Query psy14196
Match_columns 79
No_of_seqs 102 out of 660
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 21:53:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3172|consensus 99.9 9.3E-26 2E-30 148.9 5.6 72 1-72 1-88 (119)
2 cd01721 Sm_D3 The eukaryotic S 99.9 1.5E-21 3.3E-26 118.9 8.8 67 6-77 1-67 (70)
3 cd01733 LSm10 The eukaryotic S 99.8 1.7E-20 3.8E-25 116.8 8.9 70 3-77 7-76 (78)
4 cd01724 Sm_D1 The eukaryotic S 99.8 1.1E-20 2.4E-25 120.4 8.1 64 6-69 2-81 (90)
5 cd01723 LSm4 The eukaryotic Sm 99.8 3.6E-20 7.7E-25 114.3 9.2 69 5-77 1-69 (76)
6 cd01726 LSm6 The eukaryotic Sm 99.8 1.2E-19 2.6E-24 109.4 8.4 65 6-76 1-66 (67)
7 cd01725 LSm2 The eukaryotic Sm 99.8 2.5E-19 5.3E-24 112.0 8.8 70 5-77 1-70 (81)
8 PRK00737 small nuclear ribonuc 99.8 2.9E-18 6.3E-23 104.8 9.4 71 1-77 1-71 (72)
9 cd01722 Sm_F The eukaryotic Sm 99.8 2.8E-18 6E-23 103.8 8.4 66 5-76 1-67 (68)
10 cd01731 archaeal_Sm1 The archa 99.7 2.1E-17 4.6E-22 99.6 8.8 66 6-77 1-67 (68)
11 KOG3482|consensus 99.7 1.8E-17 3.9E-22 103.1 4.0 61 3-64 6-68 (79)
12 COG1958 LSM1 Small nuclear rib 99.7 1.6E-16 3.5E-21 98.1 8.1 72 3-77 5-78 (79)
13 PF01423 LSM: LSM domain ; In 99.6 7.8E-16 1.7E-20 91.3 6.7 64 8-77 1-66 (67)
14 smart00651 Sm snRNP Sm protein 99.6 1.1E-15 2.5E-20 90.5 7.4 64 8-77 1-66 (67)
15 cd01732 LSm5 The eukaryotic Sm 99.6 1.1E-15 2.4E-20 94.8 7.4 47 4-50 2-48 (76)
16 KOG3293|consensus 99.6 3.4E-16 7.3E-21 105.5 5.4 66 5-76 2-69 (134)
17 cd00600 Sm_like The eukaryotic 99.6 5.8E-15 1.3E-19 86.2 7.2 62 10-76 1-62 (63)
18 KOG3448|consensus 99.6 6.8E-15 1.5E-19 94.5 6.7 68 7-77 4-71 (96)
19 cd01730 LSm3 The eukaryotic Sm 99.6 5.3E-15 1.2E-19 92.3 5.9 46 5-50 1-46 (82)
20 cd01719 Sm_G The eukaryotic Sm 99.5 3.3E-14 7.2E-19 87.1 6.4 66 6-77 1-67 (72)
21 cd01720 Sm_D2 The eukaryotic S 99.5 8E-14 1.7E-18 88.6 6.1 74 5-78 2-85 (87)
22 cd01729 LSm7 The eukaryotic Sm 99.4 1.4E-12 3.1E-17 81.5 6.1 42 10-51 7-48 (81)
23 KOG1783|consensus 99.4 1.1E-13 2.3E-18 86.1 0.7 68 4-76 5-72 (77)
24 cd01718 Sm_E The eukaryotic Sm 99.3 3.6E-12 7.8E-17 79.9 6.5 48 4-51 5-56 (79)
25 cd01728 LSm1 The eukaryotic Sm 99.3 6.5E-12 1.4E-16 77.6 6.5 47 6-52 3-49 (74)
26 cd01717 Sm_B The eukaryotic Sm 99.3 7.1E-12 1.5E-16 77.5 5.7 42 9-50 4-45 (79)
27 KOG3428|consensus 99.2 2.8E-11 6E-16 79.9 6.6 63 6-69 3-81 (109)
28 cd06168 LSm9 The eukaryotic Sm 99.2 3.5E-11 7.7E-16 74.5 5.9 44 8-51 3-46 (75)
29 cd01727 LSm8 The eukaryotic Sm 99.2 3.8E-11 8.2E-16 73.5 5.7 42 9-50 3-44 (74)
30 KOG1775|consensus 99.1 1.2E-11 2.6E-16 77.7 1.4 61 3-63 5-69 (84)
31 PTZ00138 small nuclear ribonuc 99.0 7.6E-10 1.7E-14 70.8 5.8 67 4-76 13-85 (89)
32 KOG3460|consensus 98.8 8.5E-10 1.8E-14 70.3 -0.0 73 3-75 3-83 (91)
33 KOG1780|consensus 98.8 6.9E-09 1.5E-13 64.8 3.7 52 1-54 1-53 (77)
34 PF14438 SM-ATX: Ataxin 2 SM d 98.1 1.5E-05 3.2E-10 48.5 6.3 45 7-51 4-51 (77)
35 KOG1774|consensus 98.0 5.8E-06 1.3E-10 52.6 2.5 47 5-51 12-62 (88)
36 KOG1781|consensus 97.7 2.8E-06 6.1E-11 55.7 -2.6 43 10-52 22-64 (108)
37 KOG3168|consensus 97.6 6.1E-06 1.3E-10 58.4 -1.8 48 1-49 1-48 (177)
38 cd01739 LSm11_C The eukaryotic 97.1 0.00043 9.3E-09 42.3 2.4 38 15-52 8-49 (66)
39 KOG1784|consensus 96.5 0.0034 7.3E-08 40.7 3.2 40 10-49 5-44 (96)
40 KOG1782|consensus 95.6 0.00082 1.8E-08 45.6 -2.8 40 10-49 14-53 (129)
41 cd01716 Hfq Hfq, an abundant, 95.4 0.029 6.3E-07 33.7 3.6 33 9-41 3-37 (61)
42 TIGR02383 Hfq RNA chaperone Hf 95.3 0.031 6.6E-07 33.6 3.5 34 8-41 6-41 (61)
43 PF12701 LSM14: Scd6-like Sm d 95.2 0.071 1.5E-06 34.4 5.2 43 12-54 5-48 (96)
44 PRK00395 hfq RNA-binding prote 94.5 0.064 1.4E-06 33.8 3.5 35 8-42 10-46 (79)
45 PRK14638 hypothetical protein; 94.4 0.11 2.3E-06 35.6 4.8 41 3-44 85-128 (150)
46 PRK14639 hypothetical protein; 93.9 0.15 3.3E-06 34.5 4.8 41 3-44 73-116 (140)
47 PRK02001 hypothetical protein; 93.2 0.23 5.1E-06 34.2 4.8 40 3-43 75-117 (152)
48 PF02237 BPL_C: Biotin protein 93.1 0.41 8.8E-06 26.6 5.0 31 14-45 2-32 (48)
49 KOG3459|consensus 93.1 0.011 2.5E-07 39.4 -1.7 45 5-49 24-70 (114)
50 cd01735 LSm12_N LSm12 belongs 93.1 0.32 6.9E-06 29.1 4.7 33 13-45 4-36 (61)
51 PRK14644 hypothetical protein; 92.9 0.22 4.7E-06 33.8 4.2 41 3-44 71-117 (136)
52 PF10842 DUF2642: Protein of u 92.4 0.39 8.4E-06 29.2 4.5 30 7-37 13-42 (66)
53 COG1923 Hfq Uncharacterized ho 92.4 0.29 6.3E-06 30.7 4.0 32 8-39 10-43 (77)
54 PF11095 Gemin7: Gem-associate 92.1 0.92 2E-05 28.5 6.0 45 7-53 16-61 (80)
55 PRK14640 hypothetical protein; 91.2 0.54 1.2E-05 32.2 4.7 40 3-43 82-128 (152)
56 cd01736 LSm14_N LSm14 (also kn 91.2 1.1 2.4E-05 27.8 5.6 44 12-55 3-47 (74)
57 COG0779 Uncharacterized protei 90.3 1.2 2.5E-05 31.0 5.7 37 3-39 84-127 (153)
58 PRK14632 hypothetical protein; 89.5 0.84 1.8E-05 31.9 4.6 41 3-44 83-133 (172)
59 cd01734 YlxS_C YxlS is a Bacil 89.3 0.9 2E-05 27.8 4.1 29 10-38 20-52 (83)
60 PRK14636 hypothetical protein; 89.2 0.91 2E-05 31.9 4.6 34 9-43 92-129 (176)
61 PRK14645 hypothetical protein; 89.1 0.93 2E-05 31.3 4.5 35 3-38 87-124 (154)
62 PRK14642 hypothetical protein; 89.0 0.67 1.4E-05 33.5 3.8 40 3-43 85-140 (197)
63 PRK14647 hypothetical protein; 88.9 1 2.2E-05 31.0 4.5 36 3-38 84-131 (159)
64 PRK00092 ribosome maturation p 88.8 1.1 2.4E-05 30.4 4.7 36 3-38 83-125 (154)
65 PRK14634 hypothetical protein; 88.5 1.1 2.4E-05 30.8 4.5 40 3-43 85-131 (155)
66 PRK14633 hypothetical protein; 88.2 1.3 2.7E-05 30.3 4.7 40 3-43 79-125 (150)
67 PF02576 DUF150: Uncharacteris 87.6 1.2 2.6E-05 29.6 4.2 35 3-37 72-113 (141)
68 PF06372 Gemin6: Gemin6 protei 87.1 1.8 4E-05 30.5 5.0 38 10-48 12-50 (166)
69 PRK14091 RNA-binding protein H 86.7 1 2.2E-05 31.9 3.5 34 8-41 95-130 (165)
70 PRK14091 RNA-binding protein H 85.9 1.2 2.6E-05 31.5 3.5 34 7-40 14-49 (165)
71 PRK14646 hypothetical protein; 85.6 2 4.3E-05 29.5 4.5 40 3-43 85-131 (155)
72 PRK14631 hypothetical protein; 84.8 2.2 4.7E-05 30.0 4.5 34 3-36 102-142 (174)
73 PRK14641 hypothetical protein; 83.5 2.4 5.2E-05 29.9 4.2 34 3-36 89-129 (173)
74 PRK14637 hypothetical protein; 83.3 2.9 6.4E-05 28.7 4.5 41 3-44 83-127 (151)
75 PF07073 ROF: Modulator of Rho 81.8 1.3 2.8E-05 27.7 2.1 21 11-31 13-33 (80)
76 PRK14643 hypothetical protein; 81.4 3 6.5E-05 29.0 4.0 30 9-38 98-131 (164)
77 smart00333 TUDOR Tudor domain. 80.3 7.6 0.00016 21.2 5.1 26 13-38 4-29 (57)
78 PF10618 Tail_tube: Phage tail 80.1 3.1 6.8E-05 27.4 3.6 32 3-34 62-93 (119)
79 PRK09618 flgD flagellar basal 76.6 11 0.00023 26.0 5.6 26 11-36 88-113 (142)
80 PRK14635 hypothetical protein; 75.3 7.5 0.00016 26.8 4.6 40 3-43 84-131 (162)
81 COG2954 Uncharacterized protei 74.8 5.2 0.00011 28.1 3.6 57 5-62 72-132 (156)
82 PF11607 DUF3247: Protein of u 74.0 5.3 0.00011 26.2 3.3 23 11-33 23-46 (101)
83 PRK14630 hypothetical protein; 69.8 11 0.00024 25.5 4.3 35 3-38 82-119 (143)
84 PRK11625 Rho-binding antitermi 69.4 12 0.00026 23.6 4.1 24 12-35 20-43 (84)
85 PF03614 Flag1_repress: Repres 66.3 16 0.00034 25.9 4.5 33 15-47 29-61 (165)
86 PRK10898 serine endoprotease; 65.2 16 0.00035 27.7 4.8 32 16-47 102-133 (353)
87 PRK06789 flagellar motor switc 65.0 16 0.00035 22.5 4.0 36 10-45 36-71 (74)
88 TIGR00567 3mg DNA-3-methyladen 64.7 17 0.00038 26.0 4.7 36 5-40 9-44 (192)
89 TIGR02603 CxxCH_TIGR02603 puta 63.2 12 0.00027 24.5 3.4 21 17-37 59-79 (133)
90 TIGR02038 protease_degS peripl 58.9 24 0.00053 26.7 4.8 32 16-47 102-133 (351)
91 PRK10139 serine endoprotease; 57.3 26 0.00056 27.7 4.9 33 15-47 114-146 (455)
92 COG5316 Uncharacterized conser 57.0 39 0.00085 27.2 5.8 61 4-65 71-135 (421)
93 PF02245 Pur_DNA_glyco: Methyl 56.0 22 0.00048 25.2 3.9 35 5-40 8-42 (184)
94 PF05037 DUF669: Protein of un 55.7 8.1 0.00017 25.7 1.6 27 6-32 94-121 (141)
95 COG4568 Rof Transcriptional an 54.1 19 0.00042 22.8 3.0 24 11-34 19-42 (84)
96 PRK06955 biotin--protein ligas 53.9 38 0.00083 25.1 5.1 32 13-44 247-278 (300)
97 TIGR02037 degP_htrA_DO peripla 53.6 30 0.00066 26.6 4.6 32 16-47 82-113 (428)
98 PRK10942 serine endoprotease; 52.7 33 0.00072 27.3 4.8 31 16-46 136-166 (473)
99 PRK11911 flgD flagellar basal 51.1 29 0.00064 23.8 3.8 26 12-37 90-115 (140)
100 PF13437 HlyD_3: HlyD family s 50.2 47 0.001 20.0 4.3 33 5-37 42-78 (105)
101 TIGR03170 flgA_cterm flagella 49.1 26 0.00057 22.1 3.1 23 12-34 93-116 (122)
102 COG1886 FliN Flagellar motor s 49.0 37 0.00081 22.7 4.0 35 11-45 101-135 (136)
103 PF07076 DUF1344: Protein of u 47.9 60 0.0013 19.4 4.7 41 27-75 4-46 (61)
104 cd00540 AAG Alkyladenine DNA g 47.3 50 0.0011 23.4 4.6 35 5-40 5-39 (179)
105 PF01052 SpoA: Surface present 46.7 58 0.0012 18.9 4.2 35 13-47 40-74 (77)
106 PRK11886 bifunctional biotin-- 46.3 55 0.0012 24.1 4.9 31 13-44 270-300 (319)
107 PF09465 LBR_tudor: Lamin-B re 45.8 45 0.00097 19.6 3.5 26 13-38 7-33 (55)
108 TIGR00999 8a0102 Membrane Fusi 44.9 49 0.0011 23.0 4.3 35 6-40 132-167 (265)
109 PRK05753 nucleoside diphosphat 44.4 54 0.0012 21.9 4.2 35 2-36 90-126 (137)
110 PRK07018 flgA flagellar basal 43.5 31 0.00067 24.8 3.1 23 12-34 204-227 (235)
111 TIGR00121 birA_ligase birA, bi 43.5 65 0.0014 22.8 4.7 31 13-44 191-221 (237)
112 PF01272 GreA_GreB: Transcript 42.4 72 0.0016 18.8 4.4 32 2-34 41-74 (77)
113 PTZ00275 biotin-acetyl-CoA-car 42.2 77 0.0017 23.5 5.1 32 13-45 235-266 (285)
114 KOG1073|consensus 40.6 62 0.0013 25.5 4.5 44 12-55 6-50 (361)
115 PF05954 Phage_GPD: Phage late 39.2 45 0.00098 23.3 3.4 26 11-36 24-49 (292)
116 PF00575 S1: S1 RNA binding do 39.1 33 0.00071 19.4 2.2 18 21-38 1-18 (74)
117 PRK08330 biotin--protein ligas 39.0 93 0.002 22.1 5.0 33 12-45 185-218 (236)
118 cd05694 S1_Rrp5_repeat_hs2_sc2 37.4 33 0.00072 20.3 2.1 19 21-39 1-19 (74)
119 PRK06792 flgD flagellar basal 36.4 62 0.0013 23.4 3.7 26 12-37 115-140 (190)
120 PF09883 DUF2110: Uncharacteri 34.4 43 0.00093 24.9 2.6 31 6-37 55-87 (225)
121 PRK11713 16S ribosomal RNA met 34.4 88 0.0019 22.2 4.2 31 7-37 25-55 (234)
122 PRK13325 bifunctional biotin-- 33.0 1.1E+02 0.0025 25.1 5.2 32 13-44 276-307 (592)
123 PRK08158 type III secretion sy 32.6 88 0.0019 24.0 4.2 39 10-48 259-297 (303)
124 PRK12617 flgA flagellar basal 32.5 60 0.0013 23.4 3.2 23 12-34 183-206 (214)
125 PRK08515 flgA flagellar basal 30.7 81 0.0017 22.6 3.6 23 12-34 193-215 (222)
126 PRK14056 phenylalanine 4-monoo 30.6 1.9E+02 0.004 24.4 6.0 46 9-55 386-435 (578)
127 PF09923 DUF2155: Uncharacteri 30.6 26 0.00056 22.2 0.9 41 7-53 3-43 (90)
128 cd04453 S1_RNase_E S1_RNase_E: 30.3 96 0.0021 18.9 3.4 24 23-46 6-29 (88)
129 PRK06005 flgA flagellar basal 30.1 75 0.0016 21.8 3.2 23 12-34 128-151 (160)
130 COG0340 BirA Biotin-(acetyl-Co 29.9 2.2E+02 0.0048 20.7 6.1 34 13-46 188-221 (238)
131 PF02736 Myosin_N: Myosin N-te 29.9 43 0.00094 17.9 1.6 18 12-29 20-37 (42)
132 PF04452 Methyltrans_RNA: RNA 29.9 82 0.0018 22.2 3.5 32 8-39 13-44 (225)
133 PF06331 Tbf5: Transcription f 29.0 29 0.00064 21.0 0.9 13 27-39 4-16 (68)
134 PRK06788 flagellar motor switc 28.9 1.4E+02 0.003 19.8 4.2 39 10-48 63-101 (119)
135 cd04508 TUDOR Tudor domains ar 28.8 94 0.002 16.1 4.8 23 15-37 1-24 (48)
136 COG2094 Mpg 3-methyladenine DN 28.6 1.3E+02 0.0028 22.0 4.3 34 6-40 15-48 (200)
137 TIGR03344 VI_effect_Hcp1 type 28.5 57 0.0012 22.4 2.4 46 4-52 76-123 (166)
138 COG0265 DegQ Trypsin-like seri 27.7 1.3E+02 0.0029 22.2 4.4 34 15-48 95-128 (347)
139 cd04461 S1_Rrp5_repeat_hs8_sc7 27.4 61 0.0013 19.0 2.1 22 22-43 12-34 (83)
140 PRK12618 flgA flagellar basal 27.0 94 0.002 20.9 3.2 23 12-34 109-132 (141)
141 COG1363 FrvX Cellulase M and r 26.6 81 0.0018 24.6 3.1 24 12-35 94-117 (355)
142 PF03614 Flag1_repress: Repres 26.5 86 0.0019 22.2 3.0 25 14-38 119-143 (165)
143 cd05790 S1_Rrp40 S1_Rrp40: Rrp 26.1 1.1E+02 0.0023 19.1 3.1 26 19-44 47-72 (86)
144 PF11525 CopK: Copper resistan 25.8 56 0.0012 20.3 1.7 38 18-55 8-51 (73)
145 PRK06804 flgA flagellar basal 25.7 92 0.002 23.2 3.2 23 12-34 230-253 (261)
146 PRK10113 cell division modulat 25.5 9.5 0.00021 23.8 -1.7 23 56-78 48-71 (80)
147 TIGR01462 greA transcription e 25.4 1.8E+02 0.0038 19.4 4.3 31 2-33 116-148 (151)
148 PF10729 CedA: Cell division a 25.3 8.8 0.00019 24.0 -1.9 23 56-78 48-71 (80)
149 PRK00226 greA transcription el 24.8 1.7E+02 0.0036 19.6 4.1 32 2-34 121-154 (157)
150 PF05071 NDUFA12: NADH ubiquin 24.7 47 0.001 21.2 1.3 17 30-46 1-17 (105)
151 TIGR00046 RNA methyltransferas 24.1 1.6E+02 0.0035 21.0 4.2 37 8-44 28-65 (240)
152 PRK08477 biotin--protein ligas 24.1 2.5E+02 0.0054 20.0 5.1 38 11-49 171-208 (211)
153 PRK10708 hypothetical protein; 23.5 99 0.0021 18.5 2.4 26 14-39 3-28 (62)
154 PF14485 DUF4431: Domain of un 22.8 1.1E+02 0.0024 17.1 2.4 14 8-21 12-25 (48)
155 PF11717 Tudor-knot: RNA bindi 22.7 1.5E+02 0.0033 16.4 3.3 24 14-37 3-26 (55)
156 cd05697 S1_Rrp5_repeat_hs5 S1_ 22.5 96 0.0021 17.3 2.3 20 25-44 1-21 (69)
157 PRK00802 3-methyladenine DNA g 22.4 1.7E+02 0.0037 20.9 4.0 31 6-40 14-44 (188)
158 PF13619 KTSC: KTSC domain 21.9 1.3E+02 0.0028 17.0 2.7 18 12-29 12-29 (60)
159 PF14153 Spore_coat_CotO: Spor 21.8 81 0.0017 22.5 2.2 38 1-38 117-157 (185)
160 PRK08035 type III secretion sy 21.6 1.8E+02 0.004 22.5 4.2 36 11-46 281-316 (323)
161 PF13876 Phage_gp49_66: Phage 21.5 1.4E+02 0.0031 18.5 3.0 22 16-37 27-48 (81)
162 PF13144 SAF_2: SAF-like 21.5 1.5E+02 0.0034 20.1 3.5 23 12-34 167-190 (196)
163 PF12869 tRNA_anti-like: tRNA_ 21.3 1.3E+02 0.0029 19.1 3.0 27 13-47 118-144 (144)
164 TIGR02480 fliN flagellar motor 21.1 2E+02 0.0042 17.0 4.4 35 12-46 39-73 (77)
165 PF14563 DUF4444: Domain of un 20.9 1E+02 0.0022 17.2 2.0 22 28-49 10-31 (42)
166 PF02014 Reeler: Reeler domain 20.1 1.1E+02 0.0023 19.7 2.4 24 13-36 31-56 (132)
No 1
>KOG3172|consensus
Probab=99.92 E-value=9.3e-26 Score=148.86 Aligned_cols=72 Identities=57% Similarity=0.971 Sum_probs=68.4
Q ss_pred CCcCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE----------------ecCcccccc
Q psy14196 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY----------------YLPALVPIA 64 (79)
Q Consensus 1 m~~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~----------------~lp~~l~~~ 64 (79)
||+++|+++|++++|+.|++|+++|..|+|+|+++|++||++|+|++.|.+||++ ++||||++|
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 7899999999999999999999999999999999999999999999999999965 999999999
Q ss_pred ccccccce
Q psy14196 65 GMWNGTSG 72 (79)
Q Consensus 65 p~~~~~~~ 72 (79)
||||..++
T Consensus 81 PmFkk~~~ 88 (119)
T KOG3172|consen 81 PMFKKGKS 88 (119)
T ss_pred cccccccC
Confidence 99997543
No 2
>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=99.87 E-value=1.5e-21 Score=118.91 Aligned_cols=67 Identities=55% Similarity=0.899 Sum_probs=60.1
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
|+++|++++|+.|+||||||++|+|+|.+||+|||++|+||++++++|+. .+..-+|-|++++||+-
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~-----~~~~~v~IRG~nI~~v~ 67 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRV-----SQLEQVYIRGSKIRFFI 67 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcE-----eEcCcEEEeCCEEEEEE
Confidence 89999999999999999999999999999999999999999998888864 12245889999999973
No 3
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.84 E-value=1.7e-20 Score=116.75 Aligned_cols=70 Identities=23% Similarity=0.357 Sum_probs=61.8
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
...+..||+++.|++|+||||||.+|+|+|.+||+|||++|+||++++++|+.. ....+|-|++++||+.
T Consensus 7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~-----~~~~v~IRG~nI~yI~ 76 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQV-----QVEEIMVTGRNIRYVH 76 (78)
T ss_pred hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCcee-----ECCcEEEECCEEEEEE
Confidence 467899999999999999999999999999999999999999999998777541 2345789999999974
No 4
>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=99.84 E-value=1.1e-20 Score=120.44 Aligned_cols=64 Identities=19% Similarity=0.376 Sum_probs=57.4
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE----------------ecCccccccccccc
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY----------------YLPALVPIAGMWNG 69 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~----------------~lp~~l~~~p~~~~ 69 (79)
|+.||++++|++|+||||||++|+|+|.+||+|||++|+||+++..+|+. +|||+|...+.|-.
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 68999999999999999999999999999999999999999999777643 88999888775443
No 5
>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=99.83 E-value=3.6e-20 Score=114.26 Aligned_cols=69 Identities=25% Similarity=0.510 Sum_probs=60.4
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
.|++||+++.|++|+||||||.+|+|+|.+||+|||++|+||++++.+|+..- ....+|-|+++.||+.
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~----~~~~v~IRG~~I~~i~ 69 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFW----KMPECYIRGNTIKYLR 69 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEee----eCCcEEEeCCEEEEEE
Confidence 59999999999999999999999999999999999999999999988885410 1135788999999874
No 6
>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=99.82 E-value=1.2e-19 Score=109.41 Aligned_cols=65 Identities=15% Similarity=0.196 Sum_probs=56.3
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-ecCccccccccccccceeEEe
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~~ 76 (79)
|+++|++++|++|+||||||.+|+|+|.+||+|||++|+||+++..+++. .++. +|-|++++||.
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~------v~IRG~~I~~I 66 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGD------AFIRGNNVLYI 66 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCC------EEEECCEEEEE
Confidence 89999999999999999999999999999999999999999997544333 4443 67888888875
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=99.81 E-value=2.5e-19 Score=111.98 Aligned_cols=70 Identities=19% Similarity=0.318 Sum_probs=58.7
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
.|+.||+++.|+.|+||||||++|+|+|.+||+|||++|+||+++++++. +......-+|-|++.+||+.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~---~~~~~~~~v~IRG~~I~~I~ 70 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY---PHMLSVKNCFIRGSVVRYVQ 70 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc---ccccccCeEEEECCEEEEEE
Confidence 48899999999999999999999999999999999999999999875542 12222234788999999874
No 8
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.78 E-value=2.9e-18 Score=104.77 Aligned_cols=71 Identities=15% Similarity=0.219 Sum_probs=58.8
Q ss_pred CCcCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 1 m~~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
|+ ..|+++|+++.|++|+|+||||.+|+|+|.+||+|||++|+||+|+..++.. -+..-+|-|++++++..
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-QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVV-----RKLGKVVIRGDNVVYVS 71 (72)
T ss_pred CC-cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeE-----eEcCcEEEeCCEEEEEc
Confidence 56 6999999999999999999999999999999999999999999997533222 11223678888888763
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=99.77 E-value=2.8e-18 Score=103.78 Aligned_cols=66 Identities=17% Similarity=0.250 Sum_probs=55.5
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-ecCccccccccccccceeEEe
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~~ 76 (79)
.|+++|+++.|++|+|+||||.+|+|+|.++|+|||++|+||++...+++. .++ -+|-|+++++|.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg------~~~IRG~~I~~i 67 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLG------EVLIRCNNVLYI 67 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcC------cEEEECCEEEEE
Confidence 499999999999999999999999999999999999999999997433222 333 366888888875
No 10
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.74 E-value=2.1e-17 Score=99.55 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=56.7
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-ecCccccccccccccceeEEee
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
|+++|+++.|++|+|+||||.+|+|+|.++|+|||++|+||+|+..+++. .++ -+|-|+++++|.+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg------~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYG------RVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcC------cEEEeCCEEEEEc
Confidence 89999999999999999999999999999999999999999998655432 332 3678888888764
No 11
>KOG3482|consensus
Probab=99.69 E-value=1.8e-17 Score=103.07 Aligned_cols=61 Identities=21% Similarity=0.289 Sum_probs=53.9
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE--ecCcccccc
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY--YLPALVPIA 64 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~--~lp~~l~~~ 64 (79)
...|..||+.++|++|.|+||||.+|+|+|+++|.|||++|.+|+|. .||.. .|.+++..+
T Consensus 6 PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRC 68 (79)
T KOG3482|consen 6 PVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRC 68 (79)
T ss_pred cCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEe
Confidence 34789999999999999999999999999999999999999999995 68866 777765433
No 12
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.69 E-value=1.6e-16 Score=98.11 Aligned_cols=72 Identities=19% Similarity=0.298 Sum_probs=57.8
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEcc-CCeEecCcccccc-ccccccceeEEee
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR-DGTYYLPALVPIA-GMWNGTSGLRWAT 77 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~-~G~~~lp~~l~~~-p~~~~~~~~~~~~ 77 (79)
...|+++|++++|++|.|+||||.+|+|+|.+||+|||++|+||+|+.. +|... ..+.- -.|-||+.+++..
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~---~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKN---VRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccc---cceeccEEEEECCcEEEEe
Confidence 4578999999999999999999999999999999999999999999853 44221 11222 4677888877753
No 13
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.64 E-value=7.8e-16 Score=91.33 Aligned_cols=64 Identities=30% Similarity=0.480 Sum_probs=54.7
Q ss_pred HHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCC-eE-ecCccccccccccccceeEEee
Q psy14196 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-TY-YLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 8 ~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G-~~-~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
.+|+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++..++ +. .+ .-+|-|+++++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~------~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSL------GLVFIRGSNIRYIS 66 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEE------EEEEEEGGGEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeEC------cEEEEECCEEEEEE
Confidence 4799999999999999999999999999999999999999987554 22 33 33778888888875
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.64 E-value=1.1e-15 Score=90.46 Aligned_cols=64 Identities=25% Similarity=0.332 Sum_probs=53.9
Q ss_pred HHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccC-CeE-ecCccccccccccccceeEEee
Q psy14196 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-GTY-YLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 8 ~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~-G~~-~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
.+|+++.|+.|+|+|+||++|.|+|.++|+|||++|+||+++..+ ++. .++ -+|-|++.++++.
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~------~~~IrG~~I~~i~ 66 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLG------LVFIRGNNIVYII 66 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeC------CEEEcCCEEEEEe
Confidence 378999999999999999999999999999999999999998765 222 333 3677888888763
No 15
>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=99.64 E-value=1.1e-15 Score=94.75 Aligned_cols=47 Identities=26% Similarity=0.332 Sum_probs=45.2
Q ss_pred CchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc
Q psy14196 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF 50 (79)
Q Consensus 4 ~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~ 50 (79)
..|+++|+++.+++|.|+||||++|.|+|.+||.|||++|+||+|..
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~ 48 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYE 48 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEE
Confidence 47999999999999999999999999999999999999999999985
No 16
>KOG3293|consensus
Probab=99.64 E-value=3.4e-16 Score=105.48 Aligned_cols=66 Identities=27% Similarity=0.538 Sum_probs=58.4
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE--ecCccccccccccccceeEEe
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY--YLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~--~lp~~l~~~p~~~~~~~~~~~ 76 (79)
+||.+|..++|+++.||||||++|.|.|.+||.+||++|++|+++.+||.. .+|+ +..|++..+|.
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pE------cYirGttIkyl 69 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPE------CYIRGTTIKYL 69 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecce------eEEecceeEEE
Confidence 799999999999999999999999999999999999999999999999955 5554 45666666665
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=99.59 E-value=5.8e-15 Score=86.20 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=50.7
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEe
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~ 76 (79)
|++++|++|+|+|+||..|.|+|.++|++||++|+||+++..+++. -...-+|-|++.++++
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~-----~~~~~~~irG~~I~~I 62 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKK-----RVLGLVLIRGDNVRLV 62 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcE-----EECCeEEEECCEEEEE
Confidence 5788999999999999999999999999999999999998655332 2222366777777775
No 18
>KOG3448|consensus
Probab=99.58 E-value=6.8e-15 Score=94.46 Aligned_cols=68 Identities=19% Similarity=0.304 Sum_probs=64.2
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEee
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
..|.+.++|+.|+|||||+..++|+|-++|+|.|+.|.|+.+++++ ..|.|.....+|.|||.+||+-
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~---kyPhm~Sv~ncfIRGSvvrYv~ 71 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPD---KYPHMLSVKNCFIRGSVVRYVQ 71 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcc---cCCCeeeeeeEEEeccEEEEEE
Confidence 3688899999999999999999999999999999999999999876 7999999999999999999984
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=99.57 E-value=5.3e-15 Score=92.25 Aligned_cols=46 Identities=20% Similarity=0.334 Sum_probs=44.3
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF 50 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~ 50 (79)
.|+++|+.+.++.|.|+||||++|.|+|.+||.|||++|+||+|..
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~ 46 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETI 46 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEe
Confidence 3999999999999999999999999999999999999999999974
No 20
>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=99.52 E-value=3.3e-14 Score=87.13 Aligned_cols=66 Identities=11% Similarity=0.005 Sum_probs=52.7
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-ecCccccccccccccceeEEee
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRWAT 77 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~~~ 77 (79)
|-..|++..+++|.|+||+|.+|+|+|.++|+|||++|+||+|+..+++. .++ -+|-|++++.+..
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg------~v~IRG~~I~~i~ 67 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIG------MVVIRGNSIVMLE 67 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEec------eEEECCCEEEEEE
Confidence 45789999999999999999999999999999999999999997533221 222 2566777776643
No 21
>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=99.49 E-value=8e-14 Score=88.59 Aligned_cols=74 Identities=12% Similarity=0.128 Sum_probs=55.1
Q ss_pred chHHHHhhcC--CCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-------ecCccccccc-cccccceeE
Q psy14196 5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-------YLPALVPIAG-MWNGTSGLR 74 (79)
Q Consensus 5 ~Pl~lL~~~~--g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-------~lp~~l~~~p-~~~~~~~~~ 74 (79)
-|+++|+.+. |+.|.|+||+|.+|.|+|.+||.|||++|+||+|+...... .....-+..+ .|-|+.++=
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 89999999999999999999999999999999997422110 1111122222 667777766
Q ss_pred Eeec
Q psy14196 75 WATQ 78 (79)
Q Consensus 75 ~~~~ 78 (79)
++++
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 6554
No 22
>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=99.38 E-value=1.4e-12 Score=81.45 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=40.1
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEcc
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR 51 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~ 51 (79)
|.+.+|+.|.|.|++|++|.|+|.++|.|||++|+||+|...
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~ 48 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLR 48 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEc
Confidence 888999999999999999999999999999999999999753
No 23
>KOG1783|consensus
Probab=99.37 E-value=1.1e-13 Score=86.14 Aligned_cols=68 Identities=19% Similarity=0.298 Sum_probs=57.7
Q ss_pred CchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeEecCccccccccccccceeEEe
Q psy14196 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 4 ~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~~lp~~l~~~p~~~~~~~~~~~ 76 (79)
..|-+||.+.+|++|.|+|.+|..|+|+|+..|+|||+.|+.++|. .+|| +|.-. ..+|.|++++-|.
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~-~ngq--l~n~y--gdaFirGnnVlyI 72 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEY-VNGQ--LKNKY--GDAFIRGNNVLYI 72 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHH-hcCc--ccccc--cceeeccccEEEE
Confidence 5899999999999999999999999999999999999999999996 4774 44332 2567788877765
No 24
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.34 E-value=3.6e-12 Score=79.90 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=44.0
Q ss_pred CchHHHHhhcCCC--eEEEEec--CCcEEEEEEeEeCCccceEEeeeEEEcc
Q psy14196 4 GIPIKLLHEAEGH--IITCETT--NGDLFRGKLVEAEDNMNCAMADVTVTFR 51 (79)
Q Consensus 4 ~~Pl~lL~~~~g~--~V~VeLK--nG~~y~G~L~~~D~~MNv~L~n~~~~~~ 51 (79)
..|+++|.....+ +|.|.|+ +|.+|.|+|.++|+|||++|+||+|...
T Consensus 5 ~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~ 56 (79)
T cd01718 5 VQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHL 56 (79)
T ss_pred cCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEec
Confidence 4699999999999 7888888 9999999999999999999999999853
No 25
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.32 E-value=6.5e-12 Score=77.59 Aligned_cols=47 Identities=13% Similarity=0.062 Sum_probs=42.4
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccC
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD 52 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~ 52 (79)
+..-|.+..++.|.|.|++|++|.|+|.++|+|||++|+||.|...+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~ 49 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYV 49 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEec
Confidence 35568899999999999999999999999999999999999887433
No 26
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.29 E-value=7.1e-12 Score=77.47 Aligned_cols=42 Identities=14% Similarity=0.219 Sum_probs=39.3
Q ss_pred HHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc
Q psy14196 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF 50 (79)
Q Consensus 9 lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~ 50 (79)
=|.+.+|++|.|.|++|++|.|+|.++|.|||++|+||+|..
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~ 45 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFR 45 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEE
Confidence 367889999999999999999999999999999999999963
No 27
>KOG3428|consensus
Probab=99.24 E-value=2.8e-11 Score=79.90 Aligned_cols=63 Identities=19% Similarity=0.327 Sum_probs=54.9
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE----------------ecCccccccccccc
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY----------------YLPALVPIAGMWNG 69 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~----------------~lp~~l~~~p~~~~ 69 (79)
-+.||.++.+.+|+||||||+..+|+|.++|..||..|.+++.+.++ +. ++||.+...+.+..
T Consensus 3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ld~Llvd 81 (109)
T KOG3428|consen 3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLNLDTLLVD 81 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcCcceeeee
Confidence 36899999999999999999999999999999999999999998752 22 88998888775543
No 28
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.22 E-value=3.5e-11 Score=74.45 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=41.1
Q ss_pred HHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEcc
Q psy14196 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFR 51 (79)
Q Consensus 8 ~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~ 51 (79)
+-|.+..|++|.|.|+||+.|.|+|.++|.+||++|+||.|...
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~ 46 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRP 46 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEc
Confidence 46888999999999999999999999999999999999999853
No 29
>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=99.21 E-value=3.8e-11 Score=73.49 Aligned_cols=42 Identities=17% Similarity=0.231 Sum_probs=39.7
Q ss_pred HHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc
Q psy14196 9 LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF 50 (79)
Q Consensus 9 lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~ 50 (79)
-|.+..++.|.|.|++|..|.|+|.++|.|||++|++|+|..
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~ 44 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERV 44 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEE
Confidence 478889999999999999999999999999999999999974
No 30
>KOG1775|consensus
Probab=99.15 E-value=1.2e-11 Score=77.74 Aligned_cols=61 Identities=25% Similarity=0.287 Sum_probs=53.8
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc--cCCeE--ecCccccc
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDGTY--YLPALVPI 63 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~--~~G~~--~lp~~l~~ 63 (79)
.-.|+.++.+.+|+.+.|-+|+..++.|+|.++|+|.|++|+||+|.. ++|+. .+..+|.+
T Consensus 5 ~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLn 69 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLN 69 (84)
T ss_pred hcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeec
Confidence 458999999999999999999999999999999999999999999874 56665 66666654
No 31
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.02 E-value=7.6e-10 Score=70.78 Aligned_cols=67 Identities=12% Similarity=0.115 Sum_probs=48.3
Q ss_pred CchHHHHhhcCCCe--EEEEecC--CcEEEEEEeEeCCccceEEeeeEEEccCCeE--ecCccccccccccccceeEEe
Q psy14196 4 GIPIKLLHEAEGHI--ITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFRDGTY--YLPALVPIAGMWNGTSGLRWA 76 (79)
Q Consensus 4 ~~Pl~lL~~~~g~~--V~VeLKn--G~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~--~lp~~l~~~p~~~~~~~~~~~ 76 (79)
..|++++.++.... |.|.+++ +.+|.|+|.+||.|||++|+||+|...++.. .++. .|.|++++=|.
T Consensus 13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~------ilIRGnnV~~I 85 (89)
T PTZ00138 13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGR------ILLKGDNITLI 85 (89)
T ss_pred cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCe------EEEcCCEEEEE
Confidence 46899999977654 6666656 5899999999999999999999997533311 3333 45566655543
No 32
>KOG3460|consensus
Probab=98.80 E-value=8.5e-10 Score=70.35 Aligned_cols=73 Identities=15% Similarity=0.217 Sum_probs=56.2
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc--cCCeE-----ecCccccccc-cccccceeE
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF--RDGTY-----YLPALVPIAG-MWNGTSGLR 74 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~--~~G~~-----~lp~~l~~~p-~~~~~~~~~ 74 (79)
..-|+++|+-+....|.|+++++.+++|+|..||.|.|++|.||+++- .++.- ++...=+..| .|-||.++-
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi 82 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI 82 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence 457999999999999999999999999999999999999999998862 12211 4444445555 456665544
Q ss_pred E
Q psy14196 75 W 75 (79)
Q Consensus 75 ~ 75 (79)
.
T Consensus 83 l 83 (91)
T KOG3460|consen 83 L 83 (91)
T ss_pred E
Confidence 3
No 33
>KOG1780|consensus
Probab=98.78 E-value=6.9e-09 Score=64.76 Aligned_cols=52 Identities=23% Similarity=0.227 Sum_probs=46.1
Q ss_pred CCcC-chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCe
Q psy14196 1 MSIG-IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54 (79)
Q Consensus 1 m~~~-~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~ 54 (79)
||-+ .| =|.+...+.+.++|..|+..+|.|.+||.|||++|+++.|...+|.
T Consensus 1 Msksg~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~ 53 (77)
T KOG1780|consen 1 MSKSGHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD 53 (77)
T ss_pred CCcccCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC
Confidence 4433 67 6889999999999999999999999999999999999999876663
No 34
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.11 E-value=1.5e-05 Score=48.55 Aligned_cols=45 Identities=18% Similarity=0.337 Sum_probs=37.2
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCC---ccceEEeeeEEEcc
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED---NMNCAMADVTVTFR 51 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~---~MNv~L~n~~~~~~ 51 (79)
+-++..++|++|.|.+|||..|.|.+.+++. -+.++|+.++....
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 4567889999999999999999999999999 89999999999753
No 35
>KOG1774|consensus
Probab=97.96 E-value=5.8e-06 Score=52.62 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=34.1
Q ss_pred chHHHHhhc--CCCeEEEEecC--CcEEEEEEeEeCCccceEEeeeEEEcc
Q psy14196 5 IPIKLLHEA--EGHIITCETTN--GDLFRGKLVEAEDNMNCAMADVTVTFR 51 (79)
Q Consensus 5 ~Pl~lL~~~--~g~~V~VeLKn--G~~y~G~L~~~D~~MNv~L~n~~~~~~ 51 (79)
.|+.++... .-.+|.|=|.. |.-..|.++++|.|||++|++|+|.+.
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~ 62 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHS 62 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccc
Confidence 455444442 12345555554 888999999999999999999999863
No 36
>KOG1781|consensus
Probab=97.66 E-value=2.8e-06 Score=55.71 Aligned_cols=43 Identities=23% Similarity=0.232 Sum_probs=38.7
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccC
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD 52 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~ 52 (79)
|.+-..+.|.|++..|++..|.|.+||+-||++|+|+.|.-+|
T Consensus 22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrd 64 (108)
T KOG1781|consen 22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRD 64 (108)
T ss_pred HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcC
Confidence 4567789999999999999999999999999999999987543
No 37
>KOG3168|consensus
Probab=97.60 E-value=6.1e-06 Score=58.39 Aligned_cols=48 Identities=19% Similarity=0.299 Sum_probs=41.9
Q ss_pred CCcCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEE
Q psy14196 1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 1 m~~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
|++.-+.++|+ .++....|.+++|++|.|.+..+|.|||++|.||+|.
T Consensus 1 M~~a~sskml~-~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~ 48 (177)
T KOG3168|consen 1 MTVAKSSKMLQ-HINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEF 48 (177)
T ss_pred CCccchhHHHH-hhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHH
Confidence 56666666665 4688999999999999999999999999999999885
No 38
>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=97.09 E-value=0.00043 Score=42.34 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=29.0
Q ss_pred CCeEEEEec--CC--cEEEEEEeEeCCccceEEeeeEEEccC
Q psy14196 15 GHIITCETT--NG--DLFRGKLVEAEDNMNCAMADVTVTFRD 52 (79)
Q Consensus 15 g~~V~VeLK--nG--~~y~G~L~~~D~~MNv~L~n~~~~~~~ 52 (79)
+..|.|-++ +| -...|.|+.+|.|||+.|.||.|+...
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 345555444 43 468899999999999999999998643
No 39
>KOG1784|consensus
Probab=96.49 E-value=0.0034 Score=40.74 Aligned_cols=40 Identities=15% Similarity=0.241 Sum_probs=37.2
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEE
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
|....++.|.|-..+|+.+-|.|.+||+.-|+.++|+-+.
T Consensus 5 L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heR 44 (96)
T KOG1784|consen 5 LEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHER 44 (96)
T ss_pred HHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhh
Confidence 6778899999999999999999999999999999998764
No 40
>KOG1782|consensus
Probab=95.60 E-value=0.00082 Score=45.59 Aligned_cols=40 Identities=18% Similarity=0.109 Sum_probs=36.8
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEE
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
|-+...+.+.|-|++|+...|.|.++|+|-|++|.+|.|.
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iER 53 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIER 53 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhh
Confidence 5667788999999999999999999999999999998875
No 41
>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=95.36 E-value=0.029 Score=33.69 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=27.2
Q ss_pred HHhhc--CCCeEEEEecCCcEEEEEEeEeCCccce
Q psy14196 9 LLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNC 41 (79)
Q Consensus 9 lL~~~--~g~~V~VeLKnG~~y~G~L~~~D~~MNv 41 (79)
||+++ .+.+|+|-|.||...+|.+.++|.|+=+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl 37 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVL 37 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE
Confidence 45543 4567999999999999999999999733
No 42
>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=95.28 E-value=0.031 Score=33.64 Aligned_cols=34 Identities=18% Similarity=0.173 Sum_probs=27.9
Q ss_pred HHHhhc--CCCeEEEEecCCcEEEEEEeEeCCccce
Q psy14196 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNC 41 (79)
Q Consensus 8 ~lL~~~--~g~~V~VeLKnG~~y~G~L~~~D~~MNv 41 (79)
.+|+.+ .+.+|+|-|.||...+|.+.++|.|+=+
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVl 41 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVL 41 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEE
Confidence 455553 4678999999999999999999999743
No 43
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.17 E-value=0.071 Score=34.39 Aligned_cols=43 Identities=14% Similarity=0.164 Sum_probs=38.2
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCC-ccceEEeeeEEEccCCe
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTVTFRDGT 54 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~-~MNv~L~n~~~~~~~G~ 54 (79)
..+|+.|.+..|++--|.|+|..+|. .-.+.|+||...-.+|+
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R 48 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGR 48 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTS
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCC
Confidence 46899999999999999999999998 56999999999765554
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.46 E-value=0.064 Score=33.79 Aligned_cols=35 Identities=17% Similarity=0.167 Sum_probs=28.6
Q ss_pred HHHhhc--CCCeEEEEecCCcEEEEEEeEeCCccceE
Q psy14196 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNCA 42 (79)
Q Consensus 8 ~lL~~~--~g~~V~VeLKnG~~y~G~L~~~D~~MNv~ 42 (79)
.||+.+ .+.+|+|-|.||...+|.+.++|.|.=+.
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll 46 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLL 46 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEE
Confidence 455553 46789999999999999999999997443
No 45
>PRK14638 hypothetical protein; Provisional
Probab=94.36 E-value=0.11 Score=35.65 Aligned_cols=41 Identities=20% Similarity=0.347 Sum_probs=31.8
Q ss_pred cCchH---HHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..+|+ .=.....|+.|.|+++++..++|+|.++|+. ++.|.
T Consensus 85 ldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 85 LDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 34555 3345789999999999999999999999974 34443
No 46
>PRK14639 hypothetical protein; Provisional
Probab=93.90 E-value=0.15 Score=34.54 Aligned_cols=41 Identities=20% Similarity=0.450 Sum_probs=32.1
Q ss_pred cCchH---HHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..+|+ .-.....|+.|.|+++++..+.|+|.++|+. ++.|+
T Consensus 73 l~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 73 LERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 34555 3355789999999999999999999999984 45443
No 47
>PRK02001 hypothetical protein; Validated
Probab=93.18 E-value=0.23 Score=34.25 Aligned_cols=40 Identities=25% Similarity=0.454 Sum_probs=31.5
Q ss_pred cCchHH---HHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEE
Q psy14196 3 IGIPIK---LLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L 43 (79)
..+|+. =.....|+.|.|.++++..|.|+|.++|+. ++.|
T Consensus 75 ldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 75 LTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 345553 345789999999999999999999999985 3444
No 48
>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=93.15 E-value=0.41 Score=26.61 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=27.8
Q ss_pred CCCeEEEEecCCcEEEEEEeEeCCccceEEee
Q psy14196 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 14 ~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n 45 (79)
.|+.|+|++ ++..++|+...+|+.-.+.++.
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 6677799999999999999875
No 49
>KOG3459|consensus
Probab=93.14 E-value=0.011 Score=39.39 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=40.0
Q ss_pred chHHHHhhcC--CCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEE
Q psy14196 5 IPIKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 5 ~Pl~lL~~~~--g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
=|++++..+. ..+|.|-++|....-|++..+|-+.|++|+|+++.
T Consensus 24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkel 70 (114)
T KOG3459|consen 24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKEL 70 (114)
T ss_pred CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHH
Confidence 3788888765 56799999999999999999999999999999875
No 50
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=93.10 E-value=0.32 Score=29.11 Aligned_cols=33 Identities=15% Similarity=0.298 Sum_probs=29.0
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEee
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n 45 (79)
++|..|.+++-.|++++|.+..||..-++..=.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 579999999999999999999999988665443
No 51
>PRK14644 hypothetical protein; Provisional
Probab=92.85 E-value=0.22 Score=33.76 Aligned_cols=41 Identities=20% Similarity=0.377 Sum_probs=32.6
Q ss_pred cCchHHH--HhhcCCCeEEEEecCC----cEEEEEEeEeCCccceEEe
Q psy14196 3 IGIPIKL--LHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 3 ~~~Pl~l--L~~~~g~~V~VeLKnG----~~y~G~L~~~D~~MNv~L~ 44 (79)
..+|+.- +....|+.|.|+|++. ..+.|.|.++|+. ++.|+
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 4456644 6678999999999987 9999999999984 45554
No 52
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=92.42 E-value=0.39 Score=29.19 Aligned_cols=30 Identities=30% Similarity=0.504 Sum_probs=26.2
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCC
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
...|++++|+.|.|++-.|+. +|+|.++-.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~p 42 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKP 42 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecC
Confidence 368999999999999988776 999998865
No 53
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=92.37 E-value=0.29 Score=30.74 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=27.5
Q ss_pred HHHhh--cCCCeEEEEecCCcEEEEEEeEeCCcc
Q psy14196 8 KLLHE--AEGHIITCETTNGDLFRGKLVEAEDNM 39 (79)
Q Consensus 8 ~lL~~--~~g~~V~VeLKnG~~y~G~L~~~D~~M 39 (79)
.||+. ..+.+|+|-|.||...+|.+.++|.|-
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 46665 457789999999999999999999984
No 54
>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=92.07 E-value=0.92 Score=28.55 Aligned_cols=45 Identities=9% Similarity=0.165 Sum_probs=37.1
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCCcc-ceEEeeeEEEccCC
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNM-NCAMADVTVTFRDG 53 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~M-Nv~L~n~~~~~~~G 53 (79)
|.+|..+.|++|.+.|..+.+..|+...+|..- |+..+|-+ ++=|
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlG 61 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLG 61 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTT
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCcc
Confidence 578889999999999999999999999999966 88888843 3556
No 55
>PRK14640 hypothetical protein; Provisional
Probab=91.22 E-value=0.54 Score=32.17 Aligned_cols=40 Identities=13% Similarity=0.274 Sum_probs=30.3
Q ss_pred cCchH---HHHhhcCCCeEEEEe----cCCcEEEEEEeEeCCccceEE
Q psy14196 3 IGIPI---KLLHEAEGHIITCET----TNGDLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeL----KnG~~y~G~L~~~D~~MNv~L 43 (79)
..+|+ .=.....|+.|.|+| .++..|+|+|.++|+. ++.|
T Consensus 82 l~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 82 LDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 34555 334578999999999 5679999999999985 3444
No 56
>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=91.16 E-value=1.1 Score=27.84 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=38.4
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCCcc-ceEEeeeEEEccCCeE
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAEDNM-NCAMADVTVTFRDGTY 55 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~~M-Nv~L~n~~~~~~~G~~ 55 (79)
..+|+.+.+-.|++--|.|.|.++|..= -+.|+||...-.+|+.
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~ 47 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRP 47 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCC
Confidence 4689999999999999999999999865 7889999988666654
No 57
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.34 E-value=1.2 Score=30.99 Aligned_cols=37 Identities=19% Similarity=0.372 Sum_probs=30.9
Q ss_pred cCchHH---HHhhcCCCeEEEEe----cCCcEEEEEEeEeCCcc
Q psy14196 3 IGIPIK---LLHEAEGHIITCET----TNGDLFRGKLVEAEDNM 39 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeL----KnG~~y~G~L~~~D~~M 39 (79)
..+|+. -.....|+.|.|+| .++..+.|+|..+|+..
T Consensus 84 ldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 84 LDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred CCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 446663 44568999999999 78999999999999987
No 58
>PRK14632 hypothetical protein; Provisional
Probab=89.53 E-value=0.84 Score=31.95 Aligned_cols=41 Identities=20% Similarity=0.362 Sum_probs=30.8
Q ss_pred cCchH---HHHhhcCCCeEEEEecC-------CcEEEEEEeEeCCccceEEe
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTN-------GDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKn-------G~~y~G~L~~~D~~MNv~L~ 44 (79)
..+|| .=....+|+.|.|+|++ ...|.|+|.++|+. ++.|+
T Consensus 83 ldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 83 LERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 34555 33457899999999986 57999999999874 45554
No 59
>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=89.30 E-value=0.9 Score=27.81 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=24.9
Q ss_pred HhhcCCCeEEEEec---CC-cEEEEEEeEeCCc
Q psy14196 10 LHEAEGHIITCETT---NG-DLFRGKLVEAEDN 38 (79)
Q Consensus 10 L~~~~g~~V~VeLK---nG-~~y~G~L~~~D~~ 38 (79)
.....|+.|.|+++ +| ..+.|.|.++|+.
T Consensus 20 ~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 20 FERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 45689999999998 55 6899999999984
No 60
>PRK14636 hypothetical protein; Provisional
Probab=89.23 E-value=0.91 Score=31.95 Aligned_cols=34 Identities=21% Similarity=0.401 Sum_probs=27.1
Q ss_pred HHhhcCCCeEEEEec---CC-cEEEEEEeEeCCccceEE
Q psy14196 9 LLHEAEGHIITCETT---NG-DLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 9 lL~~~~g~~V~VeLK---nG-~~y~G~L~~~D~~MNv~L 43 (79)
=.....|+.|.|+|+ +| ..|+|+|.++|+. ++.|
T Consensus 92 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 92 DFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 345789999999998 55 6999999999883 3444
No 61
>PRK14645 hypothetical protein; Provisional
Probab=89.14 E-value=0.93 Score=31.26 Aligned_cols=35 Identities=14% Similarity=0.306 Sum_probs=27.8
Q ss_pred cCchH---HHHhhcCCCeEEEEecCCcEEEEEEeEeCCc
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~ 38 (79)
..+|| .-.....|+.|.|.+ ++..|.|+|.++|+.
T Consensus 87 ldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 87 PKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 34555 334568899999986 889999999999985
No 62
>PRK14642 hypothetical protein; Provisional
Probab=88.98 E-value=0.67 Score=33.46 Aligned_cols=40 Identities=28% Similarity=0.466 Sum_probs=31.1
Q ss_pred cCchHHH---HhhcCCCeEEEEec-------------CCcEEEEEEeEeCCccceEE
Q psy14196 3 IGIPIKL---LHEAEGHIITCETT-------------NGDLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl~l---L~~~~g~~V~VeLK-------------nG~~y~G~L~~~D~~MNv~L 43 (79)
+.+||.- .....|+.|.|+|+ +...|+|+|.++|+. +++|
T Consensus 85 ldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 85 IDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 4456643 34578999999999 789999999999985 5555
No 63
>PRK14647 hypothetical protein; Provisional
Probab=88.89 E-value=1 Score=30.99 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=28.1
Q ss_pred cCchH---HHHhhcCCCeEEEEec---------CCcEEEEEEeEeCCc
Q psy14196 3 IGIPI---KLLHEAEGHIITCETT---------NGDLFRGKLVEAEDN 38 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLK---------nG~~y~G~L~~~D~~ 38 (79)
..+|+ .=+...+|+.|.|+|+ +...|.|+|.++|+.
T Consensus 84 ~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 84 LDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred CCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 34555 3355789999999996 358999999999973
No 64
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=88.81 E-value=1.1 Score=30.42 Aligned_cols=36 Identities=14% Similarity=0.331 Sum_probs=28.6
Q ss_pred cCchH---HHHhhcCCCeEEEEe----cCCcEEEEEEeEeCCc
Q psy14196 3 IGIPI---KLLHEAEGHIITCET----TNGDLFRGKLVEAEDN 38 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeL----KnG~~y~G~L~~~D~~ 38 (79)
..+|+ .=+...+|+.|.|++ .++..+.|+|.++|+.
T Consensus 83 i~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 83 LDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 34555 335679999999997 5778999999999983
No 65
>PRK14634 hypothetical protein; Provisional
Probab=88.55 E-value=1.1 Score=30.84 Aligned_cols=40 Identities=15% Similarity=0.338 Sum_probs=29.6
Q ss_pred cCchH---HHHhhcCCCeEEEEecCC----cEEEEEEeEeCCccceEE
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKnG----~~y~G~L~~~D~~MNv~L 43 (79)
..+|+ .=.....|+.|.|+|+.. ..|.|+|.++|+. ++.|
T Consensus 85 ldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 85 IGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 34555 234568999999999853 7999999999984 3444
No 66
>PRK14633 hypothetical protein; Provisional
Probab=88.23 E-value=1.3 Score=30.32 Aligned_cols=40 Identities=23% Similarity=0.262 Sum_probs=30.1
Q ss_pred cCchHH---HHhhcCCCeEEEEec----CCcEEEEEEeEeCCccceEE
Q psy14196 3 IGIPIK---LLHEAEGHIITCETT----NGDLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeLK----nG~~y~G~L~~~D~~MNv~L 43 (79)
..+|+. =.....|+.|.|+++ ++..|+|+|.++++. ++.|
T Consensus 79 ldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 79 MNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 345553 345689999999994 679999999999985 4444
No 67
>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=87.56 E-value=1.2 Score=29.58 Aligned_cols=35 Identities=23% Similarity=0.440 Sum_probs=24.9
Q ss_pred cCchH---HHHhhcCCCeEEEEec----CCcEEEEEEeEeCC
Q psy14196 3 IGIPI---KLLHEAEGHIITCETT----NGDLFRGKLVEAED 37 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLK----nG~~y~G~L~~~D~ 37 (79)
..+|+ .-+...+|+.|.|.++ +...|.|+|.++|+
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 45666 3467799999999994 45789999999999
No 68
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=87.13 E-value=1.8 Score=30.47 Aligned_cols=38 Identities=5% Similarity=0.203 Sum_probs=29.3
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCC-ccceEEeeeEE
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAED-NMNCAMADVTV 48 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~-~MNv~L~n~~~ 48 (79)
....+|+.|.|.+.| .+|.|-|..+|+ .-|++|-+-.+
T Consensus 12 ~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 12 WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 457899999999999 999999999999 55999986555
No 69
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=86.70 E-value=1 Score=31.88 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=27.8
Q ss_pred HHHhhc--CCCeEEEEecCCcEEEEEEeEeCCccce
Q psy14196 8 KLLHEA--EGHIITCETTNGDLFRGKLVEAEDNMNC 41 (79)
Q Consensus 8 ~lL~~~--~g~~V~VeLKnG~~y~G~L~~~D~~MNv 41 (79)
.||+.+ .+.+|+|-|.||...+|.+.++|.|.=+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvl 130 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCML 130 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEE
Confidence 455554 4567999999999999999999999733
No 70
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=85.86 E-value=1.2 Score=31.55 Aligned_cols=34 Identities=12% Similarity=0.007 Sum_probs=28.2
Q ss_pred HHHHhhcC--CCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 7 IKLLHEAE--GHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 7 l~lL~~~~--g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
-.||+.+. ..+|+|-|.||...+|.+.++|.|.=
T Consensus 14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftV 49 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSI 49 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEE
Confidence 35677654 55799999999999999999999963
No 71
>PRK14646 hypothetical protein; Provisional
Probab=85.55 E-value=2 Score=29.52 Aligned_cols=40 Identities=15% Similarity=0.271 Sum_probs=29.8
Q ss_pred cCchH---HHHhhcCCCeEEEEecCC----cEEEEEEeEeCCccceEE
Q psy14196 3 IGIPI---KLLHEAEGHIITCETTNG----DLFRGKLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLKnG----~~y~G~L~~~D~~MNv~L 43 (79)
..+|+ .=.....|+.|.|+|++. ..|+|+|.++|+. ++.|
T Consensus 85 ldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 85 VSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 34555 335668999999999753 6889999999985 4555
No 72
>PRK14631 hypothetical protein; Provisional
Probab=84.78 E-value=2.2 Score=30.01 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=27.2
Q ss_pred cCchH---HHHhhcCCCeEEEEec----CCcEEEEEEeEeC
Q psy14196 3 IGIPI---KLLHEAEGHIITCETT----NGDLFRGKLVEAE 36 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLK----nG~~y~G~L~~~D 36 (79)
..+|+ .=+....|+.|.|+|+ +...|+|+|.++|
T Consensus 102 ldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 102 WDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34555 3456789999999996 5599999999998
No 73
>PRK14641 hypothetical protein; Provisional
Probab=83.47 E-value=2.4 Score=29.86 Aligned_cols=34 Identities=21% Similarity=0.333 Sum_probs=26.5
Q ss_pred cCchHH---HHhhcCCCeEEEEecC----CcEEEEEEeEeC
Q psy14196 3 IGIPIK---LLHEAEGHIITCETTN----GDLFRGKLVEAE 36 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeLKn----G~~y~G~L~~~D 36 (79)
.++||. =.....|+.|.|+|++ ...|+|+|.++|
T Consensus 89 ldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 89 LGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 345553 3566899999999976 568999999995
No 74
>PRK14637 hypothetical protein; Provisional
Probab=83.25 E-value=2.9 Score=28.65 Aligned_cols=41 Identities=17% Similarity=0.166 Sum_probs=28.9
Q ss_pred cCchHH---HHhhcCCCeEEEEecCCcEE-EEEEeEeCCccceEEe
Q psy14196 3 IGIPIK---LLHEAEGHIITCETTNGDLF-RGKLVEAEDNMNCAMA 44 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeLKnG~~y-~G~L~~~D~~MNv~L~ 44 (79)
..+|+. =.....|+.|.|++.+...+ .|+|.++|+. ++.|.
T Consensus 83 ldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 83 IERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 345553 34568999999999544456 7999999985 44443
No 75
>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=81.85 E-value=1.3 Score=27.66 Aligned_cols=21 Identities=14% Similarity=0.137 Sum_probs=14.8
Q ss_pred hhcCCCeEEEEecCCcEEEEE
Q psy14196 11 HEAEGHIITCETTNGDLFRGK 31 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~ 31 (79)
-.+.+.+|.++||||+.+.|+
T Consensus 13 AC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 13 ACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHTTTT-EEEE-TTT--EEES
T ss_pred HHhcCCeEEEEEeCCCEEEEE
Confidence 346789999999999999998
No 76
>PRK14643 hypothetical protein; Provisional
Probab=81.41 E-value=3 Score=29.02 Aligned_cols=30 Identities=20% Similarity=0.164 Sum_probs=25.8
Q ss_pred HHhhcCCCeEEEEecC----CcEEEEEEeEeCCc
Q psy14196 9 LLHEAEGHIITCETTN----GDLFRGKLVEAEDN 38 (79)
Q Consensus 9 lL~~~~g~~V~VeLKn----G~~y~G~L~~~D~~ 38 (79)
=+....|+.|.|+|+. ...|+|+|.++|+-
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 3557899999999976 69999999999975
No 77
>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=80.28 E-value=7.6 Score=21.23 Aligned_cols=26 Identities=12% Similarity=0.492 Sum_probs=23.0
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCc
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDN 38 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~ 38 (79)
..|..+.++..+|.-|+|++.++++.
T Consensus 4 ~~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 4 KVGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEECCC
Confidence 46888889888999999999999975
No 78
>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=80.10 E-value=3.1 Score=27.40 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=27.6
Q ss_pred cCchHHHHhhcCCCeEEEEecCCcEEEEEEeE
Q psy14196 3 IGIPIKLLHEAEGHIITCETTNGDLFRGKLVE 34 (79)
Q Consensus 3 ~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~ 34 (79)
-+.|+.-|+...+-+|+.||.||..|.+.=.-
T Consensus 62 ~~~~~~~i~~~~~~tvt~e~~nG~~y~l~~aw 93 (119)
T PF10618_consen 62 KDTDVDDINDITDATVTFELDNGKVYVLSNAW 93 (119)
T ss_pred CCCCHHHHhCCcccEEEEEecCCcEEEecCee
Confidence 46789999999999999999999999876333
No 79
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=76.59 E-value=11 Score=25.97 Aligned_cols=26 Identities=19% Similarity=0.419 Sum_probs=23.8
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeEeC
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVEAE 36 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~~D 36 (79)
..++|+.|+++..+|..++|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 35899999999999999999999996
No 80
>PRK14635 hypothetical protein; Provisional
Probab=75.32 E-value=7.5 Score=26.78 Aligned_cols=40 Identities=10% Similarity=0.188 Sum_probs=29.0
Q ss_pred cCchH---HHHhhcCCCeEEEEec--CCcEEEE---EEeEeCCccceEE
Q psy14196 3 IGIPI---KLLHEAEGHIITCETT--NGDLFRG---KLVEAEDNMNCAM 43 (79)
Q Consensus 3 ~~~Pl---~lL~~~~g~~V~VeLK--nG~~y~G---~L~~~D~~MNv~L 43 (79)
..+|| .=+....|+.|.|+++ ++..+.| +|.++|+. ++.|
T Consensus 84 ldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 84 AERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 34555 3355789999999986 4678888 99999885 4444
No 81
>COG2954 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.77 E-value=5.2 Score=28.09 Aligned_cols=57 Identities=19% Similarity=0.191 Sum_probs=44.9
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCcc----ceEEeeeEEEccCCeEecCcccc
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNM----NCAMADVTVTFRDGTYYLPALVP 62 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~M----Nv~L~n~~~~~~~G~~~lp~~l~ 62 (79)
-+.++|..+.|. |.-+.+--..+.|.+-.+|.|. -+++..++..+.+.+..+|++|-
T Consensus 72 DA~e~l~~~~g~-~IEK~R~~v~~~G~~wEVDvF~G~n~gLvvAEvEl~~e~~~~~lP~WLG 132 (156)
T COG2954 72 DAEEMLTTACGR-VIEKTRYPVRHGGFLWEVDVFLGDNAGLVVAEVELPDENADFDLPDWLG 132 (156)
T ss_pred CHHHHHHHhcch-heeeeEeeeeeCCEEEEEeeecCcccceEEEEEEcCccccCCcCccccC
Confidence 356889999998 6667777788999999999987 57888888866555558888873
No 82
>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=73.95 E-value=5.3 Score=26.18 Aligned_cols=23 Identities=26% Similarity=0.590 Sum_probs=16.8
Q ss_pred hhcCC-CeEEEEecCCcEEEEEEe
Q psy14196 11 HEAEG-HIITCETTNGDLFRGKLV 33 (79)
Q Consensus 11 ~~~~g-~~V~VeLKnG~~y~G~L~ 33 (79)
.++-| ..|.++|++|+.++|++.
T Consensus 23 ~~L~ge~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 23 SELDGEERVELELDDGSMLRGTVA 46 (101)
T ss_dssp HCTTTT-EEEEEETTS-EEEEEEC
T ss_pred hhcCCcceEEEEEcCCCeeeeeec
Confidence 33433 469999999999999986
No 83
>PRK14630 hypothetical protein; Provisional
Probab=69.75 E-value=11 Score=25.51 Aligned_cols=35 Identities=29% Similarity=0.295 Sum_probs=26.2
Q ss_pred cCchHH---HHhhcCCCeEEEEecCCcEEEEEEeEeCCc
Q psy14196 3 IGIPIK---LLHEAEGHIITCETTNGDLFRGKLVEAEDN 38 (79)
Q Consensus 3 ~~~Pl~---lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~ 38 (79)
..+|+. =.....|+.|.|+|+.. ...|+|.++|+.
T Consensus 82 ldRpL~~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 82 INRKIKSDREFKIFEGKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence 345553 34568999999999664 459999999884
No 84
>PRK11625 Rho-binding antiterminator; Provisional
Probab=69.37 E-value=12 Score=23.59 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=20.1
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEe
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEA 35 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~ 35 (79)
...+.+|.++||||..+.|+....
T Consensus 20 C~~~~~l~l~l~dGe~~~g~A~D~ 43 (84)
T PRK11625 20 CQHHLMLTLELKDGEVLQAKASDL 43 (84)
T ss_pred HhcCCeEEEEECCCCEEEEEEEee
Confidence 357889999999999999998433
No 85
>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=66.33 E-value=16 Score=25.89 Aligned_cols=33 Identities=15% Similarity=0.072 Sum_probs=30.0
Q ss_pred CCeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 15 g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
.-+|.|-+-||..+.|.+.+++.-=|.+|.-+.
T Consensus 29 ~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 29 DIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred CCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 567999999999999999999999999998766
No 86
>PRK10898 serine endoprotease; Provisional
Probab=65.15 E-value=16 Score=27.75 Aligned_cols=32 Identities=19% Similarity=0.331 Sum_probs=28.0
Q ss_pred CeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 16 ~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
..+.|.+.+|..|.++++.+|...++.+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 56899999999999999999999998776553
No 87
>PRK06789 flagellar motor switch protein; Validated
Probab=65.01 E-value=16 Score=22.50 Aligned_cols=36 Identities=14% Similarity=0.287 Sum_probs=30.7
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEee
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n 45 (79)
|.+..|.+|.|.+.+-..-+|.++.+|+.+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 467788889999888899999999999988777765
No 88
>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=64.75 E-value=17 Score=26.03 Aligned_cols=36 Identities=25% Similarity=0.407 Sum_probs=31.1
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
-|..+=++++|+...-++.+|....|+|++++.|+-
T Consensus 9 ~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 9 DAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred CHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 355777889999999999999888999999999974
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=63.20 E-value=12 Score=24.46 Aligned_cols=21 Identities=10% Similarity=0.260 Sum_probs=18.1
Q ss_pred eEEEEecCCcEEEEEEeEeCC
Q psy14196 17 IITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 17 ~V~VeLKnG~~y~G~L~~~D~ 37 (79)
.+.|.++||.++.|.+..=|+
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~ 79 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA 79 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC
Confidence 489999999999999988443
No 90
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=58.88 E-value=24 Score=26.69 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=28.0
Q ss_pred CeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 16 ~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
..+.|.+.+|..|.++++.+|...++.+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46889999999999999999999999886554
No 91
>PRK10139 serine endoprotease; Provisional
Probab=57.33 E-value=26 Score=27.70 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=28.5
Q ss_pred CCeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 15 g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
...+.|.+.||++|.++++..|...++.+=.+.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 357899999999999999999999998875543
No 92
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=57.05 E-value=39 Score=27.18 Aligned_cols=61 Identities=15% Similarity=0.196 Sum_probs=46.1
Q ss_pred CchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEc-cCCeE---ecCccccccc
Q psy14196 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTF-RDGTY---YLPALVPIAG 65 (79)
Q Consensus 4 ~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~-~~G~~---~lp~~l~~~p 65 (79)
-.|-++++++.||.|.- =|+|.+++++|..-|.-.=+.+.+-.+.. .|-++ -.|..|.-.|
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~~d~r~~~~~~~~~L~~~P 135 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLGCDERFVFGAVPNALRGKP 135 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEecceeEeecCCccccCCCC
Confidence 36889999999999999 79999999999999987767666655543 33333 5556666565
No 93
>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=56.03 E-value=22 Score=25.25 Aligned_cols=35 Identities=17% Similarity=0.454 Sum_probs=27.0
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
-+..+=++++|+....++.+|. ..|+|++++.|.-
T Consensus 8 ~~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 8 DTVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp BHHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred CHHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 3567778899999999999888 9999999998875
No 94
>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=55.75 E-value=8.1 Score=25.69 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=23.1
Q ss_pred hHHHHhhcCCCeEEEEecCC-cEEEEEE
Q psy14196 6 PIKLLHEAEGHIITCETTNG-DLFRGKL 32 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG-~~y~G~L 32 (79)
--.++..+.|+.+.|.+++. .+|.|+-
T Consensus 94 l~~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 94 LEQFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHHHcCCeeEEEecccccCCCCcE
Confidence 45788899999999999998 8888854
No 95
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=54.08 E-value=19 Score=22.80 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=19.0
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeE
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVE 34 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~ 34 (79)
-....-+++.+||+|..|.|+-..
T Consensus 19 ACl~hl~l~L~lkdGev~~a~A~d 42 (84)
T COG4568 19 ACLHHLPLTLELKDGEVLQAKASD 42 (84)
T ss_pred HHhhhceEEEEEcCCeEEEEEehh
Confidence 345567899999999999998543
No 96
>PRK06955 biotin--protein ligase; Provisional
Probab=53.89 E-value=38 Score=25.14 Aligned_cols=32 Identities=13% Similarity=0.148 Sum_probs=28.1
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..|+.|+|...++..+.|+..++|+.-.++++
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 67999999766677899999999999999886
No 97
>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=53.63 E-value=30 Score=26.61 Aligned_cols=32 Identities=25% Similarity=0.405 Sum_probs=27.9
Q ss_pred CeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 16 ~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
..+.|.+.+|..|.+++..+|...++.|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 46889999999999999999999998876554
No 98
>PRK10942 serine endoprotease; Provisional
Probab=52.65 E-value=33 Score=27.26 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=27.5
Q ss_pred CeEEEEecCCcEEEEEEeEeCCccceEEeee
Q psy14196 16 HIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (79)
Q Consensus 16 ~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~ 46 (79)
..+.|.+.+|.+|.++++..|...++.|=.+
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4688999999999999999999999877654
No 99
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=51.06 E-value=29 Score=23.80 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=22.9
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCC
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
.++|+.|+....+|..++|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 58999999888999999999997764
No 100
>PF13437 HlyD_3: HlyD family secretion protein
Probab=50.22 E-value=47 Score=20.01 Aligned_cols=33 Identities=21% Similarity=0.350 Sum_probs=27.1
Q ss_pred chHHHHhhc--CCCeEEEEecCC--cEEEEEEeEeCC
Q psy14196 5 IPIKLLHEA--EGHIITCETTNG--DLFRGKLVEAED 37 (79)
Q Consensus 5 ~Pl~lL~~~--~g~~V~VeLKnG--~~y~G~L~~~D~ 37 (79)
.|-+-+... .|..|++.+.++ ..+.|++.+++.
T Consensus 42 v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 42 VPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 455666665 699999999865 599999999998
No 101
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=49.11 E-value=26 Score=22.14 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=20.0
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
...|..|.|+ +.+|.+++|+..+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 4789999999 8999999999864
No 102
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=49.04 E-value=37 Score=22.68 Aligned_cols=35 Identities=14% Similarity=0.276 Sum_probs=29.3
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeEeCCccceEEee
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n 45 (79)
.+..|.+|.|-+.+-..-+|.++-+|+.+=+++.+
T Consensus 101 d~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 101 DKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred CCcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 46678888888888889999999999998887764
No 103
>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=47.91 E-value=60 Score=19.44 Aligned_cols=41 Identities=12% Similarity=0.088 Sum_probs=28.4
Q ss_pred EEEEEEeEeCCcc-ceEEeeeEEEccCCeE-ecCccccccccccccceeEE
Q psy14196 27 LFRGKLVEAEDNM-NCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRW 75 (79)
Q Consensus 27 ~y~G~L~~~D~~M-Nv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~ 75 (79)
...|++.++|... -+.|+| |+. .+|+.+. .+.++.|-.++-
T Consensus 4 ~veG~I~~id~~~~titLdD-------Gksy~lp~ef~-~~~L~~G~kV~V 46 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDD-------GKSYKLPEEFD-FDGLKPGMKVVV 46 (61)
T ss_pred cceEEEEEEcCCceEEEecC-------CCEEECCCccc-ccccCCCCEEEE
Confidence 4689999999854 666654 666 8888887 445566555543
No 104
>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=47.32 E-value=50 Score=23.35 Aligned_cols=35 Identities=17% Similarity=0.446 Sum_probs=29.0
Q ss_pred chHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 5 ~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
-++.+=++++|+.+.-++. |....|+|++++.|+-
T Consensus 5 ~~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 5 DTVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred CHHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 3567778899999987775 6689999999999974
No 105
>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=46.73 E-value=58 Score=18.94 Aligned_cols=35 Identities=11% Similarity=0.316 Sum_probs=28.4
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
..+..|.+...+-..++|++..+++..=+++.+..
T Consensus 40 ~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 40 PADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp ESSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 34578888888889999999999998888877643
No 106
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=46.30 E-value=55 Score=24.15 Aligned_cols=31 Identities=6% Similarity=-0.009 Sum_probs=27.2
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..|+.|++.. ++..+.|++.++|+.-.+.++
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 456799999999999999986
No 107
>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=45.79 E-value=45 Score=19.60 Aligned_cols=26 Identities=19% Similarity=0.456 Sum_probs=18.9
Q ss_pred cCCCeEEEEecCCcEE-EEEEeEeCCc
Q psy14196 13 AEGHIITCETTNGDLF-RGKLVEAEDN 38 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y-~G~L~~~D~~ 38 (79)
..|..|.+.=-++..| .|++.++|.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 5789999998887666 9999999874
No 108
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=44.88 E-value=49 Score=22.99 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=27.1
Q ss_pred hHHHHhh-cCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 6 PIKLLHE-AEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 6 Pl~lL~~-~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
|-..+.. ..|..|.|.+.+|..|.|++..++...+
T Consensus 132 ~~~~~~~i~~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 132 PAKDVSRIRKGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CHHHHhhCCCCCEEEEEECCCCEEEEEEEEEccccC
Confidence 4433333 4689999999999999999999997653
No 109
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=44.45 E-value=54 Score=21.86 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=27.1
Q ss_pred CcCchH--HHHhhcCCCeEEEEecCCcEEEEEEeEeC
Q psy14196 2 SIGIPI--KLLHEAEGHIITCETTNGDLFRGKLVEAE 36 (79)
Q Consensus 2 ~~~~Pl--~lL~~~~g~~V~VeLKnG~~y~G~L~~~D 36 (79)
|+..|+ .+|....|..|.+++.+|..++=++..+.
T Consensus 90 Si~SPlG~ALlG~~~Gd~v~v~~p~G~~~~~~I~~I~ 126 (137)
T PRK05753 90 SVLAPVGAALLGLSVGQSIDWPLPGGKETHLEVLEVE 126 (137)
T ss_pred cccCHHHHHHcCCCCCCEEEEECCCCCEEEEEEEEEE
Confidence 455666 68999999999999999976665565553
No 110
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=43.54 E-value=31 Score=24.79 Aligned_cols=23 Identities=22% Similarity=0.369 Sum_probs=20.7
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
...|..|.|+ +.+|.++.|+..+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4789999999 9999999999875
No 111
>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=43.45 E-value=65 Score=22.82 Aligned_cols=31 Identities=13% Similarity=0.102 Sum_probs=26.9
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..|+.|+|...+ ..+.|+..++|+.-.+.++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 569999998755 5689999999999999986
No 112
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=42.39 E-value=72 Score=18.80 Aligned_cols=32 Identities=28% Similarity=0.405 Sum_probs=22.3
Q ss_pred CcCchH--HHHhhcCCCeEEEEecCCcEEEEEEeE
Q psy14196 2 SIGIPI--KLLHEAEGHIITCETTNGDLFRGKLVE 34 (79)
Q Consensus 2 ~~~~Pl--~lL~~~~g~~V~VeLKnG~~y~G~L~~ 34 (79)
|...|+ .+|.+..|..|.+++.+| ..+=++..
T Consensus 41 S~~SPLG~ALlG~~~Gd~v~~~~~~g-~~~~~I~~ 74 (77)
T PF01272_consen 41 SIDSPLGKALLGKKVGDEVEVELPGG-ERKYEILE 74 (77)
T ss_dssp ETTSHHHHHHTT-BTT-EEEEEETTB-EEEEEEEE
T ss_pred EecCHHHHHhcCCCCCCEEEEEeCCc-eEEEEEEE
Confidence 345666 789999999999999999 55544444
No 113
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=42.18 E-value=77 Score=23.48 Aligned_cols=32 Identities=9% Similarity=0.107 Sum_probs=27.3
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEee
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n 45 (79)
..|+.|.|.. ++..+.|++.++|+.-.++++.
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 4799999975 5678999999999999888863
No 114
>KOG1073|consensus
Probab=40.61 E-value=62 Score=25.54 Aligned_cols=44 Identities=16% Similarity=0.123 Sum_probs=37.1
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCCcc-ceEEeeeEEEccCCeE
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAEDNM-NCAMADVTVTFRDGTY 55 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~~M-Nv~L~n~~~~~~~G~~ 55 (79)
..+|+.|.+--|+.--|.|.|..+|--= =|-|+||+..-.+|+.
T Consensus 6 ~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk 50 (361)
T KOG1073|consen 6 SYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRK 50 (361)
T ss_pred ccccceeEEeecccceeeeEEEeccccccceehhheeecccccCC
Confidence 4689999999999999999999998743 7889999887656644
No 115
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=39.16 E-value=45 Score=23.30 Aligned_cols=26 Identities=19% Similarity=0.345 Sum_probs=22.5
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeEeC
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVEAE 36 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~~D 36 (79)
....|+.|+|.+.....++|.+..++
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 44899999999999999999999884
No 116
>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=39.11 E-value=33 Score=19.39 Aligned_cols=18 Identities=33% Similarity=0.604 Sum_probs=15.2
Q ss_pred EecCCcEEEEEEeEeCCc
Q psy14196 21 ETTNGDLFRGKLVEAEDN 38 (79)
Q Consensus 21 eLKnG~~y~G~L~~~D~~ 38 (79)
+++-|..+.|++.+++.+
T Consensus 1 k~~~G~iv~g~V~~v~~~ 18 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDF 18 (74)
T ss_dssp -SSTTSEEEEEEEEEETT
T ss_pred CCCCCCEEEEEEEEEECC
Confidence 467899999999999984
No 117
>PRK08330 biotin--protein ligase; Provisional
Probab=39.03 E-value=93 Score=22.05 Aligned_cols=33 Identities=9% Similarity=0.122 Sum_probs=26.7
Q ss_pred hcCCCeEEEEecCCcEE-EEEEeEeCCccceEEee
Q psy14196 12 EAEGHIITCETTNGDLF-RGKLVEAEDNMNCAMAD 45 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y-~G~L~~~D~~MNv~L~n 45 (79)
...|+.|++.. ++..+ .|+..++|+.-.+.++.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 36799999975 55554 79999999999998863
No 118
>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=37.37 E-value=33 Score=20.27 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=16.3
Q ss_pred EecCCcEEEEEEeEeCCcc
Q psy14196 21 ETTNGDLFRGKLVEAEDNM 39 (79)
Q Consensus 21 eLKnG~~y~G~L~~~D~~M 39 (79)
.|+.|..+.|++.++.+|-
T Consensus 1 dl~~G~~v~g~V~si~d~G 19 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHG 19 (74)
T ss_pred CCCCCCEEEEEEEEEeCCE
Confidence 3688999999999999874
No 119
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=36.38 E-value=62 Score=23.42 Aligned_cols=26 Identities=12% Similarity=0.202 Sum_probs=22.7
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCC
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
.++|+.|++.-.+|..+.|++.++.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 46999999888899999999998864
No 120
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=34.37 E-value=43 Score=24.87 Aligned_cols=31 Identities=26% Similarity=0.491 Sum_probs=23.3
Q ss_pred hHHHHhhcCCCeEEEEecC--CcEEEEEEeEeCC
Q psy14196 6 PIKLLHEAEGHIITCETTN--GDLFRGKLVEAED 37 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKn--G~~y~G~L~~~D~ 37 (79)
...+|.+-.|..+. ++.+ |.+|+|+|.+.|.
T Consensus 55 a~Nll~eefGei~~-~le~v~Ge~y~G~l~s~~~ 87 (225)
T PF09883_consen 55 AANLLREEFGEIVY-SLEPVKGETYVGTLISWDE 87 (225)
T ss_pred HHHHHHHHhCCCCc-hhcccCCceEEEEEEeecc
Confidence 34677888887754 3333 9999999999986
No 121
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=34.36 E-value=88 Score=22.25 Aligned_cols=31 Identities=16% Similarity=0.313 Sum_probs=27.7
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCC
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
.++|+...|..|.|-.-+|..|.|++..+|.
T Consensus 25 ~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~ 55 (234)
T PRK11713 25 VRVLRLKEGDELRLFDGDGGEYLAEITEIGK 55 (234)
T ss_pred HhhccCCCCCEEEEEeCCCCEEEEEEEEecC
Confidence 4678889999999988899999999999987
No 122
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=33.01 E-value=1.1e+02 Score=25.14 Aligned_cols=32 Identities=9% Similarity=0.179 Sum_probs=28.0
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
..|+.|.+...++.++.|+..++|+.-.+.|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 67999998766677899999999999999996
No 123
>PRK08158 type III secretion system protein SpaO; Validated
Probab=32.57 E-value=88 Score=24.01 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=32.7
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEE
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTV 48 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~ 48 (79)
|.+..+..|.|...+-..-+|.|+.+|+.+=+.+.+...
T Consensus 259 L~~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i~~ 297 (303)
T PRK08158 259 LPTNAELNVEIRANGALLGNGELVQMDDTLGVEIHEWLS 297 (303)
T ss_pred CCCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEEec
Confidence 346688899999888899999999999998888877543
No 124
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=32.54 E-value=60 Score=23.40 Aligned_cols=23 Identities=13% Similarity=0.307 Sum_probs=20.2
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
...|..|.|+ +.+|.++.|+..+
T Consensus 183 G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 183 AGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCEEEEEECCCCCEEEEEEeC
Confidence 4789999999 8999999998764
No 125
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.69 E-value=81 Score=22.63 Aligned_cols=23 Identities=17% Similarity=0.439 Sum_probs=20.5
Q ss_pred hcCCCeEEEEecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~ 34 (79)
.+.|..|.|+-.+|.++.|+..+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 47899999999999999999875
No 126
>PRK14056 phenylalanine 4-monooxygenase; Provisional
Probab=30.64 E-value=1.9e+02 Score=24.40 Aligned_cols=46 Identities=22% Similarity=0.320 Sum_probs=34.3
Q ss_pred HHhhcCCCeEEEEecCCcEEEEEEeEe---CC-ccceEEeeeEEEccCCeE
Q psy14196 9 LLHEAEGHIITCETTNGDLFRGKLVEA---ED-NMNCAMADVTVTFRDGTY 55 (79)
Q Consensus 9 lL~~~~g~~V~VeLKnG~~y~G~L~~~---D~-~MNv~L~n~~~~~~~G~~ 55 (79)
-..-..|+.+..++..|-.++|.++.- ++ .+=+.+.||+.+. +|++
T Consensus 386 a~~i~~g~~~~l~f~sgi~v~G~~~~~~~~~g~~~li~f~~ctv~~-~~~~ 435 (578)
T PRK14056 386 ALGITIGNIAELEFESGIHVKGTVTDGVKNDGKIALISFINCTVTY-NGRV 435 (578)
T ss_pred hcCcccCceEEEEeecceEEEEEEeeeeccCCeEEEEEeeeeEEee-CCee
Confidence 334467999999999999999977654 22 3347888999986 4454
No 127
>PF09923 DUF2155: Uncharacterized protein conserved in bacteria (DUF2155); InterPro: IPR019225 This entry contains various hypothetical prokaryotic proteins that have no known function.
Probab=30.62 E-value=26 Score=22.18 Aligned_cols=41 Identities=12% Similarity=0.185 Sum_probs=28.8
Q ss_pred HHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCC
Q psy14196 7 IKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53 (79)
Q Consensus 7 l~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G 53 (79)
+..|.+..|+...+|++.|...+= +..-+.++.|....+++
T Consensus 3 l~~LDKitg~~~~~~v~~G~~~~~------g~L~i~~~~C~~r~p~~ 43 (90)
T PF09923_consen 3 LRGLDKITGRVTDFEVPVGETVQF------GNLTITLRACVSRPPTE 43 (90)
T ss_pred EEEEecccCeEEEEEEcCCCEEEE------ccEEEEhhheecCCCCC
Confidence 356889999999999999976541 34556677775544433
No 128
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=30.33 E-value=96 Score=18.89 Aligned_cols=24 Identities=17% Similarity=0.490 Sum_probs=19.9
Q ss_pred cCCcEEEEEEeEeCCccceEEeee
Q psy14196 23 TNGDLFRGKLVEAEDNMNCAMADV 46 (79)
Q Consensus 23 KnG~~y~G~L~~~D~~MNv~L~n~ 46 (79)
+=|..|.|++..++++|+-..-+.
T Consensus 6 ~~G~iy~g~V~~i~~~~~GaFV~l 29 (88)
T cd04453 6 IVGNIYLGRVKKIVPGLQAAFVDI 29 (88)
T ss_pred CCCCEEEEEEEEeccCCcEEEEEe
Confidence 458999999999999987766554
No 129
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.12 E-value=75 Score=21.80 Aligned_cols=23 Identities=22% Similarity=0.482 Sum_probs=19.8
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
...|..|.|+ +.+|.+++|++.+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4789999999 8999999998764
No 130
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=29.89 E-value=2.2e+02 Score=20.70 Aligned_cols=34 Identities=12% Similarity=0.155 Sum_probs=31.1
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEeee
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~ 46 (79)
..|+.|+++.-++....|+-..+|..-.+.++..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4899999999999999999999999999998864
No 131
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=29.87 E-value=43 Score=17.89 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=14.4
Q ss_pred hcCCCeEEEEecCCcEEE
Q psy14196 12 EAEGHIITCETTNGDLFR 29 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~ 29 (79)
+..|..|+|++.+|.+.+
T Consensus 20 ~~~g~~vtV~~~~G~~~t 37 (42)
T PF02736_consen 20 EEEGDKVTVKTEDGKEVT 37 (42)
T ss_dssp EEESSEEEEEETTTEEEE
T ss_pred EEcCCEEEEEECCCCEEE
Confidence 567889999999987643
No 132
>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=29.86 E-value=82 Score=22.16 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=26.2
Q ss_pred HHHhhcCCCeEEEEecCCcEEEEEEeEeCCcc
Q psy14196 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNM 39 (79)
Q Consensus 8 ~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~M 39 (79)
++|+--.|..|.|-.-+|..|.+++..++..-
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~ 44 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKS 44 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSE
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcE
Confidence 57788899999999999999999999999864
No 133
>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.
Probab=28.97 E-value=29 Score=20.95 Aligned_cols=13 Identities=31% Similarity=0.593 Sum_probs=10.3
Q ss_pred EEEEEEeEeCCcc
Q psy14196 27 LFRGKLVEAEDNM 39 (79)
Q Consensus 27 ~y~G~L~~~D~~M 39 (79)
..+|.|+.||..|
T Consensus 4 a~kGvLv~CDpa~ 16 (68)
T PF06331_consen 4 AIKGVLVECDPAI 16 (68)
T ss_dssp EEEEEEEES-HHH
T ss_pred eeeeEEEEcCHHH
Confidence 5799999999866
No 134
>PRK06788 flagellar motor switch protein; Validated
Probab=28.88 E-value=1.4e+02 Score=19.84 Aligned_cols=39 Identities=10% Similarity=0.251 Sum_probs=32.4
Q ss_pred HhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEE
Q psy14196 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTV 48 (79)
Q Consensus 10 L~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~ 48 (79)
|....+.+|.|.+-+-..|+|.+..+++.+=+.+.+...
T Consensus 63 Ldk~~~dpv~v~Vng~~~f~G~~Gv~~~~~AVrItei~~ 101 (119)
T PRK06788 63 VEKNLGHKVDVYLSNMKVGIGEAIVMDEKFGIIISEIEA 101 (119)
T ss_pred eCCcCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEecC
Confidence 356677888888888999999999999999888877654
No 135
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=28.75 E-value=94 Score=16.06 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=18.8
Q ss_pred CCeEEEEecC-CcEEEEEEeEeCC
Q psy14196 15 GHIITCETTN-GDLFRGKLVEAED 37 (79)
Q Consensus 15 g~~V~VeLKn-G~~y~G~L~~~D~ 37 (79)
|..+.+.-.+ |.-|+|++.+++.
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~ 24 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS 24 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC
Confidence 4566777765 9999999999985
No 136
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.64 E-value=1.3e+02 Score=21.97 Aligned_cols=34 Identities=21% Similarity=0.326 Sum_probs=28.1
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
|+.+=++++|+.+.=+ -+|.+++|.+++.+.|+-
T Consensus 15 ~~~vAr~LLG~~lv~~-~~g~~~~g~IVEtEAY~G 48 (200)
T COG2094 15 TLVVARELLGKTLVRR-IGGLTTSGRIVETEAYLG 48 (200)
T ss_pred HHHHHHHhcCcEEEEe-cCCcEEEEEEEEEeEecC
Confidence 4556678999987655 778999999999999995
No 137
>TIGR03344 VI_effect_Hcp1 type VI secretion system effector, Hcp1 family. This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens.
Probab=28.52 E-value=57 Score=22.42 Aligned_cols=46 Identities=13% Similarity=0.119 Sum_probs=32.6
Q ss_pred CchHHHHhhcCCCeE-EEEecCCcEEE-EEEeEeCCccceEEeeeEEEccC
Q psy14196 4 GIPIKLLHEAEGHII-TCETTNGDLFR-GKLVEAEDNMNCAMADVTVTFRD 52 (79)
Q Consensus 4 ~~Pl~lL~~~~g~~V-~VeLKnG~~y~-G~L~~~D~~MNv~L~n~~~~~~~ 52 (79)
..|+-+...+.|+.+ +|+|+.-+.-. | .-..||.+.|+||.+.+.+
T Consensus 76 ASP~L~~a~~~Ge~l~~v~l~~~r~~~~G---~~~~y~~itL~~a~Issi~ 123 (166)
T TIGR03344 76 SSPLLYQALSSGEKLEECEIKFYRTSAAG---KQELYYTIKLEGALIVDIK 123 (166)
T ss_pred CCHHHHHHHcCCCcCCEEEEEEEEeCCCC---cEEEEEEEEEeeEEEEEEE
Confidence 467777777899988 58875544211 3 3567999999999987543
No 138
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.65 E-value=1.3e+02 Score=22.23 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=28.2
Q ss_pred CCeEEEEecCCcEEEEEEeEeCCccceEEeeeEE
Q psy14196 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTV 48 (79)
Q Consensus 15 g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~ 48 (79)
...+.|.+.+|.++.++++..|....+.+-....
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~~ 128 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKIDG 128 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEecc
Confidence 5678899999999999999999988776655443
No 139
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. 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 S. cerevisiae Rrp5 and 14 S1 repeats in H. 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 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=27.37 E-value=61 Score=18.97 Aligned_cols=22 Identities=9% Similarity=0.021 Sum_probs=17.0
Q ss_pred ecCCcEEEEEEeEeCCcc-ceEE
Q psy14196 22 TTNGDLFRGKLVEAEDNM-NCAM 43 (79)
Q Consensus 22 LKnG~~y~G~L~~~D~~M-Nv~L 43 (79)
++-|..|.|++.++.++- -+.|
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l 34 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEF 34 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEc
Confidence 678999999999998853 3444
No 140
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.03 E-value=94 Score=20.89 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=19.4
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
.+.|..|.|+ +.+|.+++|+..+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4789999996 7899999998764
No 141
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=26.57 E-value=81 Score=24.62 Aligned_cols=24 Identities=29% Similarity=0.404 Sum_probs=21.1
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEe
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEA 35 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~ 35 (79)
-+.|+.|+|..++|..|.|.+-+.
T Consensus 94 ~~~gq~v~i~t~~g~~i~GvIg~~ 117 (355)
T COG1363 94 VLEGQRVTIHTDKGKKIRGVIGSK 117 (355)
T ss_pred hccCcEEEEEeCCCcEEeeeEccc
Confidence 468999999999999999999843
No 142
>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=26.53 E-value=86 Score=22.22 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=22.9
Q ss_pred CCCeEEEEecCCcEEEEEEeEeCCc
Q psy14196 14 EGHIITCETTNGDLFRGKLVEAEDN 38 (79)
Q Consensus 14 ~g~~V~VeLKnG~~y~G~L~~~D~~ 38 (79)
.|+.|.|-+.+|.++.|+=.++|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 6889999999999999999998875
No 143
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=26.11 E-value=1.1e+02 Score=19.11 Aligned_cols=26 Identities=23% Similarity=0.373 Sum_probs=22.6
Q ss_pred EEEecCCcEEEEEEeEeCCccceEEe
Q psy14196 19 TCETTNGDLFRGKLVEAEDNMNCAMA 44 (79)
Q Consensus 19 ~VeLKnG~~y~G~L~~~D~~MNv~L~ 44 (79)
.=.|+.|..+..++.++|..|+..|+
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~~~eLt 72 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDMEPELS 72 (86)
T ss_pred cccCCCCCEEEEEEEecCCCCCeEEE
Confidence 34588999999999999999998765
No 144
>PF11525 CopK: Copper resistance protein K; InterPro: IPR021604 CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation []. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site []. ; PDB: 3N7E_B 3N7D_B 3DSP_A 3DSO_A 2K0Q_A 2KM0_A 2LEL_A.
Probab=25.79 E-value=56 Score=20.26 Aligned_cols=38 Identities=16% Similarity=0.233 Sum_probs=21.1
Q ss_pred EEEEecCCcEEE----EEEeEeCCccceE-Ee-eeEEEccCCeE
Q psy14196 18 ITCETTNGDLFR----GKLVEAEDNMNCA-MA-DVTVTFRDGTY 55 (79)
Q Consensus 18 V~VeLKnG~~y~----G~L~~~D~~MNv~-L~-n~~~~~~~G~~ 55 (79)
=+|+||||++.. |++.-=|.|-+.+ ++ .......||+.
T Consensus 8 ksi~LkDGstvyiFKDGKMamEdk~Gra~rm~~g~~meTkDG~k 51 (73)
T PF11525_consen 8 KSIPLKDGSTVYIFKDGKMAMEDKFGRAVRMKKGTVMETKDGQK 51 (73)
T ss_dssp EEEEBTTSEEEEEETTS-EEEEETTSEEEE--TT-EEEBTTS-E
T ss_pred eeEecCCCCEEEEEcCCceehhhhcCceEEcCCCcEEEccCCCE
Confidence 479999998875 6666666554322 22 33333578876
No 145
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.72 E-value=92 Score=23.18 Aligned_cols=23 Identities=13% Similarity=0.330 Sum_probs=20.4
Q ss_pred hcCCCeEEEE-ecCCcEEEEEEeE
Q psy14196 12 EAEGHIITCE-TTNGDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~Ve-LKnG~~y~G~L~~ 34 (79)
...|..|.|+ +.+|.+++|+..+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4789999999 8999999999875
No 146
>PRK10113 cell division modulator; Provisional
Probab=25.48 E-value=9.5 Score=23.76 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=19.1
Q ss_pred ecCccccccccccc-cceeEEeec
Q psy14196 56 YLPALVPIAGMWNG-TSGLRWATQ 78 (79)
Q Consensus 56 ~lp~~l~~~p~~~~-~~~~~~~~~ 78 (79)
.+.+.|+.+|.|.. .++-|||.|
T Consensus 48 l~ge~FrRSPaFs~PEsAQRWAnQ 71 (80)
T PRK10113 48 LMGESFLRSPAFSVPESAQRWANQ 71 (80)
T ss_pred EechhhccCCccCCcHHHHHHHHH
Confidence 77899999997765 788899876
No 147
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=25.36 E-value=1.8e+02 Score=19.42 Aligned_cols=31 Identities=23% Similarity=0.487 Sum_probs=23.5
Q ss_pred CcCchH--HHHhhcCCCeEEEEecCCcEEEEEEe
Q psy14196 2 SIGIPI--KLLHEAEGHIITCETTNGDLFRGKLV 33 (79)
Q Consensus 2 ~~~~Pl--~lL~~~~g~~V~VeLKnG~~y~G~L~ 33 (79)
|+..|+ .+|....|..|.|++.+|. +.=++.
T Consensus 116 S~~SPlG~ALlG~~~Gd~v~v~~p~g~-~~~~I~ 148 (151)
T TIGR01462 116 SIDSPLGKALIGKKVGDVVEVQTPKGE-KEYEIL 148 (151)
T ss_pred cCCCHHHHHHcCCCCCCEEEEEeCCCc-EEEEEE
Confidence 455676 7899999999999999986 443443
No 148
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=25.33 E-value=8.8 Score=23.96 Aligned_cols=23 Identities=22% Similarity=0.315 Sum_probs=15.5
Q ss_pred ecCccccccccccc-cceeEEeec
Q psy14196 56 YLPALVPIAGMWNG-TSGLRWATQ 78 (79)
Q Consensus 56 ~lp~~l~~~p~~~~-~~~~~~~~~ 78 (79)
.+.+.|+.+|.|.- .++-|||.|
T Consensus 48 l~ge~f~rsp~fs~pesaqrwa~q 71 (80)
T PF10729_consen 48 LMGEHFRRSPAFSVPESAQRWANQ 71 (80)
T ss_dssp ESSS-EEE---BSSHHHHHHHHHH
T ss_pred EecchhccCCCcCCcHHHHHHHHH
Confidence 77899999997765 788899976
No 149
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=24.83 E-value=1.7e+02 Score=19.58 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=23.7
Q ss_pred CcCchH--HHHhhcCCCeEEEEecCCcEEEEEEeE
Q psy14196 2 SIGIPI--KLLHEAEGHIITCETTNGDLFRGKLVE 34 (79)
Q Consensus 2 ~~~~Pl--~lL~~~~g~~V~VeLKnG~~y~G~L~~ 34 (79)
|+..|+ .+|....|..|.+++.+| ...=++..
T Consensus 121 S~~SPlG~aLlGk~~Gd~v~~~~p~g-~~~~~I~~ 154 (157)
T PRK00226 121 SIESPIARALIGKKVGDTVEVTTPGG-EYEYEILS 154 (157)
T ss_pred ccCChHHHHHhCCCCCCEEEEEcCCC-cEEEEEEE
Confidence 455676 789999999999999999 33333443
No 150
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=24.73 E-value=47 Score=21.23 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=15.8
Q ss_pred EEEeEeCCccceEEeee
Q psy14196 30 GKLVEAEDNMNCAMADV 46 (79)
Q Consensus 30 G~L~~~D~~MNv~L~n~ 46 (79)
|+|++.|.+-|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999999986
No 151
>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=24.13 E-value=1.6e+02 Score=20.99 Aligned_cols=37 Identities=11% Similarity=0.362 Sum_probs=29.7
Q ss_pred HHHhhcCCCeEEEEecCCcEEEEEEeEeCCc-cceEEe
Q psy14196 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDN-MNCAMA 44 (79)
Q Consensus 8 ~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~-MNv~L~ 44 (79)
++|+.-.|..|.|---+|..|.+++..++.. .-+.+.
T Consensus 28 ~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~ 65 (240)
T TIGR00046 28 RVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELL 65 (240)
T ss_pred HcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEE
Confidence 5788889999999878899999999998765 334443
No 152
>PRK08477 biotin--protein ligase; Provisional
Probab=24.13 E-value=2.5e+02 Score=20.04 Aligned_cols=38 Identities=13% Similarity=0.075 Sum_probs=31.2
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEE
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
.-..|+.|+|. .++..++|+..++|+.--+.+..-+..
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~~ 208 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKVY 208 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEee
Confidence 34789999997 578999999999999988888765543
No 153
>PRK10708 hypothetical protein; Provisional
Probab=23.52 E-value=99 Score=18.54 Aligned_cols=26 Identities=19% Similarity=0.210 Sum_probs=22.4
Q ss_pred CCCeEEEEecCCcEEEEEEeEeCCcc
Q psy14196 14 EGHIITCETTNGDLFRGKLVEAEDNM 39 (79)
Q Consensus 14 ~g~~V~VeLKnG~~y~G~L~~~D~~M 39 (79)
++..|+|++-.|.--.|++..++.|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 47789999999999999999887764
No 154
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=22.80 E-value=1.1e+02 Score=17.11 Aligned_cols=14 Identities=14% Similarity=0.245 Sum_probs=11.9
Q ss_pred HHHhhcCCCeEEEE
Q psy14196 8 KLLHEAEGHIITCE 21 (79)
Q Consensus 8 ~lL~~~~g~~V~Ve 21 (79)
+.++.+.||.|.|.
T Consensus 12 ~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 12 SYLKSLLGKRVSVT 25 (48)
T ss_pred HHHHHhcCCeEEEE
Confidence 56778999999987
No 155
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=22.71 E-value=1.5e+02 Score=16.42 Aligned_cols=24 Identities=17% Similarity=0.605 Sum_probs=20.9
Q ss_pred CCCeEEEEecCCcEEEEEEeEeCC
Q psy14196 14 EGHIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 14 ~g~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
+|..|.++=++|..|..++..+..
T Consensus 3 vG~~v~~~~~~~~~y~A~I~~~r~ 26 (55)
T PF11717_consen 3 VGEKVLCKYKDGQWYEAKILDIRE 26 (55)
T ss_dssp TTEEEEEEETTTEEEEEEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEEe
Confidence 688899988899999999998865
No 156
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.51 E-value=96 Score=17.31 Aligned_cols=20 Identities=10% Similarity=0.287 Sum_probs=14.2
Q ss_pred CcEEEEEEeEeCCcc-ceEEe
Q psy14196 25 GDLFRGKLVEAEDNM-NCAMA 44 (79)
Q Consensus 25 G~~y~G~L~~~D~~M-Nv~L~ 44 (79)
|+.|.|++.++.++- -+.|.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~ 21 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLS 21 (69)
T ss_pred CCEEEEEEEEEeccEEEEEec
Confidence 678999999988753 44443
No 157
>PRK00802 3-methyladenine DNA glycosylase; Reviewed
Probab=22.44 E-value=1.7e+02 Score=20.85 Aligned_cols=31 Identities=23% Similarity=0.498 Sum_probs=25.4
Q ss_pred hHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccc
Q psy14196 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMN 40 (79)
Q Consensus 6 Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MN 40 (79)
++.+=++++|+.+..+ | ...|+|++++.|+-
T Consensus 14 ~~~vA~~LLGk~Lv~~---~-~~~grIvETEAY~G 44 (188)
T PRK00802 14 ALEVARDLLGKVLVHE---G-GVSGRIVETEAYIG 44 (188)
T ss_pred HHHHHHHhCCCEEEEC---C-EEEEEEEEEecccC
Confidence 4566678999999876 3 79999999999973
No 158
>PF13619 KTSC: KTSC domain
Probab=21.92 E-value=1.3e+02 Score=16.99 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=13.8
Q ss_pred hcCCCeEEEEecCCcEEE
Q psy14196 12 EAEGHIITCETTNGDLFR 29 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~ 29 (79)
+...+...|+.++|..|+
T Consensus 12 d~~~~~L~V~F~~G~~Y~ 29 (60)
T PF13619_consen 12 DPETRTLEVEFKSGSVYR 29 (60)
T ss_pred CCCCCEEEEEEcCCCEEE
Confidence 345678899999998764
No 159
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=21.79 E-value=81 Score=22.46 Aligned_cols=38 Identities=26% Similarity=0.531 Sum_probs=24.5
Q ss_pred CCcCchHHHHhhcCCCe--EEEEec-CCcEEEEEEeEeCCc
Q psy14196 1 MSIGIPIKLLHEAEGHI--ITCETT-NGDLFRGKLVEAEDN 38 (79)
Q Consensus 1 m~~~~Pl~lL~~~~g~~--V~VeLK-nG~~y~G~L~~~D~~ 38 (79)
|++.==++||-..-++. |..++. ++..|+|.|.++|.-
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 33333456666655543 444443 578999999999875
No 160
>PRK08035 type III secretion system protein SsaQ; Validated
Probab=21.59 E-value=1.8e+02 Score=22.52 Aligned_cols=36 Identities=8% Similarity=0.053 Sum_probs=28.6
Q ss_pred hhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeee
Q psy14196 11 HEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (79)
Q Consensus 11 ~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~ 46 (79)
.+..+..|.|...+-..-+|.|+.+|+..=+.+...
T Consensus 281 ~~~~~~~VdI~vNG~~ia~GElV~v~~~lGVRIt~~ 316 (323)
T PRK08035 281 GGCFYPEVTIRLNGRIIGQGELLACDNELMVRITRW 316 (323)
T ss_pred CCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEe
Confidence 345667788887777888999999999888887764
No 161
>PF13876 Phage_gp49_66: Phage protein (N4 Gp49/phage Sf6 gene 66) family
Probab=21.53 E-value=1.4e+02 Score=18.50 Aligned_cols=22 Identities=14% Similarity=0.128 Sum_probs=18.4
Q ss_pred CeEEEEecCCcEEEEEEeEeCC
Q psy14196 16 HIITCETTNGDLFRGKLVEAED 37 (79)
Q Consensus 16 ~~V~VeLKnG~~y~G~L~~~D~ 37 (79)
..+.+.|+||-++.|.=..+|+
T Consensus 27 TvC~l~L~NGF~V~g~SAcvdp 48 (81)
T PF13876_consen 27 TVCVLTLKNGFTVTGESACVDP 48 (81)
T ss_pred EEEEEEECCCcEEEEeEccCCh
Confidence 3567899999999999888776
No 162
>PF13144 SAF_2: SAF-like
Probab=21.53 E-value=1.5e+02 Score=20.06 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=19.0
Q ss_pred hcCCCeEEEEecC-CcEEEEEEeE
Q psy14196 12 EAEGHIITCETTN-GDLFRGKLVE 34 (79)
Q Consensus 12 ~~~g~~V~VeLKn-G~~y~G~L~~ 34 (79)
...|..|.|+-.+ |..++|++.+
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4789999999854 9999999875
No 163
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=21.32 E-value=1.3e+02 Score=19.12 Aligned_cols=27 Identities=15% Similarity=0.089 Sum_probs=11.3
Q ss_pred cCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeE
Q psy14196 13 AEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVT 47 (79)
Q Consensus 13 ~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~ 47 (79)
..|+.|+|. |+..++|..-++.|++|.
T Consensus 118 ~~G~~Vti~--------G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 118 KKGQKVTIK--------GICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp -TTSEEEEE--------EE-----SSS-EEEE---
T ss_pred CCCCEEEEE--------EEEEeeecCCcEEeeccC
Confidence 366776665 899888833377887763
No 164
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=21.06 E-value=2e+02 Score=17.03 Aligned_cols=35 Identities=17% Similarity=0.324 Sum_probs=27.5
Q ss_pred hcCCCeEEEEecCCcEEEEEEeEeCCccceEEeee
Q psy14196 12 EAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADV 46 (79)
Q Consensus 12 ~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~ 46 (79)
......|.+...+-..++|.+..+++.+=+.+...
T Consensus 39 ~~~~~~v~l~v~g~~~~~g~lg~~~~~~avrI~~~ 73 (77)
T TIGR02480 39 KLAGEPLDILVNGRLIARGEVVVVEDKFGIRITEI 73 (77)
T ss_pred CCCCCcEEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 34556788888888999999999999887776653
No 165
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=20.93 E-value=1e+02 Score=17.21 Aligned_cols=22 Identities=14% Similarity=0.389 Sum_probs=14.6
Q ss_pred EEEEEeEeCCccceEEeeeEEE
Q psy14196 28 FRGKLVEAEDNMNCAMADVTVT 49 (79)
Q Consensus 28 y~G~L~~~D~~MNv~L~n~~~~ 49 (79)
.+|+..++|....+-|++...+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 5799999999999999986544
No 166
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=20.15 E-value=1.1e+02 Score=19.67 Aligned_cols=24 Identities=29% Similarity=0.461 Sum_probs=18.2
Q ss_pred cCCCeEEEEe--cCCcEEEEEEeEeC
Q psy14196 13 AEGHIITCET--TNGDLFRGKLVEAE 36 (79)
Q Consensus 13 ~~g~~V~VeL--KnG~~y~G~L~~~D 36 (79)
.-|+.++|.| ..+..|+|.|...-
T Consensus 31 ~pg~~~~Vtl~~~~~~~F~GFllqAr 56 (132)
T PF02014_consen 31 EPGQTYTVTLSSSGSSSFRGFLLQAR 56 (132)
T ss_dssp -TTBEEEEEEEETTTEEBSEEEEEEE
T ss_pred cCCCEEEEEEECCCCCceeEEEEEEE
Confidence 4577888888 78889999887654
Done!