|.|+. ...++|+|.++|+.
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 3567899999999976 58999999999975
No 71
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=80.51 E-value=4.6 Score=29.64 Aligned_cols=35 Identities=23% Similarity=0.440 Sum_probs=24.5
Q ss_pred cccHH---HHHHhhCCCEEEEEEc----CCCEEEEEEEeeCC
Q psy17024 3 IGIPI---KLLHEAEGHIITCETT----NGDLFRGKLVEAED 37 (132)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VELK----nG~~y~G~L~~~D~ 37 (132)
+..|| .-+..++|+.|.|.++ +...+.|+|.++|+
T Consensus 72 ~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 72 IDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp SSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 34455 4567789999999995 45689999999998
No 72
>PRK14645 hypothetical protein; Provisional
Probab=80.50 E-value=3.1 Score=31.64 Aligned_cols=29 Identities=14% Similarity=0.289 Sum_probs=24.9
Q ss_pred HHHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y~G~L~~~D~~ 38 (132)
=+..++|+.|.|.+ ++..+.|+|.++|+.
T Consensus 96 df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 96 HFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 35567999999986 789999999999985
No 73
>PRK14631 hypothetical protein; Provisional
Probab=79.32 E-value=8 Score=30.01 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=24.6
Q ss_pred HHHHhhCCCEEEEEEc----CCCEEEEEEEeeC
Q psy17024 8 KLLHEAEGHIITCETT----NGDLFRGKLVEAE 36 (132)
Q Consensus 8 ~lL~~~~g~~V~VELK----nG~~y~G~L~~~D 36 (132)
.=+..++|+.|.|+|+ +...++|+|.++|
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 3456789999999996 4589999999998
No 74
>PRK14634 hypothetical protein; Provisional
Probab=78.88 E-value=3.7 Score=31.15 Aligned_cols=29 Identities=14% Similarity=0.350 Sum_probs=24.6
Q ss_pred HHhhCCCEEEEEEcCC----CEEEEEEEeeCCc
Q psy17024 10 LHEAEGHIITCETTNG----DLFRGKLVEAEDN 38 (132)
Q Consensus 10 L~~~~g~~V~VELKnG----~~y~G~L~~~D~~ 38 (132)
+..++|+.|.|+|++. ..|.|+|.++|+.
T Consensus 95 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~ 127 (155)
T PRK14634 95 FQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED 127 (155)
T ss_pred HHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC
Confidence 4568999999999753 6999999999984
No 75
>PRK14637 hypothetical protein; Provisional
Probab=77.99 E-value=6.1 Score=29.91 Aligned_cols=30 Identities=13% Similarity=0.156 Sum_probs=23.6
Q ss_pred HHHhhCCCEEEEEEcCCCEE-EEEEEeeCCc
Q psy17024 9 LLHEAEGHIITCETTNGDLF-RGKLVEAEDN 38 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG~~y-~G~L~~~D~~ 38 (132)
=+..++|+.|.|+|.+...+ +|+|.++|+.
T Consensus 92 ~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~ 122 (151)
T PRK14637 92 EFSIFVGETVKVWFECTGQWQVGTIAEADET 122 (151)
T ss_pred HHHHhCCCEEEEEECCCCcEEEEEEEEEeCC
Confidence 34567999999999544455 7999999985
No 76
>PRK14646 hypothetical protein; Provisional
Probab=75.31 E-value=5.5 Score=30.20 Aligned_cols=34 Identities=18% Similarity=0.272 Sum_probs=26.7
Q ss_pred HHHhhCCCEEEEEEcCC----CEEEEEEEeeCCccceEE
Q psy17024 9 LLHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 9 lL~~~~g~~V~VELKnG----~~y~G~L~~~D~~MNi~L 43 (132)
=++.++|+.|.|+|++. ..++|+|.++|+. ++.|
T Consensus 94 df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 94 DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 35668999999999753 5889999999985 4444
No 77
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=74.21 E-value=13 Score=28.16 Aligned_cols=26 Identities=19% Similarity=0.419 Sum_probs=23.7
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEEeeC
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLVEAE 36 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~~~D 36 (132)
..++|+.|+++..+++.+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 35799999999999999999999986
No 78
>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=74.06 E-value=13 Score=22.42 Aligned_cols=26 Identities=12% Similarity=0.492 Sum_probs=22.7
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDN 38 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~ 38 (132)
..|+.|.+...++.-|++++++++..
T Consensus 4 ~~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 4 KVGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEECCC
Confidence 36788888887899999999999975
No 79
>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=73.34 E-value=8.2 Score=28.05 Aligned_cols=29 Identities=14% Similarity=0.225 Sum_probs=25.9
Q ss_pred cccHHHHHHhhCCCEEEEEEcCCCEEEEE
Q psy17024 3 IGIPIKLLHEAEGHIITCETTNGDLFRGK 31 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~ 31 (132)
-++|+.-|....+-.|++||.||.+|.+.
T Consensus 62 ~~~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 62 KDTDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCCCHHHHhCCcccEEEEEecCCcEEEec
Confidence 35789999999999999999999999765
No 80
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=70.67 E-value=10 Score=29.97 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=31.7
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccce
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNC 41 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi 41 (132)
++.+=++++|+.+..++.++..+.|.|+++|.|+-.
T Consensus 10 ~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G~ 45 (192)
T TIGR00567 10 AVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMGP 45 (192)
T ss_pred HHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccCC
Confidence 567788999999999999998889999999999753
No 81
>PRK14641 hypothetical protein; Provisional
Probab=68.70 E-value=8 Score=30.04 Aligned_cols=28 Identities=14% Similarity=0.211 Sum_probs=23.4
Q ss_pred HHHhhCCCEEEEEEcC----CCEEEEEEEeeC
Q psy17024 9 LLHEAEGHIITCETTN----GDLFRGKLVEAE 36 (132)
Q Consensus 9 lL~~~~g~~V~VELKn----G~~y~G~L~~~D 36 (132)
=+..++|+.|.|.|++ ...++|+|.++|
T Consensus 98 ~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 98 QYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 3566899999999976 458999999995
No 82
>PRK06955 biotin--protein ligase; Provisional
Probab=68.39 E-value=25 Score=28.98 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=28.6
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
..|+.|+|...++++++|++..+|+.=.+.|+.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 589999997767788999999999999988853
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=68.04 E-value=8.4 Score=29.82 Aligned_cols=73 Identities=16% Similarity=0.283 Sum_probs=53.2
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-------eeecceEEEecCeEEEEecCccccc
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-------VKPMANIYIRGSKIRFLILPDMLKN 79 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-------~~~l~~vfIRGs~Ir~I~lPd~l~~ 79 (132)
+.|++ ...-+|.|.+.||.++.|.+..++.--|..|.-+... .+.+ .+.++++.+.-..=++.+-||.+++
T Consensus 22 l~f~r-~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~~~-~~nRi~~plE~I~t~Ee~~~~d~~g~~ti~~d~~~~ 99 (165)
T PF03614_consen 22 LQFWR-FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDPFK-KENRIRLPLERISTIEELIVSDFKGRLTIHPDYFNN 99 (165)
T ss_pred HHHHH-hcCCceEEEecCCcEEEEEEeccCcccCEEeccCCCC-CCceEEEEhHHhhhHhhhccccccccEEechhhccc
Confidence 34443 3567999999999999999999999999998765522 2222 2455666666666677788899988
Q ss_pred cc
Q psy17024 80 AP 81 (132)
Q Consensus 80 ap 81 (132)
.|
T Consensus 100 q~ 101 (165)
T PF03614_consen 100 QP 101 (165)
T ss_pred cc
Confidence 83
No 84
>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=67.42 E-value=5.1 Score=27.43 Aligned_cols=20 Identities=15% Similarity=0.157 Sum_probs=13.9
Q ss_pred hhCCCEEEEEEcCCCEEEEE
Q psy17024 12 EAEGHIITCETTNGDLFRGK 31 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~ 31 (132)
-+...+|+++||||+.+.|+
T Consensus 14 C~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 14 CMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HTTTT-EEEE-TTT--EEES
T ss_pred HhcCCeEEEEEeCCCEEEEE
Confidence 35678999999999999998
No 85
>PRK14635 hypothetical protein; Provisional
Probab=66.81 E-value=16 Score=27.78 Aligned_cols=33 Identities=12% Similarity=0.273 Sum_probs=25.4
Q ss_pred HHhhCCCEEEEEEc--CCCEEEE---EEEeeCCccceEE
Q psy17024 10 LHEAEGHIITCETT--NGDLFRG---KLVEAEDNMNCAM 43 (132)
Q Consensus 10 L~~~~g~~V~VELK--nG~~y~G---~L~~~D~~MNi~L 43 (132)
+..+.|+.|.|+++ ++..+.| +|.++|+. ++.|
T Consensus 94 ~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 94 LDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 45689999999986 3578888 99999975 4444
No 86
>PRK14630 hypothetical protein; Provisional
Probab=61.21 E-value=16 Score=27.29 Aligned_cols=28 Identities=25% Similarity=0.299 Sum_probs=23.0
Q ss_pred HHhhCCCEEEEEEcCCCEEEEEEEeeCCc
Q psy17024 10 LHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (132)
Q Consensus 10 L~~~~g~~V~VELKnG~~y~G~L~~~D~~ 38 (132)
++.++|+.|.|+|+.. ...|+|.++|+.
T Consensus 92 f~r~~G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 92 FKIFEGKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred HHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence 4567999999999664 459999999984
No 87
>PRK08330 biotin--protein ligase; Provisional
Probab=61.17 E-value=43 Score=26.41 Aligned_cols=32 Identities=9% Similarity=0.127 Sum_probs=26.4
Q ss_pred hCCCEEEEEEcCCCE-EEEEEEeeCCccceEEee
Q psy17024 13 AEGHIITCETTNGDL-FRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 13 ~~g~~V~VELKnG~~-y~G~L~~~D~~MNi~L~d 45 (132)
..|++|+|.. ++.. +.|+...+|+.=.+.++.
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 5899999986 4555 479999999999988874
No 88
>PRK11625 Rho-binding antiterminator; Provisional
Probab=60.87 E-value=21 Score=24.74 Aligned_cols=24 Identities=17% Similarity=0.328 Sum_probs=20.0
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeC
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAE 36 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D 36 (132)
+.+.+|.++||||+++.|+....-
T Consensus 21 ~~~~~l~l~l~dGe~~~g~A~D~~ 44 (84)
T PRK11625 21 QHHLMLTLELKDGEVLQAKASDLV 44 (84)
T ss_pred hcCCeEEEEECCCCEEEEEEEeee
Confidence 378899999999999999975443
No 89
>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=59.59 E-value=18 Score=26.14 Aligned_cols=29 Identities=7% Similarity=0.150 Sum_probs=21.2
Q ss_pred CEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 16 HIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 16 ~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
..+.|.|+||+++.|.|.+=| .-.+.|.+
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~-~~~~~l~~ 86 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET-ADGVTVKM 86 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC-CCeEEEEc
Confidence 348999999999999998844 33444443
No 90
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=59.44 E-value=39 Score=27.74 Aligned_cols=31 Identities=6% Similarity=-0.009 Sum_probs=27.3
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEe
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~ 44 (132)
..|+.|++.. ++..++|++..+|+.-.+.++
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 5799999987 556799999999999999886
No 91
>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=59.35 E-value=14 Score=26.52 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=15.4
Q ss_pred CCEEEEEEcCCCEEEEEEE
Q psy17024 15 GHIITCETTNGDLFRGKLV 33 (132)
Q Consensus 15 g~~V~VELKnG~~y~G~L~ 33 (132)
...|.++|++|+.+.||+.
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 3579999999999999985
No 92
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=59.23 E-value=16 Score=28.61 Aligned_cols=34 Identities=18% Similarity=0.505 Sum_probs=27.1
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
++.+=++++|+.+..++.++. +.|.|+++|.|+-
T Consensus 9 ~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 9 TVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 577889999999999999888 9999999998876
No 93
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=58.77 E-value=24 Score=27.58 Aligned_cols=35 Identities=17% Similarity=0.452 Sum_probs=29.8
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccce
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNC 41 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi 41 (132)
++.+=++++|+.+..++. +.++.|.|+++|.|+--
T Consensus 6 ~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G~ 40 (179)
T cd00540 6 TVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLGP 40 (179)
T ss_pred HHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCCC
Confidence 577889999999988775 67899999999999753
No 94
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=58.54 E-value=18 Score=27.17 Aligned_cols=40 Identities=30% Similarity=0.398 Sum_probs=32.5
Q ss_pred CCCEEEEEEEeeC---CccceEEeeEEEEecCCceeecceEEEecCe
Q psy17024 24 NGDLFRGKLVEAE---DNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67 (132)
Q Consensus 24 nG~~y~G~L~~~D---~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~ 67 (132)
-+..+.|.+..+- -+||++|.|| ++|+...-..+-|||++
T Consensus 81 Ad~~lvG~VqKvS~Lil~~~~~v~Dv----~tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 81 ADYVLVGEVQKVSNLILNMNVYVRDV----ETGKVVRGRSVDIRGNT 123 (140)
T ss_pred CCEEEEEEEechhhhheeeeEEEEEC----CCCCEEeeeeeeEecCc
Confidence 3557788888776 4899999998 67888888889999986
No 95
>KOG3262|consensus
Probab=56.23 E-value=25 Score=28.25 Aligned_cols=14 Identities=14% Similarity=0.480 Sum_probs=6.3
Q ss_pred eeCCccceEEeeEE
Q psy17024 34 EAEDNMNCAMADVT 47 (132)
Q Consensus 34 ~~D~~MNi~L~dv~ 47 (132)
.|+..+-|.|++..
T Consensus 62 ~Cegd~Vck~~~~k 75 (215)
T KOG3262|consen 62 MCEGDLVCKLTNKK 75 (215)
T ss_pred hcCCceEEeecccc
Confidence 44444444444433
No 96
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=55.01 E-value=53 Score=30.00 Aligned_cols=49 Identities=14% Similarity=0.246 Sum_probs=36.1
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc-eeecceEEEecC
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK-VKPMANIYIRGS 66 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs 66 (132)
..|+.|+|...++.+++|+...+|+.=.+.|+. .+|. ...-++|.+|..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~-----~~g~~~~~sGEVslr~~ 325 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET-----AEGKQTVVSGEISLRSD 325 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE-----CCCeEEEEEEeEEEeec
Confidence 689999997666778999999999999998863 2332 344556666543
No 97
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=52.89 E-value=34 Score=25.87 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=23.1
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCC
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAED 37 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~ 37 (132)
.++|+.|+....+|..++|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 57999999888999999999998764
No 98
>PRK06789 flagellar motor switch protein; Validated
Probab=50.98 E-value=28 Score=23.58 Aligned_cols=35 Identities=11% Similarity=0.257 Sum_probs=27.0
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
.++.+.+|.|.+.+--.-+|.++.+|+++=+.+.+
T Consensus 37 dk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 37 ENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred CCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 45667777777777778889999999988777655
No 99
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=47.31 E-value=76 Score=28.14 Aligned_cols=42 Identities=17% Similarity=0.278 Sum_probs=34.5
Q ss_pred cccHHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
+-.|-+++.++.||.|+- =|+|++++++|.+-|--.-+.+.|
T Consensus 70 l~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~ 111 (421)
T COG5316 70 LLSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGD 111 (421)
T ss_pred ccCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCC
Confidence 456889999999999999 899999999999988755444443
No 100
>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=46.47 E-value=88 Score=24.59 Aligned_cols=31 Identities=13% Similarity=0.102 Sum_probs=26.9
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEe
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~ 44 (132)
..|+.|+|...+ ..+.|+...+|+.=.+.|+
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 579999998755 5799999999999999886
No 101
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=44.82 E-value=26 Score=24.31 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=18.7
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
.--+++++||+|+.|.|+- .|-+-|
T Consensus 22 ~hl~l~L~lkdGev~~a~A--~d~~~r 46 (84)
T COG4568 22 HHLPLTLELKDGEVLQAKA--SDLQRR 46 (84)
T ss_pred hhceEEEEEcCCeEEEEEe--hhhhhh
Confidence 3458999999999999974 444444
No 102
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=44.11 E-value=93 Score=22.63 Aligned_cols=57 Identities=16% Similarity=0.112 Sum_probs=40.6
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccc-eEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMN-CAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MN-i~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 73 (132)
.|..|.|.-=...=.+|++..+|..-| +.++.+.+..++|.. -++-|.-|||.++-|
T Consensus 44 kGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~---~e~pIh~SnV~l~~l 101 (114)
T TIGR01080 44 KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTE---VPVPIHPSNVMITKL 101 (114)
T ss_pred cCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeE---EEeeechHHeEEEec
Confidence 466666666555667799999996555 889999988777732 344577777777655
No 103
>PRK10898 serine endoprotease; Provisional
Probab=42.19 E-value=1.2e+02 Score=25.62 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=38.6
Q ss_pred CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecc--eEEEecCeEEEEecCcc
Q psy17024 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMA--NIYIRGSKIRFLILPDM 76 (132)
Q Consensus 15 g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~--~vfIRGs~Ir~I~lPd~ 76 (132)
...+.|.+.+|+.|..+++.+|...++-|-.+.-. +-....+. .-.-.|..|..+-.|-.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~l~~~~l~~~~~~~~G~~V~aiG~P~g 162 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--NLPVIPINPKRVPHIGDVVLAIGNPYN 162 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--CCCeeeccCcCcCCCCCEEEEEeCCCC
Confidence 35789999999999999999999999877655321 11111111 12234666666666643
No 104
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=42.14 E-value=39 Score=24.99 Aligned_cols=34 Identities=15% Similarity=0.280 Sum_probs=24.7
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
+..+.+|.|-+.+-..-+|.|+-+|+++=+.+.+
T Consensus 102 ~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 102 KLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred CcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 3445666666666667889999999988777764
No 105
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=42.00 E-value=87 Score=20.14 Aligned_cols=47 Identities=23% Similarity=0.396 Sum_probs=28.7
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccc-------------eEEeeEEEEecCCceeecce
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMN-------------CAMADVTVTFRDGKVKPMAN 60 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MN-------------i~L~dv~~t~~dg~~~~l~~ 60 (132)
++|-+|+|+ .++.++.=.+..-..||. -.++.++++.+||+...++.
T Consensus 2 AiGA~V~v~-~~~~~q~~~v~~g~gy~s~~~~~lhFGLG~~~~v~~v~V~WP~G~~~~~~~ 61 (71)
T PF07593_consen 2 AIGARVTVT-ADGRTQTREVTSGGGYLSQSEPRLHFGLGDATSVDSVEVRWPDGKVQTLEN 61 (71)
T ss_pred CCCeEEEEE-ECCeEEEEEEeCCCCEeecCCCCEEEECCCCCCEEEEEEECCCCCEEEEEc
Confidence 678899999 666666555555444443 33445666667776544443
No 106
>PF13437 HlyD_3: HlyD family secretion protein
Probab=41.86 E-value=58 Score=21.74 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=27.5
Q ss_pred ccHHHHHHhh--CCCEEEEEEcCC--CEEEEEEEeeCC
Q psy17024 4 GIPIKLLHEA--EGHIITCETTNG--DLFRGKLVEAED 37 (132)
Q Consensus 4 ~~Pl~lL~~~--~g~~V~VELKnG--~~y~G~L~~~D~ 37 (132)
.+|-+.+..+ .|..|++.+.++ ..+.|++..++.
T Consensus 41 ~v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 41 YVPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EEChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 3566666676 699999999865 599999999998
No 107
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=40.34 E-value=1.2e+02 Score=22.39 Aligned_cols=57 Identities=23% Similarity=0.177 Sum_probs=39.9
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccc-eEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMN-CAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MN-i~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 73 (132)
.|..|.|.-=...=-+|++..+|..-| +.+++|.+..++|. --++.|.=|||.++-|
T Consensus 48 kGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~---~~e~pIh~SNV~l~~l 105 (120)
T PRK01191 48 KGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGT---EVPRPIHPSNVMITKL 105 (120)
T ss_pred CCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCe---EEEcccchhHeEEEeC
Confidence 455666655554555699999997666 99999998877773 2356677777776554
No 108
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=39.47 E-value=1e+02 Score=23.46 Aligned_cols=57 Identities=14% Similarity=0.081 Sum_probs=41.7
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCcc-ceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNM-NCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~M-Ni~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 73 (132)
.|..|.|..=...=-+|++..+|..- -+.+++|.+...++++. ++-|--|||.++-+
T Consensus 49 kGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~---e~PIh~SNV~iv~l 106 (143)
T PTZ00194 49 KDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPV---QIGIHPSNVIITKL 106 (143)
T ss_pred cCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEe---ecCcCchheEEEcc
Confidence 45566665555444569999999644 59999999998888763 66788888877664
No 109
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=39.29 E-value=21 Score=28.01 Aligned_cols=61 Identities=16% Similarity=0.239 Sum_probs=36.0
Q ss_pred HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCcc-ceEEeeEEEEecCCc-eeecceEEEecCeE
Q psy17024 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNM-NCAMADVTVTFRDGK-VKPMANIYIRGSKI 68 (132)
Q Consensus 8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~M-Ni~L~dv~~t~~dg~-~~~l~~vfIRGs~I 68 (132)
++|+.-.|..|.|-.-+|..|.++|.++|... -+.+..-.....+.. ...+=..++|++..
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~~~~~~~~~~~~i~L~~al~K~~~~ 75 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRILEELEIPPEPPPEITLAQALPKGDRM 75 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SSSSEEEEEEE--STTHH
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEeeeccCCCCCcceEEEEEEEEcCccH
Confidence 55667789999999999999999999999654 344443333322222 25555556665543
No 110
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=39.12 E-value=19 Score=26.77 Aligned_cols=17 Identities=29% Similarity=0.247 Sum_probs=12.4
Q ss_pred EEecCcccccccccccc
Q psy17024 70 FLILPDMLKNAPMFKGK 86 (132)
Q Consensus 70 ~I~lPd~l~~ap~lk~~ 86 (132)
|++||+++.-+.+.+..
T Consensus 80 yL~LP~eivP~T~k~~~ 96 (124)
T PTZ00034 80 YLHLPPDVFPATHKKKS 96 (124)
T ss_pred HhCCCcccCchhhcccc
Confidence 67899888777775543
No 111
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=38.50 E-value=74 Score=24.63 Aligned_cols=37 Identities=16% Similarity=0.219 Sum_probs=28.5
Q ss_pred ccHHHHHHhh-CCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 4 GIPIKLLHEA-EGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 4 ~~Pl~lL~~~-~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
.+|-..+..+ .|..|+|.+.++..|.|++..++...+
T Consensus 130 ~v~~~~~~~i~~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 130 EVPAKDVSRIRKGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred EECHHHHhhCCCCCEEEEEECCCCEEEEEEEEEccccC
Confidence 3454444443 789999999999999999999997554
No 112
>PRK04313 30S ribosomal protein S4e; Validated
Probab=38.32 E-value=1.3e+02 Score=24.60 Aligned_cols=45 Identities=24% Similarity=0.363 Sum_probs=28.3
Q ss_pred EEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecCeEEEEecC
Q psy17024 30 GKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGSKIRFLILP 74 (132)
Q Consensus 30 G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lP 74 (132)
|++.+++.++--.-+-|++.+.+|+ ...++.||+=|..=-+|.||
T Consensus 190 G~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~~kp~isl~ 236 (237)
T PRK04313 190 GKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGKEKPVIKLP 236 (237)
T ss_pred EEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcCCCcceeCC
Confidence 8888888666222222444445664 56788899888655566665
No 113
>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=38.19 E-value=1.5e+02 Score=24.96 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=27.9
Q ss_pred CEEEEEEcCCCEEEEEEEeeCCccceEEeeEE
Q psy17024 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (132)
Q Consensus 16 ~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~ 47 (132)
..+.|.+.+|..|.++++.+|...++-|-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46889999999999999999999998886553
No 114
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=38.06 E-value=81 Score=25.89 Aligned_cols=32 Identities=9% Similarity=0.107 Sum_probs=27.3
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEee
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~d 45 (132)
..|+.|+|.. +++.+.|++.++|+.-.+.|+.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 3799999976 5689999999999998888864
No 115
>PRK10708 hypothetical protein; Provisional
Probab=37.88 E-value=37 Score=22.24 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=23.6
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
++..|+|++..+..-.|++..++.|--
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~E 29 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFSE 29 (62)
T ss_pred cccEEEEecCCCccccceEEEEeeccC
Confidence 577899999999999999999998654
No 116
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=37.55 E-value=1.3e+02 Score=24.02 Aligned_cols=26 Identities=12% Similarity=0.202 Sum_probs=22.7
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCC
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAED 37 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~ 37 (132)
.++|+.|++.-.+|+.+.|++..+.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 46999999988899999999998763
No 117
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.20 E-value=84 Score=25.22 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=31.8
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEE
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t 49 (132)
|+.+=++++|+.+.=+ -+|.++.|.+++.|.|+- .+|.-..
T Consensus 15 ~~~vAr~LLG~~lv~~-~~g~~~~g~IVEtEAY~G--~~D~A~H 55 (200)
T COG2094 15 TLVVARELLGKTLVRR-IGGLTTSGRIVETEAYLG--PDDPACH 55 (200)
T ss_pred HHHHHHHhcCcEEEEe-cCCcEEEEEEEEEeEecC--CCchhhh
Confidence 4567788999988766 788999999999999996 3454333
No 118
>PRK10139 serine endoprotease; Provisional
Probab=37.15 E-value=68 Score=28.14 Aligned_cols=63 Identities=17% Similarity=0.165 Sum_probs=40.4
Q ss_pred CCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecc--eEEEecCeEEEEecCcccc
Q psy17024 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMA--NIYIRGSKIRFLILPDMLK 78 (132)
Q Consensus 15 g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~--~vfIRGs~Ir~I~lPd~l~ 78 (132)
...|+|.+.++++|..+|+..|....+-|-.+... .+=....+. .-.--|..|..|--|.-+.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~-~~l~~~~lg~s~~~~~G~~V~aiG~P~g~~ 178 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP-SKLTQIAIADSDKLRVGDFAVAVGNPFGLG 178 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC-CCCceeEecCccccCCCCEEEEEecCCCCC
Confidence 45889999999999999999999999877555310 011122221 1123466777666665443
No 119
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=36.58 E-value=1.7e+02 Score=23.61 Aligned_cols=34 Identities=12% Similarity=0.155 Sum_probs=31.0
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeE
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv 46 (132)
..|+.|++++.++.+..|+...+|+.-.+.|+.-
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 3899999999999999999999999999988763
No 120
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=36.02 E-value=48 Score=26.05 Aligned_cols=38 Identities=26% Similarity=0.482 Sum_probs=28.6
Q ss_pred CCcccHHHHHHhhCCC--EEEEEEcC-CCEEEEEEEeeCCc
Q psy17024 1 MSIGIPIKLLHEAEGH--IITCETTN-GDLFRGKLVEAEDN 38 (132)
Q Consensus 1 ms~~~Pl~lL~~~~g~--~V~VELKn-G~~y~G~L~~~D~~ 38 (132)
||+.-=|.||-.+=++ +|.+++.. +.+|+|.|.++|+-
T Consensus 117 M~~~EKI~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 117 MNIEEKIDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred ccHHHHHHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 6666778888887544 46666655 67999999999975
No 121
>PF14262 DUF4353: Domain of unknown function (DUF4353)
Probab=35.96 E-value=73 Score=26.33 Aligned_cols=58 Identities=22% Similarity=0.460 Sum_probs=37.7
Q ss_pred hCCCEEEEEEcCCCEEEEEEE------ee--CCccceEEeeEEEEecCCceeecceEEEecCeEEEEecCc
Q psy17024 13 AEGHIITCETTNGDLFRGKLV------EA--EDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPD 75 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~------~~--D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lPd 75 (132)
..+..|+|.-..-.++.|+|. +. ++...|+|.+|+++..++- -+||.-..=.||.|.+
T Consensus 4 v~~~~vtIt~~GtY~lsGs~~~g~i~V~a~~~~~v~lvL~gv~it~~~~a-----~I~v~~a~k~~i~la~ 69 (264)
T PF14262_consen 4 VSGSTVTITKAGTYVLSGSLSDGQIVVDAGDTDKVRLVLDGVSITNSSGA-----AIYVKSADKVFITLAE 69 (264)
T ss_pred EeCCEEEEcCCEEEEEEEEccCcEEEEEcCCCceEEEEECCeEEeCCCCC-----CEEEEeCCeEEEEEcC
Confidence 346777776654456777776 44 5678999999999976653 2444444444556654
No 122
>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=35.15 E-value=76 Score=27.17 Aligned_cols=32 Identities=25% Similarity=0.405 Sum_probs=27.9
Q ss_pred CEEEEEEcCCCEEEEEEEeeCCccceEEeeEE
Q psy17024 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (132)
Q Consensus 16 ~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~ 47 (132)
..+.|.+.++..|..+++.+|...++-|-.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47889999999999999999999998876553
No 123
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=35.11 E-value=1e+02 Score=23.94 Aligned_cols=35 Identities=20% Similarity=0.346 Sum_probs=28.4
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCc
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGK 54 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~ 54 (132)
.|+-|.|-|.+|.+++|+-.++|.- .|++..+||.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac------qVgl~~~~Gn 153 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC------QVGLILPNGN 153 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE------EEEEEcCCCC
Confidence 7899999999999999999998863 2555556665
No 124
>PRK00802 3-methyladenine DNA glycosylase; Reviewed
Probab=35.07 E-value=73 Score=25.11 Aligned_cols=32 Identities=19% Similarity=0.420 Sum_probs=26.7
Q ss_pred HHHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccce
Q psy17024 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNC 41 (132)
Q Consensus 6 Pl~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi 41 (132)
++.+=++++|+.+..+ ..+.|.|+++|.|+--
T Consensus 14 ~~~vA~~LLGk~Lv~~----~~~~grIvETEAY~G~ 45 (188)
T PRK00802 14 ALEVARDLLGKVLVHE----GGVSGRIVETEAYIGA 45 (188)
T ss_pred HHHHHHHhCCCEEEEC----CEEEEEEEEEecccCC
Confidence 4667788999999877 4899999999999744
No 125
>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=33.63 E-value=42 Score=21.96 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=23.6
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
++..|+|++..+..-.|++.+++.|--
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~E 29 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFNE 29 (62)
T ss_pred cccEEEEecCCcccccceEEEEeeccC
Confidence 567899999999999999999998754
No 126
>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=33.28 E-value=1.3e+02 Score=19.25 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=26.6
Q ss_pred CCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEE
Q psy17024 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (132)
Q Consensus 14 ~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~ 47 (132)
....|.|.+.+-..++|++..+|+++=+.+.+..
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 4567788776667899999999998888887653
No 127
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.75 E-value=41 Score=21.97 Aligned_cols=52 Identities=12% Similarity=0.162 Sum_probs=29.4
Q ss_pred EEcCCCEEEEEEEeeCCc---cceEEeeEEEEecCCceeecceEEEecCeEEEEec
Q psy17024 21 ETTNGDLFRGKLVEAEDN---MNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 21 ELKnG~~y~G~L~~~D~~---MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 73 (132)
.|+.|..+.|++.++++| +++-+.+++=.-+..... -+..|-.|..+...++
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~-~~~~~~~Gq~v~~~V~ 55 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG-NFSKLKVGQLLLCVVE 55 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC-cccccCCCCEEEEEEE
Confidence 368899999999999985 344333432221111111 0155666777666554
No 128
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=32.72 E-value=1.3e+02 Score=18.99 Aligned_cols=39 Identities=13% Similarity=0.279 Sum_probs=25.8
Q ss_pred cCCCEEEEEEEe---eCCccceEEeeEEEEec-CCceeecceE
Q psy17024 23 TNGDLFRGKLVE---AEDNMNCAMADVTVTFR-DGKVKPMANI 61 (132)
Q Consensus 23 KnG~~y~G~L~~---~D~~MNi~L~dv~~t~~-dg~~~~l~~v 61 (132)
|+-.++.|.|.. ||+-+=..|+|+++... +.+..+.+.+
T Consensus 3 k~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkv 45 (52)
T PF02751_consen 3 KNKLSFKGHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKV 45 (52)
T ss_dssp --EEEEEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEE
T ss_pred ceeEEEEEeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeE
Confidence 344567788875 78999999999999863 3334444443
No 129
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.15 E-value=33 Score=25.14 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=22.5
Q ss_pred HHHHHhhCCCEEEEEEcCC-CEEEEEEE
Q psy17024 7 IKLLHEAEGHIITCETTNG-DLFRGKLV 33 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG-~~y~G~L~ 33 (132)
-.++..++|+.|.|+++.. ..|.|+..
T Consensus 95 ~~~~~~l~gk~l~V~v~~~~~e~nGk~y 122 (141)
T PF05037_consen 95 EQFLNQLLGKPLRVTVKWEENEYNGKTY 122 (141)
T ss_pred HHHHHHHcCCeeEEEecccccCCCCcEe
Confidence 4678889999999999998 78888544
No 130
>KOG4401|consensus
Probab=32.07 E-value=61 Score=25.68 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=35.7
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEEEecCCceeecc
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMA 59 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~t~~dg~~~~l~ 59 (132)
++|..|.|+.-++....|.+++||-.-++..-++. ..++++.+..
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~--~s~~~P~~~~ 53 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP--SSNGKPNHAK 53 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc--ccCCCCccch
Confidence 57888999999999999999999988888877766 3455544433
No 131
>PRK10942 serine endoprotease; Provisional
Probab=31.74 E-value=91 Score=27.51 Aligned_cols=32 Identities=19% Similarity=0.356 Sum_probs=27.7
Q ss_pred CCEEEEEEcCCCEEEEEEEeeCCccceEEeeE
Q psy17024 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (132)
Q Consensus 15 g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv 46 (132)
...|+|.+.++++|..+++..|...++-|-.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999999877544
No 132
>COG4907 Predicted membrane protein [Function unknown]
Probab=31.54 E-value=49 Score=30.15 Aligned_cols=12 Identities=50% Similarity=0.880 Sum_probs=5.4
Q ss_pred CCCCCCCCCCCC
Q psy17024 121 RGGWGGPSRGGR 132 (132)
Q Consensus 121 ~~~~~~~~~~~~ 132 (132)
.|+.+||++|+|
T Consensus 584 gGg~GGGGGGar 595 (595)
T COG4907 584 GGGSGGGGGGAR 595 (595)
T ss_pred CCCCCCCCCCCC
Confidence 344444444444
No 133
>TIGR03344 VI_effect_Hcp1 type VI secretion system effector, Hcp1 family. This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens.
Probab=31.29 E-value=1e+02 Score=23.34 Aligned_cols=69 Identities=14% Similarity=0.178 Sum_probs=42.6
Q ss_pred ccHHHHHHhhCCCEE-EEEEcCCCEE-EEEEEeeCCccceEEeeEEEEecC---------CceeecceEEEecCeEEEEe
Q psy17024 4 GIPIKLLHEAEGHII-TCETTNGDLF-RGKLVEAEDNMNCAMADVTVTFRD---------GKVKPMANIYIRGSKIRFLI 72 (132)
Q Consensus 4 ~~Pl~lL~~~~g~~V-~VELKnG~~y-~G~L~~~D~~MNi~L~dv~~t~~d---------g~~~~l~~vfIRGs~Ir~I~ 72 (132)
..|.-+..-+.|+.+ +|+|.--++- -| .-+.||.+.|+||.++.-+ +.....+.|-+.=..|.+-+
T Consensus 76 ASP~L~~a~~~Ge~l~~v~l~~~r~~~~G---~~~~y~~itL~~a~Issi~~~~~~~~~~~~~~~~E~vs~~y~~I~~~y 152 (166)
T TIGR03344 76 SSPLLYQALSSGEKLEECEIKFYRTSAAG---KQELYYTIKLEGALIVDIKPYMPHCLDPNNAQPLEDVSFRYRKITWTH 152 (166)
T ss_pred CCHHHHHHHcCCCcCCEEEEEEEEeCCCC---cEEEEEEEEEeeEEEEEEEcccCcccCCCCCCceEEEEEEeeEEEEEE
Confidence 457666667788877 4777432211 13 3567999999999987422 12234566666666777666
Q ss_pred cCc
Q psy17024 73 LPD 75 (132)
Q Consensus 73 lPd 75 (132)
.+.
T Consensus 153 ~~~ 155 (166)
T TIGR03344 153 HIA 155 (166)
T ss_pred ECC
Confidence 543
No 134
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=30.94 E-value=1.4e+02 Score=19.07 Aligned_cols=31 Identities=19% Similarity=0.359 Sum_probs=21.7
Q ss_pred CCCEEEEEEcCCC----EEEEEEEeeCCccceEEe
Q psy17024 14 EGHIITCETTNGD----LFRGKLVEAEDNMNCAMA 44 (132)
Q Consensus 14 ~g~~V~VELKnG~----~y~G~L~~~D~~MNi~L~ 44 (132)
.|+.|.||+.++. .|.-+++++++.=.+.++
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~ 37 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIIS 37 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEE
Confidence 5889999995543 599999999987444443
No 135
>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=30.50 E-value=1.9e+02 Score=20.88 Aligned_cols=45 Identities=20% Similarity=0.383 Sum_probs=30.4
Q ss_pred CCEEEEEEEeeCCccceEEe-----eEEEEecCCceeecceEEEecCeEEEEecC
Q psy17024 25 GDLFRGKLVEAEDNMNCAMA-----DVTVTFRDGKVKPMANIYIRGSKIRFLILP 74 (132)
Q Consensus 25 G~~y~G~L~~~D~~MNi~L~-----dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lP 74 (132)
|..+.|++..+.+. ++.++ .|.+.. +..-.+-|.||+.|+...-.
T Consensus 24 gk~V~G~I~hvv~d-dLYIDfG~KFhcVc~r----p~~~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 24 GKIVIGKIFHVVDD-DLYIDFGGKFHCVCKR----PAVNGEKYVRGSRVRLRLKD 73 (104)
T ss_pred CCEEEEEEEEEecC-ceEEEeCCceeEEEec----ccccccccccCCEEEEEECC
Confidence 77889999998765 55444 344442 22334569999999987743
No 136
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=30.06 E-value=52 Score=20.52 Aligned_cols=53 Identities=17% Similarity=0.390 Sum_probs=29.1
Q ss_pred EEcCCCEEEEEEEeeCC-ccceEEe-eEEEEecC-----CceeecceEEEecCeEEEEec
Q psy17024 21 ETTNGDLFRGKLVEAED-NMNCAMA-DVTVTFRD-----GKVKPMANIYIRGSKIRFLIL 73 (132)
Q Consensus 21 ELKnG~~y~G~L~~~D~-~MNi~L~-dv~~t~~d-----g~~~~l~~vfIRGs~Ir~I~l 73 (132)
+++-|+++.|++.++++ .+-+.|. .+...-+- .........|--|..|+..++
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~ 60 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVI 60 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEE
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEE
Confidence 46789999999999996 3333333 22221111 112234455666666665554
No 137
>PF11347 DUF3148: Protein of unknown function (DUF3148); InterPro: IPR021495 This family of proteins has no known function.
Probab=29.53 E-value=43 Score=22.18 Aligned_cols=21 Identities=43% Similarity=0.806 Sum_probs=16.9
Q ss_pred cCeEEEEecCcccccc---ccccc
Q psy17024 65 GSKIRFLILPDMLKNA---PMFKG 85 (132)
Q Consensus 65 Gs~Ir~I~lPd~l~~a---p~lk~ 85 (132)
|+.|+.+..|..||.| |||.-
T Consensus 3 G~~V~l~~~ppylKTAdpMPmLRp 26 (63)
T PF11347_consen 3 GDKVRLIEAPPYLKTADPMPMLRP 26 (63)
T ss_pred CCeEEEeecCCceeccCCccccCC
Confidence 7899999999999855 66653
No 138
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=29.12 E-value=62 Score=19.79 Aligned_cols=20 Identities=10% Similarity=0.386 Sum_probs=13.9
Q ss_pred EEEEEEeeCCccceEEeeEE
Q psy17024 28 FRGKLVEAEDNMNCAMADVT 47 (132)
Q Consensus 28 y~G~L~~~D~~MNi~L~dv~ 47 (132)
.+|+-..+|+++.+.|.+-.
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~ 29 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDD 29 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS
T ss_pred cceeEEeeccccceEEEeCC
Confidence 57999999999999999854
No 139
>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....
Probab=28.97 E-value=34 Score=17.13 Aligned_cols=19 Identities=11% Similarity=0.434 Sum_probs=13.3
Q ss_pred cceEEEecCeEEEEecCcccc
Q psy17024 58 MANIYIRGSKIRFLILPDMLK 78 (132)
Q Consensus 58 l~~vfIRGs~Ir~I~lPd~l~ 78 (132)
+..+.+.+++|. .+|+.+.
T Consensus 2 L~~Ldls~n~l~--~ip~~~~ 20 (22)
T PF00560_consen 2 LEYLDLSGNNLT--SIPSSFS 20 (22)
T ss_dssp ESEEEETSSEES--EEGTTTT
T ss_pred ccEEECCCCcCE--eCChhhc
Confidence 567888888777 5666553
No 140
>PRK08477 biotin--protein ligase; Provisional
Probab=28.89 E-value=2.2e+02 Score=22.49 Aligned_cols=37 Identities=14% Similarity=0.094 Sum_probs=30.0
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEE
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTV 48 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~ 48 (132)
.-..++.|+|.. +++.++|+..++|++--+.++.-.+
T Consensus 171 ~~~~~~~v~v~~-~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 171 EFEKSKSFSFHI-DGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HHHcCCEEEEEE-CCEEEEEEEeeECCCCeEEECCEEe
Confidence 346899999974 7899999999999988887765443
No 141
>PRK14056 phenylalanine 4-monooxygenase; Provisional
Probab=27.47 E-value=1.4e+02 Score=27.56 Aligned_cols=41 Identities=20% Similarity=0.293 Sum_probs=32.3
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEee---C-CccceEEeeEEEEecC
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEA---E-DNMNCAMADVTVTFRD 52 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~---D-~~MNi~L~dv~~t~~d 52 (132)
-.+|+.|.+|+.+|.+++|.++.. | ..+=+.++||+++..+
T Consensus 389 i~~g~~~~l~f~sgi~v~G~~~~~~~~~g~~~li~f~~ctv~~~~ 433 (578)
T PRK14056 389 ITIGNIAELEFESGIHVKGTVTDGVKNDGKIALISFINCTVTYNG 433 (578)
T ss_pred cccCceEEEEeecceEEEEEEeeeeccCCeEEEEEeeeeEEeeCC
Confidence 357999999999999999977664 2 3445888899999644
No 142
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=27.11 E-value=92 Score=24.71 Aligned_cols=38 Identities=11% Similarity=0.379 Sum_probs=29.9
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCCc-cceEEe
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDN-MNCAMA 44 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~-MNi~L~ 44 (132)
.++|+.-.|..|.|-.-+|..|.++|.+++.. ..+.+.
T Consensus 27 ~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~ 65 (240)
T TIGR00046 27 VRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELL 65 (240)
T ss_pred HHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEE
Confidence 35777789999999888899999999999864 344443
No 143
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=26.89 E-value=98 Score=24.41 Aligned_cols=31 Identities=16% Similarity=0.313 Sum_probs=27.4
Q ss_pred HHHHHhhCCCEEEEEEcCCCEEEEEEEeeCC
Q psy17024 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED 37 (132)
Q Consensus 7 l~lL~~~~g~~V~VELKnG~~y~G~L~~~D~ 37 (132)
.++|+.-.|..|.|-.-+|..|.++|..+|.
T Consensus 25 ~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~ 55 (234)
T PRK11713 25 VRVLRLKEGDELRLFDGDGGEYLAEITEIGK 55 (234)
T ss_pred HhhccCCCCCEEEEEeCCCCEEEEEEEEecC
Confidence 4677888999999988889999999999986
No 144
>cd01343 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
Probab=26.32 E-value=2.2e+02 Score=22.76 Aligned_cols=51 Identities=12% Similarity=0.214 Sum_probs=35.6
Q ss_pred EEEEEEcCCCEEEEEEEeeCCccceEEe-eEEEEecCCceeecceEEEecCeEEEE
Q psy17024 17 IITCETTNGDLFRGKLVEAEDNMNCAMA-DVTVTFRDGKVKPMANIYIRGSKIRFL 71 (132)
Q Consensus 17 ~V~VELKnG~~y~G~L~~~D~~MNi~L~-dv~~t~~dg~~~~l~~vfIRGs~Ir~I 71 (132)
.+.+.|.++..++|.+...+ -++.|. +..-. ..+ .+.+..+-+.+..|.|-
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~-~tg-~S~v~~L~l~~g~v~f~ 125 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWT-LTG-DSNVNNLTLNGGTVDFN 125 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEE-EeC-CcccceeEecCCEEEec
Confidence 68899999999999999988 445555 33322 222 34567778888887765
No 145
>PRK08158 type III secretion system protein SpaO; Validated
Probab=26.29 E-value=96 Score=26.28 Aligned_cols=37 Identities=14% Similarity=0.185 Sum_probs=30.0
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeEEE
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTV 48 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv~~ 48 (132)
+..+.+|.|....--.-+|.|+.+|+.+=+.+.++.-
T Consensus 261 ~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i~~ 297 (303)
T PRK08158 261 TNAELNVEIRANGALLGNGELVQMDDTLGVEIHEWLS 297 (303)
T ss_pred CCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEEec
Confidence 4577788888877778899999999998888877643
No 146
>PLN00036 40S ribosomal protein S4; Provisional
Probab=24.97 E-value=3.7e+02 Score=22.38 Aligned_cols=46 Identities=17% Similarity=0.358 Sum_probs=29.1
Q ss_pred EEEEeeCCccceEEeeEEEEecCCc--eeecceEEEecC-eEEEEecCcc
Q psy17024 30 GKLVEAEDNMNCAMADVTVTFRDGK--VKPMANIYIRGS-KIRFLILPDM 76 (132)
Q Consensus 30 G~L~~~D~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs-~Ir~I~lPd~ 76 (132)
|++.+++.+..- -+-|++.+.+|. ...++.||+=|. +=-+|.||..
T Consensus 193 G~I~~i~~~~~~-~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~ 241 (261)
T PLN00036 193 GVIKNREKHKGS-FEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKG 241 (261)
T ss_pred EEEEEEEecCCC-CCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCC
Confidence 888888844321 122444445664 457889999987 6567777654
No 147
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=24.37 E-value=78 Score=24.63 Aligned_cols=26 Identities=19% Similarity=0.345 Sum_probs=22.3
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEEeeC
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLVEAE 36 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~~~D 36 (132)
..++|+.|+|.+.....++|.+.+++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 44899999999998889999999985
No 148
>PF04234 CopC: CopC domain; InterPro: IPR007348 CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm [].; GO: 0005507 copper ion binding, 0046688 response to copper ion, 0042597 periplasmic space; PDB: 1IX2_B 1LYQ_A 2C9P_C 2C9R_A 2C9Q_A 1M42_A 1OT4_A 1NM4_A.
Probab=24.03 E-value=1e+02 Score=20.97 Aligned_cols=46 Identities=26% Similarity=0.290 Sum_probs=29.2
Q ss_pred EeeCCccceEEeeEEEEecCCceeecceEEEec-CeEEEEecCcccc
Q psy17024 33 VEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG-SKIRFLILPDMLK 78 (132)
Q Consensus 33 ~~~D~~MNi~L~dv~~t~~dg~~~~l~~vfIRG-s~Ir~I~lPd~l~ 78 (132)
..|++.+...++.+++++.+|+...+....+.+ ..-..+.+|..|.
T Consensus 24 L~F~e~v~~~~s~v~v~~~~g~~v~~~~~~~~~~~~~~~~~l~~~l~ 70 (97)
T PF04234_consen 24 LTFSEPVEPGFSSVTVTDPDGKRVDLGEPTVDGDGKTLTVPLPPPLP 70 (97)
T ss_dssp EEESS---CCC-EEEEEEEEETTSCTCEEEEEESTTEEEEEESS---
T ss_pred EEeCCCCccCccEEEEEcCCCceeecCcceecCCceEEEEECCCCCC
Confidence 467777777899999999888888888888888 3344456666454
No 149
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=23.11 E-value=98 Score=26.70 Aligned_cols=23 Identities=30% Similarity=0.442 Sum_probs=20.8
Q ss_pred HhhCCCEEEEEEcCCCEEEEEEE
Q psy17024 11 HEAEGHIITCETTNGDLFRGKLV 33 (132)
Q Consensus 11 ~~~~g~~V~VELKnG~~y~G~L~ 33 (132)
+-+.|+.|+|.+.+|..|.|+|-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 34689999999999999999998
No 150
>KOG1596|consensus
Probab=22.91 E-value=1.1e+02 Score=26.02 Aligned_cols=42 Identities=45% Similarity=0.642 Sum_probs=0.0
Q ss_pred CCccCCchhhhhhhhhccCCCCCCCC---CCCCCCCCCCCCCCCC
Q psy17024 91 AGAAGRGKSGILRAQAARGRGRGGPP---QRGGRGGWGGPSRGGR 132 (132)
Q Consensus 91 ~~~~~~g~~~~~r~~~~rg~grgg~~---~~~~~~~~~~~~~~~~ 132 (132)
..+..++-..-.++..+-+|++.+.. +.++|++|.|++++++
T Consensus 7 ~~g~~~gg~~gg~gg~gg~rg~~gg~~g~~~~~rg~g~gg~~~g~ 51 (317)
T KOG1596|consen 7 SRGGSRGGSRGGRGGFGGGRGTSGGGEGIGGGGRGGGRGGSRGGR 51 (317)
T ss_pred CCCCCCCCCccCcCCCCCCccccCCCCCcCCCcCCCCCCCCCCCC
No 151
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=22.15 E-value=85 Score=27.02 Aligned_cols=11 Identities=9% Similarity=0.383 Sum_probs=5.5
Q ss_pred ecCeEEEEecC
Q psy17024 64 RGSKIRFLILP 74 (132)
Q Consensus 64 RGs~Ir~I~lP 74 (132)
.|..|.++...
T Consensus 342 ~G~ai~l~~~~ 352 (456)
T PRK10590 342 TGEALSLVCVD 352 (456)
T ss_pred CeeEEEEecHH
Confidence 35555555443
No 152
>PLN02432 putative pectinesterase
Probab=21.92 E-value=4.8e+02 Score=21.85 Aligned_cols=35 Identities=14% Similarity=0.263 Sum_probs=22.1
Q ss_pred HHHHhhCCCEEEEEEcCCCEEEEEEEeeCCccceEE
Q psy17024 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (132)
Q Consensus 8 ~lL~~~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L 43 (132)
..+.+...++++|.+|+| +|+-+|.==-.--||.|
T Consensus 31 da~p~~~~~~~~I~I~~G-~Y~E~V~ip~~k~~itl 65 (293)
T PLN02432 31 DAVPSNNSQLVFIWVKPG-IYREKVVVPADKPFITL 65 (293)
T ss_pred hhccccCCceEEEEEeCc-eeEEEEEEeccCceEEE
Confidence 334444456899999999 77777653233445555
No 153
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=21.65 E-value=2.6e+02 Score=21.12 Aligned_cols=26 Identities=15% Similarity=0.225 Sum_probs=19.3
Q ss_pred hhCCCEEEEEEcCCCEEEEEEEeeCCccc
Q psy17024 12 EAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (132)
Q Consensus 12 ~~~g~~V~VELKnG~~y~G~L~~~D~~MN 40 (132)
.++|+.|++ .++ .+.|++.++.-+.|
T Consensus 94 slIGk~V~~--~~~-~~~G~V~sV~~~~~ 119 (140)
T PRK06009 94 GLIGRTVTS--ADG-SITGVVKSVTVYSD 119 (140)
T ss_pred HhcCCEEEe--cCC-cEEEEEEEEEEeCC
Confidence 479999986 344 68999999874433
No 154
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=21.63 E-value=1.4e+02 Score=20.76 Aligned_cols=26 Identities=27% Similarity=0.417 Sum_probs=19.7
Q ss_pred cccHHHHHHhh---CCCEEEEEEcCCCEE
Q psy17024 3 IGIPIKLLHEA---EGHIITCETTNGDLF 28 (132)
Q Consensus 3 ~~~Pl~lL~~~---~g~~V~VELKnG~~y 28 (132)
+-+|-.+++++ +|..|+|++-|+..+
T Consensus 14 vrIP~~l~kql~l~~g~~v~v~v~n~~~i 42 (82)
T COG2336 14 VRIPAALLKQLNLTIGDEVEVEVGNDQSI 42 (82)
T ss_pred eeccHHHHHHhCCCcCceEEEEEcCCcEE
Confidence 45677777776 899999999987543
No 155
>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=21.62 E-value=1.9e+02 Score=18.62 Aligned_cols=39 Identities=23% Similarity=0.451 Sum_probs=24.8
Q ss_pred hCCCEEEEEEcCCCEE-EEEEEeeCCccceEEeeEEEEecCCce
Q psy17024 13 AEGHIITCETTNGDLF-RGKLVEAEDNMNCAMADVTVTFRDGKV 55 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y-~G~L~~~D~~MNi~L~dv~~t~~dg~~ 55 (132)
..|..|.+.--+...| .|++.++|.---. .++...||..
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~----y~V~Y~DGte 46 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDR----YTVLYEDGTE 46 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTE----EEEEETTS-E
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCce----EEEEEcCCCE
Confidence 4788999999888766 9999999864332 3445567754
No 156
>PRK06788 flagellar motor switch protein; Validated
Probab=21.22 E-value=1.7e+02 Score=21.45 Aligned_cols=34 Identities=12% Similarity=0.255 Sum_probs=19.0
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCccceEEeeE
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~MNi~L~dv 46 (132)
..+.+|.|.+.+-..++|++..+++++=+.+.++
T Consensus 66 ~~~dpv~v~Vng~~~f~G~~Gv~~~~~AVrItei 99 (119)
T PRK06788 66 NLGHKVDVYLSNMKVGIGEAIVMDEKFGIIISEI 99 (119)
T ss_pred cCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEe
Confidence 3444555555555566666666666655555544
No 157
>KOG0921|consensus
Probab=20.92 E-value=1e+02 Score=30.58 Aligned_cols=36 Identities=22% Similarity=0.354 Sum_probs=25.5
Q ss_pred CCcccHHHHHHhhCCCEEEEEEcCCCEEEEE-EEeeCCccceEEee
Q psy17024 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGK-LVEAEDNMNCAMAD 45 (132)
Q Consensus 1 ms~~~Pl~lL~~~~g~~V~VELKnG~~y~G~-L~~~D~~MNi~L~d 45 (132)
||+--||.||--.--| | ..-|. |+-+|++.|++++.
T Consensus 1056 MslVsPLQLLLF~SrK---V------qsdgq~IV~VDdWIklqIsh 1092 (1282)
T KOG0921|consen 1056 MSLVSPLQLLLFGSRK---V------QSDGQGIVRVDDWIKLQISH 1092 (1282)
T ss_pred ccccChHHHhhhhhhh---c------cccCcceEEeeceeeEeccH
Confidence 7888899888543322 1 23455 77899999999874
No 158
>PF11634 IPI_T4: Nuclease inhibitor from bacteriophage T4; InterPro: IPR024373 This family of proteins represents IPI from bacteriophage T4. This protein is a nuclease inhibitor which is injected by T4 to protect its DNA from gmrS/gmrD CT of pathogenic Escherichia coli into the infected host []. The structure of this protein consists of two small beta-sheets flanked by N and C termini by alpha-helices. The protein has a gmrS/gmrD hydrophobic binding site [].; PDB: 2JUB_A.
Probab=20.84 E-value=70 Score=21.48 Aligned_cols=26 Identities=19% Similarity=0.320 Sum_probs=15.5
Q ss_pred hCCCEEEEEEcCCCEEEEEEEeeCCcc
Q psy17024 13 AEGHIITCETTNGDLFRGKLVEAEDNM 39 (132)
Q Consensus 13 ~~g~~V~VELKnG~~y~G~L~~~D~~M 39 (132)
-+|++| |-|.||+++.||+.--|.+-
T Consensus 14 regkp~-i~lv~gee~kgtvylgdg~~ 39 (76)
T PF11634_consen 14 REGKPM-ISLVNGEEIKGTVYLGDGWS 39 (76)
T ss_dssp S-SSEE-E-TTT--EEES-SSTTTT-E
T ss_pred CCCCce-EeeccccceeeeEEecCccc
Confidence 356665 78999999999998777654
No 159
>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=20.13 E-value=1e+02 Score=20.23 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=14.9
Q ss_pred EEEEEEEeeCC-ccceEEee
Q psy17024 27 LFRGKLVEAED-NMNCAMAD 45 (132)
Q Consensus 27 ~y~G~L~~~D~-~MNi~L~d 45 (132)
..+|++.++|. .|-|.|+|
T Consensus 4 ~veG~I~~id~~~~titLdD 23 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDD 23 (61)
T ss_pred cceEEEEEEcCCceEEEecC
Confidence 56899999995 66777765
Done!