Query 032863
Match_columns 132
No_of_seqs 180 out of 1178
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:52:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032863.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032863hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3172 Small nuclear ribonucl 100.0 4.4E-41 9.5E-46 240.1 9.9 118 4-132 2-119 (119)
2 cd01724 Sm_D1 The eukaryotic S 100.0 6.5E-30 1.4E-34 178.4 11.4 85 8-92 2-86 (90)
3 cd01721 Sm_D3 The eukaryotic S 100.0 5.6E-28 1.2E-32 161.2 10.2 70 8-77 1-70 (70)
4 cd01733 LSm10 The eukaryotic S 99.9 2.4E-26 5.3E-31 156.6 10.4 72 5-76 7-78 (78)
5 KOG3293 Small nuclear ribonucl 99.9 8E-27 1.7E-31 170.2 7.4 75 7-81 2-77 (134)
6 cd01723 LSm4 The eukaryotic Sm 99.9 3.2E-26 7E-31 154.8 9.5 73 7-79 1-74 (76)
7 cd01725 LSm2 The eukaryotic Sm 99.9 2.9E-25 6.3E-30 152.0 9.9 75 7-81 1-77 (81)
8 KOG3428 Small nuclear ribonucl 99.9 1.7E-23 3.7E-28 149.7 10.8 90 8-98 3-92 (109)
9 cd01726 LSm6 The eukaryotic Sm 99.9 1.9E-23 4.1E-28 138.0 9.6 67 8-74 1-67 (67)
10 cd01722 Sm_F The eukaryotic Sm 99.9 1.5E-22 3.2E-27 134.2 9.5 68 7-74 1-68 (68)
11 PRK00737 small nuclear ribonuc 99.9 7.9E-22 1.7E-26 132.1 10.3 69 6-74 3-71 (72)
12 cd01731 archaeal_Sm1 The archa 99.9 4.1E-21 8.8E-26 126.9 9.7 67 8-74 1-67 (68)
13 PF01423 LSM: LSM domain ; In 99.8 3.3E-20 7.2E-25 121.1 9.7 66 10-75 1-67 (67)
14 smart00651 Sm snRNP Sm protein 99.8 3.1E-20 6.7E-25 121.1 9.2 65 11-75 2-67 (67)
15 COG1958 LSM1 Small nuclear rib 99.8 1E-19 2.3E-24 123.3 10.1 75 1-75 1-79 (79)
16 cd00600 Sm_like The eukaryotic 99.8 2.8E-19 6.1E-24 114.9 8.6 63 12-74 1-63 (63)
17 cd01732 LSm5 The eukaryotic Sm 99.8 5.7E-19 1.2E-23 119.8 10.1 70 6-75 2-74 (76)
18 KOG3448 Predicted snRNP core p 99.8 1.6E-18 3.4E-23 120.4 8.4 82 8-89 3-86 (96)
19 cd01719 Sm_G The eukaryotic Sm 99.8 4.1E-18 8.9E-23 114.4 9.2 70 8-77 1-70 (72)
20 cd01730 LSm3 The eukaryotic Sm 99.7 3.5E-17 7.6E-22 112.0 9.2 68 7-74 1-81 (82)
21 KOG3482 Small nuclear ribonucl 99.7 1.6E-17 3.4E-22 111.8 6.7 71 3-74 4-75 (79)
22 cd01720 Sm_D2 The eukaryotic S 99.7 5.8E-17 1.3E-21 112.7 9.5 69 7-75 2-85 (87)
23 cd01729 LSm7 The eukaryotic Sm 99.7 6.3E-16 1.4E-20 105.9 9.2 66 12-77 7-80 (81)
24 cd01718 Sm_E The eukaryotic Sm 99.7 6.8E-16 1.5E-20 105.7 9.4 72 3-74 2-78 (79)
25 KOG1783 Small nuclear ribonucl 99.6 1E-16 2.2E-21 107.8 1.8 75 1-77 1-76 (77)
26 cd01717 Sm_B The eukaryotic Sm 99.6 7.6E-15 1.7E-19 99.6 9.0 65 11-75 4-78 (79)
27 cd01728 LSm1 The eukaryotic Sm 99.6 1.7E-14 3.8E-19 97.4 9.6 68 8-75 3-73 (74)
28 cd01727 LSm8 The eukaryotic Sm 99.5 6.9E-14 1.5E-18 93.9 9.1 67 11-77 3-73 (74)
29 PTZ00138 small nuclear ribonuc 99.5 5.1E-14 1.1E-18 98.4 8.6 73 3-75 10-87 (89)
30 cd06168 LSm9 The eukaryotic Sm 99.5 1.1E-13 2.4E-18 93.7 9.5 66 10-75 3-74 (75)
31 KOG1780 Small Nuclear ribonucl 99.4 5.2E-13 1.1E-17 90.1 6.9 72 1-75 1-72 (77)
32 KOG3460 Small nuclear ribonucl 99.4 1.2E-13 2.6E-18 95.2 3.3 76 4-79 2-90 (91)
33 KOG1775 U6 snRNA-associated Sm 99.3 1.9E-12 4.1E-17 88.0 3.8 74 2-75 2-78 (84)
34 KOG1774 Small nuclear ribonucl 98.6 6.7E-08 1.5E-12 66.6 4.0 71 5-75 10-85 (88)
35 KOG3168 U1 snRNP component [Tr 98.5 4.3E-08 9.4E-13 75.4 2.0 82 5-87 3-94 (177)
36 KOG1781 Small Nuclear ribonucl 98.4 4.7E-08 1E-12 69.4 -0.2 72 9-80 19-98 (108)
37 PF14438 SM-ATX: Ataxin 2 SM d 98.1 1.5E-05 3.3E-10 53.3 6.6 45 9-53 4-51 (77)
38 KOG1784 Small Nuclear ribonucl 97.9 3E-05 6.4E-10 54.5 5.0 77 12-89 5-85 (96)
39 KOG1782 Small Nuclear ribonucl 97.6 1.2E-05 2.5E-10 59.3 -0.3 66 12-77 14-82 (129)
40 PF12701 LSM14: Scd6-like Sm d 97.4 0.00088 1.9E-08 47.4 7.2 67 14-80 5-81 (96)
41 cd01739 LSm11_C The eukaryotic 97.1 0.0005 1.1E-08 45.7 2.8 39 16-54 7-49 (66)
42 KOG3459 Small nuclear ribonucl 97.1 0.00012 2.6E-09 53.0 -0.2 68 7-74 24-106 (114)
43 PF11095 Gemin7: Gem-associate 96.4 0.029 6.3E-07 38.6 7.7 64 8-76 15-79 (80)
44 cd01736 LSm14_N LSm14 (also kn 96.0 0.045 9.7E-07 37.2 7.0 58 14-71 3-71 (74)
45 PF10842 DUF2642: Protein of u 96.0 0.074 1.6E-06 35.3 7.7 52 9-74 13-65 (66)
46 PF02237 BPL_C: Biotin protein 95.5 0.091 2E-06 32.1 6.3 31 16-47 2-32 (48)
47 cd01716 Hfq Hfq, an abundant, 95.3 0.062 1.4E-06 35.2 5.4 35 11-45 3-39 (61)
48 TIGR02383 Hfq RNA chaperone Hf 95.0 0.089 1.9E-06 34.5 5.4 36 10-45 6-43 (61)
49 PRK00395 hfq RNA-binding prote 94.7 0.14 3.1E-06 35.1 6.1 69 1-81 1-71 (79)
50 KOG1073 Uncharacterized mRNA-a 93.2 0.21 4.6E-06 42.9 5.7 67 13-79 5-82 (361)
51 PF06372 Gemin6: Gemin6 protei 92.6 0.7 1.5E-05 35.8 7.3 61 11-78 11-72 (166)
52 PRK14644 hypothetical protein; 92.2 0.42 9E-06 35.6 5.4 44 2-46 68-117 (136)
53 cd01735 LSm12_N LSm12 belongs 91.7 0.51 1.1E-05 30.8 4.7 30 15-44 4-33 (61)
54 COG1923 Hfq Uncharacterized ho 91.5 0.53 1.1E-05 32.2 4.8 33 9-41 9-43 (77)
55 PRK02001 hypothetical protein; 90.4 0.84 1.8E-05 34.7 5.5 41 4-45 74-117 (152)
56 PRK14638 hypothetical protein; 89.9 0.71 1.5E-05 34.8 4.8 41 4-45 84-127 (150)
57 PRK14639 hypothetical protein; 88.6 1.4 3E-05 32.9 5.5 42 4-46 72-116 (140)
58 cd01734 YlxS_C YxlS is a Bacil 88.6 2.5 5.3E-05 28.4 6.3 39 2-40 7-52 (83)
59 PF05918 API5: Apoptosis inhib 86.9 0.19 4.2E-06 45.3 0.0 7 122-128 545-551 (556)
60 PRK00092 ribosome maturation p 86.7 3.6 7.7E-05 30.8 6.8 37 4-40 82-125 (154)
61 PRK14642 hypothetical protein; 86.7 2.5 5.5E-05 33.5 6.2 77 2-80 82-183 (197)
62 PRK14091 RNA-binding protein H 86.7 2.6 5.6E-05 32.7 6.0 37 9-45 14-52 (165)
63 PRK14091 RNA-binding protein H 85.8 2.3 5E-05 32.9 5.4 58 10-79 95-154 (165)
64 PRK14632 hypothetical protein; 85.0 3.7 8E-05 31.6 6.2 43 3-46 81-133 (172)
65 PF02576 DUF150: Uncharacteris 84.7 3.2 6.9E-05 30.4 5.6 37 3-39 70-113 (141)
66 PRK14633 hypothetical protein; 84.1 4.6 9.9E-05 30.4 6.3 41 4-45 78-125 (150)
67 COG0779 Uncharacterized protei 83.7 3.4 7.3E-05 31.5 5.5 38 4-41 83-127 (153)
68 PRK14640 hypothetical protein; 83.6 3.7 8E-05 30.9 5.6 37 4-40 81-124 (152)
69 PRK14647 hypothetical protein; 82.3 6.1 0.00013 29.9 6.4 36 4-39 83-130 (159)
70 PRK14636 hypothetical protein; 82.0 7.4 0.00016 30.1 6.9 37 4-40 82-125 (176)
71 PRK14645 hypothetical protein; 81.4 4.4 9.5E-05 30.7 5.3 37 3-40 85-124 (154)
72 PRK14643 hypothetical protein; 80.8 4.1 8.9E-05 31.2 5.0 36 5-40 89-131 (164)
73 PRK14646 hypothetical protein; 77.9 6.1 0.00013 29.9 5.1 41 4-45 84-131 (155)
74 PRK14637 hypothetical protein; 77.9 9.7 0.00021 28.7 6.2 42 3-45 81-126 (151)
75 PRK14634 hypothetical protein; 76.1 8.1 0.00018 29.2 5.4 37 4-40 84-127 (155)
76 PRK14631 hypothetical protein; 75.8 12 0.00026 28.9 6.3 35 4-38 101-142 (174)
77 PRK06955 biotin--protein ligas 74.3 18 0.0004 29.7 7.5 48 15-67 247-295 (300)
78 PRK14635 hypothetical protein; 69.8 18 0.00039 27.4 6.0 41 4-45 83-131 (162)
79 PF07073 ROF: Modulator of Rho 69.4 4.4 9.6E-05 27.7 2.3 21 14-34 14-34 (80)
80 PRK09618 flgD flagellar basal 69.0 17 0.00036 27.5 5.5 26 13-38 88-113 (142)
81 smart00333 TUDOR Tudor domain. 68.4 20 0.00044 21.5 5.0 25 16-40 5-29 (57)
82 PF10618 Tail_tube: Phage tail 68.1 12 0.00026 27.1 4.5 32 6-37 63-94 (119)
83 TIGR00567 3mg DNA-3-methyladen 67.2 13 0.00028 29.3 4.8 36 7-42 9-44 (192)
84 PRK14641 hypothetical protein; 66.3 15 0.00032 28.5 4.9 36 3-38 87-129 (173)
85 PRK11886 bifunctional biotin-- 65.4 33 0.00072 28.1 7.2 31 15-46 270-300 (319)
86 PRK08330 biotin--protein ligas 64.1 42 0.00091 26.4 7.3 46 15-66 186-234 (236)
87 PRK11625 Rho-binding antitermi 62.3 19 0.0004 24.9 4.3 24 14-37 20-43 (84)
88 PRK13325 bifunctional biotin-- 60.6 44 0.00095 30.4 7.6 49 15-68 276-325 (592)
89 TIGR02603 CxxCH_TIGR02603 puta 60.0 35 0.00075 24.6 5.7 21 18-38 58-78 (133)
90 KOG3262 H/ACA small nucleolar 60.0 11 0.00023 30.2 3.1 13 9-21 57-69 (215)
91 PF03614 Flag1_repress: Repres 57.4 14 0.0003 28.5 3.3 69 15-83 27-101 (165)
92 PRK14630 hypothetical protein; 57.3 30 0.00066 25.8 5.1 37 3-40 80-119 (143)
93 PF11607 DUF3247: Protein of u 56.9 16 0.00036 26.0 3.3 26 11-36 21-47 (101)
94 PF02245 Pur_DNA_glyco: Methyl 56.5 20 0.00044 28.0 4.2 35 7-42 8-42 (184)
95 TIGR00121 birA_ligase birA, bi 55.5 71 0.0015 25.1 7.2 31 15-46 191-221 (237)
96 PRK11911 flgD flagellar basal 53.5 36 0.00078 25.6 4.9 25 14-38 90-114 (140)
97 cd00540 AAG Alkyladenine DNA g 52.7 33 0.00071 26.7 4.8 35 7-42 5-39 (179)
98 TIGR03344 VI_effect_Hcp1 type 52.5 77 0.0017 24.0 6.7 71 6-79 76-157 (166)
99 PRK06789 flagellar motor switc 49.8 39 0.00085 22.7 4.2 36 13-48 37-72 (74)
100 PF11684 DUF3280: Protein of u 47.2 45 0.00098 24.9 4.6 40 26-69 81-123 (140)
101 COG4568 Rof Transcriptional an 46.2 29 0.00063 23.9 3.1 22 14-35 20-41 (84)
102 PTZ00034 40S ribosomal protein 45.9 7.3 0.00016 28.9 0.1 16 72-87 80-95 (124)
103 TIGR01080 rplX_A_E ribosomal p 45.2 1E+02 0.0022 22.3 6.1 57 16-75 44-101 (114)
104 PF03614 Flag1_repress: Repres 43.2 74 0.0016 24.6 5.2 35 16-56 119-153 (165)
105 PRK05163 rpsL 30S ribosomal pr 42.3 72 0.0016 23.7 4.9 61 13-90 46-113 (124)
106 COG3157 Hcp Type VI protein se 41.5 88 0.0019 24.1 5.5 73 6-81 70-150 (162)
107 PF04452 Methyltrans_RNA: RNA 40.7 36 0.00078 26.6 3.4 60 10-69 13-74 (225)
108 PRK01191 rpl24p 50S ribosomal 40.4 1.3E+02 0.0029 22.0 6.1 56 17-75 49-105 (120)
109 COG2336 MazE Growth regulator 39.8 40 0.00087 23.3 3.1 28 2-29 11-41 (82)
110 PF07593 UnbV_ASPIC: ASPIC and 39.6 1E+02 0.0022 19.7 5.4 49 14-63 1-62 (71)
111 CHL00051 rps12 ribosomal prote 39.6 79 0.0017 23.4 4.8 61 13-89 46-112 (123)
112 PTZ00275 biotin-acetyl-CoA-car 39.2 75 0.0016 26.0 5.2 32 15-47 235-266 (285)
113 COG5316 Uncharacterized conser 39.0 1.2E+02 0.0026 26.9 6.5 39 6-45 71-109 (421)
114 COG0340 BirA Biotin-(acetyl-Co 38.6 1.5E+02 0.0033 23.8 6.7 34 15-48 188-221 (238)
115 TIGR00981 rpsL_bact ribosomal 38.5 83 0.0018 23.4 4.7 62 13-91 46-114 (124)
116 COG1886 FliN Flagellar motor s 38.0 64 0.0014 23.7 4.2 34 14-47 102-135 (136)
117 PRK10898 serine endoprotease; 37.7 66 0.0014 27.1 4.7 32 17-48 101-132 (353)
118 COG2094 Mpg 3-methyladenine DN 37.4 71 0.0015 25.5 4.5 36 6-42 13-48 (200)
119 PTZ00194 60S ribosomal protein 34.8 1.2E+02 0.0027 22.9 5.3 58 16-76 49-107 (143)
120 PF14262 DUF4353: Domain of un 34.6 1.3E+02 0.0029 24.7 5.9 57 16-77 5-69 (264)
121 PRK09798 antitoxin MazE; Provi 33.9 49 0.0011 22.5 2.7 29 2-30 12-43 (82)
122 PRK06792 flgD flagellar basal 31.5 1.3E+02 0.0028 23.9 5.1 25 14-38 115-139 (190)
123 PRK10139 serine endoprotease; 31.4 96 0.0021 27.1 4.8 32 17-48 114-145 (455)
124 cd05694 S1_Rrp5_repeat_hs2_sc2 30.8 45 0.00098 21.7 2.1 52 23-75 1-55 (74)
125 PRK08477 biotin--protein ligas 30.5 1.9E+02 0.0041 22.8 6.0 36 13-49 171-206 (211)
126 PF13437 HlyD_3: HlyD family s 30.3 1.1E+02 0.0024 20.3 4.1 34 6-39 41-78 (105)
127 TIGR02037 degP_htrA_DO peripla 30.2 97 0.0021 26.5 4.6 32 18-49 82-113 (428)
128 PRK00802 3-methyladenine DNA g 28.5 1E+02 0.0023 24.2 4.1 32 7-42 13-44 (188)
129 TIGR03170 flgA_cterm flagella 28.4 84 0.0018 21.9 3.3 22 15-36 94-116 (122)
130 PF00560 LRR_1: Leucine Rich R 28.3 40 0.00086 16.8 1.2 19 60-80 2-20 (22)
131 PF05037 DUF669: Protein of un 28.0 42 0.00091 24.5 1.8 30 7-36 93-123 (141)
132 PF00575 S1: S1 RNA binding do 27.5 61 0.0013 20.1 2.3 24 23-46 1-25 (74)
133 PF01052 SpoA: Surface present 27.5 1.7E+02 0.0037 18.6 5.3 34 16-49 41-74 (77)
134 PF14563 DUF4444: Domain of un 26.7 81 0.0018 19.2 2.5 21 30-50 10-30 (42)
135 PRK14056 phenylalanine 4-monoo 26.4 1.7E+02 0.0037 27.0 5.6 40 15-54 390-433 (578)
136 TIGR00046 RNA methyltransferas 26.4 1.5E+02 0.0032 23.4 4.8 61 9-69 27-89 (240)
137 PF02751 TFIIA_gamma_C: Transc 26.4 1.7E+02 0.0038 18.4 5.9 39 25-63 3-45 (52)
138 PRK11713 16S ribosomal RNA met 26.3 1.5E+02 0.0033 23.2 4.8 31 9-39 25-55 (234)
139 PRK10942 serine endoprotease; 26.1 1.2E+02 0.0027 26.6 4.6 32 17-48 135-166 (473)
140 PRK04313 30S ribosomal protein 26.0 2.9E+02 0.0062 22.6 6.4 45 32-76 190-236 (237)
141 TIGR00999 8a0102 Membrane Fusi 25.7 1.3E+02 0.0027 23.3 4.2 36 7-42 131-167 (265)
142 PRK10113 cell division modulat 25.5 60 0.0013 22.0 2.0 28 61-88 35-62 (80)
143 TIGR02038 protease_degS peripl 24.7 3.2E+02 0.007 22.8 6.7 32 18-49 102-133 (351)
144 cd01737 LSm16_N LSm16 belongs 24.3 2.1E+02 0.0046 18.7 5.4 55 14-71 3-59 (62)
145 PRK10708 hypothetical protein; 24.3 87 0.0019 20.4 2.5 27 16-42 3-29 (62)
146 PF05954 Phage_GPD: Phage late 23.8 90 0.0019 24.2 3.1 26 13-38 24-49 (292)
147 PF12945 YcgR_2: Flagellar pro 23.4 2.1E+02 0.0045 18.2 4.4 29 16-44 3-35 (87)
148 KOG1219 Uncharacterized conser 23.2 1.3E+02 0.0027 33.2 4.5 81 2-89 1583-1673(4289)
149 PRK08158 type III secretion sy 22.8 1.7E+02 0.0036 24.8 4.6 37 14-50 261-297 (303)
150 COG1363 FrvX Cellulase M and r 22.7 1E+02 0.0022 26.6 3.3 23 13-35 93-115 (355)
151 PF07076 DUF1344: Protein of u 22.7 96 0.0021 20.2 2.5 20 29-48 4-24 (61)
152 cd00319 Ribosomal_S12_like Rib 22.3 1.4E+02 0.0031 21.1 3.5 24 13-36 31-54 (95)
153 KOG4401 Uncharacterized conser 21.9 1.2E+02 0.0026 24.0 3.3 45 15-61 9-53 (184)
154 PRK07018 flgA flagellar basal 21.1 1.2E+02 0.0026 24.0 3.3 22 15-36 205-227 (235)
155 cd01343 PL1_Passenger_AT Perta 20.7 4.3E+02 0.0093 21.1 6.4 52 19-74 74-126 (233)
156 PF10781 DSRB: Dextransucrase 20.6 1E+02 0.0022 20.1 2.3 27 16-42 3-29 (62)
157 PF12541 DUF3737: Protein of u 20.4 1.4E+02 0.0031 25.0 3.7 33 36-69 151-183 (277)
158 PF09465 LBR_tudor: Lamin-B re 20.1 2.1E+02 0.0046 18.3 3.6 25 15-39 7-32 (55)
No 1
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=100.00 E-value=4.4e-41 Score=240.07 Aligned_cols=118 Identities=70% Similarity=1.162 Sum_probs=100.1
Q ss_pred CCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCccccccc
Q 032863 4 SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAP 83 (132)
Q Consensus 4 ~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap 83 (132)
++++|++||||++||.|++|+++|++|+|+|.++||+|||+|+|+++|.+||+.+++++||||||+|||+++||+|++||
T Consensus 2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnAP 81 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNAP 81 (119)
T ss_pred ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcCc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhchhhhhcCCCCCcccccchhHHHHHHHhhcCCCCCCCCCCCCCCCC
Q 032863 84 MFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPGRGVVPPVRR 132 (132)
Q Consensus 84 ~l~~~~~~~~~~~~~~~~~rg~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 132 (132)
||+. +++++.+.+.+|+.+.+ ++|+| +||||.++++||
T Consensus 82 mFkk------~~~~~~g~~~~RG~~~~----~~grg-~g~rg~~~p~~r 119 (119)
T KOG3172|consen 82 MFKK------GKSRSLGGGPGRGRARR----ARGRG-RGGRGAGPPVRR 119 (119)
T ss_pred cccc------ccCCcCCCCCCcccccc----ccCCC-CCCCCCCCCCCC
Confidence 9993 33444444444443333 33333 556888888775
No 2
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.97 E-value=6.5e-30 Score=178.45 Aligned_cols=85 Identities=26% Similarity=0.497 Sum_probs=80.9
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcccccccchhc
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKR 87 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~l~~ 87 (132)
|++||++++|++|+||||||++|+|+|.+||+||||+|+||+++..++....++++||||++|+||+|||+++..++|.+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~ 81 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVD 81 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhh
Confidence 78999999999999999999999999999999999999999999988889999999999999999999999999999998
Q ss_pred hhhhh
Q 032863 88 LDARI 92 (132)
Q Consensus 88 ~~~~~ 92 (132)
..+..
T Consensus 82 ~~~~~ 86 (90)
T cd01724 82 STPKP 86 (90)
T ss_pred cCCcc
Confidence 76543
No 3
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.95 E-value=5.6e-28 Score=161.24 Aligned_cols=70 Identities=69% Similarity=1.218 Sum_probs=68.5
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCc
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++|+...++++||||++|+||+|||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 8999999999999999999999999999999999999999999999999899999999999999999997
No 4
>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=99.94 E-value=2.4e-26 Score=156.60 Aligned_cols=72 Identities=29% Similarity=0.514 Sum_probs=69.2
Q ss_pred CCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecC
Q 032863 5 LGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIP 76 (132)
Q Consensus 5 i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lp 76 (132)
-.++++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++++..+++++||||++|+||+||
T Consensus 7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 357899999999999999999999999999999999999999999999888888999999999999999998
No 5
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.94 E-value=8e-27 Score=170.17 Aligned_cols=75 Identities=36% Similarity=0.748 Sum_probs=72.5
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCeEEEEecCccccc
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSKVRFMVIPDMLKN 81 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~lpd~l~~ 81 (132)
.|+.||+.++++++.||||||++|.|.|++||.+||++|++|++|.+|| +++.+++|||||++|+|+.|||.+..
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHH
Confidence 6999999999999999999999999999999999999999999999999 69999999999999999999999764
No 6
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.94 E-value=3.2e-26 Score=154.79 Aligned_cols=73 Identities=36% Similarity=0.757 Sum_probs=69.5
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCc-eeeeeeEEEeCCeEEEEecCccc
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGK-VSQLEHVFIRGSKVRFMVIPDML 79 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lpd~l 79 (132)
.|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++|+ ...++++||||++|+||++||++
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 59999999999999999999999999999999999999999999988885 56789999999999999999986
No 7
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.93 E-value=2.9e-25 Score=152.04 Aligned_cols=75 Identities=29% Similarity=0.457 Sum_probs=68.9
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC--ceeeeeeEEEeCCeEEEEecCccccc
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG--KVSQLEHVFIRGSKVRFMVIPDMLKN 81 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg--~~~~l~~vfIRGs~Ir~I~lpd~l~~ 81 (132)
.|+.||++++|++|+||||||++|+|+|.+||+|||++|+||+++.+++ ....++++||||++|+||++||++-.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence 4899999999999999999999999999999999999999999998665 35678999999999999999998743
No 8
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.90 E-value=1.7e-23 Score=149.70 Aligned_cols=90 Identities=26% Similarity=0.483 Sum_probs=84.3
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcccccccchhc
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKR 87 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~l~~ 87 (132)
.+.||+.+.+++|+||||||++++|+|.++|.+||.+|.+|+++.+ |++..++.++|||++|||+++||.+..++++.+
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 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-GEPVRLDTLSIRGNNIRYYILPDSLNLDTLLVD 81 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-CCceeEEEEEeecceEEEEEccCCcCcceeeee
Confidence 5789999999999999999999999999999999999999999986 488899999999999999999999999999999
Q ss_pred hhhhhcCCCCC
Q 032863 88 LDARIKGKSSS 98 (132)
Q Consensus 88 ~~~~~~~~~~~ 98 (132)
+.+..+.++..
T Consensus 82 ~~~~~~~~~~~ 92 (109)
T KOG3428|consen 82 DAPRLHLRKNE 92 (109)
T ss_pred hhhhhhhhccc
Confidence 99887776654
No 9
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=1.9e-23 Score=137.99 Aligned_cols=67 Identities=28% Similarity=0.422 Sum_probs=63.5
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
|++||++++|++|+||||||++|+|+|.+||+|||++|+||+++..+++...++++||||++|+||.
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 8999999999999999999999999999999999999999999876667889999999999999984
No 10
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.89 E-value=1.5e-22 Score=134.16 Aligned_cols=68 Identities=29% Similarity=0.435 Sum_probs=63.3
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
.|+.+|++++|++|+|||+||.+|+|+|.++|+|||++|+||+++...++...++++||||++|+||.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 49999999999999999999999999999999999999999998864556789999999999999984
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.87 E-value=7.9e-22 Score=132.10 Aligned_cols=69 Identities=29% Similarity=0.422 Sum_probs=64.9
Q ss_pred CcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 6 GIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
..|+++|++++|++|+|+|+||.+|+|+|.+||+|||++|+||+++..++....++.+||||++|.||.
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 589999999999999999999999999999999999999999999875556778999999999999985
No 12
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.86 E-value=4.1e-21 Score=126.94 Aligned_cols=67 Identities=28% Similarity=0.452 Sum_probs=64.1
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
|+++|++++|++|+|+|+||.+|.|+|.+||+|||++|+||+++..++....++.+||||++|.||.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 8999999999999999999999999999999999999999999887777889999999999999986
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=99.83 E-value=3.3e-20 Score=121.06 Aligned_cols=66 Identities=39% Similarity=0.665 Sum_probs=63.0
Q ss_pred HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCeEEEEec
Q 032863 10 KLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 10 ~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l 75 (132)
.+|++++|++|+|+|+||.+|+|+|.+||++||++|+||+++..++ +...++.+||||++|+||++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4799999999999999999999999999999999999999998777 88999999999999999985
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.83 E-value=3.1e-20 Score=121.05 Aligned_cols=65 Identities=37% Similarity=0.604 Sum_probs=62.1
Q ss_pred HHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC-CceeeeeeEEEeCCeEEEEec
Q 032863 11 LLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD-GKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 11 lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d-g~~~~l~~vfIRGs~Ir~I~l 75 (132)
+|++++|+.|+|+|+||++|.|+|.++|+|||++|+||+++.++ ++..+++.+||||++|+||++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 79999999999999999999999999999999999999999877 688999999999999999974
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.82 E-value=1e-19 Score=123.34 Aligned_cols=75 Identities=28% Similarity=0.436 Sum_probs=64.9
Q ss_pred CCCCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEcc-CCce--ee-eeeEEEeCCeEEEEec
Q 032863 1 MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAK-DGKV--SQ-LEHVFIRGSKVRFMVI 75 (132)
Q Consensus 1 ms~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~-dg~~--~~-l~~vfIRGs~Ir~I~l 75 (132)
|+.....|+.+|+++++++|.|+||||++|+|+|.+||+|||++|+||+++.. ++.. .. .+.+||||++|.||.+
T Consensus 1 ~~~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 1 MSMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CCcccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 44555689999999999999999999999999999999999999999999874 4432 34 4499999999999863
No 16
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.80 E-value=2.8e-19 Score=114.92 Aligned_cols=63 Identities=37% Similarity=0.584 Sum_probs=60.3
Q ss_pred HHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 12 LHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 12 L~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
|++++|++|+|+|+||.+|.|+|.++|++||++|+|++++..+.+...++.+||||++|+||+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 578999999999999999999999999999999999999988888999999999999999985
No 17
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.80 E-value=5.7e-19 Score=119.81 Aligned_cols=70 Identities=21% Similarity=0.471 Sum_probs=63.9
Q ss_pred CcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEc--cC-CceeeeeeEEEeCCeEEEEec
Q 032863 6 GIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTA--KD-GKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~--~d-g~~~~l~~vfIRGs~Ir~I~l 75 (132)
..|+++|+++++++|.|+|++|.+|.|+|.+||.|||++|+||++.. ++ +....++.+||||++|.+|+.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 47999999999999999999999999999999999999999998875 23 356789999999999999983
No 18
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.77 E-value=1.6e-18 Score=120.44 Aligned_cols=82 Identities=24% Similarity=0.394 Sum_probs=73.9
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC--ceeeeeeEEEeCCeEEEEecCcccccccch
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG--KVSQLEHVFIRGSKVRFMVIPDMLKNAPMF 85 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg--~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~l 85 (132)
-..|++.++|+.|+|||||+..+.|+|.++|+|+|+.|+|+++++++. .-.....|||||+.||||.+|..-.....+
T Consensus 3 FysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtqll 82 (96)
T KOG3448|consen 3 FYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQLL 82 (96)
T ss_pred hHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHHH
Confidence 368999999999999999999999999999999999999999998765 457788999999999999999888777777
Q ss_pred hchh
Q 032863 86 KRLD 89 (132)
Q Consensus 86 ~~~~ 89 (132)
.++.
T Consensus 83 ~da~ 86 (96)
T KOG3448|consen 83 QDAA 86 (96)
T ss_pred HHHH
Confidence 7654
No 19
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=4.1e-18 Score=114.35 Aligned_cols=70 Identities=14% Similarity=0.208 Sum_probs=63.7
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCc
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
|-..|+++++++|.|+|++|.+|.|+|.+||+|||++|+||+++..+.....++.++|||++|.+|..-|
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 3457999999999999999999999999999999999999999875557789999999999999998654
No 20
>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=99.72 E-value=3.5e-17 Score=111.99 Aligned_cols=68 Identities=21% Similarity=0.346 Sum_probs=61.0
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC-------------CceeeeeeEEEeCCeEEEE
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD-------------GKVSQLEHVFIRGSKVRFM 73 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d-------------g~~~~l~~vfIRGs~Ir~I 73 (132)
.|+.||+.+.+++|.|+|++|..|.|+|.+||.|||++|+||+++... .....++.+||||++|.+|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 489999999999999999999999999999999999999999987532 1245789999999999998
Q ss_pred e
Q 032863 74 V 74 (132)
Q Consensus 74 ~ 74 (132)
.
T Consensus 81 ~ 81 (82)
T cd01730 81 S 81 (82)
T ss_pred C
Confidence 5
No 21
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.72 E-value=1.6e-17 Score=111.77 Aligned_cols=71 Identities=30% Similarity=0.463 Sum_probs=65.0
Q ss_pred CCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCeEEEEe
Q 032863 3 RSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 3 ~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~ 74 (132)
...-.|-.||+.+.|++|.|+||.|.+|+|+|.++|.|||++|.++++.. || ..-.+++++||.+||.||.
T Consensus 4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i-dG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI-DGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh-cccccccceeEEEEeccEEEEe
Confidence 34457899999999999999999999999999999999999999999876 55 6788999999999999994
No 22
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.72 E-value=5.8e-17 Score=112.66 Aligned_cols=69 Identities=22% Similarity=0.315 Sum_probs=60.9
Q ss_pred cHHHHHHhhC--CCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-------------ceeeeeeEEEeCCeEE
Q 032863 7 IPVKLLHEAS--GHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-------------KVSQLEHVFIRGSKVR 71 (132)
Q Consensus 7 ~P~~lL~~~~--g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-------------~~~~l~~vfIRGs~Ir 71 (132)
-|+.+|+.+. +++|.|.|++|..|.|+|.+||.|||++|+||+++.... +...++.+||||++|.
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 5999999996 899999999999999999999999999999999875331 1346899999999999
Q ss_pred EEec
Q 032863 72 FMVI 75 (132)
Q Consensus 72 ~I~l 75 (132)
||..
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9864
No 23
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.66 E-value=6.3e-16 Score=105.85 Aligned_cols=66 Identities=23% Similarity=0.294 Sum_probs=59.2
Q ss_pred HHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC--------CceeeeeeEEEeCCeEEEEecCc
Q 032863 12 LHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD--------GKVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 12 L~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d--------g~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
|+++++++|.|.|++|.+|.|+|.++|.|||++|+||++...+ .....++.++|||++|.+|...|
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 8899999999999999999999999999999999999987643 14577899999999999997654
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=99.66 E-value=6.8e-16 Score=105.66 Aligned_cols=72 Identities=13% Similarity=0.241 Sum_probs=63.5
Q ss_pred CCCCcHHHHHHhhCCC--EEEEEeC--CCcEEEEEEEeeCCceeeEEeeeEEEcc-CCceeeeeeEEEeCCeEEEEe
Q 032863 3 RSLGIPVKLLHEASGH--VVTVELK--SGELYRGSMVECEDNWNCQLENITYTAK-DGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 3 ~~i~~P~~lL~~~~g~--~V~VELk--nG~~y~G~L~~vD~~MNi~L~dv~~t~~-dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
+.+..|+.+|+++..+ +|+|.|+ +|.+|.|+|.++|.|||++|+||++... ......++.++|||++|.+|+
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 3467899999999999 7888887 8999999999999999999999998764 335678999999999999987
No 25
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.62 E-value=1e-16 Score=107.76 Aligned_cols=75 Identities=31% Similarity=0.482 Sum_probs=68.5
Q ss_pred CCCCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCc-eeeeeeEEEeCCeEEEEecCc
Q 032863 1 MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGK-VSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 1 ms~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~lpd 77 (132)
|| .-..|-.||.+.+|++|.|+|.+|..|+|+|...|.|||+.|+.+++.. ||+ +..++.+||||++|.||...+
T Consensus 1 ~s-~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 1 MS-EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred CC-cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCcccccccceeeccccEEEEEecc
Confidence 56 3478999999999999999999999999999999999999999999876 664 788999999999999998753
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=99.60 E-value=7.6e-15 Score=99.62 Aligned_cols=65 Identities=18% Similarity=0.272 Sum_probs=57.7
Q ss_pred HHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC----------CceeeeeeEEEeCCeEEEEec
Q 032863 11 LLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD----------GKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 11 lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d----------g~~~~l~~vfIRGs~Ir~I~l 75 (132)
-|++++|++|.|.|++|..|.|+|.++|.|||++|+||+++... .+...++.+||||++|.+|.+
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 37889999999999999999999999999999999999986522 135679999999999999975
No 27
>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=99.58 E-value=1.7e-14 Score=97.43 Aligned_cols=68 Identities=19% Similarity=0.126 Sum_probs=59.3
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC---ceeeeeeEEEeCCeEEEEec
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG---KVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg---~~~~l~~vfIRGs~Ir~I~l 75 (132)
++.-|.++++++|.|.|++|..|.|+|.++|.|||++|+||.++..++ ....++.++|||++|.+|.+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 356688999999999999999999999999999999999998765333 35678999999999999864
No 28
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.53 E-value=6.9e-14 Score=93.94 Aligned_cols=67 Identities=19% Similarity=0.231 Sum_probs=58.9
Q ss_pred HHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEcc---CC-ceeeeeeEEEeCCeEEEEecCc
Q 032863 11 LLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAK---DG-KVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 11 lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~---dg-~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
-|.++++++|.|.|++|..|.|+|.++|.|||++|++|.+... ++ ....++.++|||++|.+|..-|
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 4788999999999999999999999999999999999988642 23 3567999999999999998654
No 29
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.53 E-value=5.1e-14 Score=98.38 Aligned_cols=73 Identities=11% Similarity=0.237 Sum_probs=60.5
Q ss_pred CCCCcHHHHHHhhCCC--EEEEEeCC--CcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCeEEEEec
Q 032863 3 RSLGIPVKLLHEASGH--VVTVELKS--GELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 3 ~~i~~P~~lL~~~~g~--~V~VELkn--G~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~Ir~I~l 75 (132)
+.+..|+++|+++... +|.|.|.+ +..|.|+|.+||.|||++|+||++...++ ....++.++|||++|.+|..
T Consensus 10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 4467899999999765 45555556 58999999999999999999999876433 56789999999999999875
No 30
>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=99.52 E-value=1.1e-13 Score=93.67 Aligned_cols=66 Identities=15% Similarity=0.213 Sum_probs=60.2
Q ss_pred HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC------CceeeeeeEEEeCCeEEEEec
Q 032863 10 KLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD------GKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 10 ~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d------g~~~~l~~vfIRGs~Ir~I~l 75 (132)
+-|++++|++|.|.|++|..|.|+|.++|.+||+.|+||.++..+ .....++.++|||++|..|++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 468899999999999999999999999999999999999997643 357789999999999999976
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.42 E-value=5.2e-13 Score=90.13 Aligned_cols=72 Identities=24% Similarity=0.357 Sum_probs=65.9
Q ss_pred CCCCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEec
Q 032863 1 MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 1 ms~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 75 (132)
||++ +.| =|+++.++.+.+.|..+..+.|+|.++|.|||++|+++++...++....+..++|||++|..+.-
T Consensus 1 Msks-g~P--eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 1 MSKS-GHP--ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred CCcc-cCc--hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEee
Confidence 6654 678 78999999999999999999999999999999999999999889988999999999999987654
No 32
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.41 E-value=1.2e-13 Score=95.15 Aligned_cols=76 Identities=25% Similarity=0.359 Sum_probs=65.9
Q ss_pred CCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEc--cCC-----------ceeeeeeEEEeCCeE
Q 032863 4 SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTA--KDG-----------KVSQLEHVFIRGSKV 70 (132)
Q Consensus 4 ~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~--~dg-----------~~~~l~~vfIRGs~I 70 (132)
.+..|++||+-.+++.|-|+|+++++++|+|.+||+|+|++|.||.+|- .+. ....++.+||||.+|
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence 4678999999999999999999999999999999999999999987543 222 235689999999999
Q ss_pred EEEecCccc
Q 032863 71 RFMVIPDML 79 (132)
Q Consensus 71 r~I~lpd~l 79 (132)
.+|..|-.+
T Consensus 82 ilvspp~~~ 90 (91)
T KOG3460|consen 82 ILVSPPLRL 90 (91)
T ss_pred EEEcCcccC
Confidence 999988543
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.30 E-value=1.9e-12 Score=88.01 Aligned_cols=74 Identities=23% Similarity=0.490 Sum_probs=66.1
Q ss_pred CCCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEE--EccCC-ceeeeeeEEEeCCeEEEEec
Q 032863 2 SRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITY--TAKDG-KVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 2 s~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~--t~~dg-~~~~l~~vfIRGs~Ir~I~l 75 (132)
+.+.-.|+.|+.+++|+.|.|-+|++.++.|+|.+||+|.|++|+||++ +.++| ...+++++++.|++|..+..
T Consensus 2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvP 78 (84)
T KOG1775|consen 2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVP 78 (84)
T ss_pred ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEec
Confidence 3445789999999999999999999999999999999999999999996 44566 47899999999999987764
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=98.57 E-value=6.7e-08 Score=66.56 Aligned_cols=71 Identities=17% Similarity=0.287 Sum_probs=54.7
Q ss_pred CCcHHHHHHhhC--CCEEEEEeCC--CcEEEEEEEeeCCceeeEEeeeEEEccCCc-eeeeeeEEEeCCeEEEEec
Q 032863 5 LGIPVKLLHEAS--GHVVTVELKS--GELYRGSMVECEDNWNCQLENITYTAKDGK-VSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 5 i~~P~~lL~~~~--g~~V~VELkn--G~~y~G~L~~vD~~MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~Ir~I~l 75 (132)
.-.|+.++..++ -.+|.|=|.. +..+.|.+.+||+|||++|+|+.+.....+ -..++.++++|.+|..|.-
T Consensus 10 mv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 10 MVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred ecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 346766555543 3456666665 789999999999999999999998765443 3479999999999998864
No 35
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.51 E-value=4.3e-08 Score=75.39 Aligned_cols=82 Identities=22% Similarity=0.334 Sum_probs=65.8
Q ss_pred CCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEcc---------CC-ceeeeeeEEEeCCeEEEEe
Q 032863 5 LGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAK---------DG-KVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 5 i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~---------dg-~~~~l~~vfIRGs~Ir~I~ 74 (132)
+.-+.++|+ .+++.+.|.++||.+|.|++..||.|||++|.||.+... |+ ....|..|.+||.+|....
T Consensus 3 ~a~sskml~-~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~t 81 (177)
T KOG3168|consen 3 VAKSSKMLQ-HINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMT 81 (177)
T ss_pred ccchhHHHH-hhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEe
Confidence 556666665 579999999999999999999999999999999875321 22 3567999999999999999
Q ss_pred cCcccccccchhc
Q 032863 75 IPDMLKNAPMFKR 87 (132)
Q Consensus 75 lpd~l~~ap~l~~ 87 (132)
+.+-...++=|..
T Consensus 82 Vegppp~s~s~~~ 94 (177)
T KOG3168|consen 82 VEGPPPPSDSFRR 94 (177)
T ss_pred ccCCCCCcccccc
Confidence 9776665555543
No 36
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.40 E-value=4.7e-08 Score=69.44 Aligned_cols=72 Identities=17% Similarity=0.196 Sum_probs=63.1
Q ss_pred HHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC--------ceeeeeeEEEeCCeEEEEecCcccc
Q 032863 9 VKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG--------KVSQLEHVFIRGSKVRFMVIPDMLK 80 (132)
Q Consensus 9 ~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg--------~~~~l~~vfIRGs~Ir~I~lpd~l~ 80 (132)
+--|.+++++.|.|++..|..+.|+|.++|..||++|+|+.++-+|. ...+++.+.+||..+..|...|-.+
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 45578899999999999999999999999999999999998766542 3478999999999999999887665
No 37
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.09 E-value=1.5e-05 Score=53.28 Aligned_cols=45 Identities=27% Similarity=0.408 Sum_probs=37.0
Q ss_pred HHHHHhhCCCEEEEEeCCCcEEEEEEEeeCC---ceeeEEeeeEEEcc
Q 032863 9 VKLLHEASGHVVTVELKSGELYRGSMVECED---NWNCQLENITYTAK 53 (132)
Q Consensus 9 ~~lL~~~~g~~V~VELknG~~y~G~L~~vD~---~MNi~L~dv~~t~~ 53 (132)
+-++..++|++|+|.++||..|.|.|.+++. -+.+.|+.+.....
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 4477889999999999999999999999998 99999999988764
No 38
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=97.87 E-value=3e-05 Score=54.53 Aligned_cols=77 Identities=18% Similarity=0.173 Sum_probs=63.1
Q ss_pred HHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEc---cCC-ceeeeeeEEEeCCeEEEEecCcccccccchhc
Q 032863 12 LHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTA---KDG-KVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKR 87 (132)
Q Consensus 12 L~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~---~dg-~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~l~~ 87 (132)
|..+.++.|.|-+.+|+.+-|.|.+||..-|+.|+++-+-. ..| ...-++...|||.||..|-+-|+- .+|+|++
T Consensus 5 L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe-~d~~ld~ 83 (96)
T KOG1784|consen 5 LEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEE-LDSRLDL 83 (96)
T ss_pred HHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchh-hhhhhhh
Confidence 78889999999999999999999999999999999986521 123 467788999999999999876653 3467776
Q ss_pred hh
Q 032863 88 LD 89 (132)
Q Consensus 88 ~~ 89 (132)
.+
T Consensus 84 tk 85 (96)
T KOG1784|consen 84 TK 85 (96)
T ss_pred hh
Confidence 53
No 39
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=97.61 E-value=1.2e-05 Score=59.28 Aligned_cols=66 Identities=21% Similarity=0.151 Sum_probs=54.7
Q ss_pred HHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEE-EccCCc--eeeeeeEEEeCCeEEEEecCc
Q 032863 12 LHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITY-TAKDGK--VSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 12 L~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~-t~~dg~--~~~l~~vfIRGs~Ir~I~lpd 77 (132)
|-+.+.+.+.|-|++|....|.|.+||+|-|++|++|.+ +..+.+ -...+.+.|||.||..+-.-|
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 667789999999999999999999999999999999986 333332 345677999999999987643
No 40
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.41 E-value=0.00088 Score=47.41 Aligned_cols=67 Identities=16% Similarity=0.262 Sum_probs=55.3
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeCC-ceeeEEeeeEEEccCCc---------eeeeeeEEEeCCeEEEEecCcccc
Q 032863 14 EASGHVVTVELKSGELYRGSMVECED-NWNCQLENITYTAKDGK---------VSQLEHVFIRGSKVRFMVIPDMLK 80 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD~-~MNi~L~dv~~t~~dg~---------~~~l~~vfIRGs~Ir~I~lpd~l~ 80 (132)
.++|+.|.+..+++..|.|+|..+|. .-.|.|+||.....+++ ...++.+..||+-|.-+.+-+.-.
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 57899999999999999999999994 88999999987665443 345889999999999888755433
No 41
>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=97.08 E-value=0.0005 Score=45.65 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=31.8
Q ss_pred CCCEEEEEeCCC----cEEEEEEEeeCCceeeEEeeeEEEccC
Q 032863 16 SGHVVTVELKSG----ELYRGSMVECEDNWNCQLENITYTAKD 54 (132)
Q Consensus 16 ~g~~V~VELknG----~~y~G~L~~vD~~MNi~L~dv~~t~~d 54 (132)
....|.|-++.- -.++|.|.+||.|||+.|.||+++...
T Consensus 7 er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 7 ERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 457777777743 378899999999999999999998754
No 42
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=97.07 E-value=0.00012 Score=52.99 Aligned_cols=68 Identities=21% Similarity=0.322 Sum_probs=55.6
Q ss_pred cHHHHHHhhC--CCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEcc------CCc-------eeeeeeEEEeCCeEE
Q 032863 7 IPVKLLHEAS--GHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAK------DGK-------VSQLEHVFIRGSKVR 71 (132)
Q Consensus 7 ~P~~lL~~~~--g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~------dg~-------~~~l~~vfIRGs~Ir 71 (132)
-|+++|..+. ..+|.|-++|....-|.+.++|-|.|++|+|+.+..- +|+ ...++.+||||.+|.
T Consensus 24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI 103 (114)
T KOG3459|consen 24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI 103 (114)
T ss_pred CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence 5888888875 6789999999999999999999999999999986331 222 245788999999887
Q ss_pred EEe
Q 032863 72 FMV 74 (132)
Q Consensus 72 ~I~ 74 (132)
.+.
T Consensus 104 ~v~ 106 (114)
T KOG3459|consen 104 LVL 106 (114)
T ss_pred EEE
Confidence 664
No 43
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=96.40 E-value=0.029 Score=38.59 Aligned_cols=64 Identities=20% Similarity=0.241 Sum_probs=51.0
Q ss_pred HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeC-CceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecC
Q 032863 8 PVKLLHEASGHVVTVELKSGELYRGSMVECE-DNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIP 76 (132)
Q Consensus 8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lp 76 (132)
-+.+|..+.|++|.+.|....++.|+...+| +..|+..+|-. .+=|. .++-.+|.+-|..+.+.
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~--TPlGv---~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ--TPLGV---QPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE--TTTTE---EEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC--CCccc---ChhheeecCCEEEEEec
Confidence 3678999999999999999999999999999 78899988863 33443 47899999999988874
No 44
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=96.04 E-value=0.045 Score=37.18 Aligned_cols=58 Identities=19% Similarity=0.336 Sum_probs=46.3
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeC-CceeeEEeeeEEEccCCc----------eeeeeeEEEeCCeEE
Q 032863 14 EASGHVVTVELKSGELYRGSMVECE-DNWNCQLENITYTAKDGK----------VSQLEHVFIRGSKVR 71 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD-~~MNi~L~dv~~t~~dg~----------~~~l~~vfIRGs~Ir 71 (132)
+++|+.|.+-.|++..|.|+|.++| +.--+.|+||.....+|. ..-++.+.-||+.|.
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 5789999999999999999999999 566688999987665542 233666777777765
No 45
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=95.97 E-value=0.074 Score=35.31 Aligned_cols=52 Identities=29% Similarity=0.535 Sum_probs=39.8
Q ss_pred HHHHHhhCCCEEEEEeCCCcEEEEEEEeeC-CceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 9 VKLLHEASGHVVTVELKSGELYRGSMVECE-DNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 9 ~~lL~~~~g~~V~VELknG~~y~G~L~~vD-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
+..|++++|+.|+|++-.|.. +|+|.++. ||. .|+. .++ .+|||=.+|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDhI--vl~~------~~~-----~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDHI--VLEE------NGT-----PFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCEE--EEEe------CCc-----EEEEEeeeEEEEc
Confidence 688999999999999977766 99999987 444 2221 222 4899988888874
No 46
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=95.49 E-value=0.091 Score=32.09 Aligned_cols=31 Identities=19% Similarity=0.158 Sum_probs=28.2
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCceeeEEee
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWNCQLEN 47 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MNi~L~d 47 (132)
+|++|+|++ ++..++|+...+|+.=.+.++.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 689999999 7778899999999999999876
No 47
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.34 E-value=0.062 Score=35.17 Aligned_cols=35 Identities=20% Similarity=0.164 Sum_probs=29.2
Q ss_pred HHHhh--CCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 11 LLHEA--SGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 11 lL~~~--~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
||+++ ...+|+|-|.||..++|++.++|.|+=+.-
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~ 39 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLE 39 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEE
Confidence 55555 578999999999999999999999875544
No 48
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.03 E-value=0.089 Score=34.47 Aligned_cols=36 Identities=19% Similarity=0.121 Sum_probs=29.6
Q ss_pred HHHHhh--CCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 10 KLLHEA--SGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 10 ~lL~~~--~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
.||.++ ...+|+|-|.||..+.|++.++|.|+=+.-
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 355554 578999999999999999999999875554
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.74 E-value=0.14 Score=35.13 Aligned_cols=69 Identities=14% Similarity=0.144 Sum_probs=46.5
Q ss_pred CCCCCCcHHHHHHhh--CCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcc
Q 032863 1 MSRSLGIPVKLLHEA--SGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDM 78 (132)
Q Consensus 1 ms~~i~~P~~lL~~~--~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~ 78 (132)
|.....+==.||..+ ...+|+|-|.||..++|.+.++|.|.=+... +|+ +-+|-=..|..|.....
T Consensus 1 m~~~~nlQd~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~-------~gk-----qqLIYKHAISTI~p~~~ 68 (79)
T PRK00395 1 MAKGQNLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRN-------TGK-----SQLVYKHAISTVVPARP 68 (79)
T ss_pred CccccchHHHHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEE-------CCc-----EEEEEEeeeEEEecCCc
Confidence 333333334566665 5789999999999999999999998755543 343 13555566777766555
Q ss_pred ccc
Q 032863 79 LKN 81 (132)
Q Consensus 79 l~~ 81 (132)
+..
T Consensus 69 i~~ 71 (79)
T PRK00395 69 VSL 71 (79)
T ss_pred ccc
Confidence 543
No 50
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.24 E-value=0.21 Score=42.89 Aligned_cols=67 Identities=15% Similarity=0.315 Sum_probs=54.1
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeC-CceeeEEeeeEEEccCCc---------ee-eeeeEEEeCCeEEEEecCccc
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECE-DNWNCQLENITYTAKDGK---------VS-QLEHVFIRGSKVRFMVIPDML 79 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD-~~MNi~L~dv~~t~~dg~---------~~-~l~~vfIRGs~Ir~I~lpd~l 79 (132)
..++|+.|.+--|++..|.|+|..+| +.-=|-|++|.....++. .. .++.|.-||+.|+-+++-|..
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 46799999999999999999999999 677789999966554331 11 578899999999988876643
No 51
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=92.63 E-value=0.7 Score=35.75 Aligned_cols=61 Identities=23% Similarity=0.266 Sum_probs=43.2
Q ss_pred HHHhhCCCEEEEEeCCCcEEEEEEEeeC-CceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcc
Q 032863 11 LLHEASGHVVTVELKSGELYRGSMVECE-DNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDM 78 (132)
Q Consensus 11 lL~~~~g~~V~VELknG~~y~G~L~~vD-~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~ 78 (132)
.+..++++.|.|.+.| .+|.|-|..+| ..-|++|-+.. .|++ ...-+|-|..|+.|.+-+.
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~---e~~~---~sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQ---EDGK---RSVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE----TTS----EEEEEE-GGGEEEEEEEE-
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcc---cCCc---eeEEEEEccceEEEEEccC
Confidence 4578999999999999 99999999999 57788886543 2343 2358899999999987554
No 52
>PRK14644 hypothetical protein; Provisional
Probab=92.20 E-value=0.42 Score=35.62 Aligned_cols=44 Identities=18% Similarity=0.385 Sum_probs=33.9
Q ss_pred CCCCCcHHHH--HHhhCCCEEEEEeCCC----cEEEEEEEeeCCceeeEEe
Q 032863 2 SRSLGIPVKL--LHEASGHVVTVELKSG----ELYRGSMVECEDNWNCQLE 46 (132)
Q Consensus 2 s~~i~~P~~l--L~~~~g~~V~VELknG----~~y~G~L~~vD~~MNi~L~ 46 (132)
|-.+..|+.- +..++|+.|.|.|++. ..+.|+|.++|+. ++.|+
T Consensus 68 SPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 68 SPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred CCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 3445666654 6778999999999987 8999999999973 34443
No 53
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=91.68 E-value=0.51 Score=30.84 Aligned_cols=30 Identities=13% Similarity=0.098 Sum_probs=26.6
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeE
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQ 44 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~ 44 (132)
.+|..|.+++-.|+.++|.+..||..-++.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~l 33 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKML 33 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEE
Confidence 479999999999999999999999765554
No 54
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.54 E-value=0.53 Score=32.19 Aligned_cols=33 Identities=18% Similarity=0.134 Sum_probs=27.9
Q ss_pred HHHHHhh--CCCEEEEEeCCCcEEEEEEEeeCCce
Q 032863 9 VKLLHEA--SGHVVTVELKSGELYRGSMVECEDNW 41 (132)
Q Consensus 9 ~~lL~~~--~g~~V~VELknG~~y~G~L~~vD~~M 41 (132)
=.||..+ ...+|+|-|.||...+|.+.+||.|-
T Consensus 9 D~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~ 43 (77)
T COG1923 9 DPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV 43 (77)
T ss_pred hHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE
Confidence 3456654 68899999999999999999999874
No 55
>PRK02001 hypothetical protein; Validated
Probab=90.38 E-value=0.84 Score=34.66 Aligned_cols=41 Identities=22% Similarity=0.411 Sum_probs=32.0
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 4 SLGIPV---KLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
.+..|+ .=+..++|+.|.|.|.++..+.|+|.++|+. ++.|
T Consensus 74 GldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 74 GLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 345554 3455789999999999999999999999975 3444
No 56
>PRK14638 hypothetical protein; Provisional
Probab=89.85 E-value=0.71 Score=34.79 Aligned_cols=41 Identities=20% Similarity=0.344 Sum_probs=31.9
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 4 SLGIPV---KLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
.+..|+ .=+..++|+.|.|.|+++..++|+|.++|+. ++.|
T Consensus 84 GldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 84 GLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred CCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 345554 3456789999999999999999999999974 3444
No 57
>PRK14639 hypothetical protein; Provisional
Probab=88.64 E-value=1.4 Score=32.89 Aligned_cols=42 Identities=24% Similarity=0.443 Sum_probs=32.7
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEe
Q 032863 4 SLGIPV---KLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLE 46 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~ 46 (132)
.+..|+ .=++.++|+.|.|+|.+...+.|+|.++|+. ++.|+
T Consensus 72 Gl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 72 GLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred CCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 345554 4466789999999999999999999999983 44443
No 58
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=88.61 E-value=2.5 Score=28.45 Aligned_cols=39 Identities=26% Similarity=0.468 Sum_probs=29.2
Q ss_pred CCCCCcHH---HHHHhhCCCEEEEEeC---CC-cEEEEEEEeeCCc
Q 032863 2 SRSLGIPV---KLLHEASGHVVTVELK---SG-ELYRGSMVECEDN 40 (132)
Q Consensus 2 s~~i~~P~---~lL~~~~g~~V~VELk---nG-~~y~G~L~~vD~~ 40 (132)
|-.+..|+ .=+..++|+.|.|+|+ +| ..+.|.|.++|+.
T Consensus 7 SPGl~RpL~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 7 SPGAERPLKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred CCCCCCcCCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 33455554 3345679999999998 55 5899999999984
No 59
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=86.91 E-value=0.19 Score=45.35 Aligned_cols=7 Identities=43% Similarity=0.482 Sum_probs=0.0
Q ss_pred CCCCCCC
Q 032863 122 PGRGVVP 128 (132)
Q Consensus 122 ~g~~~~~ 128 (132)
||||+|+
T Consensus 545 gg~grg~ 551 (556)
T PF05918_consen 545 GGRGRGR 551 (556)
T ss_dssp -------
T ss_pred CCCCCcc
Confidence 3444444
No 60
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=86.73 E-value=3.6 Score=30.81 Aligned_cols=37 Identities=19% Similarity=0.408 Sum_probs=29.3
Q ss_pred CCCcHH---HHHHhhCCCEEEEEe----CCCcEEEEEEEeeCCc
Q 032863 4 SLGIPV---KLLHEASGHVVTVEL----KSGELYRGSMVECEDN 40 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VEL----knG~~y~G~L~~vD~~ 40 (132)
.+..|+ .=+..++|+.|.|+| .+...+.|+|.++|+.
T Consensus 82 Gi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 82 GLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred CCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 455564 346678999999998 4678999999999983
No 61
>PRK14642 hypothetical protein; Provisional
Probab=86.72 E-value=2.5 Score=33.51 Aligned_cols=77 Identities=18% Similarity=0.348 Sum_probs=48.2
Q ss_pred CCCCCcHHHH---HHhhCCCEEEEEeC-------------CCcEEEEEEEeeCCceeeEE--eeeEEEccCC------c-
Q 032863 2 SRSLGIPVKL---LHEASGHVVTVELK-------------SGELYRGSMVECEDNWNCQL--ENITYTAKDG------K- 56 (132)
Q Consensus 2 s~~i~~P~~l---L~~~~g~~V~VELk-------------nG~~y~G~L~~vD~~MNi~L--~dv~~t~~dg------~- 56 (132)
|-.+..|++- +..++|+.|.|.|+ +...|+|+|.++|+. +++| ++.-+- +++ +
T Consensus 82 SPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~-k~g~~~~k~~~ 159 (197)
T PRK14642 82 SPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPV-KPGQRVSKKRV 159 (197)
T ss_pred CCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccC-CCccccccccc
Confidence 3446667544 45578999999998 679999999999974 4444 221010 122 1
Q ss_pred eeeeeeEEEeCCeEEEEecCcccc
Q 032863 57 VSQLEHVFIRGSKVRFMVIPDMLK 80 (132)
Q Consensus 57 ~~~l~~vfIRGs~Ir~I~lpd~l~ 80 (132)
+..+..+-|-=+.|++..|-..++
T Consensus 160 ~~~~~~~~~~~~eik~a~l~p~~~ 183 (197)
T PRK14642 160 PAPLQALGFTLDELREARLAPIVD 183 (197)
T ss_pred cccceeEEeehhheeeEEEEEEEe
Confidence 134456666667777777654444
No 62
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=86.66 E-value=2.6 Score=32.69 Aligned_cols=37 Identities=16% Similarity=0.022 Sum_probs=30.7
Q ss_pred HHHHHhh--CCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 9 VKLLHEA--SGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 9 ~~lL~~~--~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
=.||+.+ ...+|+|-|.||..++|++.++|.|.=+..
T Consensus 14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~ 52 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLR 52 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEE
Confidence 4677776 477899999999999999999999865544
No 63
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=85.80 E-value=2.3 Score=32.93 Aligned_cols=58 Identities=19% Similarity=0.166 Sum_probs=39.8
Q ss_pred HHHHhh--CCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCccc
Q 032863 10 KLLHEA--SGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDML 79 (132)
Q Consensus 10 ~lL~~~--~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l 79 (132)
.||..+ ...+|+|-|.||..++|.+.++|.|.=+... +|+ +-+|-=..|.-|.....+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~-------~gk-----qqLIYKHAISTI~P~~~v 154 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLER-------DGY-----VQLVYKHAVSTVQPAGPV 154 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEe-------CCc-----EEEEEEeEEEEEccCCCc
Confidence 456655 5789999999999999999999998755443 343 124444455555554444
No 64
>PRK14632 hypothetical protein; Provisional
Probab=84.99 E-value=3.7 Score=31.63 Aligned_cols=43 Identities=19% Similarity=0.366 Sum_probs=31.9
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeCC-------CcEEEEEEEeeCCceeeEEe
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELKS-------GELYRGSMVECEDNWNCQLE 46 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELkn-------G~~y~G~L~~vD~~MNi~L~ 46 (132)
-.+..|+ .=++.++|+.|.|+|++ ...+.|+|.++|+. ++.|+
T Consensus 81 PGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 81 PGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred CCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 3455564 44567899999999986 56999999999974 44443
No 65
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=84.65 E-value=3.2 Score=30.43 Aligned_cols=37 Identities=22% Similarity=0.462 Sum_probs=25.6
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeC----CCcEEEEEEEeeCC
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELK----SGELYRGSMVECED 39 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELk----nG~~y~G~L~~vD~ 39 (132)
-.+..|+ .-+..++|+.|.|.++ +...+.|+|.++|+
T Consensus 70 PG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 70 PGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp -SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 3456676 4567889999999994 45689999999998
No 66
>PRK14633 hypothetical protein; Provisional
Probab=84.12 E-value=4.6 Score=30.37 Aligned_cols=41 Identities=20% Similarity=0.229 Sum_probs=30.7
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeC----CCcEEEEEEEeeCCceeeEE
Q 032863 4 SLGIPV---KLLHEASGHVVTVELK----SGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELk----nG~~y~G~L~~vD~~MNi~L 45 (132)
.+..|+ .=+..++|+.|.|.|+ +...++|+|.++|+. ++.|
T Consensus 78 GldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 78 GMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 355564 3456689999999994 568999999999974 4444
No 67
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.71 E-value=3.4 Score=31.52 Aligned_cols=38 Identities=21% Similarity=0.385 Sum_probs=30.9
Q ss_pred CCCcHH---HHHHhhCCCEEEEEe----CCCcEEEEEEEeeCCce
Q 032863 4 SLGIPV---KLLHEASGHVVTVEL----KSGELYRGSMVECEDNW 41 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VEL----knG~~y~G~L~~vD~~M 41 (132)
.+..|+ .=+..+.|+.|.|+| .+...+.|+|.++|...
T Consensus 83 GldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 83 GLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred CCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 355665 345667999999999 68899999999999865
No 68
>PRK14640 hypothetical protein; Provisional
Probab=83.58 E-value=3.7 Score=30.91 Aligned_cols=37 Identities=16% Similarity=0.371 Sum_probs=29.4
Q ss_pred CCCcHH---HHHHhhCCCEEEEEe----CCCcEEEEEEEeeCCc
Q 032863 4 SLGIPV---KLLHEASGHVVTVEL----KSGELYRGSMVECEDN 40 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VEL----knG~~y~G~L~~vD~~ 40 (132)
.+..|+ .=++.++|+.|.|.| .+...++|+|.++|+.
T Consensus 81 Gl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~ 124 (152)
T PRK14640 81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD 124 (152)
T ss_pred CCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 455564 445678999999999 4678999999999974
No 69
>PRK14647 hypothetical protein; Provisional
Probab=82.31 E-value=6.1 Score=29.88 Aligned_cols=36 Identities=19% Similarity=0.284 Sum_probs=28.2
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeC---------CCcEEEEEEEeeCC
Q 032863 4 SLGIPV---KLLHEASGHVVTVELK---------SGELYRGSMVECED 39 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELk---------nG~~y~G~L~~vD~ 39 (132)
.+..|+ .=+..++|+.|.|+|+ +...+.|+|.++|+
T Consensus 83 G~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 83 GLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 345554 4456789999999996 34899999999997
No 70
>PRK14636 hypothetical protein; Provisional
Probab=81.98 E-value=7.4 Score=30.13 Aligned_cols=37 Identities=22% Similarity=0.507 Sum_probs=28.8
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeC---CC-cEEEEEEEeeCCc
Q 032863 4 SLGIPV---KLLHEASGHVVTVELK---SG-ELYRGSMVECEDN 40 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELk---nG-~~y~G~L~~vD~~ 40 (132)
.+..|+ .=+..++|+.|.|+|+ +| ..++|+|.++|+.
T Consensus 82 GldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~ 125 (176)
T PRK14636 82 GIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD 125 (176)
T ss_pred CCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC
Confidence 344554 4456789999999998 55 6999999999873
No 71
>PRK14645 hypothetical protein; Provisional
Probab=81.39 E-value=4.4 Score=30.72 Aligned_cols=37 Identities=16% Similarity=0.275 Sum_probs=29.0
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCc
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELKSGELYRGSMVECEDN 40 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELknG~~y~G~L~~vD~~ 40 (132)
-.+..|+ .=+..+.|+.|.|.+ ++..+.|+|.++|+.
T Consensus 85 PGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 85 PGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred CCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 3455564 445678899999986 789999999999984
No 72
>PRK14643 hypothetical protein; Provisional
Probab=80.84 E-value=4.1 Score=31.20 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=28.5
Q ss_pred CCcHH---HHHHhhCCCEEEEEeCC----CcEEEEEEEeeCCc
Q 032863 5 LGIPV---KLLHEASGHVVTVELKS----GELYRGSMVECEDN 40 (132)
Q Consensus 5 i~~P~---~lL~~~~g~~V~VELkn----G~~y~G~L~~vD~~ 40 (132)
+..|+ .=++.+.|+.|.|.|+. ...+.|+|.++|+.
T Consensus 89 leRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 89 IEKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred CCCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 44554 34667899999999975 58999999999964
No 73
>PRK14646 hypothetical protein; Provisional
Probab=77.91 E-value=6.1 Score=29.87 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=30.1
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeCCC----cEEEEEEEeeCCceeeEE
Q 032863 4 SLGIPV---KLLHEASGHVVTVELKSG----ELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELknG----~~y~G~L~~vD~~MNi~L 45 (132)
.+..|+ .=++.+.|+.|.|+|++. ..+.|+|.++|+. ++.|
T Consensus 84 GldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 84 GVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 345554 446678999999999643 5889999999974 4444
No 74
>PRK14637 hypothetical protein; Provisional
Probab=77.89 E-value=9.7 Score=28.73 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=29.3
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeCCCcEE-EEEEEeeCCceeeEE
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELKSGELY-RGSMVECEDNWNCQL 45 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELknG~~y-~G~L~~vD~~MNi~L 45 (132)
-.+..|+ .=+..++|+.|.|+|.+...+ .|+|.++|+. ++.|
T Consensus 81 PGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 81 PGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred CCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 3455664 345667999999999544455 7999999975 3444
No 75
>PRK14634 hypothetical protein; Provisional
Probab=76.12 E-value=8.1 Score=29.20 Aligned_cols=37 Identities=16% Similarity=0.327 Sum_probs=28.2
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeCCC----cEEEEEEEeeCCc
Q 032863 4 SLGIPV---KLLHEASGHVVTVELKSG----ELYRGSMVECEDN 40 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELknG----~~y~G~L~~vD~~ 40 (132)
.+..|+ .=+..++|+.|.|+|++. ..|.|+|.++|+.
T Consensus 84 GldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~ 127 (155)
T PRK14634 84 GIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED 127 (155)
T ss_pred CCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC
Confidence 344554 345678999999999743 6999999999974
No 76
>PRK14631 hypothetical protein; Provisional
Probab=75.83 E-value=12 Score=28.92 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=28.0
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeC----CCcEEEEEEEeeC
Q 032863 4 SLGIPV---KLLHEASGHVVTVELK----SGELYRGSMVECE 38 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELk----nG~~y~G~L~~vD 38 (132)
.+..|+ .=+..+.|+.|.|+|+ +...++|+|.++|
T Consensus 101 GldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 101 GWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 345554 4567789999999996 4589999999998
No 77
>PRK06955 biotin--protein ligase; Provisional
Probab=74.34 E-value=18 Score=29.74 Aligned_cols=48 Identities=21% Similarity=0.238 Sum_probs=35.1
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeC
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRG 67 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRG 67 (132)
..|+.|+|...++.++.|++.++|+.-.+.+++ .+| +....++|.++.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~-----~~g~~~~~sGeV~~~~ 295 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT-----PAGRQAIAAGDVSLRE 295 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe-----CCCeEEEEEEEEEEec
Confidence 579999997767788999999999999988863 244 233445555543
No 78
>PRK14635 hypothetical protein; Provisional
Probab=69.76 E-value=18 Score=27.43 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=29.2
Q ss_pred CCCcHH---HHHHhhCCCEEEEEeC--CCcEEEE---EEEeeCCceeeEE
Q 032863 4 SLGIPV---KLLHEASGHVVTVELK--SGELYRG---SMVECEDNWNCQL 45 (132)
Q Consensus 4 ~i~~P~---~lL~~~~g~~V~VELk--nG~~y~G---~L~~vD~~MNi~L 45 (132)
.+..|+ .=+..+.|+.|.|++. ++..+.| +|.++|+. ++.|
T Consensus 83 GldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 83 GAERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CCCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 345554 3456789999999986 4578887 99999974 3444
No 79
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=69.38 E-value=4.4 Score=27.65 Aligned_cols=21 Identities=29% Similarity=0.265 Sum_probs=14.5
Q ss_pred hhCCCEEEEEeCCCcEEEEEE
Q 032863 14 EASGHVVTVELKSGELYRGSM 34 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L 34 (132)
.+.+.+|.++|+||+.+.|+-
T Consensus 14 C~~~~~v~L~l~dG~~~~g~A 34 (80)
T PF07073_consen 14 CMYRYPVKLTLKDGEQIEGKA 34 (80)
T ss_dssp HTTTT-EEEE-TTT--EEESS
T ss_pred HhcCCeEEEEEeCCCEEEEEE
Confidence 456889999999999999983
No 80
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=68.96 E-value=17 Score=27.50 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=23.6
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeC
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECE 38 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD 38 (132)
..++|+.|+++..+|..+.|++.+|.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 35799999999999999999999975
No 81
>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=68.38 E-value=20 Score=21.47 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=22.1
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCc
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDN 40 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~ 40 (132)
.|+.|.+...++.-|++++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5788888888899999999999964
No 82
>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=68.10 E-value=12 Score=27.08 Aligned_cols=32 Identities=25% Similarity=0.280 Sum_probs=27.4
Q ss_pred CcHHHHHHhhCCCEEEEEeCCCcEEEEEEEee
Q 032863 6 GIPVKLLHEASGHVVTVELKSGELYRGSMVEC 37 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~VELknG~~y~G~L~~v 37 (132)
+.|+.-|....+-.|+.||.||.+|.+.=.-+
T Consensus 63 ~~~~~~i~~~~~~tvt~e~~nG~~y~l~~aw~ 94 (119)
T PF10618_consen 63 DTDVDDINDITDATVTFELDNGKVYVLSNAWT 94 (119)
T ss_pred CCCHHHHhCCcccEEEEEecCCcEEEecCeeE
Confidence 57899999999999999999999998754333
No 83
>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=67.19 E-value=13 Score=29.32 Aligned_cols=36 Identities=28% Similarity=0.346 Sum_probs=31.9
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
-++.+=++++|+.+..++.++..+.|.|+++|.|+-
T Consensus 9 ~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 9 DAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred CHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 467788899999999999999888999999999864
No 84
>PRK14641 hypothetical protein; Provisional
Probab=66.34 E-value=15 Score=28.48 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=27.5
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeCC----CcEEEEEEEeeC
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELKS----GELYRGSMVECE 38 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELkn----G~~y~G~L~~vD 38 (132)
-.+..|+ .=+..++|+.|.|.|++ ...++|+|.++|
T Consensus 87 PGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 87 PGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCCCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 3455564 44567899999999976 458999999995
No 85
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=65.37 E-value=33 Score=28.09 Aligned_cols=31 Identities=16% Similarity=0.118 Sum_probs=27.2
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEe
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLE 46 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~ 46 (132)
..|+.|++.. ++..+.|++.++|+.-.+.++
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 5799999987 456799999999999999986
No 86
>PRK08330 biotin--protein ligase; Provisional
Probab=64.10 E-value=42 Score=26.39 Aligned_cols=46 Identities=22% Similarity=0.186 Sum_probs=32.7
Q ss_pred hCCCEEEEEeCCCcE-EEEEEEeeCCceeeEEeeeEEEccCCc--eeeeeeEEEe
Q 032863 15 ASGHVVTVELKSGEL-YRGSMVECEDNWNCQLENITYTAKDGK--VSQLEHVFIR 66 (132)
Q Consensus 15 ~~g~~V~VELknG~~-y~G~L~~vD~~MNi~L~dv~~t~~dg~--~~~l~~vfIR 66 (132)
..|+.|+|.. ++.. +.|+..++|+.-.+.++.. +|. ....+++.+|
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~-----~g~~~~~~~gev~~~ 234 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD-----DGTVKKVLYGDVSLR 234 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC-----CCCEEEEEEEEEEEe
Confidence 6799999986 4555 4799999999988888742 443 2334556554
No 87
>PRK11625 Rho-binding antiterminator; Provisional
Probab=62.32 E-value=19 Score=24.88 Aligned_cols=24 Identities=25% Similarity=0.361 Sum_probs=20.1
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEee
Q 032863 14 EASGHVVTVELKSGELYRGSMVEC 37 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~v 37 (132)
.+.+.+|.++|+||+++.|+....
T Consensus 20 C~~~~~l~l~l~dGe~~~g~A~D~ 43 (84)
T PRK11625 20 CQHHLMLTLELKDGEVLQAKASDL 43 (84)
T ss_pred HhcCCeEEEEECCCCEEEEEEEee
Confidence 347889999999999999998543
No 88
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=60.64 E-value=44 Score=30.45 Aligned_cols=49 Identities=14% Similarity=0.270 Sum_probs=37.0
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCC
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGS 68 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs 68 (132)
..|+.|+|...++.++.|+..++|+.-.+.|+. .+| +...-++|.+|..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~-----~~g~~~~~sGEVslr~~ 325 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET-----AEGKQTVVSGEISLRSD 325 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE-----CCCeEEEEEEeEEEeec
Confidence 679999997667778999999999999999864 244 3445566766543
No 89
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=59.98 E-value=35 Score=24.62 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=18.1
Q ss_pred CEEEEEeCCCcEEEEEEEeeC
Q 032863 18 HVVTVELKSGELYRGSMVECE 38 (132)
Q Consensus 18 ~~V~VELknG~~y~G~L~~vD 38 (132)
..+.|.|+||+++.|.|.+=|
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET 78 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC
Confidence 358999999999999998844
No 90
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=59.97 E-value=11 Score=30.16 Aligned_cols=13 Identities=38% Similarity=0.572 Sum_probs=10.5
Q ss_pred HHHHHhhCCCEEE
Q 032863 9 VKLLHEASGHVVT 21 (132)
Q Consensus 9 ~~lL~~~~g~~V~ 21 (132)
-.|||.+++..|+
T Consensus 57 g~flh~Cegd~Vc 69 (215)
T KOG3262|consen 57 GKFLHMCEGDLVC 69 (215)
T ss_pred hhhhhhcCCceEE
Confidence 4789999998775
No 91
>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=57.35 E-value=14 Score=28.53 Aligned_cols=69 Identities=19% Similarity=0.280 Sum_probs=51.4
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccC------CceeeeeeEEEeCCeEEEEecCccccccc
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKD------GKVSQLEHVFIRGSKVRFMVIPDMLKNAP 83 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~d------g~~~~l~~vfIRGs~Ir~I~lpd~l~~ap 83 (132)
.-.-+|.|-+.||.++.|.+..++.--|..|.-+.....+ ...+.+++..+.-..=++.+-||.+++.|
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~~~~~nRi~~plE~I~t~Ee~~~~d~~g~~ti~~d~~~~q~ 101 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDPFKKENRIRLPLERISTIEELIVSDFKGRLTIHPDYFNNQP 101 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCCCCCCceEEEEhHHhhhHhhhccccccccEEechhhccccc
Confidence 3567999999999999999999999999998776522211 12345566666666667788889888883
No 92
>PRK14630 hypothetical protein; Provisional
Probab=57.27 E-value=30 Score=25.75 Aligned_cols=37 Identities=11% Similarity=0.267 Sum_probs=27.3
Q ss_pred CCCCcHH---HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCc
Q 032863 3 RSLGIPV---KLLHEASGHVVTVELKSGELYRGSMVECEDN 40 (132)
Q Consensus 3 ~~i~~P~---~lL~~~~g~~V~VELknG~~y~G~L~~vD~~ 40 (132)
-.+..|+ .=++.+.|+.|.|.|... ...|+|.++|+.
T Consensus 80 PGldRpL~~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 80 PGINRKIKSDREFKIFEGKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred CCCCCcCCCHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence 3455664 345567999999999664 459999999973
No 93
>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=56.90 E-value=16 Score=26.00 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=18.4
Q ss_pred HHHhhC-CCEEEEEeCCCcEEEEEEEe
Q 032863 11 LLHEAS-GHVVTVELKSGELYRGSMVE 36 (132)
Q Consensus 11 lL~~~~-g~~V~VELknG~~y~G~L~~ 36 (132)
++.++- ...|.++|++|..+.|++..
T Consensus 21 lv~~L~ge~~V~l~L~DGs~l~Gtv~v 47 (101)
T PF11607_consen 21 LVSELDGEERVELELDDGSMLRGTVAV 47 (101)
T ss_dssp HHHCTTTT-EEEEEETTS-EEEEEECC
T ss_pred HHhhcCCcceEEEEEcCCCeeeeeecc
Confidence 334443 46899999999999999864
No 94
>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=56.52 E-value=20 Score=27.99 Aligned_cols=35 Identities=26% Similarity=0.400 Sum_probs=27.5
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
-++.+=++++|+.+..++.++. +.|.|+++|.|+-
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 4678889999999999999888 9999999988765
No 95
>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=55.48 E-value=71 Score=25.06 Aligned_cols=31 Identities=16% Similarity=0.107 Sum_probs=26.9
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEe
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLE 46 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~ 46 (132)
..|+.|+|...+ ..+.|++.++|+.-.+.|+
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 569999998755 5689999999999999886
No 96
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=53.50 E-value=36 Score=25.64 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=22.5
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeC
Q 032863 14 EASGHVVTVELKSGELYRGSMVECE 38 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD 38 (132)
.++|+.|+....+|..+.|++.++.
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~ 114 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQ 114 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEE
Confidence 5799999988899999999999876
No 97
>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=52.70 E-value=33 Score=26.74 Aligned_cols=35 Identities=26% Similarity=0.393 Sum_probs=29.9
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
-++.+=++++|+.+..++. +.++.|.|++++.|+-
T Consensus 5 ~~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 5 DTVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred CHHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 4678889999999988885 6689999999999864
No 98
>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=52.55 E-value=77 Score=24.01 Aligned_cols=71 Identities=20% Similarity=0.147 Sum_probs=46.0
Q ss_pred CcHHHHHHhhCCCEE-EEEeCCCcEE-EEEEEeeCCceeeEEeeeEEEccC---------CceeeeeeEEEeCCeEEEEe
Q 032863 6 GIPVKLLHEASGHVV-TVELKSGELY-RGSMVECEDNWNCQLENITYTAKD---------GKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V-~VELknG~~y-~G~L~~vD~~MNi~L~dv~~t~~d---------g~~~~l~~vfIRGs~Ir~I~ 74 (132)
..|.-+...+.|+.+ +|+|.--.+- -| .-+.||.+.|+||.++.-+ +.....+.|-+.=..|.+-+
T Consensus 76 ASP~L~~a~~~Ge~l~~v~l~~~r~~~~G---~~~~y~~itL~~a~Issi~~~~~~~~~~~~~~~~E~vs~~y~~I~~~y 152 (166)
T TIGR03344 76 SSPLLYQALSSGEKLEECEIKFYRTSAAG---KQELYYTIKLEGALIVDIKPYMPHCLDPNNAQPLEDVSFRYRKITWTH 152 (166)
T ss_pred CCHHHHHHHcCCCcCCEEEEEEEEeCCCC---cEEEEEEEEEeeEEEEEEEcccCcccCCCCCCceEEEEEEeeEEEEEE
Confidence 467777777888877 4777422210 13 3457999999999975522 22335678888778888877
Q ss_pred cCccc
Q 032863 75 IPDML 79 (132)
Q Consensus 75 lpd~l 79 (132)
.+...
T Consensus 153 ~~~~~ 157 (166)
T TIGR03344 153 HIAGT 157 (166)
T ss_pred ECCCe
Confidence 65543
No 99
>PRK06789 flagellar motor switch protein; Validated
Probab=49.80 E-value=39 Score=22.75 Aligned_cols=36 Identities=11% Similarity=0.264 Sum_probs=28.4
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeee
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECEDNWNCQLENI 48 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv 48 (132)
.+..+.+|.|.+.+-..-+|.+..+|+.+=+.+.+.
T Consensus 37 dk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIteL 72 (74)
T PRK06789 37 ENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVEL 72 (74)
T ss_pred CCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEEc
Confidence 556677777877777788999999999888877653
No 100
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=47.24 E-value=45 Score=24.89 Aligned_cols=40 Identities=25% Similarity=0.342 Sum_probs=32.2
Q ss_pred CCcEEEEEEEeeC---CceeeEEeeeEEEccCCceeeeeeEEEeCCe
Q 032863 26 SGELYRGSMVECE---DNWNCQLENITYTAKDGKVSQLEHVFIRGSK 69 (132)
Q Consensus 26 nG~~y~G~L~~vD---~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~ 69 (132)
-+-.+.|.+..+- -+||+.|.|| ..|+...-..+-|||++
T Consensus 81 Ad~~lvG~VqKvS~Lil~~~~~v~Dv----~tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 81 ADYVLVGEVQKVSNLILNMNVYVRDV----ETGKVVRGRSVDIRGNT 123 (140)
T ss_pred CCEEEEEEEechhhhheeeeEEEEEC----CCCCEEeeeeeeEecCc
Confidence 3456778877766 5999999999 68888888889999985
No 101
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=46.23 E-value=29 Score=23.92 Aligned_cols=22 Identities=27% Similarity=0.309 Sum_probs=18.0
Q ss_pred hhCCCEEEEEeCCCcEEEEEEE
Q 032863 14 EASGHVVTVELKSGELYRGSMV 35 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~ 35 (132)
.+-.-+++.+||+|+.|.|+-.
T Consensus 20 Cl~hl~l~L~lkdGev~~a~A~ 41 (84)
T COG4568 20 CLHHLPLTLELKDGEVLQAKAS 41 (84)
T ss_pred HhhhceEEEEEcCCeEEEEEeh
Confidence 3445689999999999999754
No 102
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=45.86 E-value=7.3 Score=28.92 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=12.9
Q ss_pred EEecCcccccccchhc
Q 032863 72 FMVIPDMLKNAPMFKR 87 (132)
Q Consensus 72 ~I~lpd~l~~ap~l~~ 87 (132)
|++||+++-.+++-+.
T Consensus 80 yL~LP~eivP~T~k~~ 95 (124)
T PTZ00034 80 YLHLPPDVFPATHKKK 95 (124)
T ss_pred HhCCCcccCchhhccc
Confidence 7899999988887554
No 103
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=45.16 E-value=1e+02 Score=22.33 Aligned_cols=57 Identities=18% Similarity=0.107 Sum_probs=41.2
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCcee-eEEeeeEEEccCCceeeeeeEEEeCCeEEEEec
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWN-CQLENITYTAKDGKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MN-i~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 75 (132)
.|-.|.|.-=...=..|++..+|..=| +.++++.+..++|. --++-|.-|||.++.|
T Consensus 44 kGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~---~~e~pIh~SnV~l~~l 101 (114)
T TIGR01080 44 KGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGT---EVPVPIHPSNVMITKL 101 (114)
T ss_pred cCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCe---EEEeeechHHeEEEec
Confidence 466666666555567799999995444 99999998877772 2345588888887766
No 104
>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=43.19 E-value=74 Score=24.61 Aligned_cols=35 Identities=14% Similarity=0.276 Sum_probs=28.8
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCc
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGK 56 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~ 56 (132)
+|+-|.|-+.+|.+++|+-.++|. ..|++..+||.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna------cqVgl~~~~Gn 153 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA------CQVGLILPNGN 153 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce------EEEEEEcCCCC
Confidence 699999999999999999999886 23555556775
No 105
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=42.30 E-value=72 Score=23.67 Aligned_cols=61 Identities=25% Similarity=0.382 Sum_probs=40.0
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCe------EEEEecCcccccccch
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSK------VRFMVIPDMLKNAPMF 85 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~------Ir~I~lpd~l~~ap~l 85 (132)
++++-+.+.|.|+||.++..-+=. +| .....+.|+|||-. |+|=++--.+|.+.+.
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPG-----------------eGhnlqehs~VLvrGGrv~DlPGVrykvVrG~~D~~gv~ 108 (124)
T PRK05163 46 NSALRKVARVRLTNGFEVTAYIPG-----------------EGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVK 108 (124)
T ss_pred CchhheEEEEEeCCCCEEEEEcCC-----------------CCCCccccCEEEEeCCccCCCCCcEEEEeeeeecccccc
Confidence 345667899999999887655544 33 23345567888764 5677777777777665
Q ss_pred hchhh
Q 032863 86 KRLDA 90 (132)
Q Consensus 86 ~~~~~ 90 (132)
.+.+.
T Consensus 109 ~R~~~ 113 (124)
T PRK05163 109 DRKQG 113 (124)
T ss_pred ccccc
Confidence 54433
No 106
>COG3157 Hcp Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.51 E-value=88 Score=24.05 Aligned_cols=73 Identities=15% Similarity=0.094 Sum_probs=52.9
Q ss_pred CcHHHHHHhhCCCEEE-EEeCCCcEE-EEEEEeeCCceeeEEeeeEEEccC------CceeeeeeEEEeCCeEEEEecCc
Q 032863 6 GIPVKLLHEASGHVVT-VELKSGELY-RGSMVECEDNWNCQLENITYTAKD------GKVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~-VELknG~~y-~G~L~~vD~~MNi~L~dv~~t~~d------g~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
..|+-+...+.|+.+. ++|.--++- .|.+. .|..+.|+||.+..-+ +.+...++|-++=..|.+-+.+.
T Consensus 70 sSPlL~~a~~~ge~l~~~~~~~~R~~~~G~~~---~y~~~~Ltna~Is~is~~~~~~~~~~p~EtvsL~y~kI~w~~~~~ 146 (162)
T COG3157 70 ASPLLYKACSSGETLKTAVLTWYRTGDAGQQE---EYLTIKLTNALISDISVSGSHGGDFLPTETVSLSYTKITWEYTVQ 146 (162)
T ss_pred cChHHHHHHhCCCccceEEEEEEEeCCCCCce---EEEEEEEeeeEEEEEecccCCCccccceEEEEEEEEEEEEEEecC
Confidence 4788788888899888 887654442 45544 4788999999875532 12468899999999999988876
Q ss_pred cccc
Q 032863 78 MLKN 81 (132)
Q Consensus 78 ~l~~ 81 (132)
.-..
T Consensus 147 ~t~g 150 (162)
T COG3157 147 GTSG 150 (162)
T ss_pred CCCc
Confidence 5443
No 107
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=40.74 E-value=36 Score=26.58 Aligned_cols=60 Identities=17% Similarity=0.210 Sum_probs=36.4
Q ss_pred HHHHhhCCCEEEEEeCCCcEEEEEEEeeCCc-eeeEEeeeEEEccCCc-eeeeeeEEEeCCe
Q 032863 10 KLLHEASGHVVTVELKSGELYRGSMVECEDN-WNCQLENITYTAKDGK-VSQLEHVFIRGSK 69 (132)
Q Consensus 10 ~lL~~~~g~~V~VELknG~~y~G~L~~vD~~-MNi~L~dv~~t~~dg~-~~~l~~vfIRGs~ 69 (132)
++|.--.|..|.|-.-+|..|.++|.++|.. .-+.+..-........ ...+=..++++..
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~~~~~~~~~~~~i~L~~al~K~~~ 74 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRILEELEIPPEPPPEITLAQALPKGDR 74 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SSSSEEEEEEE--STTH
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEeeeccCCCCCcceEEEEEEEEcCcc
Confidence 5566678999999999999999999999954 3355554333333332 3566666666654
No 108
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=40.39 E-value=1.3e+02 Score=22.01 Aligned_cols=56 Identities=23% Similarity=0.168 Sum_probs=39.6
Q ss_pred CCEEEEEeCCCcEEEEEEEeeCCcee-eEEeeeEEEccCCceeeeeeEEEeCCeEEEEec
Q 032863 17 GHVVTVELKSGELYRGSMVECEDNWN-CQLENITYTAKDGKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 17 g~~V~VELknG~~y~G~L~~vD~~MN-i~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 75 (132)
|-.|.|--=...=-+|++..+|..-| +.+++|.+..++|. --+..|.=|||.++.|
T Consensus 49 GD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~---~~e~pIh~SNV~l~~l 105 (120)
T PRK01191 49 GDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGT---EVPRPIHPSNVMITKL 105 (120)
T ss_pred CCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCe---EEEcccchhHeEEEeC
Confidence 45555554444445699999996555 99999998887772 3457777788877665
No 109
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=39.80 E-value=40 Score=23.28 Aligned_cols=28 Identities=32% Similarity=0.463 Sum_probs=22.0
Q ss_pred CCCCCcHHHHHHhh---CCCEEEEEeCCCcE
Q 032863 2 SRSLGIPVKLLHEA---SGHVVTVELKSGEL 29 (132)
Q Consensus 2 s~~i~~P~~lL~~~---~g~~V~VELknG~~ 29 (132)
|..+.+|-.+++.+ +|..|+|++.|+..
T Consensus 11 S~avrIP~~l~kql~l~~g~~v~v~v~n~~~ 41 (82)
T COG2336 11 SAAVRIPAALLKQLNLTIGDEVEVEVGNDQS 41 (82)
T ss_pred cceeeccHHHHHHhCCCcCceEEEEEcCCcE
Confidence 34567898888876 69999999998743
No 110
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=39.59 E-value=1e+02 Score=19.74 Aligned_cols=49 Identities=27% Similarity=0.343 Sum_probs=30.5
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeCCcee-------------eEEeeeEEEccCCceeeeeeE
Q 032863 14 EASGHVVTVELKSGELYRGSMVECEDNWN-------------CQLENITYTAKDGKVSQLEHV 63 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD~~MN-------------i~L~dv~~t~~dg~~~~l~~v 63 (132)
+++|-.|+|+ .++.++.=.+..-..||. -.++.++++.+||+...++.+
T Consensus 1 dAiGA~V~v~-~~~~~q~~~v~~g~gy~s~~~~~lhFGLG~~~~v~~v~V~WP~G~~~~~~~~ 62 (71)
T PF07593_consen 1 DAIGARVTVT-ADGRTQTREVTSGGGYLSQSEPRLHFGLGDATSVDSVEVRWPDGKVQTLENV 62 (71)
T ss_pred CCCCeEEEEE-ECCeEEEEEEeCCCCEeecCCCCEEEECCCCCCEEEEEEECCCCCEEEEEcc
Confidence 3678899999 666666555555444443 344556677778766555544
No 111
>CHL00051 rps12 ribosomal protein S12
Probab=39.58 E-value=79 Score=23.44 Aligned_cols=61 Identities=23% Similarity=0.313 Sum_probs=39.0
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCe------EEEEecCcccccccchh
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSK------VRFMVIPDMLKNAPMFK 86 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~------Ir~I~lpd~l~~ap~l~ 86 (132)
++++=+.+.|.|+||.++..-+=+.- | |+ ...+.|+|||-. |+|=++--.+|.+.+..
T Consensus 46 NSA~RKvarVrLsngk~v~AyIPGeG-h-nl--------------qehs~VLvrGGrv~DlPGVrykvVRG~~D~~gv~~ 109 (123)
T CHL00051 46 NSALRKVARVRLTSGFEITAYIPGIG-H-NL--------------QEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKD 109 (123)
T ss_pred ChhheeEEEEEccCCCEEEEEcCCCC-c-cc--------------cccCEEEEeCCccCCCCCeeEEEEeeeeccccccc
Confidence 34566789999999998876655422 2 22 334457777764 56767767777776655
Q ss_pred chh
Q 032863 87 RLD 89 (132)
Q Consensus 87 ~~~ 89 (132)
+.+
T Consensus 110 R~~ 112 (123)
T CHL00051 110 RQQ 112 (123)
T ss_pred ccc
Confidence 433
No 112
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=39.24 E-value=75 Score=26.04 Aligned_cols=32 Identities=16% Similarity=0.083 Sum_probs=27.1
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEee
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLEN 47 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~d 47 (132)
..|+.|+|.. ++..+.|++.++|+.-.+.|+.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 3799999976 5688999999999988888864
No 113
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=39.04 E-value=1.2e+02 Score=26.87 Aligned_cols=39 Identities=21% Similarity=0.216 Sum_probs=32.5
Q ss_pred CcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEE
Q 032863 6 GIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQL 45 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L 45 (132)
-.|-+++..+.||.|.- =|+|.+++++|.+-|--.-+.+
T Consensus 71 ~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~ 109 (421)
T COG5316 71 LSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRT 109 (421)
T ss_pred cCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEec
Confidence 46889999999999999 8999999999999886443333
No 114
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=38.59 E-value=1.5e+02 Score=23.81 Aligned_cols=34 Identities=21% Similarity=0.287 Sum_probs=30.9
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeee
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLENI 48 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv 48 (132)
..|+.|++++-++.+..|+...+|+.-.+.|+.-
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4899999999999999999999999999888763
No 115
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=38.55 E-value=83 Score=23.35 Aligned_cols=62 Identities=26% Similarity=0.402 Sum_probs=39.9
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCC-ceeeeeeEEEeCCe------EEEEecCcccccccch
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDG-KVSQLEHVFIRGSK------VRFMVIPDMLKNAPMF 85 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~------Ir~I~lpd~l~~ap~l 85 (132)
++++=+.+.|.|+||.++..-+=+ +| .....+.|+|||-. |+|=.+--.+|.+.+.
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPG-----------------~Ghnlqehs~VLvrGGrv~DlPGVkykvVrG~~D~~gv~ 108 (124)
T TIGR00981 46 NSALRKVARVRLTNGFEVTAYIPG-----------------EGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVK 108 (124)
T ss_pred CchhheeEEEEeCCCCEEEEEcCC-----------------CCCCccccCEEEEeCCccCCCCCeEEEEEeEeecccccc
Confidence 345667899999999887655443 33 23445667888764 5666666677777665
Q ss_pred hchhhh
Q 032863 86 KRLDAR 91 (132)
Q Consensus 86 ~~~~~~ 91 (132)
.+.+.+
T Consensus 109 ~R~~~R 114 (124)
T TIGR00981 109 NRKQGR 114 (124)
T ss_pred cccccc
Confidence 544433
No 116
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=38.04 E-value=64 Score=23.73 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=25.3
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEee
Q 032863 14 EASGHVVTVELKSGELYRGSMVECEDNWNCQLEN 47 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~d 47 (132)
+..+.+|.|-+.+=.+-+|.|+-+|+++=+.+.+
T Consensus 102 ~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIte 135 (136)
T COG1886 102 KLAGEPVDILVNGRLIGRGEVVVVDDKFGVRITE 135 (136)
T ss_pred CcCCCceEEEECCEEEEEEeEEEECCeEEEEEEe
Confidence 4446666666666678899999999998887765
No 117
>PRK10898 serine endoprotease; Provisional
Probab=37.70 E-value=66 Score=27.09 Aligned_cols=32 Identities=16% Similarity=0.319 Sum_probs=27.9
Q ss_pred CCEEEEEeCCCcEEEEEEEeeCCceeeEEeee
Q 032863 17 GHVVTVELKSGELYRGSMVECEDNWNCQLENI 48 (132)
Q Consensus 17 g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv 48 (132)
...+.|.+.+|..|.+++..+|...++-|=.+
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 35789999999999999999999998877655
No 118
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.40 E-value=71 Score=25.54 Aligned_cols=36 Identities=19% Similarity=0.187 Sum_probs=30.4
Q ss_pred CcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 6 GIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 6 ~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
..|+.+=++++|+.+.=+ -+|.++.|.+++.+.|+-
T Consensus 13 rd~~~vAr~LLG~~lv~~-~~g~~~~g~IVEtEAY~G 48 (200)
T COG2094 13 RDTLVVARELLGKTLVRR-IGGLTTSGRIVETEAYLG 48 (200)
T ss_pred cCHHHHHHHhcCcEEEEe-cCCcEEEEEEEEEeEecC
Confidence 356778889999988766 788999999999999985
No 119
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=34.76 E-value=1.2e+02 Score=22.91 Aligned_cols=58 Identities=19% Similarity=0.209 Sum_probs=42.4
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCC-ceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecC
Q 032863 16 SGHVVTVELKSGELYRGSMVECED-NWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIP 76 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~-~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lp 76 (132)
.|-.|.|-.=+..=-+|++..+|. ..-+.+++|.....++++ -++-|--|||.++.+-
T Consensus 49 kGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~---~e~PIh~SNV~iv~l~ 107 (143)
T PTZ00194 49 KDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP---VQIGIHPSNVIITKLK 107 (143)
T ss_pred cCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE---eecCcCchheEEEccc
Confidence 355555555444445699999994 445999999998888876 3678888888887763
No 120
>PF14262 DUF4353: Domain of unknown function (DUF4353)
Probab=34.57 E-value=1.3e+02 Score=24.70 Aligned_cols=57 Identities=19% Similarity=0.439 Sum_probs=38.6
Q ss_pred CCCEEEEEeCCCcEEEEEEE------ee--CCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCc
Q 032863 16 SGHVVTVELKSGELYRGSMV------EC--EDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPD 77 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~------~v--D~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd 77 (132)
.+..|+|.-..--++.|+|. ++ ++...|+|.+|+++..++.+ ++|.-..=.||.|++
T Consensus 5 ~~~~vtIt~~GtY~lsGs~~~g~i~V~a~~~~~v~lvL~gv~it~~~~a~-----I~v~~a~k~~i~la~ 69 (264)
T PF14262_consen 5 SGSTVTITKAGTYVLSGSLSDGQIVVDAGDTDKVRLVLDGVSITNSSGAA-----IYVKSADKVFITLAE 69 (264)
T ss_pred eCCEEEEcCCEEEEEEEEccCcEEEEEcCCCceEEEEECCeEEeCCCCCC-----EEEEeCCeEEEEEcC
Confidence 46677776654446677776 34 57899999999999877653 455555555566655
No 121
>PRK09798 antitoxin MazE; Provisional
Probab=33.90 E-value=49 Score=22.46 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=22.4
Q ss_pred CCCCCcHHHHHHhh---CCCEEEEEeCCCcEE
Q 032863 2 SRSLGIPVKLLHEA---SGHVVTVELKSGELY 30 (132)
Q Consensus 2 s~~i~~P~~lL~~~---~g~~V~VELknG~~y 30 (132)
|..|.+|-.||.++ .|..|.|++.+|..+
T Consensus 12 S~~vRIPk~~l~~l~l~~g~~vei~v~~~~ii 43 (82)
T PRK09798 12 SPAVRIPATLMQALNLNIDDEVKIDLVDGKLI 43 (82)
T ss_pred cceEEcCHHHHHHcCCCCCCEEEEEEECCEEE
Confidence 34577898888875 589999999887654
No 122
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=31.50 E-value=1.3e+02 Score=23.88 Aligned_cols=25 Identities=16% Similarity=0.159 Sum_probs=22.2
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeC
Q 032863 14 EASGHVVTVELKSGELYRGSMVECE 38 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD 38 (132)
.++|+.|++.-.+|..+.|++..+.
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 5699999998889999999999865
No 123
>PRK10139 serine endoprotease; Provisional
Probab=31.38 E-value=96 Score=27.15 Aligned_cols=32 Identities=16% Similarity=0.429 Sum_probs=27.9
Q ss_pred CCEEEEEeCCCcEEEEEEEeeCCceeeEEeee
Q 032863 17 GHVVTVELKSGELYRGSMVECEDNWNCQLENI 48 (132)
Q Consensus 17 g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv 48 (132)
...|.|.+.||..|..++...|....+-+=.+
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 45889999999999999999999888877555
No 124
>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=30.78 E-value=45 Score=21.67 Aligned_cols=52 Identities=15% Similarity=0.128 Sum_probs=28.3
Q ss_pred EeCCCcEEEEEEEeeCCc---eeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEec
Q 032863 23 ELKSGELYRGSMVECEDN---WNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVI 75 (132)
Q Consensus 23 ELknG~~y~G~L~~vD~~---MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~l 75 (132)
+|+.|.++.|++.++++| +++-+.+++-.-+....+ .+..|=.|..+...++
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~-~~~~~~~Gq~v~~~V~ 55 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG-NFSKLKVGQLLLCVVE 55 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC-cccccCCCCEEEEEEE
Confidence 368899999999999974 444333443211111110 0145555666655544
No 125
>PRK08477 biotin--protein ligase; Provisional
Probab=30.51 E-value=1.9e+02 Score=22.76 Aligned_cols=36 Identities=8% Similarity=0.011 Sum_probs=28.4
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeE
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECEDNWNCQLENIT 49 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~ 49 (132)
.-..|+.|+|. .++..++|+..++|+.--+.++.-.
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 34689999997 4789999999999987776665443
No 126
>PF13437 HlyD_3: HlyD family secretion protein
Probab=30.35 E-value=1.1e+02 Score=20.26 Aligned_cols=34 Identities=26% Similarity=0.382 Sum_probs=26.8
Q ss_pred CcHHHHHHhh--CCCEEEEEeCCC--cEEEEEEEeeCC
Q 032863 6 GIPVKLLHEA--SGHVVTVELKSG--ELYRGSMVECED 39 (132)
Q Consensus 6 ~~P~~lL~~~--~g~~V~VELknG--~~y~G~L~~vD~ 39 (132)
.+|-+.+..+ .|..|++.+.++ ..+.|++.+++.
T Consensus 41 ~v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 41 YVPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EEChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 3455666665 699999999855 599999999987
No 127
>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=30.24 E-value=97 Score=26.46 Aligned_cols=32 Identities=19% Similarity=0.321 Sum_probs=27.8
Q ss_pred CEEEEEeCCCcEEEEEEEeeCCceeeEEeeeE
Q 032863 18 HVVTVELKSGELYRGSMVECEDNWNCQLENIT 49 (132)
Q Consensus 18 ~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~ 49 (132)
..+.|.+.++..|.+++..+|...++-|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47889999999999999999999998776553
No 128
>PRK00802 3-methyladenine DNA glycosylase; Reviewed
Probab=28.49 E-value=1e+02 Score=24.17 Aligned_cols=32 Identities=22% Similarity=0.247 Sum_probs=26.9
Q ss_pred cHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 7 IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
.++.+=++++|+.+..+ ..+.|.|+++|.|+-
T Consensus 13 ~~~~vA~~LLGk~Lv~~----~~~~grIvETEAY~G 44 (188)
T PRK00802 13 DALEVARDLLGKVLVHE----GGVSGRIVETEAYIG 44 (188)
T ss_pred CHHHHHHHhCCCEEEEC----CEEEEEEEEEecccC
Confidence 45677789999999877 489999999998864
No 129
>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=28.40 E-value=84 Score=21.86 Aligned_cols=22 Identities=32% Similarity=0.534 Sum_probs=18.0
Q ss_pred hCCCEEEEE-eCCCcEEEEEEEe
Q 032863 15 ASGHVVTVE-LKSGELYRGSMVE 36 (132)
Q Consensus 15 ~~g~~V~VE-LknG~~y~G~L~~ 36 (132)
.+|..|.|+ +.++.++.|++.+
T Consensus 94 ~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 94 AVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 478888888 7888888888765
No 130
>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....
Probab=28.26 E-value=40 Score=16.79 Aligned_cols=19 Identities=26% Similarity=0.475 Sum_probs=13.5
Q ss_pred eeeEEEeCCeEEEEecCcccc
Q 032863 60 LEHVFIRGSKVRFMVIPDMLK 80 (132)
Q Consensus 60 l~~vfIRGs~Ir~I~lpd~l~ 80 (132)
+..+.+.+++|. .+|+.+.
T Consensus 2 L~~Ldls~n~l~--~ip~~~~ 20 (22)
T PF00560_consen 2 LEYLDLSGNNLT--SIPSSFS 20 (22)
T ss_dssp ESEEEETSSEES--EEGTTTT
T ss_pred ccEEECCCCcCE--eCChhhc
Confidence 567888888777 5666553
No 131
>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=28.03 E-value=42 Score=24.52 Aligned_cols=30 Identities=20% Similarity=0.257 Sum_probs=24.1
Q ss_pred cHHHHHHhhCCCEEEEEeCCC-cEEEEEEEe
Q 032863 7 IPVKLLHEASGHVVTVELKSG-ELYRGSMVE 36 (132)
Q Consensus 7 ~P~~lL~~~~g~~V~VELknG-~~y~G~L~~ 36 (132)
..-.++..++|+.|.|+++.. ..|.|+...
T Consensus 93 sl~~~~~~l~gk~l~V~v~~~~~e~nGk~y~ 123 (141)
T PF05037_consen 93 SLEQFLNQLLGKPLRVTVKWEENEYNGKTYP 123 (141)
T ss_pred cHHHHHHHHcCCeeEEEecccccCCCCcEee
Confidence 345788899999999999988 788886543
No 132
>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=27.55 E-value=61 Score=20.14 Aligned_cols=24 Identities=29% Similarity=0.495 Sum_probs=17.3
Q ss_pred EeCCCcEEEEEEEeeCC-ceeeEEe
Q 032863 23 ELKSGELYRGSMVECED-NWNCQLE 46 (132)
Q Consensus 23 ELknG~~y~G~L~~vD~-~MNi~L~ 46 (132)
+++-|+++.|++.++++ .+-+.|.
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~ 25 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLG 25 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEES
T ss_pred CCCCCCEEEEEEEEEECCEEEEEEC
Confidence 46789999999999985 3444444
No 133
>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=27.54 E-value=1.7e+02 Score=18.63 Aligned_cols=34 Identities=9% Similarity=0.332 Sum_probs=27.1
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeE
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWNCQLENIT 49 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~ 49 (132)
.+..|.+...+-..++|.+..+|+++=+.+.+..
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 4567888887777999999999998888887753
No 134
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=26.66 E-value=81 Score=19.17 Aligned_cols=21 Identities=10% Similarity=0.327 Sum_probs=14.0
Q ss_pred EEEEEEeeCCceeeEEeeeEE
Q 032863 30 YRGSMVECEDNWNCQLENITY 50 (132)
Q Consensus 30 y~G~L~~vD~~MNi~L~dv~~ 50 (132)
..|+-.++|+++.+.|.+-..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 579999999999999987643
No 135
>PRK14056 phenylalanine 4-monooxygenase; Provisional
Probab=26.43 E-value=1.7e+02 Score=27.00 Aligned_cols=40 Identities=20% Similarity=0.268 Sum_probs=31.9
Q ss_pred hCCCEEEEEeCCCcEEEEEEEee---C-CceeeEEeeeEEEccC
Q 032863 15 ASGHVVTVELKSGELYRGSMVEC---E-DNWNCQLENITYTAKD 54 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~v---D-~~MNi~L~dv~~t~~d 54 (132)
..|+.+..|+.+|.+++|.+..- + ..+=+.++||+++..+
T Consensus 390 ~~g~~~~l~f~sgi~v~G~~~~~~~~~g~~~li~f~~ctv~~~~ 433 (578)
T PRK14056 390 TIGNIAELEFESGIHVKGTVTDGVKNDGKIALISFINCTVTYNG 433 (578)
T ss_pred ccCceEEEEeecceEEEEEEeeeeccCCeEEEEEeeeeEEeeCC
Confidence 46899999999999999976553 3 4555889999999744
No 136
>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=26.42 E-value=1.5e+02 Score=23.44 Aligned_cols=61 Identities=20% Similarity=0.288 Sum_probs=38.2
Q ss_pred HHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCc-eeeEEeeeEEEccCC-ceeeeeeEEEeCCe
Q 032863 9 VKLLHEASGHVVTVELKSGELYRGSMVECEDN-WNCQLENITYTAKDG-KVSQLEHVFIRGSK 69 (132)
Q Consensus 9 ~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~-MNi~L~dv~~t~~dg-~~~~l~~vfIRGs~ 69 (132)
.++|..-.|..|.|-.-+|..|.++|..++.. ..+.+.......... ....+=...+|+..
T Consensus 27 ~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~~~~~~~~~~~~~i~l~~al~K~~~ 89 (240)
T TIGR00046 27 VRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELLEGESEKRELPLKIHLAIVLIKGKK 89 (240)
T ss_pred HHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEEecccCCCCCCcEEEEEEeecCCcc
Confidence 35677788999999877899999999998754 444444332221111 22344444555543
No 137
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=26.39 E-value=1.7e+02 Score=18.36 Aligned_cols=39 Identities=18% Similarity=0.589 Sum_probs=26.6
Q ss_pred CCCcEEEEEEEe---eCCceeeEEeeeEEEcc-CCceeeeeeE
Q 032863 25 KSGELYRGSMVE---CEDNWNCQLENITYTAK-DGKVSQLEHV 63 (132)
Q Consensus 25 knG~~y~G~L~~---vD~~MNi~L~dv~~t~~-dg~~~~l~~v 63 (132)
++-.++.|.|.. ||+-+=..|+|+++... +....+.+.+
T Consensus 3 k~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkv 45 (52)
T PF02751_consen 3 KNKLSFKGHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKV 45 (52)
T ss_dssp --EEEEEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEE
T ss_pred ceeEEEEEeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeE
Confidence 455678898876 89999999999998763 3334444433
No 138
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=26.34 E-value=1.5e+02 Score=23.23 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=27.1
Q ss_pred HHHHHhhCCCEEEEEeCCCcEEEEEEEeeCC
Q 032863 9 VKLLHEASGHVVTVELKSGELYRGSMVECED 39 (132)
Q Consensus 9 ~~lL~~~~g~~V~VELknG~~y~G~L~~vD~ 39 (132)
.++|..-.|..|.|-.-+|..|.++|..+|.
T Consensus 25 ~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~ 55 (234)
T PRK11713 25 VRVLRLKEGDELRLFDGDGGEYLAEITEIGK 55 (234)
T ss_pred HhhccCCCCCEEEEEeCCCCEEEEEEEEecC
Confidence 4677778899999988889999999999985
No 139
>PRK10942 serine endoprotease; Provisional
Probab=26.06 E-value=1.2e+02 Score=26.59 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=27.4
Q ss_pred CCEEEEEeCCCcEEEEEEEeeCCceeeEEeee
Q 032863 17 GHVVTVELKSGELYRGSMVECEDNWNCQLENI 48 (132)
Q Consensus 17 g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv 48 (132)
...|.|.+.+|.+|.+++...|...++-|=.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999988876544
No 140
>PRK04313 30S ribosomal protein S4e; Validated
Probab=26.01 E-value=2.9e+02 Score=22.59 Aligned_cols=45 Identities=27% Similarity=0.422 Sum_probs=26.5
Q ss_pred EEEEeeCCceeeEEeeeEEEccCCc--eeeeeeEEEeCCeEEEEecC
Q 032863 32 GSMVECEDNWNCQLENITYTAKDGK--VSQLEHVFIRGSKVRFMVIP 76 (132)
Q Consensus 32 G~L~~vD~~MNi~L~dv~~t~~dg~--~~~l~~vfIRGs~Ir~I~lp 76 (132)
|++.+.+.+.--.-+-|++.+.+|+ .+.++.+|+=|..=-+|.||
T Consensus 190 G~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~~kp~isl~ 236 (237)
T PRK04313 190 GKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGKEKPVIKLP 236 (237)
T ss_pred EEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcCCCcceeCC
Confidence 8888887554211122333334664 46678888888765566665
No 141
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=25.70 E-value=1.3e+02 Score=23.26 Aligned_cols=36 Identities=19% Similarity=0.228 Sum_probs=27.9
Q ss_pred cHHHHHHhh-CCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 7 IPVKLLHEA-SGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 7 ~P~~lL~~~-~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
+|-..+..+ .|..|+|.+.++..|.|++..++...+
T Consensus 131 v~~~~~~~i~~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 131 VPAKDVSRIRKGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred ECHHHHhhCCCCCEEEEEECCCCEEEEEEEEEccccC
Confidence 454444444 699999999999999999999986544
No 142
>PRK10113 cell division modulator; Provisional
Probab=25.45 E-value=60 Score=21.96 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=24.1
Q ss_pred eeEEEeCCeEEEEecCcccccccchhch
Q 032863 61 EHVFIRGSKVRFMVIPDMLKNAPMFKRL 88 (132)
Q Consensus 61 ~~vfIRGs~Ir~I~lpd~l~~ap~l~~~ 88 (132)
+.-.+||..|.|+.+-|.+.-+|.|...
T Consensus 35 DVW~LrGKYVAFvl~ge~FrRSPaFs~P 62 (80)
T PRK10113 35 DVWMLRGKYVAFVLMGESFLRSPAFSVP 62 (80)
T ss_pred hhheeccceEEEEEechhhccCCccCCc
Confidence 3457899999999999999999999643
No 143
>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=24.71 E-value=3.2e+02 Score=22.82 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=27.9
Q ss_pred CEEEEEeCCCcEEEEEEEeeCCceeeEEeeeE
Q 032863 18 HVVTVELKSGELYRGSMVECEDNWNCQLENIT 49 (132)
Q Consensus 18 ~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~ 49 (132)
..+.|.+.+|..|.+++...|...++-|=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46889999999999999999999998886554
No 144
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=24.34 E-value=2.1e+02 Score=18.71 Aligned_cols=55 Identities=16% Similarity=0.275 Sum_probs=36.0
Q ss_pred hhCCCEEEEEeCCCc-EEEEEEEeeCC-ceeeEEeeeEEEccCCceeeeeeEEEeCCeEE
Q 032863 14 EASGHVVTVELKSGE-LYRGSMVECED-NWNCQLENITYTAKDGKVSQLEHVFIRGSKVR 71 (132)
Q Consensus 14 ~~~g~~V~VELknG~-~y~G~L~~vD~-~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir 71 (132)
.-+|+.|.|...+.- +|.|.+..+|. .--++|.... .+|-.-...++..+..-|+
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~---~ngik~~~~EVt~~~~DI~ 59 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF---HNGVKCLVPEVTFRAGDIR 59 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc---cCCccccCceEEEEEcchh
Confidence 457899999998874 99999999995 3334444432 3443444556666655443
No 145
>PRK10708 hypothetical protein; Provisional
Probab=24.33 E-value=87 Score=20.40 Aligned_cols=27 Identities=22% Similarity=0.235 Sum_probs=23.0
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
++..|+|++..+..-.|++..++.+--
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~E 29 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFSE 29 (62)
T ss_pred cccEEEEecCCCccccceEEEEeeccC
Confidence 467899999999999999999987543
No 146
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=23.85 E-value=90 Score=24.24 Aligned_cols=26 Identities=27% Similarity=0.455 Sum_probs=22.4
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEeeC
Q 032863 13 HEASGHVVTVELKSGELYRGSMVECE 38 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~vD 38 (132)
..++|+.|+|.+.....++|.+.+++
T Consensus 24 ~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 24 KDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp GGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 44899999999998899999999984
No 147
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=23.42 E-value=2.1e+02 Score=18.18 Aligned_cols=29 Identities=14% Similarity=0.353 Sum_probs=20.2
Q ss_pred CCCEEEEEeCCCc----EEEEEEEeeCCceeeE
Q 032863 16 SGHVVTVELKSGE----LYRGSMVECEDNWNCQ 44 (132)
Q Consensus 16 ~g~~V~VELknG~----~y~G~L~~vD~~MNi~ 44 (132)
.|..|.||+.++. .|.-++.++++.=.+.
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~ 35 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLI 35 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEE
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEE
Confidence 5889999995543 5999999999763333
No 148
>KOG1219 consensus Uncharacterized conserved protein, contains laminin, cadherin and EGF domains [Signal transduction mechanisms]
Probab=23.19 E-value=1.3e+02 Score=33.23 Aligned_cols=81 Identities=26% Similarity=0.266 Sum_probs=53.0
Q ss_pred CCCCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEcc--CCceeeeeeEEEeCCe--------EE
Q 032863 2 SRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAK--DGKVSQLEHVFIRGSK--------VR 71 (132)
Q Consensus 2 s~~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~--dg~~~~l~~vfIRGs~--------Ir 71 (132)
|..++.|+-++.......|+.||++|.+|-= + +|| .++....+.+ |=+....-++-|+|.+ +.
T Consensus 1583 S~~~gSpig~v~a~~~s~Vtyel~d~~t~~~----f--~~~-~~sg~ii~qk~ld~e~~~s~~~~i~gtn~aG~~t~~~v 1655 (4289)
T KOG1219|consen 1583 SFNSGSPIGKVPADSDSDVTYELIDGNTYVR----F--FEN-FVSGHIITQKLLDLEHRKSYFLDIKGTNMAGKLTAPIV 1655 (4289)
T ss_pred cCCCCCeeEEEeccCCCceEEEEecCCccee----E--EEe-eecceeeehhhccccccceEEEEEEEeeccccccCcEE
Confidence 4567899999999999999999999988521 1 111 2222222221 1123334456677764 66
Q ss_pred EEecCcccccccchhchh
Q 032863 72 FMVIPDMLKNAPMFKRLD 89 (132)
Q Consensus 72 ~I~lpd~l~~ap~l~~~~ 89 (132)
.+++-|+=+++|+|.+..
T Consensus 1656 vv~ii~en~nsp~fr~~e 1673 (4289)
T KOG1219|consen 1656 VVLIIDENDNSPEFRENE 1673 (4289)
T ss_pred EEEEeccccCChHHhhhh
Confidence 777888899999997643
No 149
>PRK08158 type III secretion system protein SpaO; Validated
Probab=22.78 E-value=1.7e+02 Score=24.78 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=29.8
Q ss_pred hhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEE
Q 032863 14 EASGHVVTVELKSGELYRGSMVECEDNWNCQLENITY 50 (132)
Q Consensus 14 ~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~ 50 (132)
...+.+|.|...+-..-+|.|+.+|+.+=+.+.++.-
T Consensus 261 ~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i~~ 297 (303)
T PRK08158 261 TNAELNVEIRANGALLGNGELVQMDDTLGVEIHEWLS 297 (303)
T ss_pred CCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEEec
Confidence 4567778887777778899999999999888887743
No 150
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=22.72 E-value=1e+02 Score=26.56 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=20.9
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEE
Q 032863 13 HEASGHVVTVELKSGELYRGSMV 35 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~ 35 (132)
+-+.|+.|+|...+|..|.|+|-
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg 115 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIG 115 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEc
Confidence 45689999999999999999998
No 151
>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=22.70 E-value=96 Score=20.25 Aligned_cols=20 Identities=10% Similarity=0.202 Sum_probs=15.6
Q ss_pred EEEEEEEeeC-CceeeEEeee
Q 032863 29 LYRGSMVECE-DNWNCQLENI 48 (132)
Q Consensus 29 ~y~G~L~~vD-~~MNi~L~dv 48 (132)
...|++.++| ..|-|+|+|=
T Consensus 4 ~veG~I~~id~~~~titLdDG 24 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDG 24 (61)
T ss_pred cceEEEEEEcCCceEEEecCC
Confidence 4689999999 5777777653
No 152
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=22.33 E-value=1.4e+02 Score=21.12 Aligned_cols=24 Identities=25% Similarity=0.187 Sum_probs=16.9
Q ss_pred HhhCCCEEEEEeCCCcEEEEEEEe
Q 032863 13 HEASGHVVTVELKSGELYRGSMVE 36 (132)
Q Consensus 13 ~~~~g~~V~VELknG~~y~G~L~~ 36 (132)
++++=+.+.|.|.||.++..-+=.
T Consensus 31 NSA~RK~arV~L~ngk~v~ayIPg 54 (95)
T cd00319 31 NSALRKVAKVRLTSGYEVTAYIPG 54 (95)
T ss_pred ChhhceEEEEEccCCCEEEEECCC
Confidence 345667889999999887654433
No 153
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.88 E-value=1.2e+02 Score=23.96 Aligned_cols=45 Identities=13% Similarity=0.171 Sum_probs=34.4
Q ss_pred hCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeee
Q 032863 15 ASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLE 61 (132)
Q Consensus 15 ~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~ 61 (132)
++|..|.++.-++....|.+.+||-.-++..-++. ..++++.+..
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~--~s~~~P~~~~ 53 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP--SSNGKPNHAK 53 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc--ccCCCCccch
Confidence 46788999999999999999999987777766665 3355544433
No 154
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.14 E-value=1.2e+02 Score=24.02 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=19.3
Q ss_pred hCCCEEEEE-eCCCcEEEEEEEe
Q 032863 15 ASGHVVTVE-LKSGELYRGSMVE 36 (132)
Q Consensus 15 ~~g~~V~VE-LknG~~y~G~L~~ 36 (132)
.+|..|.|+ +.+|.++.|++.+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 578999999 9999999999876
No 155
>cd01343 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
Probab=20.71 E-value=4.3e+02 Score=21.07 Aligned_cols=52 Identities=19% Similarity=0.314 Sum_probs=35.7
Q ss_pred EEEEEeCCCcEEEEEEEeeCCceeeEEe-eeEEEccCCceeeeeeEEEeCCeEEEEe
Q 032863 19 VVTVELKSGELYRGSMVECEDNWNCQLE-NITYTAKDGKVSQLEHVFIRGSKVRFMV 74 (132)
Q Consensus 19 ~V~VELknG~~y~G~L~~vD~~MNi~L~-dv~~t~~dg~~~~l~~vfIRGs~Ir~I~ 74 (132)
.+.+.|.++..++|.+...+ -++.|. +..-.. .+ .+.+..+.+.+..|.|-.
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~~-tg-~S~v~~L~l~~g~v~f~~ 126 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWTL-TG-DSNVNNLTLNGGTVDFNG 126 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEEE-eC-CcccceeEecCCEEEecc
Confidence 68899999999999999987 345555 443332 22 234577777877777653
No 156
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=20.60 E-value=1e+02 Score=20.05 Aligned_cols=27 Identities=22% Similarity=0.217 Sum_probs=23.0
Q ss_pred CCCEEEEEeCCCcEEEEEEEeeCCcee
Q 032863 16 SGHVVTVELKSGELYRGSMVECEDNWN 42 (132)
Q Consensus 16 ~g~~V~VELknG~~y~G~L~~vD~~MN 42 (132)
++..|+|++..+..-.|++..++.+--
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~E 29 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFNE 29 (62)
T ss_pred cccEEEEecCCcccccceEEEEeeccC
Confidence 467899999999999999999987644
No 157
>PF12541 DUF3737: Protein of unknown function (DUF3737) ; InterPro: IPR022208 This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 281 and 297 amino acids in length.
Probab=20.44 E-value=1.4e+02 Score=24.95 Aligned_cols=33 Identities=21% Similarity=0.167 Sum_probs=20.3
Q ss_pred eeCCceeeEEeeeEEEccCCceeeeeeEEEeCCe
Q 032863 36 ECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSK 69 (132)
Q Consensus 36 ~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~ 69 (132)
.||.--|+.+.|+++..+| .+++.+.|.|+-|-
T Consensus 151 ~Fq~~kNvei~ns~l~sKD-AFWn~eNVtVyDS~ 183 (277)
T PF12541_consen 151 SFQYCKNVEIHNSKLDSKD-AFWNCENVTVYDSV 183 (277)
T ss_pred EeeceeeEEEEccEEeccc-ccccCCceEEEcce
Confidence 3666667777777776654 45555555555543
No 158
>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=20.05 E-value=2.1e+02 Score=18.27 Aligned_cols=25 Identities=32% Similarity=0.567 Sum_probs=18.2
Q ss_pred hCCCEEEEEeCCCcEE-EEEEEeeCC
Q 032863 15 ASGHVVTVELKSGELY-RGSMVECED 39 (132)
Q Consensus 15 ~~g~~V~VELknG~~y-~G~L~~vD~ 39 (132)
..|..|.+.--++..| .|++.++|.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecc
Confidence 4688999999887765 999999885
Done!