Query 030131
Match_columns 182
No_of_seqs 110 out of 218
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 09:00:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4401 Uncharacterized conser 100.0 2.7E-34 5.7E-39 225.5 10.6 173 5-177 1-182 (184)
2 PF09793 AD: Anticodon-binding 100.0 3.3E-32 7.1E-37 195.3 9.3 87 80-166 1-91 (91)
3 PF06372 Gemin6: Gemin6 protei 99.9 7.2E-24 1.6E-28 166.4 8.3 145 13-172 15-163 (166)
4 cd01735 LSm12_N LSm12 belongs 99.7 1.8E-17 3.8E-22 110.0 7.0 59 10-68 1-61 (61)
5 PF12701 LSM14: Scd6-like Sm d 97.8 0.00015 3.3E-09 52.4 7.8 64 12-75 5-82 (96)
6 cd00600 Sm_like The eukaryotic 96.7 0.0064 1.4E-07 39.7 5.9 54 13-67 4-62 (63)
7 PF01423 LSM: LSM domain ; In 96.4 0.013 2.9E-07 38.8 5.9 55 13-68 6-66 (67)
8 cd01719 Sm_G The eukaryotic Sm 96.2 0.026 5.7E-07 38.5 6.7 57 14-71 9-70 (72)
9 cd01731 archaeal_Sm1 The archa 96.0 0.044 9.6E-07 36.7 6.8 55 13-67 8-66 (68)
10 cd06168 LSm9 The eukaryotic Sm 95.9 0.04 8.6E-07 38.0 6.3 57 13-69 8-74 (75)
11 PRK00737 small nuclear ribonuc 95.8 0.057 1.2E-06 36.7 6.8 55 13-67 12-70 (72)
12 cd01726 LSm6 The eukaryotic Sm 95.8 0.051 1.1E-06 36.4 6.4 55 13-67 8-66 (67)
13 cd01717 Sm_B The eukaryotic Sm 95.5 0.055 1.2E-06 37.4 6.1 58 12-69 7-78 (79)
14 smart00651 Sm snRNP Sm protein 95.4 0.063 1.4E-06 35.4 5.7 56 13-68 6-66 (67)
15 PF03614 Flag1_repress: Repres 95.3 0.026 5.7E-07 43.8 4.0 50 16-68 30-79 (165)
16 COG1958 LSM1 Small nuclear rib 95.3 0.091 2E-06 36.2 6.4 57 11-67 13-77 (79)
17 PF14438 SM-ATX: Ataxin 2 SM d 95.2 0.051 1.1E-06 37.2 5.0 35 13-47 10-46 (77)
18 cd01736 LSm14_N LSm14 (also kn 95.1 0.14 3E-06 35.3 6.8 56 12-67 3-73 (74)
19 cd01722 Sm_F The eukaryotic Sm 95.0 0.15 3.1E-06 34.3 6.7 55 13-67 9-67 (68)
20 cd01723 LSm4 The eukaryotic Sm 94.2 0.47 1E-05 32.5 7.8 57 13-69 9-70 (76)
21 cd01724 Sm_D1 The eukaryotic S 94.1 0.37 8E-06 34.3 7.3 58 13-70 9-70 (90)
22 KOG1073 Uncharacterized mRNA-a 93.8 0.15 3.3E-06 44.9 5.8 62 13-74 7-83 (361)
23 cd01725 LSm2 The eukaryotic Sm 93.7 0.46 1E-05 33.0 7.2 57 13-69 9-71 (81)
24 cd01721 Sm_D3 The eukaryotic S 93.6 0.54 1.2E-05 31.7 7.1 57 12-68 7-67 (70)
25 cd01727 LSm8 The eukaryotic Sm 92.7 0.29 6.2E-06 33.4 4.7 33 14-46 8-40 (74)
26 cd01729 LSm7 The eukaryotic Sm 92.6 0.3 6.6E-06 34.0 4.8 56 13-68 10-77 (81)
27 cd01733 LSm10 The eukaryotic S 92.4 1.1 2.4E-05 30.9 7.5 56 13-68 17-76 (78)
28 cd01728 LSm1 The eukaryotic Sm 92.0 0.38 8.3E-06 33.0 4.7 33 13-45 10-42 (74)
29 cd01730 LSm3 The eukaryotic Sm 91.8 0.32 7E-06 33.8 4.2 31 13-43 9-39 (82)
30 cd01737 LSm16_N LSm16 belongs 91.7 0.55 1.2E-05 31.0 4.8 38 14-51 5-43 (62)
31 cd01732 LSm5 The eukaryotic Sm 90.5 0.56 1.2E-05 32.3 4.3 55 13-67 11-72 (76)
32 KOG1783 Small nuclear ribonucl 89.9 0.077 1.7E-06 36.3 -0.4 66 2-68 3-73 (77)
33 cd01720 Sm_D2 The eukaryotic S 89.6 0.3 6.4E-06 34.6 2.4 31 12-42 11-41 (87)
34 PF01245 Ribosomal_L19: Riboso 88.1 1.8 3.9E-05 32.2 5.8 71 4-74 11-90 (113)
35 PF02237 BPL_C: Biotin protein 88.1 1.5 3.2E-05 27.2 4.6 33 13-47 1-33 (48)
36 TIGR01024 rplS_bact ribosomal 85.5 6.3 0.00014 29.3 7.4 71 4-74 11-90 (113)
37 CHL00084 rpl19 ribosomal prote 84.7 8.8 0.00019 28.7 7.9 71 4-74 15-94 (117)
38 PF08863 YolD: YolD-like prote 84.1 5 0.00011 27.6 6.2 50 13-67 40-92 (92)
39 KOG1784 Small Nuclear ribonucl 83.1 1.6 3.4E-05 31.2 3.2 61 14-74 9-77 (96)
40 PRK05338 rplS 50S ribosomal pr 82.9 8.5 0.00018 28.7 7.2 71 4-74 11-90 (116)
41 cd01716 Hfq Hfq, an abundant, 79.8 15 0.00032 24.3 6.9 46 15-68 11-56 (61)
42 TIGR02383 Hfq RNA chaperone Hf 79.4 13 0.00028 24.6 6.4 46 15-68 15-60 (61)
43 KOG1775 U6 snRNA-associated Sm 76.7 2.1 4.6E-05 29.6 2.1 55 11-66 13-75 (84)
44 PF10842 DUF2642: Protein of u 76.3 20 0.00044 24.0 6.7 45 14-67 20-64 (66)
45 PF07073 ROF: Modulator of Rho 73.0 5.9 0.00013 27.6 3.6 54 15-74 17-73 (80)
46 KOG3482 Small nuclear ribonucl 70.8 7.8 0.00017 26.6 3.7 33 14-46 17-49 (79)
47 PRK14638 hypothetical protein; 69.6 24 0.00052 27.3 6.7 49 13-69 98-146 (150)
48 PF09981 DUF2218: Uncharacteri 69.4 8.5 0.00018 27.1 3.8 60 112-177 11-81 (89)
49 PRK14632 hypothetical protein; 69.1 27 0.00058 27.7 7.1 59 13-73 96-163 (172)
50 PF09465 LBR_tudor: Lamin-B re 69.0 24 0.00053 22.9 5.5 36 10-45 4-40 (55)
51 KOG3172 Small nuclear ribonucl 68.7 37 0.00079 25.0 7.0 60 13-73 13-76 (119)
52 PRK02001 hypothetical protein; 64.9 40 0.00087 26.2 7.2 32 13-46 88-119 (152)
53 PF11095 Gemin7: Gem-associate 64.9 45 0.00097 23.3 7.1 57 13-69 22-78 (80)
54 PRK00395 hfq RNA-binding prote 63.1 49 0.0011 23.1 6.6 48 15-70 19-66 (79)
55 PF02576 DUF150: Uncharacteris 60.9 47 0.001 25.0 6.9 32 14-47 86-121 (141)
56 COG0335 RplS Ribosomal protein 60.9 65 0.0014 24.0 7.2 67 8-74 17-92 (115)
57 KOG3448 Predicted snRNP core p 60.2 50 0.0011 23.5 6.2 60 13-72 10-75 (96)
58 PRK00092 ribosome maturation p 59.1 52 0.0011 25.3 6.9 51 13-69 96-150 (154)
59 COG0779 Uncharacterized protei 58.4 39 0.00084 26.4 6.0 32 13-46 97-132 (153)
60 COG1923 Hfq Uncharacterized ho 57.3 62 0.0013 22.4 6.6 48 15-70 19-66 (77)
61 PRK14640 hypothetical protein; 55.8 63 0.0014 25.0 6.8 51 13-71 95-149 (152)
62 PRK14639 hypothetical protein; 54.3 29 0.00064 26.5 4.7 50 14-69 87-136 (140)
63 smart00739 KOW KOW (Kyprides, 53.5 29 0.00062 18.1 3.4 26 12-37 2-27 (28)
64 PF14894 Lsm_C: Lsm C-terminal 52.5 65 0.0014 21.5 5.5 50 118-173 4-61 (64)
65 PRK14644 hypothetical protein; 52.0 62 0.0013 24.6 6.1 31 13-45 83-117 (136)
66 PRK10898 serine endoprotease; 51.6 37 0.00081 29.7 5.5 33 15-47 101-133 (353)
67 PF07076 DUF1344: Protein of u 51.3 18 0.0004 23.9 2.7 23 26-48 3-25 (61)
68 PRK09618 flgD flagellar basal 48.7 1E+02 0.0023 23.7 6.9 29 13-41 90-118 (142)
69 PRK14636 hypothetical protein; 47.7 60 0.0013 25.8 5.7 52 13-71 96-151 (176)
70 cd01718 Sm_E The eukaryotic Sm 47.3 47 0.001 23.0 4.4 50 17-67 20-77 (79)
71 TIGR02038 protease_degS peripl 47.2 47 0.001 29.0 5.5 32 16-47 102-133 (351)
72 PRK14641 hypothetical protein; 46.5 72 0.0016 25.3 6.0 53 14-66 103-166 (173)
73 PRK10942 serine endoprotease; 45.3 85 0.0018 28.7 7.0 32 15-46 135-166 (473)
74 PTZ00138 small nuclear ribonuc 45.0 52 0.0011 23.3 4.4 53 16-68 27-86 (89)
75 PRK10708 hypothetical protein; 44.3 38 0.00083 22.2 3.3 31 14-44 3-33 (62)
76 PRK11911 flgD flagellar basal 42.4 65 0.0014 24.8 4.9 32 13-44 91-122 (140)
77 cd01734 YlxS_C YxlS is a Bacil 42.4 1.1E+02 0.0024 20.9 7.5 54 13-70 23-80 (83)
78 PRK10139 serine endoprotease; 41.8 62 0.0013 29.4 5.5 33 15-47 114-146 (455)
79 cd01739 LSm11_C The eukaryotic 41.7 57 0.0012 21.9 3.9 36 11-46 4-43 (66)
80 PRK14631 hypothetical protein; 41.4 1.5E+02 0.0032 23.6 7.0 53 13-70 115-171 (174)
81 PF01011 PQQ: PQQ enzyme repea 40.4 21 0.00047 20.5 1.6 19 28-46 8-26 (38)
82 KOG1780 Small Nuclear ribonucl 39.9 90 0.002 21.5 4.7 63 9-71 8-74 (77)
83 TIGR01955 RfaH transcriptional 39.8 66 0.0014 24.3 4.7 38 9-46 106-143 (159)
84 PF10133 RNA_bind_2: Predicted 39.4 1.1E+02 0.0024 20.1 5.8 33 13-45 26-60 (61)
85 PRK14633 hypothetical protein; 39.3 1.2E+02 0.0026 23.4 6.1 51 13-70 92-146 (150)
86 PRK14643 hypothetical protein; 39.3 64 0.0014 25.4 4.6 32 13-44 102-137 (164)
87 PF10781 DSRB: Dextransucrase 38.5 48 0.001 21.7 3.1 31 14-44 3-33 (62)
88 KOG3293 Small nuclear ribonucl 37.8 1E+02 0.0022 23.3 5.1 55 13-69 10-71 (134)
89 PRK14645 hypothetical protein; 36.7 66 0.0014 25.0 4.3 30 14-46 101-130 (154)
90 PF00467 KOW: KOW motif; Inte 35.1 83 0.0018 17.4 3.6 31 14-44 1-31 (32)
91 PRK14642 hypothetical protein; 33.9 87 0.0019 25.5 4.7 58 14-71 99-180 (197)
92 KOG3460 Small nuclear ribonucl 33.7 9.4 0.0002 26.8 -0.8 30 14-43 14-43 (91)
93 PRK14091 RNA-binding protein H 33.5 2.1E+02 0.0045 22.7 6.5 49 14-70 23-71 (165)
94 PRK04183 glutamyl-tRNA(Gln) am 32.8 2.2E+02 0.0047 25.8 7.5 55 12-74 3-58 (419)
95 PRK08559 nusG transcription an 32.6 90 0.0019 23.9 4.4 37 10-46 93-129 (153)
96 PF14564 Membrane_bind: Membra 32.3 2E+02 0.0044 21.0 7.1 33 14-46 51-86 (110)
97 COG4847 Uncharacterized protei 32.1 39 0.00085 24.4 2.1 27 17-44 6-32 (103)
98 cd05703 S1_Rrp5_repeat_hs12_sc 31.5 90 0.0019 20.6 3.8 22 24-45 49-70 (73)
99 PRK06792 flgD flagellar basal 31.4 2.5E+02 0.0055 22.8 6.9 48 13-68 116-164 (190)
100 PF13570 PQQ_3: PQQ-like domai 31.1 27 0.00059 20.1 1.0 11 29-39 30-40 (40)
101 PF05593 RHS_repeat: RHS Repea 31.0 1.1E+02 0.0024 17.5 4.8 32 13-47 3-34 (38)
102 PF15490 Ten1_2: Telomere-capp 31.0 1.9E+02 0.004 21.6 5.7 47 12-68 18-64 (118)
103 PF15200 KRTDAP: Keratinocyte 31.0 29 0.00063 23.8 1.2 37 81-131 24-61 (77)
104 smart00564 PQQ beta-propeller 30.7 43 0.00094 18.0 1.8 14 30-43 16-29 (33)
105 KOG3428 Small nuclear ribonucl 30.7 99 0.0021 22.8 4.0 54 14-67 11-67 (109)
106 PRK14635 hypothetical protein; 30.2 2.6E+02 0.0057 21.7 6.9 54 14-69 98-158 (162)
107 PRK14091 RNA-binding protein H 30.1 2.6E+02 0.0056 22.2 6.6 48 15-70 104-151 (165)
108 PRK14646 hypothetical protein; 29.8 2.6E+02 0.0057 21.6 7.0 49 14-70 99-151 (155)
109 COG4520 LipA Surface antigen [ 29.4 41 0.00088 25.7 1.9 27 127-153 77-105 (136)
110 PF14153 Spore_coat_CotO: Spor 29.2 1.4E+02 0.0031 23.9 5.2 49 17-71 135-184 (185)
111 TIGR02603 CxxCH_TIGR02603 puta 28.8 1.3E+02 0.0028 22.3 4.7 47 17-70 59-105 (133)
112 COG2100 Predicted Fe-S oxidore 28.6 1.9E+02 0.004 25.9 6.0 54 8-62 348-405 (414)
113 TIGR02037 degP_htrA_DO peripla 28.4 1.3E+02 0.0029 26.7 5.4 32 16-47 82-113 (428)
114 PRK14634 hypothetical protein; 27.8 1.1E+02 0.0024 23.7 4.2 50 13-70 98-151 (155)
115 cd07885 RHD-n_RelA N-terminal 27.6 51 0.0011 26.2 2.3 28 123-150 37-68 (169)
116 cd05696 S1_Rrp5_repeat_hs4 S1_ 27.1 1.2E+02 0.0026 19.8 3.8 22 24-45 49-70 (71)
117 PF09153 DUF1938: Domain of un 26.9 56 0.0012 23.0 2.1 24 14-37 10-33 (86)
118 PF14157 YmzC: YmzC-like prote 26.8 89 0.0019 20.8 2.9 16 31-46 42-57 (63)
119 cd07883 RHD-n_NFkB N-terminal 26.7 52 0.0011 26.8 2.2 28 123-150 37-68 (197)
120 cd01206 Homer Homer type EVH1 26.4 1.6E+02 0.0034 21.9 4.5 36 28-63 9-52 (111)
121 smart00333 TUDOR Tudor domain. 26.3 1.6E+02 0.0034 17.9 5.1 34 11-44 2-35 (57)
122 PF03088 Str_synth: Strictosid 26.1 93 0.002 21.9 3.2 21 26-46 33-54 (89)
123 PF11717 Tudor-knot: RNA bindi 25.9 1.3E+02 0.0028 18.9 3.6 29 12-40 1-29 (55)
124 CHL00132 psaF photosystem I su 25.9 1.6E+02 0.0034 23.8 4.7 39 87-125 36-83 (185)
125 PF02393 US22: US22 like; Int 24.9 65 0.0014 23.2 2.3 18 29-46 90-107 (125)
126 TIGR01080 rplX_A_E ribosomal p 24.9 1.6E+02 0.0034 21.9 4.3 35 11-45 41-75 (114)
127 PF10835 DUF2573: Protein of u 24.9 1.3E+02 0.0029 20.9 3.7 37 117-175 35-74 (82)
128 cd07933 RHD-n_c-Rel N-terminal 24.6 63 0.0014 25.8 2.3 28 123-150 37-68 (172)
129 CHL00141 rpl24 ribosomal prote 24.5 2E+02 0.0042 20.0 4.6 35 11-45 8-42 (83)
130 cd07887 RHD-n_Dorsal_Dif N-ter 24.4 64 0.0014 25.8 2.3 27 123-149 37-67 (173)
131 cd05695 S1_Rrp5_repeat_hs3 S1_ 24.3 1.3E+02 0.0027 19.4 3.4 22 23-44 44-65 (66)
132 PF09943 DUF2175: Uncharacteri 24.2 73 0.0016 23.2 2.4 29 18-47 3-31 (101)
133 PRK09014 rfaH transcriptional 24.1 1.2E+02 0.0027 23.1 3.9 37 11-47 109-145 (162)
134 PF05735 TSP_C: Thrombospondin 23.6 1.2E+02 0.0027 24.8 3.8 27 18-44 41-67 (201)
135 PRK14630 hypothetical protein; 23.4 3.4E+02 0.0074 20.7 6.7 47 14-69 96-142 (143)
136 cd07935 RHD-n_NFkB1 N-terminal 23.3 67 0.0015 26.3 2.3 27 123-149 37-67 (202)
137 PLN02150 terpene synthase/cycl 23.1 1.1E+02 0.0023 21.8 3.1 20 156-175 21-40 (96)
138 PF07317 YcgR: Flagellar regul 23.0 2.2E+02 0.0049 20.3 4.8 35 15-49 21-55 (108)
139 PRK12281 rplX 50S ribosomal pr 23.0 2.4E+02 0.0051 19.2 4.7 35 11-45 6-40 (76)
140 COG3553 Uncharacterized protei 22.8 2.6E+02 0.0056 20.1 4.9 60 116-175 18-83 (96)
141 PF12658 Ten1: Telomere cappin 22.3 1.4E+02 0.003 22.3 3.7 28 12-47 22-49 (124)
142 PRK06955 biotin--protein ligas 22.3 1.6E+02 0.0035 25.1 4.6 35 11-46 245-279 (300)
143 KOG3350 Uncharacterized conser 22.1 52 0.0011 26.8 1.4 25 138-162 136-160 (217)
144 PF14208 DUF4320: Domain of un 22.0 3.3E+02 0.0072 20.1 5.9 25 107-131 38-66 (116)
145 PRK01191 rpl24p 50S ribosomal 21.9 2.2E+02 0.0048 21.3 4.7 35 11-45 45-79 (120)
146 PF06094 AIG2: AIG2-like famil 21.8 1.5E+02 0.0033 20.2 3.7 20 17-36 83-102 (102)
147 COG4806 RhaA L-rhamnose isomer 21.5 45 0.00097 29.1 0.9 14 127-140 290-303 (419)
148 COG0340 BirA Biotin-(acetyl-Co 21.4 1.8E+02 0.0039 24.2 4.5 36 11-47 186-221 (238)
149 PF00447 HSF_DNA-bind: HSF-typ 20.5 1E+02 0.0022 21.8 2.5 24 116-139 4-32 (103)
No 1
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.7e-34 Score=225.50 Aligned_cols=173 Identities=28% Similarity=0.381 Sum_probs=144.7
Q ss_pred CCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEE---EEecCCeeEEEEecCCCC--CCC-
Q 030131 5 VGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIR---LLNANYIKDFSFLGQADD--PLD- 78 (182)
Q Consensus 5 m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~---iIn~~~Ik~i~vl~~~~~--~~~- 78 (182)
|++...++++|+.|+|+|++|...+|+||+||..+++|+|.++++++.+.... ++|.+|++.++++.+... ++.
T Consensus 1 m~p~s~~vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~~s~~~P~~~~~~~~~~~~~~~~~e~~~~k~~fp~~~~ 80 (184)
T KOG4401|consen 1 MKPASATVAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTPSSNGKPNHAKFDIVINNNYSQLVESYLDKEAFPPAKS 80 (184)
T ss_pred CCCCcceeEEEEEEEecccccceeeeEEEEEEcccCeeEecccccCCCCccchhhHHHHHHHHHHHHHhcccccCCchhh
Confidence 78889999999999999999999999999999999999999996655444444 799999999988876541 111
Q ss_pred CCCCCCCHHHHH-HHHHHHHHHH-HHHHHHcCCCCCHHHHHHHHHHhhhcc-eEEcCCcEEEeeeEEEcCCCCCCCccCC
Q 030131 79 PKKCFLDLSRLQ-AREHLAVRQA-EADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEVRVSSPYLPESVSGG 155 (182)
Q Consensus 79 ~~l~~v~~~~l~-~r~~~ai~~~-~~~~~~~g~gvs~egQ~lFd~L~Kt~p-v~W~~~~IvV~d~V~I~pPY~~~n~~~~ 155 (182)
..+-++|++.+. .++..+.+.+ ....+..|+|||+|||+||+.|.||+| ++|.+++|+||++|.|.|||..+||.+.
T Consensus 81 qq~~~~~lnglr~~k~~~~~~~~~t~s~r~~~~gvS~egQ~lf~~l~Kti~D~~W~nkdI~Il~eV~v~~PY~ve~i~g~ 160 (184)
T KOG4401|consen 81 QQCFPVDLNGLRIEKELTKTEPALTKSLRMSNPGVSAEGQQLFRQLEKTIGDTKWVNKDILILKEVVVISPYVVEDIFGL 160 (184)
T ss_pred cccccccCchhHHHhhhhcccccccHhHhhcCCCcCHHHHHHHHHHHhhcCCceEeecCcEEEeeeeecCCceeeeeecc
Confidence 123356666555 4555555554 455556679999999999999999999 9999999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHHHHHhhh
Q 030131 156 TAAANERVKKVLEFERKRLQAR 177 (182)
Q Consensus 156 ~~~~l~rV~kIl~~~~~~~~~~ 177 (182)
+..+..+||||+++..+.++++
T Consensus 161 ~~aan~~v~kI~~~~~r~~~~~ 182 (184)
T KOG4401|consen 161 TKAANGQVQKILEKVSRTYESR 182 (184)
T ss_pred chhhhhHHHHHHHHHHhhhhhc
Confidence 8889999999999999998865
No 2
>PF09793 AD: Anticodon-binding domain; InterPro: IPR019181 Sm and Sm-like proteins of the Lsm (like Sm) domain family are generally involved in essential RNA-processing tasks []. All the LSM proteins are evolutionarily conserved in eukaryotes with an N-terminal Lsm domain to bind nucleic acids, followed by an as yet uncharacterised C-terminal region, some of which have a C-terminal methyltransferase domain. This entry represents the central region of approximately 100 residues, which is conserved from plants to humans and is frequently found in association with Lsm domain-containing proteins.
Probab=99.97 E-value=3.3e-32 Score=195.31 Aligned_cols=87 Identities=51% Similarity=0.777 Sum_probs=83.8
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhcc-eEEcCCcEEEeeeEEEcCCCCCCCcc---CC
Q 030131 80 KKCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLP-VRWDKTVIVVMNEVRVSSPYLPESVS---GG 155 (182)
Q Consensus 80 ~l~~v~~~~l~~r~~~ai~~~~~~~~~~g~gvs~egQ~lFd~L~Kt~p-v~W~~~~IvV~d~V~I~pPY~~~n~~---~~ 155 (182)
+|++||+++|++|+++++++++..++++|+|||++||+||++|+||+| |+|+|++|+|||+|+|+|||+++||+ ++
T Consensus 1 ~~~~l~i~~l~~r~~~ai~~~~~~~~~~~~~vs~egQ~lF~~l~Kt~~dv~W~g~~IiV~d~V~I~pPY~~~nv~~~~~~ 80 (91)
T PF09793_consen 1 PPPPLDIERLQKRLRKAIEEAKRKLSSIGPGVSPEGQKLFDALSKTIPDVRWDGKNIIVLDEVKISPPYKVENVSSLGGG 80 (91)
T ss_pred CCCcCCHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHhhCCCCEECCCeEEEeCceEEcCCCCccceeeCCCC
Confidence 478999999999999999999999999999999999999999999999 99999999999999999999999998 67
Q ss_pred ChhHHHHHHHH
Q 030131 156 TAAANERVKKV 166 (182)
Q Consensus 156 ~~~~l~rV~kI 166 (182)
+..+++|||||
T Consensus 81 ~~~al~~VkKI 91 (91)
T PF09793_consen 81 DSKALERVKKI 91 (91)
T ss_pred ChHHHhheecC
Confidence 88999999986
No 3
>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=99.90 E-value=7.2e-24 Score=166.36 Aligned_cols=145 Identities=19% Similarity=0.300 Sum_probs=47.6
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCCCCCCCCCCCCCHHHHHHH
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQADDPLDPKKCFLDLSRLQAR 92 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~~~~~~~l~~v~~~~l~~r 92 (182)
-+|+.|+|++.+ .++.|+|||+||.|..|||.+....+ ..++++|.+++|++++++.+.+.. ..++
T Consensus 15 yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~~-~~sv~~I~ghaVk~vevl~~~~~~------------~~e~ 80 (166)
T PF06372_consen 15 YVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQEDG-KRSVKVIMGHAVKSVEVLSEGDQE------------VPEK 80 (166)
T ss_dssp TTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TTS--EEEEEE-GGGEEEEEEEE---HH------------HHHH
T ss_pred hhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccCC-ceeEEEEEccceEEEEEccCCchh------------hHHH
Confidence 489999999999 99999999999999999998876644 578999999999999999975421 1111
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhh-hcceEEcC---CcEEEeeeEEEcCCCCCCCccCCChhHHHHHHHHHH
Q 030131 93 EHLAVRQAEADAQRIGVGVTTEAQNIFDALSK-TLPVRWDK---TVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLE 168 (182)
Q Consensus 93 ~~~ai~~~~~~~~~~g~gvs~egQ~lFd~L~K-t~pv~W~~---~~IvV~d~V~I~pPY~~~n~~~~~~~~l~rV~kIl~ 168 (182)
+..-........ ...+........|-.||.+ .+||.-+| +.++|.|.|+|.|||+++||+++|+..|.|||++|+
T Consensus 81 l~~~~~~~~~~~-~s~edl~~RK~~l~~wL~~N~ipV~E~g~~~~~l~V~gvvtI~pPY~~e~C~ssN~IIL~RVQ~Li~ 159 (166)
T PF06372_consen 81 LQHLFMPEESSG-YSPEDLEKRKESLKQWLEKNRIPVTEQGDPDGTLCVAGVVTIEPPYGPENCSSSNEIILSRVQKLIQ 159 (166)
T ss_dssp HHT-----------------------------------------------------------------------------
T ss_pred HHhccCCccccc-CCHHHHHHHHHHHHHHHHHCCCceEeecCCCCeEEEeeEEEECCCCChHhcCCccHHHHHHHHHHHH
Confidence 111101000000 0012334445678889998 77999994 469999999999999999999999999999999999
Q ss_pred HHHH
Q 030131 169 FERK 172 (182)
Q Consensus 169 ~~~~ 172 (182)
++..
T Consensus 160 ~~~~ 163 (166)
T PF06372_consen 160 NMPD 163 (166)
T ss_dssp ----
T ss_pred hCcc
Confidence 8753
No 4
>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=99.72 E-value=1.8e-17 Score=110.01 Aligned_cols=59 Identities=32% Similarity=0.558 Sum_probs=53.5
Q ss_pred CceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCC--CcceEEEEecCCeeEEE
Q 030131 10 EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSG--PRRNIRLLNANYIKDFS 68 (182)
Q Consensus 10 ~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~--~~~~~~iIn~~~Ik~i~ 68 (182)
++|++|+.|+|+|++|++++|+|+|||+.+++|+|+++++.+ +.+|++|||+++|++++
T Consensus 1 ~~f~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s~~~~~~~~dv~ivnls~~~dv~ 61 (61)
T cd01735 1 ECFSVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPSSSGKPNHADILLVNLSYVSEVE 61 (61)
T ss_pred CccccccEEEEEecCCceEEEEEEEecCCCcEEEEECccccCCCCcceEEEEEhhhEEecC
Confidence 479999999999999999999999999999999999876433 46899999999999985
No 5
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.79 E-value=0.00015 Score=52.41 Aligned_cols=64 Identities=11% Similarity=0.173 Sum_probs=52.9
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCC--------------CCcceEEEEecCCeeEEEEecCCCC
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKS--------------GPRRNIRLLNANYIKDFSFLGQADD 75 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~--------------~~~~~~~iIn~~~Ik~i~vl~~~~~ 75 (182)
.-+|++|++.+..+-.|+|.++..|+...+|+|..-... .....+-+++++-||+++|+.....
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~~ 82 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPPP 82 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-S
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCCC
Confidence 458999999999999999999999999999999764221 1246888999999999999987663
No 6
>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=96.72 E-value=0.0064 Score=39.69 Aligned_cols=54 Identities=20% Similarity=0.386 Sum_probs=40.1
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-----CCCcceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-----SGPRRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-----~~~~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|++.+|..+.|.+.+||...+ ++|..... .......-+|+++.|+.+
T Consensus 4 ~~g~~V~V~l~~g~~~~G~L~~~D~~~N-i~L~~~~~~~~~~~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 4 LVGKTVRVELKDGRVLEGVLVAFDKYMN-LVLDDVEETIKEGKKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred HCCCEEEEEECCCcEEEEEEEEECCCCC-EEECCEEEEecCCcEEECCeEEEECCEEEEE
Confidence 4799999999999999999999998774 45543311 112345678888888765
No 7
>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=96.39 E-value=0.013 Score=38.77 Aligned_cols=55 Identities=20% Similarity=0.440 Sum_probs=39.5
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCC--C----CcceEEEEecCCeeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKS--G----PRRNIRLLNANYIKDFS 68 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~--~----~~~~~~iIn~~~Ik~i~ 68 (182)
.+|++|+|.+.+|.+++|.+.+||.--+ |+|...... . ..-...+|+++.|..|.
T Consensus 6 ~~g~~V~V~l~~g~~~~G~L~~~D~~~N-l~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 6 LIGKRVRVELKNGRTYRGTLVSFDQFMN-LVLSDVTETIKNGPEKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp TTTSEEEEEETTSEEEEEEEEEEETTEE-EEEEEEEEEETTESEEEEEEEEEEEGGGEEEEE
T ss_pred hCCcEEEEEEeCCEEEEEEEEEeechhe-EEeeeEEEEECCCCcEeECcEEEEECCEEEEEE
Confidence 4699999999999999999999997444 555443211 1 11245688888888764
No 8
>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=96.23 E-value=0.026 Score=38.49 Aligned_cols=57 Identities=23% Similarity=0.369 Sum_probs=42.3
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC--CC---CcceEEEEecCCeeEEEEec
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK--SG---PRRNIRLLNANYIKDFSFLG 71 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~--~~---~~~~~~iIn~~~Ik~i~vl~ 71 (182)
+|++|.|++.+|..+.|.+.+||.-.|++ |..... .+ ..-..-+|+++.|..+..++
T Consensus 9 i~k~V~V~L~~g~~~~G~L~~~D~~mNlv-L~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 9 MDKKLSLKLNGNRKVSGILRGFDPFMNLV-LDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred CCCeEEEEECCCeEEEEEEEEEcccccEE-eccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 89999999999999999999999766654 433211 01 12245689999999887664
No 9
>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=95.98 E-value=0.044 Score=36.71 Aligned_cols=55 Identities=13% Similarity=0.237 Sum_probs=39.4
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC-CC---CcceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK-SG---PRRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~-~~---~~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|++.+|..++|++.+||.--+++.-.+... .+ ..-..-+|+++.|..|
T Consensus 8 ~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i 66 (68)
T cd01731 8 SLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFI 66 (68)
T ss_pred hcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEE
Confidence 4799999999999999999999998777665544211 11 1223457777777654
No 10
>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=95.88 E-value=0.04 Score=37.99 Aligned_cols=57 Identities=16% Similarity=0.184 Sum_probs=41.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---CC-----CC--cceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---KS-----GP--RRNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~~-----~~--~~~~~iIn~~~Ik~i~v 69 (182)
.+|.+|+|++.+|..+.|...|||...|+|.=.|.. .+ .. .-..-+|+++.|.++++
T Consensus 8 ~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 8 LLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 389999999999999999999999877766433321 00 11 12456888999988875
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=95.77 E-value=0.057 Score=36.70 Aligned_cols=55 Identities=15% Similarity=0.295 Sum_probs=39.2
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCCC---cceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSGP---RRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~~---~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|++.+|.+++|.+.+||.--+++.-.+.. .++. .-..-+|+++.|..|
T Consensus 12 ~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i 70 (72)
T PRK00737 12 ALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV 70 (72)
T ss_pred hCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEE
Confidence 489999999999999999999999866665544421 1111 122347888887765
No 12
>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=95.76 E-value=0.051 Score=36.37 Aligned_cols=55 Identities=16% Similarity=0.300 Sum_probs=39.0
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCCC---cceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSGP---RRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~~---~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|++.+|.+++|++.+||+--+++.=.+.. ..++ .-..-+|+++.|..|
T Consensus 8 ~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I 66 (67)
T cd01726 8 IIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYI 66 (67)
T ss_pred hCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEE
Confidence 489999999999999999999999766655433321 1111 123457888887765
No 13
>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=95.55 E-value=0.055 Score=37.38 Aligned_cols=58 Identities=21% Similarity=0.297 Sum_probs=42.4
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---CC--------C---CcceEEEEecCCeeEEEE
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---KS--------G---PRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~~--------~---~~~~~~iIn~~~Ik~i~v 69 (182)
.-+|++|.|++.+|..+.|.+.|||.-.|++.=.+.. .. . ..-..-+|+++.|.+|.|
T Consensus 7 ~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 7 QLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred HHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 3489999999999999999999999888876432210 00 0 112456889999888875
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=95.35 E-value=0.063 Score=35.40 Aligned_cols=56 Identities=18% Similarity=0.333 Sum_probs=38.8
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CC--CCCcceEEEEecCCeeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LK--SGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~--~~~~~~~~iIn~~~Ik~i~ 68 (182)
.+|++|.|++.+|.++.|.+.+||+--+++.=.+. .. .......-+|+++.|.-|.
T Consensus 6 ~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 6 LIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEe
Confidence 47999999999999999999999986665543322 11 0112234478888877653
No 15
>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=95.27 E-value=0.026 Score=43.84 Aligned_cols=50 Identities=16% Similarity=0.050 Sum_probs=40.5
Q ss_pred cEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131 16 CLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 16 ~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~ 68 (182)
..|++++.+|++|.|.|+.|++..+.| |- +.. ....+--.|.+.+|..++
T Consensus 30 ~pVrvv~~ng~~f~myV~gf~~~~n~i-L~-p~~-~~~~nRi~~plE~I~t~E 79 (165)
T PF03614_consen 30 IPVRVVSENGQVFCMYVSGFMSKENKI-LA-PDP-FKKENRIRLPLERISTIE 79 (165)
T ss_pred CceEEEecCCcEEEEEEeccCcccCEE-ec-cCC-CCCCceEEEEhHHhhhHh
Confidence 469999999999999999999999999 53 332 234466678899999887
No 16
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=95.26 E-value=0.091 Score=36.21 Aligned_cols=57 Identities=18% Similarity=0.294 Sum_probs=40.5
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC---CCCc-----ceEEEEecCCeeEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK---SGPR-----RNIRLLNANYIKDF 67 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~---~~~~-----~~~~iIn~~~Ik~i 67 (182)
.-.+|.+|.|++.+|.++.|.+.+||.--|++.-.+..- .+.. ...-+|+++.|.-|
T Consensus 13 ~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I 77 (79)
T COG1958 13 KKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLI 77 (79)
T ss_pred HHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEE
Confidence 345889999999999999999999998777665433211 1111 12567888888765
No 17
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=95.19 E-value=0.051 Score=37.19 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=27.0
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCC--CCeEEEEec
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRF--TNMLVIQEG 47 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~--~~~lvL~~~ 47 (182)
.+|..|.|+|.+|..|+|..-++++. .-.++|+.+
T Consensus 10 lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a 46 (77)
T PF14438_consen 10 LVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMA 46 (77)
T ss_dssp TTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEE
T ss_pred CcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEee
Confidence 48999999999999999999999996 466788775
No 18
>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=95.10 E-value=0.14 Score=35.28 Aligned_cols=56 Identities=13% Similarity=0.205 Sum_probs=44.0
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC---C------------CCCcceEEEEecCCeeEE
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL---K------------SGPRRNIRLLNANYIKDF 67 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~---~------------~~~~~~~~iIn~~~Ik~i 67 (182)
..+|+++.+.+..+-.++|.++.+|+...+|+|+.-. . .....++-+.+++-||++
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence 3589999999999999999999999999999996521 0 112346667777777765
No 19
>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=95.04 E-value=0.15 Score=34.26 Aligned_cols=55 Identities=18% Similarity=0.287 Sum_probs=37.9
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC-CCC---CcceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL-KSG---PRRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~-~~~---~~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|.+.+|.++.|.+.+||.--+++.=.+.. ..+ .....-+|+++.|.-|
T Consensus 9 ~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 9 LTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYI 67 (68)
T ss_pred cCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEE
Confidence 489999999999999999999999766554433321 111 1235567777776644
No 20
>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=94.21 E-value=0.47 Score=32.50 Aligned_cols=57 Identities=18% Similarity=0.275 Sum_probs=43.2
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc---ceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR---RNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~---~~~~iIn~~~Ik~i~v 69 (182)
..|++|.|.+.+|.+++|.+.+||.--++..-.+. ..++.. -.--+|+++.|..+.+
T Consensus 9 ~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~ 70 (76)
T cd01723 9 AQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRV 70 (76)
T ss_pred cCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEc
Confidence 47999999999999999999999998887765542 122222 1346799999998753
No 21
>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=94.08 E-value=0.37 Score=34.28 Aligned_cols=58 Identities=17% Similarity=0.153 Sum_probs=42.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC--CCC--CcceEEEEecCCeeEEEEe
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL--KSG--PRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~--~~~--~~~~~~iIn~~~Ik~i~vl 70 (182)
..|..|.|.+.+|.+++|.+.++|.--|+..-.+.. ..+ ....--+|+++.|+-|.+-
T Consensus 9 l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lP 70 (90)
T cd01724 9 LTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILP 70 (90)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcC
Confidence 479999999999999999999999877665544321 111 1224458999999988543
No 22
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.78 E-value=0.15 Score=44.95 Aligned_cols=62 Identities=15% Similarity=0.210 Sum_probs=51.8
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CC---C--------CCcceEEEEecCCeeEEEEecCCC
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LK---S--------GPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~---~--------~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
-||+.|.+....|=.|||.+|+.|..-.+|.|+.- .+ . ...+++-+.+++-||+|.|.+...
T Consensus 7 yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p~ 83 (361)
T KOG1073|consen 7 YIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETPA 83 (361)
T ss_pred cccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCcc
Confidence 48999999999999999999999999999999542 11 0 125689999999999999998543
No 23
>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=93.74 E-value=0.46 Score=33.02 Aligned_cols=57 Identities=9% Similarity=0.123 Sum_probs=41.5
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc----ceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR----RNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~----~~~~iIn~~~Ik~i~v 69 (182)
..|+.|.|.+.+|.+++|.+.++|+--++..-.+. ...+.. ..--+|+++.|+-|.+
T Consensus 9 l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~l 71 (81)
T cd01725 9 LVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQL 71 (81)
T ss_pred CCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEe
Confidence 47999999999999999999999987766554432 111111 1235899999998864
No 24
>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=93.59 E-value=0.54 Score=31.68 Aligned_cols=57 Identities=14% Similarity=0.256 Sum_probs=39.9
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEE
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFS 68 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~ 68 (182)
-..|+.|.|.+.+|.+++|++.++|.--++..-.+. ...+. ...--+|+++.|.-+.
T Consensus 7 ~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~ 67 (70)
T cd01721 7 EAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFI 67 (70)
T ss_pred hCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEE
Confidence 358999999999999999999999986654433331 11121 1234578888888664
No 25
>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=92.68 E-value=0.29 Score=33.37 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=29.0
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
++++|.|++.+|..+.|++-+||.-.|++.=.+
T Consensus 8 l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~ 40 (74)
T cd01727 8 LNKTVSVITVDGRVIVGTLKGFDQATNLILDDS 40 (74)
T ss_pred cCCEEEEEECCCcEEEEEEEEEccccCEEccce
Confidence 899999999999999999999999877665443
No 26
>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=92.58 E-value=0.3 Score=33.97 Aligned_cols=56 Identities=14% Similarity=0.174 Sum_probs=39.4
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec---CCCC---------CcceEEEEecCCeeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG---LKSG---------PRRNIRLLNANYIKDFS 68 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~---~~~~---------~~~~~~iIn~~~Ik~i~ 68 (182)
.+|++|.|++.+|..+.|++-+||.--|++.=.+- ..+. ..-..-+|+++.|..+.
T Consensus 10 ~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 10 YVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred hcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEe
Confidence 48999999999999999999999987776543331 1100 11245677887776654
No 27
>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=92.44 E-value=1.1 Score=30.94 Aligned_cols=56 Identities=11% Similarity=0.219 Sum_probs=39.8
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec-CCCCC---cceEEEEecCCeeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG-LKSGP---RRNIRLLNANYIKDFS 68 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~-~~~~~---~~~~~iIn~~~Ik~i~ 68 (182)
.+|+.|.|.+.+|.+++|.+.++|.--++..-.+. ..+++ ...--+|+++.|.-|.
T Consensus 17 l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~ 76 (78)
T cd01733 17 LQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVH 76 (78)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEE
Confidence 47999999999999999999999987765544332 11111 1234478888887664
No 28
>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=92.04 E-value=0.38 Score=32.97 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=28.4
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
.++++|.|++.+|..+.|.+-+||+-.+++.=.
T Consensus 10 ~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d 42 (74)
T cd01728 10 DLDKKVVVLLRDGRKLIGILRSFDQFANLVLQD 42 (74)
T ss_pred hcCCEEEEEEcCCeEEEEEEEEECCcccEEecc
Confidence 489999999999999999999999876665433
No 29
>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=91.83 E-value=0.32 Score=33.81 Aligned_cols=31 Identities=23% Similarity=0.397 Sum_probs=27.6
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLV 43 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lv 43 (182)
..+++|.|++.+|..+.|.+-+||.-.+++.
T Consensus 9 ~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL 39 (82)
T cd01730 9 SLDERVYVKLRGDRELRGRLHAYDQHLNMIL 39 (82)
T ss_pred hCCCEEEEEECCCCEEEEEEEEEccceEEec
Confidence 4789999999999999999999998776653
No 30
>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=91.73 E-value=0.55 Score=30.96 Aligned_cols=38 Identities=21% Similarity=0.363 Sum_probs=32.5
Q ss_pred eccEEEEEecCC-CEEEEEEEEEeCCCCeEEEEecCCCC
Q 030131 14 VGCLLSIKTTLG-DEFDGQVMAFDRFTNMLVIQEGLKSG 51 (182)
Q Consensus 14 vG~~V~vtt~~~-~~~~G~V~~~D~~~~~lvL~~~~~~~ 51 (182)
+|+.|+|..-.. .+|+|.|-..|+.+.+|+|..+..++
T Consensus 5 iGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~~ng 43 (62)
T cd01737 5 LGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPFHNG 43 (62)
T ss_pred cceEEEEecCCceEEEEEEEEEeCccceEEEEeecccCC
Confidence 789999986555 69999999999999999998876654
No 31
>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=90.54 E-value=0.56 Score=32.30 Aligned_cols=55 Identities=27% Similarity=0.419 Sum_probs=38.3
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCCC---CcceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKSG---PRRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~~---~~~~~~iIn~~~Ik~i 67 (182)
.+|++|.|++.+|.++.|.+-+||.--|++.=.+. ...+ .....-+|+++.|.-|
T Consensus 11 ~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i 72 (76)
T cd01732 11 CIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICML 72 (76)
T ss_pred hCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEE
Confidence 47999999999999999999999987776532221 0111 1224457788777655
No 32
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=89.90 E-value=0.077 Score=36.28 Aligned_cols=66 Identities=17% Similarity=0.331 Sum_probs=46.1
Q ss_pred CCCCCCCCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC--CC---CcceEEEEecCCeeEEE
Q 030131 2 EGQVGGSGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK--SG---PRRNIRLLNANYIKDFS 68 (182)
Q Consensus 2 ~~~m~~~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~--~~---~~~~~~iIn~~~Ik~i~ 68 (182)
+++|.++-....+|..|.|+.+.|-.+.|...|.|-=- .|.|..... ++ +...=-+|+++.|-.|.
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgym-NiaLe~tee~~ngql~n~ygdaFirGnnVlyIs 73 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYM-NIALESTEEYVNGQLKNKYGDAFIRGNNVLYIS 73 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHH-HHHHHHHHHHhcCcccccccceeeccccEEEEE
Confidence 57787777788899999999999999999999999532 344533311 12 22334577777766554
No 33
>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=89.58 E-value=0.3 Score=34.63 Aligned_cols=31 Identities=29% Similarity=0.377 Sum_probs=27.1
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeE
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNML 42 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~l 42 (182)
...|++|.|++..|..+.|++-+||.--+++
T Consensus 11 ~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlv 41 (87)
T cd01720 11 VKNNTQVLINCRNNKKLLGRVKAFDRHCNMV 41 (87)
T ss_pred HcCCCEEEEEEcCCCEEEEEEEEecCccEEE
Confidence 3358999999999999999999999877655
No 34
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=88.15 E-value=1.8 Score=32.16 Aligned_cols=71 Identities=20% Similarity=0.271 Sum_probs=50.5
Q ss_pred CCCCCCCceeeccEEEEEecCC-------CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 4 QVGGSGEEFAVGCLLSIKTTLG-------DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 4 ~m~~~~~~~~vG~~V~vtt~~~-------~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
++...-+.|.+|..|+|++... +.|+|.|.+..- ...+++|+.-....+---.--++...|++|+|+....
T Consensus 11 ~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~k 90 (113)
T PF01245_consen 11 QIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRGK 90 (113)
T ss_dssp TCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEBE
T ss_pred HhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEecc
Confidence 4566778999999999998644 489999999985 4566777664331122223346778999999998653
No 35
>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=88.10 E-value=1.5 Score=27.23 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=26.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
++|..|++.+ .++.++|.+..+|+. +.|+|++.
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~-G~L~v~~~ 33 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDD-GALLVRTE 33 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETT-SEEEEEET
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCC-CEEEEEEC
Confidence 3699999999 888999999999964 55666653
No 36
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=85.50 E-value=6.3 Score=29.31 Aligned_cols=71 Identities=15% Similarity=0.193 Sum_probs=50.4
Q ss_pred CCCCCCCceeeccEEEEEecCC-------CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 4 QVGGSGEEFAVGCLLSIKTTLG-------DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 4 ~m~~~~~~~~vG~~V~vtt~~~-------~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
+|...-+.|.+|..|+|+.... +.|+|.|.+..- .+.+++|+.-...-+---.--++...|++|+|+....
T Consensus 11 ~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~~~k 90 (113)
T TIGR01024 11 QLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLHSPNIDSIEVVRRGK 90 (113)
T ss_pred HhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcCCCccceEEEEEeCc
Confidence 4555678899999999998653 379999999983 4556788765442233333345678899999997654
No 37
>CHL00084 rpl19 ribosomal protein L19
Probab=84.75 E-value=8.8 Score=28.72 Aligned_cols=71 Identities=13% Similarity=0.227 Sum_probs=49.9
Q ss_pred CCCCCCCceeeccEEEEEe--cCCC-----EEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 4 QVGGSGEEFAVGCLLSIKT--TLGD-----EFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 4 ~m~~~~~~~~vG~~V~vtt--~~~~-----~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
||...-+.|.+|..|+|+. ..|. .|+|.|.+..- .+.+++|+.-...-+---.--++...|.+|+|+....
T Consensus 15 ~~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gk 94 (117)
T CHL00084 15 FLKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFLLHSPKLASIEVLRRSK 94 (117)
T ss_pred HhhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEecCCCccceEEEEEeCc
Confidence 4555678899999999998 3443 79999999863 4556777765432223333345778899999998654
No 38
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=84.08 E-value=5 Score=27.63 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=37.7
Q ss_pred eeccEEEEEecCC---CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEE
Q 030131 13 AVGCLLSIKTTLG---DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDF 67 (182)
Q Consensus 13 ~vG~~V~vtt~~~---~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i 67 (182)
.-+..|.++.-.+ .+++|.|..+|+..+.|.+.... .....|+.+.|.+|
T Consensus 40 ~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~-----~~~~~I~~~~I~~I 92 (92)
T PF08863_consen 40 QENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKDED-----GETEKIPFDDIIDI 92 (92)
T ss_pred cCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCC-----CCEEEEEhhhEEEC
Confidence 3467888887554 58889999999999999998632 35566676776653
No 39
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=83.09 E-value=1.6 Score=31.19 Aligned_cols=61 Identities=13% Similarity=0.178 Sum_probs=44.4
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCC----CCcceEEEEecCCeeEEEEecCCC
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKS----GPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~----~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
++..|.|-|.+|+.+-|.+-+||..++.++=.+. +.. .-.--+.||++.-+..+--+++..
T Consensus 9 ~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~ 77 (96)
T KOG1784|consen 9 MNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEEL 77 (96)
T ss_pred hhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhh
Confidence 5789999999999999999999998887764432 111 112247788888887776665543
No 40
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=82.89 E-value=8.5 Score=28.74 Aligned_cols=71 Identities=15% Similarity=0.190 Sum_probs=50.3
Q ss_pred CCCCCCCceeeccEEEEEec--CC-----CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 4 QVGGSGEEFAVGCLLSIKTT--LG-----DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 4 ~m~~~~~~~~vG~~V~vtt~--~~-----~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
+|...-+.|.+|..|+|+.. .| +.|+|.|.+..- ...+++|+.-...-+---.--++...|++|+|+....
T Consensus 11 ~~~~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~gk 90 (116)
T PRK05338 11 QLRKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHSPRIDSIEVVRRGK 90 (116)
T ss_pred HhhcCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCCCcccEEEEEEecc
Confidence 45556788999999999875 34 379999999983 3556778765432233333345678899999997653
No 41
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=79.75 E-value=15 Score=24.30 Aligned_cols=46 Identities=20% Similarity=0.371 Sum_probs=34.1
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~ 68 (182)
...|.+-..+|..++|.|.+||. -++.|... + + -.+|.-++|+-|.
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~--ftVll~~~---g-~--qqLIYKhAISTI~ 56 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDN--FTVLLESD---G-K--QQLVYKHAISTIT 56 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcc--eEEEEEEC---C-c--EEEEEeeeeEEEe
Confidence 35688889999999999999995 34444432 1 2 2578889998875
No 42
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=79.45 E-value=13 Score=24.62 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=33.1
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~ 68 (182)
+..|.|-..+|-.++|.|-+||. -++.|... + .-.+|.-++|+-|.
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~--ftVll~~~---g---~qqLIYKhAISTI~ 60 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDN--FTVLLESQ---G---KQQLIYKHAISTIT 60 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEee--eEEEEEEC---C---cEEEEEEEEEEEEc
Confidence 45788889999999999999995 33444431 2 22588888888663
No 43
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=76.71 E-value=2.1 Score=29.56 Aligned_cols=55 Identities=27% Similarity=0.445 Sum_probs=38.9
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec----CCCC----CcceEEEEecCCeeE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG----LKSG----PRRNIRLLNANYIKD 66 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~----~~~~----~~~~~~iIn~~~Ik~ 66 (182)
+-.+|+++.|....+.++.|++..||---+++. ..- ..+. .+.+-.++|++.|.=
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~VNmvL-eDvtEye~~~egr~~tk~~~iLLnGNni~m 75 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVL-EDVTEYEITPEGRRMTKLDQILLNGNNITM 75 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHHHHHH-HhhhheeeCCCcceeeeeeeeeecCCcEEE
Confidence 456999999999999999999999997666653 211 0111 234556777777763
No 44
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=76.27 E-value=20 Score=24.03 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=34.9
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDF 67 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i 67 (182)
+|++|.|.|..|.. +|.+-...| .-|+|... ...-+|+.+.|.++
T Consensus 20 iG~~vvV~T~~g~v-~G~L~~V~p--DhIvl~~~------~~~~~IR~~~IV~v 64 (66)
T PF10842_consen 20 IGQRVVVQTTRGSV-RGILVDVKP--DHIVLEEN------GTPFFIRIAQIVWV 64 (66)
T ss_pred cCCEEEEEEcCCcE-EEEEEeecC--CEEEEEeC------CcEEEEEeeeEEEE
Confidence 89999999976655 999998887 66788753 24567777888766
No 45
>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=72.96 E-value=5.9 Score=27.60 Aligned_cols=54 Identities=13% Similarity=0.251 Sum_probs=30.4
Q ss_pred ccEEEEEecCCCEEEEEEEEE--e-CCCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 15 GCLLSIKTTLGDEFDGQVMAF--D-RFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~--D-~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
+..|+++..+|+.++|.-... + .....|+|... ..-+-|.++.|.+++++.+.+
T Consensus 17 ~~~v~L~l~dG~~~~g~A~dt~~~~~k~E~L~l~~~------~~~~~i~Ld~I~~~~al~~nP 73 (80)
T PF07073_consen 17 RYPVKLTLKDGEQIEGKALDTRTNAKKEECLVLEQD------GGEQEIRLDQIASMSALTDNP 73 (80)
T ss_dssp TT-EEEE-TTT--EEESS-EEE---SSS-EEEEEET------TEEEEESTT--SEEE----ET
T ss_pred CCeEEEEEeCCCEEEEEEEEEEEecCceEEEEEecC------CcEEEEEhhheeeeeecCCCC
Confidence 468999999999999974322 2 44567888763 245788999999999887643
No 46
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=70.76 E-value=7.8 Score=26.55 Aligned_cols=33 Identities=21% Similarity=0.503 Sum_probs=29.2
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
.|+.|.|+..-|+++.|++.+.|.=-++....+
T Consensus 17 ~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~ 49 (79)
T KOG3482|consen 17 TGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANA 49 (79)
T ss_pred cCCeEEEEEecCcEEEEEEEEecchhheehhhh
Confidence 789999999999999999999998777766654
No 47
>PRK14638 hypothetical protein; Provisional
Probab=69.56 E-value=24 Score=27.31 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=35.8
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v 69 (182)
.+|..|+|++..++.++|.+-.+|. ..++|... +. . .-|+.+.|+...+
T Consensus 98 ~~G~~v~V~~~~~k~~~G~L~~~~~--~~i~l~~~---~~--~-~~i~~~~I~~a~l 146 (150)
T PRK14638 98 FTGKLAKIVTKDGKTFIGRIESFVD--GTITISDE---KE--K-YEINIDDVKRANL 146 (150)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeC--CEEEEEEC---Cc--E-EEEEhHHcceEEE
Confidence 3899999999999999999999985 45666531 11 2 4457777776654
No 48
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=69.40 E-value=8.5 Score=27.15 Aligned_cols=60 Identities=20% Similarity=0.348 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHhhhcceEEcCCcEEEeeeEEEcCCCCCCC-----------ccCCChhHHHHHHHHHHHHHHHHhhh
Q 030131 112 TTEAQNIFDALSKTLPVRWDKTVIVVMNEVRVSSPYLPES-----------VSGGTAAANERVKKVLEFERKRLQAR 177 (182)
Q Consensus 112 s~egQ~lFd~L~Kt~pv~W~~~~IvV~d~V~I~pPY~~~n-----------~~~~~~~~l~rV~kIl~~~~~~~~~~ 177 (182)
+...++|-.+++-.+|+.|+++. -.|.=|++... |.+.++..|++++.||..+-.+...+
T Consensus 11 ~ryl~qLc~Hf~hk~~v~~d~~~------g~i~f~~G~~~l~a~~~~L~l~vea~~~~~L~~~~~vv~~HL~rFa~r 81 (89)
T PF09981_consen 11 SRYLKQLCKHFAHKFEVEWDEDS------GRITFPFGTCTLSAEPDALTLRVEAPDAEALARLEDVVARHLERFAFR 81 (89)
T ss_dssp HHHHHHHHHHTTTSSEEEE-SSE------EEEE-SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTSTT
T ss_pred HHHHHHHHHHhcCCCceEEcCCc------eEEEeCCEEEEEEeCCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHhcc
Confidence 34456677777777899999863 34444555432 23567899999999999998876433
No 49
>PRK14632 hypothetical protein; Provisional
Probab=69.11 E-value=27 Score=27.70 Aligned_cols=59 Identities=10% Similarity=0.166 Sum_probs=40.3
Q ss_pred eeccEEEEEecC-------CCEEEEEEEEEeCCCCeEEEEecCCC--CCcceEEEEecCCeeEEEEecCC
Q 030131 13 AVGCLLSIKTTL-------GDEFDGQVMAFDRFTNMLVIQEGLKS--GPRRNIRLLNANYIKDFSFLGQA 73 (182)
Q Consensus 13 ~vG~~V~vtt~~-------~~~~~G~V~~~D~~~~~lvL~~~~~~--~~~~~~~iIn~~~Ik~i~vl~~~ 73 (182)
.+|..|+|++.. ...++|.+..+|. +.|+|....++ .......-|..+.|+...+.-+.
T Consensus 96 ~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~--~~i~l~~~~~~~~~~~~~~~~i~~~~I~ka~l~~~f 163 (172)
T PRK14632 96 YVGRQIELTLIDPTPEWPGRRKFRGELLAVEG--DTVVLRPEGAPAPEAEEAVLRTSWQGVRKANLIHVF 163 (172)
T ss_pred hCCCEEEEEEeccccccCCceEEEEEEEEEeC--CEEEEEEcCcccccCCceeEEEEhHHccEEEEEEEc
Confidence 389999999865 4699999999985 45666543221 11112345788999988776655
No 50
>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=69.00 E-value=24 Score=22.86 Aligned_cols=36 Identities=17% Similarity=0.455 Sum_probs=26.9
Q ss_pred CceeeccEEEEEecCCCEE-EEEEEEEeCCCCeEEEE
Q 030131 10 EEFAVGCLLSIKTTLGDEF-DGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 10 ~~~~vG~~V~vtt~~~~~~-~G~V~~~D~~~~~lvL~ 45 (182)
-.|..|..|.+.=..+..+ +|.|..||+.++.=.+.
T Consensus 4 ~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~ 40 (55)
T PF09465_consen 4 RKFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVL 40 (55)
T ss_dssp SSS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEE
T ss_pred ccccCCCEEEEECCCCCcEEEEEEEEecccCceEEEE
Confidence 5688999999998777655 99999999988876554
No 51
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=68.68 E-value=37 Score=25.05 Aligned_cols=60 Identities=15% Similarity=0.290 Sum_probs=40.5
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCC--cceEEEEecCCeeEEEEecCC
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGP--RRNIRLLNANYIKDFSFLGQA 73 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~--~~~~~iIn~~~Ik~i~vl~~~ 73 (182)
+-|+-|.|.|..|++|.|.+.-.+..-|.-.=... ...+. .-+--+|+++.|+=+ |+++.
T Consensus 13 aqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFl-vlPdm 76 (119)
T KOG3172|consen 13 AQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFL-VLPDM 76 (119)
T ss_pred ccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEE-ECchH
Confidence 35899999999999999999988866554322111 11121 224468999999844 66654
No 52
>PRK02001 hypothetical protein; Validated
Probab=64.87 E-value=40 Score=26.20 Aligned_cols=32 Identities=19% Similarity=0.346 Sum_probs=26.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
.+|..|+|++..+..++|.+..+|.. .++|..
T Consensus 88 ~~G~~v~V~l~~~~~~~G~L~~~~~~--~i~l~~ 119 (152)
T PRK02001 88 NIGRELEVLTKNGKKIEGELKSADEN--DITLEV 119 (152)
T ss_pred hCCCEEEEEECCCCEEEEEEEEEeCC--EEEEEE
Confidence 38999999999899999999999964 455543
No 53
>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=64.87 E-value=45 Score=23.26 Aligned_cols=57 Identities=14% Similarity=0.047 Sum_probs=41.6
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v 69 (182)
..|..|.+++..+.++.|+.-++|+....+.+..-..|-+...--+++++-|.++..
T Consensus 22 ~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 22 MVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLGVQPEALLRCSDVISISF 78 (80)
T ss_dssp CTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTTEEEEEEEEGGGEEEEEE
T ss_pred hcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcccChhheeecCCEEEEEe
Confidence 368999999999999999999999977777665544444556667888887777653
No 54
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=63.08 E-value=49 Score=23.05 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=34.8
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
+..|.|-.++|-.++|.|.+||. -++.|... + .-.+|.-++|+-|..-
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~--ftVll~~~---g---kqqLIYKHAISTI~p~ 66 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDN--FVVLLRNT---G---KSQLVYKHAISTVVPA 66 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEcc--EEEEEEEC---C---cEEEEEEeeeEEEecC
Confidence 45788889999999999999994 33444432 2 1258889999987633
No 55
>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=60.94 E-value=47 Score=25.00 Aligned_cols=32 Identities=22% Similarity=0.548 Sum_probs=23.8
Q ss_pred eccEEEEEec---CC-CEEEEEEEEEeCCCCeEEEEec
Q 030131 14 VGCLLSIKTT---LG-DEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 14 vG~~V~vtt~---~~-~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
+|..|+|++. .| ..++|.+..++. +.++|...
T Consensus 86 iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~ 121 (141)
T PF02576_consen 86 IGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITLEVE 121 (141)
T ss_dssp -SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEEEEE
T ss_pred cCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEEEEC
Confidence 8999999983 33 689999999998 66666543
No 56
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=60.88 E-value=65 Score=24.03 Aligned_cols=67 Identities=13% Similarity=0.203 Sum_probs=42.4
Q ss_pred CCCceeeccEEEEEe--cCC-----CEEEEEEEEEeC--CCCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 8 SGEEFAVGCLLSIKT--TLG-----DEFDGQVMAFDR--FTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 8 ~~~~~~vG~~V~vtt--~~~-----~~~~G~V~~~D~--~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
.-++|.+|..|++.. ..| +.|+|.|.+.+- .+.+.++..-+..-+---.=-++...|.+|+|+....
T Consensus 17 ~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~rrGk 92 (115)
T COG0335 17 DIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPLHSPLIESIEVVRRGK 92 (115)
T ss_pred hCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeecCCCceeEEEEEecCc
Confidence 356788888777654 334 589999999995 3444444433221122223346778899999998764
No 57
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=60.18 E-value=50 Score=23.50 Aligned_cols=60 Identities=8% Similarity=0.078 Sum_probs=42.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCc----ceEEEEecCCeeEEEEecC
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPR----RNIRLLNANYIKDFSFLGQ 72 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~----~~~~iIn~~~Ik~i~vl~~ 72 (182)
.||+.|.|...+|-.+.|++-+.|+--|+=.+... ....-+ -..-+|+++-|+-+++-++
T Consensus 10 lvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 10 LVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred hcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence 48999999999999999999999987666444332 111111 1335788888888876544
No 58
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=59.07 E-value=52 Score=25.31 Aligned_cols=51 Identities=16% Similarity=0.201 Sum_probs=35.3
Q ss_pred eeccEEEEEe----cCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131 13 AVGCLLSIKT----TLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt----~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v 69 (182)
.+|..|+|++ ..+..++|.+..+|. +.++|....+ . ...-|+.+.|+...+
T Consensus 96 ~~G~~v~V~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~~~---~-~~~~i~~~~I~~a~l 150 (154)
T PRK00092 96 FIGREVKVKLYEPIDGRKKFQGILLAVDG--ETVTLEVEGK---E-KEVEIPLDNIAKARL 150 (154)
T ss_pred hCCCeEEEEEEcccCCceEEEEEEEEeeC--CEEEEEECCC---e-EEEEEEHHHcceEEE
Confidence 3899999997 455799999999998 4466664322 1 234467777776654
No 59
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.39 E-value=39 Score=26.40 Aligned_cols=32 Identities=22% Similarity=0.388 Sum_probs=27.0
Q ss_pred eeccEEEEEe----cCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 13 AVGCLLSIKT----TLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 13 ~vG~~V~vtt----~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
.+|..|+|+| ...+.++|.|..+|..+ +++..
T Consensus 97 ~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~--v~~~~ 132 (153)
T COG0779 97 FIGEKVKVKLRLPIEGRKKFEGKIVAVDGET--VTLEV 132 (153)
T ss_pred hcCcEEEEEEecccCCceEEEEEEEEEcCCe--EEEEE
Confidence 4899999999 67789999999999866 66654
No 60
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=57.28 E-value=62 Score=22.40 Aligned_cols=48 Identities=23% Similarity=0.262 Sum_probs=35.8
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
+..|+|=..+|-..+|.|-+|| +..+|..... --.+|.-|+|+-+..-
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD---~f~VlL~~~g-----~qqlVYKHAISTi~p~ 66 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFD---NFVVLLKNTG-----KQQLVYKHAISTIVPS 66 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeee---eEEEEEEcCC-----eeEEEEeeeeeEEccc
Confidence 5688999999999999999999 4555543221 2368888999887543
No 61
>PRK14640 hypothetical protein; Provisional
Probab=55.77 E-value=63 Score=24.95 Aligned_cols=51 Identities=18% Similarity=0.247 Sum_probs=36.2
Q ss_pred eeccEEEEEec----CCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131 13 AVGCLLSIKTT----LGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG 71 (182)
Q Consensus 13 ~vG~~V~vtt~----~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~ 71 (182)
.+|..|+|++. ....++|.+..+|. ..++|....+ . .-|+.+-|+...+..
T Consensus 95 ~~G~~v~V~l~~~~~~~k~~~G~L~~v~~--~~v~l~~~~~-----~-~~i~~~~I~ka~l~~ 149 (152)
T PRK14640 95 YVGQEAAVTLRMATNNRRKFKGVIKAVQG--DMITLTVDGK-----D-EVLAFTNIQKANIVP 149 (152)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEEeC--CEEEEEECCe-----E-EEEEhHHeeeEEEec
Confidence 38999999983 45899999999986 4566654211 2 345778888776653
No 62
>PRK14639 hypothetical protein; Provisional
Probab=54.28 E-value=29 Score=26.49 Aligned_cols=50 Identities=22% Similarity=0.323 Sum_probs=34.3
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v 69 (182)
+|..|+|++..++.++|.+..+|.. .++|..... + .-.-|+.+.|+...+
T Consensus 87 ~G~~v~v~l~~~~~~~G~L~~~~~~--~i~l~~~~~-~---~~~~i~~~~I~ka~l 136 (140)
T PRK14639 87 IGELVKITTNEKEKFEGKIVSVDDE--NITLENLEN-K---EKTTINFNDIKKAKT 136 (140)
T ss_pred CCCEEEEEECCCcEEEEEEEEEeCC--EEEEEEccC-C---cEEEEEhHHeeeEEE
Confidence 8999999998889999999999974 444432111 1 113456677766554
No 63
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=53.53 E-value=29 Score=18.10 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=21.4
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeC
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDR 37 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~ 37 (182)
+..|..|+|+.-...-..|.|..+|.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 56899999998777788899888774
No 64
>PF14894 Lsm_C: Lsm C-terminal; PDB: 1M5Q_1.
Probab=52.49 E-value=65 Score=21.51 Aligned_cols=50 Identities=30% Similarity=0.429 Sum_probs=33.1
Q ss_pred HHHHHhh---hcc--eEEcC--CcEEEeeeEEEcCCCCCCCc-cCCChhHHHHHHHHHHHHHHH
Q 030131 118 IFDALSK---TLP--VRWDK--TVIVVMNEVRVSSPYLPESV-SGGTAAANERVKKVLEFERKR 173 (182)
Q Consensus 118 lFd~L~K---t~p--v~W~~--~~IvV~d~V~I~pPY~~~n~-~~~~~~~l~rV~kIl~~~~~~ 173 (182)
+-+.|.| .+| |+.-. ..|+|+|.|+++ ++- -|+. ...+||..+.+.|-++
T Consensus 4 Fa~~~~r~l~l~p~~VK~~eea~vV~V~drirVs-----e~GVEGsG-PlAerv~~ly~eyi~~ 61 (64)
T PF14894_consen 4 FAEYLERELNLFPGMVKVYEEANVVVVMDRIRVS-----ENGVEGSG-PLAERVYDLYNEYIEK 61 (64)
T ss_dssp HHHHHHH---HSTTTEEEETTTTEEEETTTEEEE-----TTEEE--S-HHHHHHHHHHHHHHH-
T ss_pred HHHHHHHhcccCccceEEeccCCEEEEeeeEEEe-----ccccccCC-hHHHHHHHHHHHHHHh
Confidence 4456666 556 76644 579999999987 333 3444 4669999999888764
No 65
>PRK14644 hypothetical protein; Provisional
Probab=51.97 E-value=62 Score=24.62 Aligned_cols=31 Identities=10% Similarity=0.343 Sum_probs=25.8
Q ss_pred eeccEEEEEecCC----CEEEEEEEEEeCCCCeEEEE
Q 030131 13 AVGCLLSIKTTLG----DEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 13 ~vG~~V~vtt~~~----~~~~G~V~~~D~~~~~lvL~ 45 (182)
.+|..|+|++... +.++|.+..+|. +.++|.
T Consensus 83 ~~G~~v~V~l~~~~~~~~~~~G~L~~v~~--~~i~l~ 117 (136)
T PRK14644 83 HIGEIIDVSLNKEVNKTDFITGELLENNP--ETITLK 117 (136)
T ss_pred hCCCeEEEEEccCcCCeEEEEEEEEEEeC--CEEEEE
Confidence 4899999998766 899999999997 456664
No 66
>PRK10898 serine endoprotease; Provisional
Probab=51.58 E-value=37 Score=29.71 Aligned_cols=33 Identities=15% Similarity=0.268 Sum_probs=29.3
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
...+.|++.+|.++.++|.++|+.+.+-+|+..
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 357889999999999999999999999888764
No 67
>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=51.27 E-value=18 Score=23.91 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=20.1
Q ss_pred CEEEEEEEEEeCCCCeEEEEecC
Q 030131 26 DEFDGQVMAFDRFTNMLVIQEGL 48 (182)
Q Consensus 26 ~~~~G~V~~~D~~~~~lvL~~~~ 48 (182)
...+|.|-.+|+.+.+|+|..+.
T Consensus 3 ~~veG~I~~id~~~~titLdDGk 25 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDDGK 25 (61)
T ss_pred ccceEEEEEEcCCceEEEecCCC
Confidence 35799999999999999998753
No 68
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=48.72 E-value=1e+02 Score=23.73 Aligned_cols=29 Identities=14% Similarity=0.152 Sum_probs=25.1
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCe
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNM 41 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~ 41 (182)
-||+.|.+++.+|+.++|.|-+.....+.
T Consensus 90 lVGk~V~~~~~~g~~~tG~V~~V~~~~g~ 118 (142)
T PRK09618 90 LIGKEVEWEGEDGEIVSGTVTSVKQKDGD 118 (142)
T ss_pred HhCCEEEEEeCCCCEEEEEEEEEEEcCCc
Confidence 58999999999999999999998865554
No 69
>PRK14636 hypothetical protein; Provisional
Probab=47.75 E-value=60 Score=25.82 Aligned_cols=52 Identities=17% Similarity=0.201 Sum_probs=35.7
Q ss_pred eeccEEEEEec---CC-CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131 13 AVGCLLSIKTT---LG-DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG 71 (182)
Q Consensus 13 ~vG~~V~vtt~---~~-~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~ 71 (182)
.+|..|+|++. .| +.++|.+..+|.. .++|.... +. . .-|+.+-|+...+.-
T Consensus 96 ~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~--~v~l~~~~--~~--~-~~i~~~~I~kA~l~~ 151 (176)
T PRK14636 96 WAGHEARIALSEPLDGRKQFRGELKGIDGD--TVTIADNK--AG--E-VILPFAAIESAKLIL 151 (176)
T ss_pred hCCCeEEEEEecccCCeEEEEEEEEEEeCC--EEEEEEcC--Cc--E-EEEEhHHcceEEEec
Confidence 38999999986 45 6999999999874 45554311 11 2 356777777776553
No 70
>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=47.25 E-value=47 Score=22.96 Aligned_cols=50 Identities=16% Similarity=0.266 Sum_probs=30.3
Q ss_pred EEEEEec--CCCEEEEEEEEEeCCCCeEEEEecCC---CC---CcceEEEEecCCeeEE
Q 030131 17 LLSIKTT--LGDEFDGQVMAFDRFTNMLVIQEGLK---SG---PRRNIRLLNANYIKDF 67 (182)
Q Consensus 17 ~V~vtt~--~~~~~~G~V~~~D~~~~~lvL~~~~~---~~---~~~~~~iIn~~~Ik~i 67 (182)
+|.|... .|..++|.+-+||.--|++ |.+... .+ ..-..-+|+++.|.-|
T Consensus 20 ~V~V~l~~~~g~~~~G~L~gfD~~mNlv-L~d~~E~~~~~~~~~~lG~iliRGnnV~~I 77 (79)
T cd01718 20 RVQIWLYEQTDLRIEGVIIGFDEYMNLV-LDDAEEVHLKTKTRKPLGRILLKGDNITLI 77 (79)
T ss_pred EEEEEEEeCCCcEEEEEEEEEccceeEE-EcCEEEEecCCceEeEcCcEEEeCCEEEEE
Confidence 5555554 8899999999999877554 433211 01 1123357777766543
No 71
>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=47.16 E-value=47 Score=28.99 Aligned_cols=32 Identities=16% Similarity=0.326 Sum_probs=28.4
Q ss_pred cEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 16 CLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 16 ~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
..+.|++.+|..+.++|..+|+.+.+-+|+-.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 36888899999999999999999999888764
No 72
>PRK14641 hypothetical protein; Provisional
Probab=46.52 E-value=72 Score=25.34 Aligned_cols=53 Identities=19% Similarity=0.213 Sum_probs=32.0
Q ss_pred eccEEEEEecC----CCEEEEEEEEEe---CCCCeEEEEecCCC--C--CcceEEEEecCCeeE
Q 030131 14 VGCLLSIKTTL----GDEFDGQVMAFD---RFTNMLVIQEGLKS--G--PRRNIRLLNANYIKD 66 (182)
Q Consensus 14 vG~~V~vtt~~----~~~~~G~V~~~D---~~~~~lvL~~~~~~--~--~~~~~~iIn~~~Ik~ 66 (182)
+|..|+|+|.. ...++|.+..++ .....++|...... + .....+-|..+.|+.
T Consensus 103 ~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~v~~ 166 (173)
T PRK14641 103 VGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPEQKKKKGKQEETENITLELDAVIR 166 (173)
T ss_pred CCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEeccccccccCCCCceEEEEhHHccc
Confidence 89999999865 358999999997 11334544333211 1 113445556655554
No 73
>PRK10942 serine endoprotease; Provisional
Probab=45.29 E-value=85 Score=28.73 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=28.6
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
+..+.|++.+|.++.++|..+|+.+.+-+|+-
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35688999999999999999999999999865
No 74
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=45.01 E-value=52 Score=23.34 Aligned_cols=53 Identities=19% Similarity=0.204 Sum_probs=33.8
Q ss_pred cEEEEEecCC--CEEEEEEEEEeCCCCeEEEEecC---CC--CCcceEEEEecCCeeEEE
Q 030131 16 CLLSIKTTLG--DEFDGQVMAFDRFTNMLVIQEGL---KS--GPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 16 ~~V~vtt~~~--~~~~G~V~~~D~~~~~lvL~~~~---~~--~~~~~~~iIn~~~Ik~i~ 68 (182)
.+|.|.+.++ ..++|.+-+||.--|++.=.+.. .. ......-+|+++.|..|.
T Consensus 27 ~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~ 86 (89)
T PTZ00138 27 TRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIM 86 (89)
T ss_pred cEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEE
Confidence 4778887664 78999999999887655433311 00 112244677887776653
No 75
>PRK10708 hypothetical protein; Provisional
Probab=44.29 E-value=38 Score=22.15 Aligned_cols=31 Identities=26% Similarity=0.334 Sum_probs=26.0
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
++.+|.|+|-.+..-+|.|.+..+-+.-++-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~EG~My 33 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFSEGTMY 33 (62)
T ss_pred cccEEEEecCCCccccceEEEEeeccCcEEE
Confidence 5778999999999999999999986665443
No 76
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=42.43 E-value=65 Score=24.84 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=25.1
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
.||+.|......|+.++|.|-+.....+-+.+
T Consensus 91 lIGk~V~~~~~~g~~~tG~V~sV~~~~~~~~~ 122 (140)
T PRK11911 91 FIGKDIKGVSLNGEVISGKVESVQQTTNGVML 122 (140)
T ss_pred hhCceeEEEecCCCEEEEEEEEEEEcCCceEE
Confidence 48999998889999999999877655444444
No 77
>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=42.36 E-value=1.1e+02 Score=20.87 Aligned_cols=54 Identities=22% Similarity=0.339 Sum_probs=35.2
Q ss_pred eeccEEEEEec---CC-CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 13 AVGCLLSIKTT---LG-DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 13 ~vG~~V~vtt~---~~-~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
.+|..|+|++. .| ..++|.+-.+|.. .++|....+ +...-.-|+.+-|+...+.
T Consensus 23 ~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~--~v~l~~~~~--~~~~~~~i~~~~I~ka~l~ 80 (83)
T cd01734 23 AVGKYVHVKLYQPIDGQKEFEGTLLGVDDD--TVTLEVDIK--TRGKTVEIPLDKIAKARLA 80 (83)
T ss_pred hCCCEEEEEEEcccCCeEEEEEEEEeEeCC--EEEEEEecC--CCCeEEEEEhHHeeEEEEE
Confidence 48999999986 45 4899999999984 455554321 1122344566777766543
No 78
>PRK10139 serine endoprotease; Provisional
Probab=41.78 E-value=62 Score=29.44 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=29.4
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
+..+.|++.+|+++.++|..+|+.+.+-+|+-.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 457889999999999999999999999999763
No 79
>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=41.68 E-value=57 Score=21.92 Aligned_cols=36 Identities=22% Similarity=0.322 Sum_probs=25.8
Q ss_pred ceeeccEEEEEec----CCCEEEEEEEEEeCCCCeEEEEe
Q 030131 11 EFAVGCLLSIKTT----LGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 11 ~~~vG~~V~vtt~----~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
++.-+.+|+|-|- .+...+|.+.+||---|++....
T Consensus 4 ~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV 43 (66)
T cd01739 4 CVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDV 43 (66)
T ss_pred hhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhh
Confidence 3344666777653 34799999999998888876543
No 80
>PRK14631 hypothetical protein; Provisional
Probab=41.41 E-value=1.5e+02 Score=23.55 Aligned_cols=53 Identities=11% Similarity=0.250 Sum_probs=35.7
Q ss_pred eeccEEEEEecC----CCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 13 AVGCLLSIKTTL----GDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 13 ~vG~~V~vtt~~----~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
.+|..|+|++.. ...++|.+..+|-....|+|.... ...+ -|..+-|+...++
T Consensus 115 ~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~----~~~~-~i~~~~I~ka~L~ 171 (174)
T PRK14631 115 YIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEG----KHVL-DIDSNNIDKANLI 171 (174)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcC----CcEE-EEEhHHcceEEEe
Confidence 389999999853 389999999999555677776421 1122 3466666665544
No 81
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=40.43 E-value=21 Score=20.51 Aligned_cols=19 Identities=26% Similarity=0.238 Sum_probs=14.8
Q ss_pred EEEEEEEEeCCCCeEEEEe
Q 030131 28 FDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 28 ~~G~V~~~D~~~~~lvL~~ 46 (182)
..|.||++|..++-++=+-
T Consensus 8 ~~g~l~AlD~~TG~~~W~~ 26 (38)
T PF01011_consen 8 PDGYLYALDAKTGKVLWKF 26 (38)
T ss_dssp TTSEEEEEETTTTSEEEEE
T ss_pred CCCEEEEEECCCCCEEEee
Confidence 3478999999998887654
No 82
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=39.88 E-value=90 Score=21.50 Aligned_cols=63 Identities=19% Similarity=0.235 Sum_probs=42.4
Q ss_pred CCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec--CCCCCcceEE--EEecCCeeEEEEec
Q 030131 9 GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG--LKSGPRRNIR--LLNANYIKDFSFLG 71 (182)
Q Consensus 9 ~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~~~~~~--iIn~~~Ik~i~vl~ 71 (182)
+..--..+++.++...|..++|.+-.|||--++++=.+- ...+.+.+++ +|++..|..++-++
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~ 74 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALE 74 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeecc
Confidence 333446788999999999999999999997775533221 1223344444 67777777776654
No 83
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=39.77 E-value=66 Score=24.35 Aligned_cols=38 Identities=11% Similarity=-0.001 Sum_probs=30.3
Q ss_pred CCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 9 GEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 9 ~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
...+..|.+|+|+.-.=.-++|.|..+|+.....++..
T Consensus 106 ~~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~ 143 (159)
T TIGR01955 106 TTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLN 143 (159)
T ss_pred ccCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEh
Confidence 34577999999997777899999999997766555544
No 84
>PF10133 RNA_bind_2: Predicted RNA-binding protein; InterPro: IPR019300 This entry represents a family of bacterial proteins predicted to have RNA-binding properties, though their exact function has not yet been defined.
Probab=39.43 E-value=1.1e+02 Score=20.06 Aligned_cols=33 Identities=15% Similarity=0.465 Sum_probs=27.5
Q ss_pred eeccEEEEEecCCC--EEEEEEEEEeCCCCeEEEE
Q 030131 13 AVGCLLSIKTTLGD--EFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 13 ~vG~~V~vtt~~~~--~~~G~V~~~D~~~~~lvL~ 45 (182)
+-|-.|.++..+|+ .++|.|--.|-..+-|+|.
T Consensus 26 ~~~~~i~l~dIfG~~k~v~g~I~~idl~~hkIile 60 (61)
T PF10133_consen 26 PEGDKIRLTDIFGEQKEVEGRIKEIDLVDHKIILE 60 (61)
T ss_pred EeCCEEEEEeccCCeEEEEEEEEEEEccCCEEEEe
Confidence 45677888998885 7889999999998888875
No 85
>PRK14633 hypothetical protein; Provisional
Probab=39.34 E-value=1.2e+02 Score=23.37 Aligned_cols=51 Identities=14% Similarity=0.137 Sum_probs=34.4
Q ss_pred eeccEEEEEec----CCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 13 AVGCLLSIKTT----LGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 13 ~vG~~V~vtt~----~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
.+|..|+|++. ....++|.+-.++.. .++|.... + .-.-|+.+.|+...+.
T Consensus 92 ~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~--~i~l~~~~--~---~~~~i~~~~I~ka~l~ 146 (150)
T PRK14633 92 LVGFNVKAVTLAPVGSQTKFKGVLERVEGN--NVILNLED--G---KEISFDFDELKKLRVS 146 (150)
T ss_pred hCCCeEEEEEecccCCcEEEEEEEEEEeCC--EEEEEEcC--C---cEEEEEhHHeeeEEEe
Confidence 38999999983 447999999999874 55554311 1 1234577777776654
No 86
>PRK14643 hypothetical protein; Provisional
Probab=39.29 E-value=64 Score=25.37 Aligned_cols=32 Identities=22% Similarity=0.303 Sum_probs=26.0
Q ss_pred eeccEEEEEecC----CCEEEEEEEEEeCCCCeEEE
Q 030131 13 AVGCLLSIKTTL----GDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 13 ~vG~~V~vtt~~----~~~~~G~V~~~D~~~~~lvL 44 (182)
.+|.+|+|++.. ...++|.+..+|...-.|.|
T Consensus 102 ~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 102 ALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred hcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 489999999854 47999999999987666654
No 87
>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=38.53 E-value=48 Score=21.71 Aligned_cols=31 Identities=23% Similarity=0.342 Sum_probs=26.1
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
++..|.|+|-.+..-+|.|.+..+-+.-++-
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~EG~MY 33 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFNEGTMY 33 (62)
T ss_pred cccEEEEecCCcccccceEEEEeeccCcEEE
Confidence 5778999999999999999999986665543
No 88
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=37.78 E-value=1e+02 Score=23.32 Aligned_cols=55 Identities=15% Similarity=0.300 Sum_probs=36.7
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEE---EecCCCCCcceEEE----EecCCeeEEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI---QEGLKSGPRRNIRL----LNANYIKDFSF 69 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL---~~~~~~~~~~~~~i----In~~~Ik~i~v 69 (182)
+-|..+.|...+|+++.|-+...|.--++ .| .+.++ .+..-|++ |++++||-+.+
T Consensus 10 aq~~pmlvELKNget~nGhL~~cD~wMNl-~L~~Vi~ts~-Dgdkf~r~pEcYirGttIkylri 71 (134)
T KOG3293|consen 10 AQNHPMLVELKNGETYNGHLVNCDNWMNL-HLREVICTSE-DGDKFFRMPECYIRGTTIKYLRI 71 (134)
T ss_pred cCCCeEEEEecCCCEecceeecchhhhhc-chheeEEecc-CCCceeecceeEEecceeEEEec
Confidence 45788999999999999999999963332 22 12222 22334444 78888887754
No 89
>PRK14645 hypothetical protein; Provisional
Probab=36.68 E-value=66 Score=25.02 Aligned_cols=30 Identities=17% Similarity=0.406 Sum_probs=25.0
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
+|..|+|++ .++.++|.+..+|. +.|+|..
T Consensus 101 ~G~~v~v~~-~~k~~~G~L~~~~d--~~i~l~~ 130 (154)
T PRK14645 101 AGLKAKVRG-PGENFTGRIKAVSG--DQVTFDV 130 (154)
T ss_pred CCCEEEEEc-CCeEEEEEEEEEeC--CEEEEEE
Confidence 899999975 77999999999986 4666654
No 90
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=35.15 E-value=83 Score=17.44 Aligned_cols=31 Identities=16% Similarity=0.168 Sum_probs=24.4
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
+|..|+|+.-...-..|.|.-.|+....+++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 3778888876667789999999988866654
No 91
>PRK14642 hypothetical protein; Provisional
Probab=33.95 E-value=87 Score=25.50 Aligned_cols=58 Identities=12% Similarity=0.197 Sum_probs=36.4
Q ss_pred eccEEEEEec-------------CCCEEEEEEEEEeCCCCeEEEEec--CCCCC---cc------eEEEEecCCeeEEEE
Q 030131 14 VGCLLSIKTT-------------LGDEFDGQVMAFDRFTNMLVIQEG--LKSGP---RR------NIRLLNANYIKDFSF 69 (182)
Q Consensus 14 vG~~V~vtt~-------------~~~~~~G~V~~~D~~~~~lvL~~~--~~~~~---~~------~~~iIn~~~Ik~i~v 69 (182)
+|..|+|+|. ....|+|.+-.+|...-.|.+... .+++. +. .-.-+..+-|+...+
T Consensus 99 iG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~~~~~k~g~~~~k~~~~~~~~~~~~~~~eik~a~l 178 (197)
T PRK14642 99 AGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSDEPPVKPGQRVSKKRVPAPLQALGFTLDELREARL 178 (197)
T ss_pred CCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEeecccCCCccccccccccccceeEEeehhheeeEEE
Confidence 8999999986 568999999999975444444432 12221 10 123455666777666
Q ss_pred ec
Q 030131 70 LG 71 (182)
Q Consensus 70 l~ 71 (182)
..
T Consensus 179 ~p 180 (197)
T PRK14642 179 AP 180 (197)
T ss_pred EE
Confidence 64
No 92
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=33.72 E-value=9.4 Score=26.85 Aligned_cols=30 Identities=27% Similarity=0.404 Sum_probs=26.4
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLV 43 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lv 43 (182)
..-+|-|++..|.++.|.+-+||.--|++.
T Consensus 14 LdErVyVKlr~drel~G~L~afD~HlNmvL 43 (91)
T KOG3460|consen 14 LDERVYVKLRSDRELRGTLHAFDEHLNMVL 43 (91)
T ss_pred ccceEEEEecCChhhhcchhhhHHhhhhhh
Confidence 567899999999999999999998877754
No 93
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=33.50 E-value=2.1e+02 Score=22.72 Aligned_cols=49 Identities=14% Similarity=0.221 Sum_probs=35.3
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
-...|.|-..+|-.++|.|.+||. -+|.|... + .-.+|.-++|+-|.--
T Consensus 23 ~k~~VtvfL~nG~rl~G~I~~fD~--ftVlL~~~---g---kqqLIYKHAISTI~p~ 71 (165)
T PRK14091 23 TKTPVTMFLVKGVKLQGIITWFDN--FSILLRRD---G---QSQLVYKHAISTIMPA 71 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcc--eEEEEEeC---C---ceEEEEeeeeeeeccc
Confidence 455778889999999999999995 33444432 1 1258999999987533
No 94
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=32.77 E-value=2.2e+02 Score=25.82 Aligned_cols=55 Identities=16% Similarity=0.311 Sum_probs=39.3
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCC-CCeEEEEecCCCCCcceEEEEecCCeeEEEEecCCC
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRF-TNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLGQAD 74 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~-~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~~~~ 74 (182)
..+|..|+|++.+ .+++|.+. .+. .+.|||+-. +.+| -=|..+.|+++++++...
T Consensus 3 ~~~gd~v~~~~~~-~~~~g~~~--p~~~~~~~~~kl~----~gyn-~g~~~~~~~~~~~~~~~~ 58 (419)
T PRK04183 3 MEVGDRVRVEKDD-VVYEGILM--PSYEDDHIVIKLD----NGYN-IGIDIDKIAEIELLEKGE 58 (419)
T ss_pred CCCCCEEEEEECC-eEEEEEEe--cCCCCCEEEEEcC----CCce-eeeccccccceEEccccc
Confidence 4579999998754 99999998 223 368998853 2334 345668888999997654
No 95
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=32.58 E-value=90 Score=23.94 Aligned_cols=37 Identities=11% Similarity=0.095 Sum_probs=31.5
Q ss_pred CceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 10 EEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 10 ~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
..+.+|..|+|+.-.-.-++|.|..+|...+.+.|.-
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~l 129 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVEL 129 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEE
Confidence 4588999999998777889999999999888876654
No 96
>PF14564 Membrane_bind: Membrane binding; PDB: 1YHP_A 2B1O_A.
Probab=32.30 E-value=2e+02 Score=21.05 Aligned_cols=33 Identities=24% Similarity=0.447 Sum_probs=24.5
Q ss_pred eccEEEEEecC-CC-EEEEEEEE-EeCCCCeEEEEe
Q 030131 14 VGCLLSIKTTL-GD-EFDGQVMA-FDRFTNMLVIQE 46 (182)
Q Consensus 14 vG~~V~vtt~~-~~-~~~G~V~~-~D~~~~~lvL~~ 46 (182)
+=+.|.|.-.. |. ...|.||- |||+++.|....
T Consensus 51 iv~~I~Vr~~~~g~~v~nGsvYFkY~~s~g~V~~~~ 86 (110)
T PF14564_consen 51 IVCQISVRDTDWGQYVANGSVYFKYNPSTGEVSIRK 86 (110)
T ss_dssp EEEEEEEEESST-SEEEEEEEEEEEETTTTEEEEE-
T ss_pred EEEEEEEEeccCCceEecceEEEEECCCCCeEEEee
Confidence 44667777666 76 55699988 999999999987
No 97
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.13 E-value=39 Score=24.44 Aligned_cols=27 Identities=15% Similarity=0.172 Sum_probs=21.0
Q ss_pred EEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 17 LLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 17 ~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
.-+|--|.+..++|+.|||=+ -+.+=-
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~ 32 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHY 32 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchH
Confidence 457888999999999999987 444433
No 98
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.45 E-value=90 Score=20.59 Aligned_cols=22 Identities=18% Similarity=0.489 Sum_probs=17.8
Q ss_pred CCCEEEEEEEEEeCCCCeEEEE
Q 030131 24 LGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 24 ~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
-|+.+++.|..+|+..+.|.|.
T Consensus 49 vG~~v~~kV~~id~~~~~i~Ls 70 (73)
T cd05703 49 IGQALKAKVVGVDKEHKLLRLS 70 (73)
T ss_pred CCCEEEEEEEEEeCCCCEEEEE
Confidence 4677888899999988888874
No 99
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=31.36 E-value=2.5e+02 Score=22.75 Aligned_cols=48 Identities=15% Similarity=0.209 Sum_probs=33.8
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCC-CCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRF-TNMLVIQEGLKSGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~-~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~ 68 (182)
.||+.|..+..+|..++|.|.+.... .+.+.|... + +-|.++.|.+|.
T Consensus 116 lIGK~V~~~~~dG~~vtG~V~sV~~~~~g~v~l~vd---g-----~~v~l~~V~~Vs 164 (190)
T PRK06792 116 FLGKYVRGVSNDGKQVTGQVETVRLAENNDVQLIVD---N-----QVVSLRFVERVS 164 (190)
T ss_pred hcCcEEEEEcCCCCEEEEEEEEEEEccCCcEEEEEC---C-----EEEeccceeEec
Confidence 48999999989999999999988753 345555432 1 455556666554
No 100
>PF13570 PQQ_3: PQQ-like domain; PDB: 3HXJ_B 3Q54_A.
Probab=31.08 E-value=27 Score=20.12 Aligned_cols=11 Identities=45% Similarity=0.676 Sum_probs=8.0
Q ss_pred EEEEEEEeCCC
Q 030131 29 DGQVMAFDRFT 39 (182)
Q Consensus 29 ~G~V~~~D~~~ 39 (182)
.|.|||+|+.+
T Consensus 30 dg~l~ald~~t 40 (40)
T PF13570_consen 30 DGNLYALDAAT 40 (40)
T ss_dssp TSEEEEEETT-
T ss_pred CCEEEEEeCCC
Confidence 47889998754
No 101
>PF05593 RHS_repeat: RHS Repeat; InterPro: IPR006530 These sequences contain two tandem copies of a 21-residue extracellular repeat that is found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin [, , ].
Probab=31.04 E-value=1.1e+02 Score=17.54 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=26.2
Q ss_pred eeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 13 AVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 13 ~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
..|..++++...|.+.+ |.||+..+++.+..+
T Consensus 3 ~~G~l~~~~d~~G~~~~---y~YD~~g~l~~~t~~ 34 (38)
T PF05593_consen 3 ANGRLTSVTDPDGRTTR---YTYDAAGRLTSVTDP 34 (38)
T ss_pred CCCCEEEEEcCCCCEEE---EEECCCCCEEEEECC
Confidence 45778889988888884 999999998887654
No 102
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=31.02 E-value=1.9e+02 Score=21.57 Aligned_cols=47 Identities=11% Similarity=0.189 Sum_probs=30.3
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEE
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFS 68 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~ 68 (182)
+..|..|++ .|.+.+||..+...+|.+... ....--.|++.++..++
T Consensus 18 ~~~g~svR~--------~GrL~~yD~~~~~a~l~~~~~--~~~~~l~V~t~~l~~~~ 64 (118)
T PF15490_consen 18 VPEGKSVRT--------FGRLQSYDVATSRATLTAQHE--SDQHSLKVDTKLLEPFQ 64 (118)
T ss_pred ccCCCeEEE--------EEEEEEEeccCCEEEEEeecc--CCCcEEEEEeeEccccc
Confidence 445666655 499999999999999954432 22234556666655544
No 103
>PF15200 KRTDAP: Keratinocyte differentiation-associated
Probab=30.95 E-value=29 Score=23.76 Aligned_cols=37 Identities=27% Similarity=0.609 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhcc-eEEc
Q 030131 81 KCFLDLSRLQAREHLAVRQAEADAQRIGVGVTTEAQNIFDALSKTLP-VRWD 131 (182)
Q Consensus 81 l~~v~~~~l~~r~~~ai~~~~~~~~~~g~gvs~egQ~lFd~L~Kt~p-v~W~ 131 (182)
.+.+|++++++-++- .+- - -=.+||++|++.+| ..|+
T Consensus 24 ~qFLNvdklrsafk~----~eF--l--------NWHalfe~iK~kLPFlNWd 61 (77)
T PF15200_consen 24 TQFLNVDKLRSAFKS----EEF--L--------NWHALFEAIKRKLPFLNWD 61 (77)
T ss_pred chhccHHHHHHhhCh----Hhh--h--------hHHHHHHHHHHhCcccchh
Confidence 568888877654432 111 0 12469999999999 8996
No 104
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=30.74 E-value=43 Score=17.96 Aligned_cols=14 Identities=29% Similarity=0.451 Sum_probs=10.3
Q ss_pred EEEEEEeCCCCeEE
Q 030131 30 GQVMAFDRFTNMLV 43 (182)
Q Consensus 30 G~V~~~D~~~~~lv 43 (182)
|.++++|..++-+.
T Consensus 16 g~l~a~d~~~G~~~ 29 (33)
T smart00564 16 GTLYALDAKTGEIL 29 (33)
T ss_pred CEEEEEEcccCcEE
Confidence 78888888766554
No 105
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=30.70 E-value=99 Score=22.81 Aligned_cols=54 Identities=15% Similarity=0.154 Sum_probs=36.1
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec-CCCCCc--ceEEEEecCCeeEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG-LKSGPR--RNIRLLNANYIKDF 67 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~-~~~~~~--~~~~iIn~~~Ik~i 67 (182)
-+-.|.|.+.+|..+.|+|-..|+..+....... .-++.+ -...-|.++-|.-+
T Consensus 11 ~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~~pv~l~~lsirgnniRy~ 67 (109)
T KOG3428|consen 11 LNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKGEPVRLDTLSIRGNNIRYY 67 (109)
T ss_pred hCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCCCceeEEEEEeecceEEEE
Confidence 3568999999999999999999998888755332 111211 23344455666544
No 106
>PRK14635 hypothetical protein; Provisional
Probab=30.17 E-value=2.6e+02 Score=21.69 Aligned_cols=54 Identities=11% Similarity=0.075 Sum_probs=32.6
Q ss_pred eccEEEEEecC--CCEEEE---EEEEEeCCCCeEEEEecCC--CCCcceEEEEecCCeeEEEE
Q 030131 14 VGCLLSIKTTL--GDEFDG---QVMAFDRFTNMLVIQEGLK--SGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 14 vG~~V~vtt~~--~~~~~G---~V~~~D~~~~~lvL~~~~~--~~~~~~~~iIn~~~Ik~i~v 69 (182)
+|..|+|++.. +..+.| .+..+|.. .++|....+ ........-|..+-|+...+
T Consensus 98 ~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~--~v~l~~~~k~~~~~~~~~~~ip~~~I~ka~l 158 (162)
T PRK14635 98 RGIPVRLVFRSEESEKWQEGIFRLVNRDGD--QVELEKFQKGKKSKVKKQTTLNLKDILKGNL 158 (162)
T ss_pred CCCEEEEEEecCCCcEEEecceEEEEEcCC--EEEEEEecccccccCCeEEEEEhHHeeeeEE
Confidence 89999998753 568887 89999875 444443111 01112234556677776654
No 107
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=30.06 E-value=2.6e+02 Score=22.17 Aligned_cols=48 Identities=17% Similarity=0.301 Sum_probs=34.9
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
...|.|-.++|-.++|.|-+||. -++.|... + . -.+|.-++|+-|.-.
T Consensus 104 k~~VtvfL~NG~~l~G~I~~fD~--ftvlL~~~---g-k--qqLIYKHAISTI~P~ 151 (165)
T PRK14091 104 GEPVTMFLVNGVMLQGEIAAFDL--FCMLLERD---G-Y--VQLVYKHAVSTVQPA 151 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcc--eEEEEEeC---C-c--EEEEEEeEEEEEccC
Confidence 45688889999999999999994 33444432 2 1 258889999987643
No 108
>PRK14646 hypothetical protein; Provisional
Probab=29.80 E-value=2.6e+02 Score=21.57 Aligned_cols=49 Identities=16% Similarity=0.257 Sum_probs=34.2
Q ss_pred eccEEEEEecCC----CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 14 VGCLLSIKTTLG----DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 14 vG~~V~vtt~~~----~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
+|..|+|++... ..++|.+..+|. ..|+|... + ...-|+.+.|+...+.
T Consensus 99 ~G~~v~V~l~~~~~~~~~~~G~L~~~~~--~~v~l~~~---g---~~~~i~~~~I~ka~L~ 151 (155)
T PRK14646 99 KGFPVNVELNQKNSKIKFLNGLLYEKSK--DYLAINIK---G---KIKKIPFNEVLKISLC 151 (155)
T ss_pred CCCEEEEEEecCcCCeEEEEEEEEEEeC--CEEEEEEC---C---EEEEEEHHHeeeEEeC
Confidence 899999998542 588999999997 46666542 1 1234566777776554
No 109
>COG4520 LipA Surface antigen [Cell envelope biogenesis, outer membrane]
Probab=29.37 E-value=41 Score=25.72 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=23.4
Q ss_pred ceEEcCCcEEEeeeEEEcCCCCCC--Ccc
Q 030131 127 PVRWDKTVIVVMNEVRVSSPYLPE--SVS 153 (182)
Q Consensus 127 pv~W~~~~IvV~d~V~I~pPY~~~--n~~ 153 (182)
||.|.+..=+|+++|+-..||... ||+
T Consensus 77 ~v~W~g~~~~v~G~Vv~~~py~vgsq~cR 105 (136)
T COG4520 77 PVAWYGADGVVYGSVVAAQPYQVGSQNCR 105 (136)
T ss_pred ceeEECCCCceeeeEeeccccchhhhhhh
Confidence 599998776999999999999986 664
No 110
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=29.22 E-value=1.4e+02 Score=23.94 Aligned_cols=49 Identities=14% Similarity=0.272 Sum_probs=33.7
Q ss_pred EEEEEe-cCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEec
Q 030131 17 LLSIKT-TLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFLG 71 (182)
Q Consensus 17 ~V~vtt-~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl~ 71 (182)
.++|.- +.+.+|.|.|..|+. +.|.|..+.. + .---|+...|.+|..++
T Consensus 135 ~i~C~i~t~~~~Y~G~I~~~~~--~~v~i~~~~~-~---~~~~i~~~~I~sI~~iG 184 (185)
T PF14153_consen 135 PIKCEIETKDKSYRGIILSYDE--GEVSIMPFNQ-G---EEIEIPIDDITSIKMIG 184 (185)
T ss_pred CCceEEEeCCceEEEEEEeccC--CEEEEeccCC-C---cceEeehhheeeeeecc
Confidence 344543 467899999999997 4676776532 2 33556778888887764
No 111
>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=28.85 E-value=1.3e+02 Score=22.29 Aligned_cols=47 Identities=15% Similarity=0.072 Sum_probs=30.8
Q ss_pred EEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 17 LLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 17 ~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
.+.|+|.+|+++.|.+..=|. ..++|..+. + ..+.|..+-|++....
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~--~~~~l~~~~--g---~~~~i~~~~I~~~~~~ 105 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA--DGVTVKMPG--G---VEQSVPREEIKSREAL 105 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC--CeEEEEcCC--C---cEEEEEHHHHHHhhcC
Confidence 478999999999999887654 556665432 2 2355555556655433
No 112
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=28.61 E-value=1.9e+02 Score=25.90 Aligned_cols=54 Identities=17% Similarity=0.366 Sum_probs=41.3
Q ss_pred CCCceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecC----CCCCcceEEEEecC
Q 030131 8 SGEEFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGL----KSGPRRNIRLLNAN 62 (182)
Q Consensus 8 ~~~~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~----~~~~~~~~~iIn~~ 62 (182)
...+|..|..|++..++...+.|+..|.+- ...|.+.... ..|..-.+||+.+.
T Consensus 348 lp~PF~rGevv~aevV~~Gr~kGEmlavAr-dRvIav~~~~~~~~~vG~~vkvrIvr~k 405 (414)
T COG2100 348 LPKPFKRGEVVKAEVVLPGRLKGEMLAVAR-DRVIAVINSNEGALLVGDRVKVRIVRTK 405 (414)
T ss_pred CCCccccCcEEEEEEEecceecceEEEEec-ccEEEEecCchhhhccCceEEEEEEEcc
Confidence 456789999999999999999999999996 6667665543 23445567777654
No 113
>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=28.42 E-value=1.3e+02 Score=26.73 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=28.5
Q ss_pred cEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 16 CLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 16 ~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
..+.|++.+|..+.++|+.+|+...+-+|+-.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 47888899999999999999999999888764
No 114
>PRK14634 hypothetical protein; Provisional
Probab=27.79 E-value=1.1e+02 Score=23.70 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=33.9
Q ss_pred eeccEEEEEecCC----CEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEEe
Q 030131 13 AVGCLLSIKTTLG----DEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSFL 70 (182)
Q Consensus 13 ~vG~~V~vtt~~~----~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~vl 70 (182)
.+|..|+|+|... ..++|.+..+|. ..|+|... + ...-|+.+.|+...+.
T Consensus 98 ~~G~~V~V~l~~~~~~~k~~~G~L~~~~~--~~v~l~~~---~---~~~~i~~~~I~ka~l~ 151 (155)
T PRK14634 98 FRGFPVEVSHRDDDGSEQRLEGLLLERNE--DHLQINIR---G---RIKRIPRDSVISVRLT 151 (155)
T ss_pred hCCCeEEEEEecCCCCeEEEEEEEEEEeC--CEEEEEEC---C---EEEEEEHHHeeeEEeC
Confidence 3899999998632 699999999986 45656542 1 1234566777766544
No 115
>cd07885 RHD-n_RelA N-terminal sub-domain of the Rel homology domain (RHD) of RelA. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD domain of the RelA family of transcription factors, categorized as a class II member of the NF-kappa B family. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which
Probab=27.61 E-value=51 Score=26.20 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=24.1
Q ss_pred hhhcc----eEEcCCcEEEeeeEEEcCCCCCC
Q 030131 123 SKTLP----VRWDKTVIVVMNEVRVSSPYLPE 150 (182)
Q Consensus 123 ~Kt~p----v~W~~~~IvV~d~V~I~pPY~~~ 150 (182)
.||+| +.|+|...|+..=|+-.+||.+-
T Consensus 37 ~KT~Pti~i~nY~G~a~V~vslVT~d~p~rpH 68 (169)
T cd07885 37 TKTHPTIKINNYTGPGRVRISLVTKDPPHKPH 68 (169)
T ss_pred CCcCCeEEEecCcCCEEEEEEEEeCCCCCCCC
Confidence 38998 57889999999999999999884
No 116
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=27.10 E-value=1.2e+02 Score=19.78 Aligned_cols=22 Identities=9% Similarity=0.437 Sum_probs=18.6
Q ss_pred CCCEEEEEEEEEeCCCCeEEEE
Q 030131 24 LGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 24 ~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
-|+.++..|..+|+..+.|.|.
T Consensus 49 vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 49 AGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CCCEEEEEEEEEeCCCCEEEEe
Confidence 4788899999999999888774
No 117
>PF09153 DUF1938: Domain of unknown function (DUF1938); InterPro: IPR015236 This domain, which is predominantly found in the archaeal protein O6-alkylguanine-DNA alkyltransferase, adopts a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. The exact function has not, as yet, been defined, though it has been postulated that this domain may confer thermostability to the protein []. ; GO: 0005737 cytoplasm; PDB: 1MGT_A.
Probab=26.93 E-value=56 Score=23.03 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=20.2
Q ss_pred eccEEEEEecCCCEEEEEEEEEeC
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDR 37 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~ 37 (182)
-|..|.|-+...+.++|..|++|-
T Consensus 10 ~~rei~I~vi~e~kIqGItfslDg 33 (86)
T PF09153_consen 10 GGREIWIAVIFEEKIQGITFSLDG 33 (86)
T ss_dssp TTEEEEEEEEESSSEEEEEEESSH
T ss_pred CCeEEEEEEEEcCceeeEEEEecc
Confidence 466788888888889999999983
No 118
>PF14157 YmzC: YmzC-like protein; PDB: 3KVP_E.
Probab=26.77 E-value=89 Score=20.79 Aligned_cols=16 Identities=19% Similarity=0.503 Sum_probs=14.1
Q ss_pred EEEEEeCCCCeEEEEe
Q 030131 31 QVMAFDRFTNMLVIQE 46 (182)
Q Consensus 31 ~V~~~D~~~~~lvL~~ 46 (182)
.||-|||.++-|.|..
T Consensus 42 KIfkyd~~tNei~L~K 57 (63)
T PF14157_consen 42 KIFKYDEDTNEITLKK 57 (63)
T ss_dssp EEEEEETTTTEEEEEE
T ss_pred EEEEeCCCCCeEEEEE
Confidence 5899999999999964
No 119
>cd07883 RHD-n_NFkB N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-kappa B). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 and B2 families of transcription factors, also referred to as class I members of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. Family members include NF-kappa B1 and NF-kappa B2. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form), while NF-kappa B2 is called p100 or p52 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large
Probab=26.71 E-value=52 Score=26.82 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=23.9
Q ss_pred hhhcc----eEEcCCcEEEeeeEEEcCCCCCC
Q 030131 123 SKTLP----VRWDKTVIVVMNEVRVSSPYLPE 150 (182)
Q Consensus 123 ~Kt~p----v~W~~~~IvV~d~V~I~pPY~~~ 150 (182)
.|||| +.|+|..+|+..=|+-.+||.+-
T Consensus 37 ~KT~PtVki~nY~G~a~I~VslVT~d~p~rpH 68 (197)
T cd07883 37 KKSYPTVKICNYQGPARIVVQLVTNSEPPRLH 68 (197)
T ss_pred CCcCCeEEEecCcCCEEEEEEEEeCCCCCCCC
Confidence 48998 57899998888899999999873
No 120
>cd01206 Homer Homer type EVH1 domain. Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=26.39 E-value=1.6e+02 Score=21.86 Aligned_cols=36 Identities=14% Similarity=0.114 Sum_probs=21.2
Q ss_pred EEEEEEEEeCCCC-eEEEEecC-------CCCCcceEEEEecCC
Q 030131 28 FDGQVMAFDRFTN-MLVIQEGL-------KSGPRRNIRLLNANY 63 (182)
Q Consensus 28 ~~G~V~~~D~~~~-~lvL~~~~-------~~~~~~~~~iIn~~~ 63 (182)
....|+.|||.++ .-+--... .+...+.||||-...
T Consensus 9 arA~V~~yd~~tKk~WvPs~~~~~~V~~y~~~~~ntfRIi~~~~ 52 (111)
T cd01206 9 TRAHVFQIDPKTKKNWIPASKHAVTVSYFYDSTRNVYRIISVGG 52 (111)
T ss_pred eeeEEEEECCCCcceeEeCCCCceeEEEEecCCCcEEEEEEecC
Confidence 4678999999875 33221111 123456888877554
No 121
>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=26.32 E-value=1.6e+02 Score=17.89 Aligned_cols=34 Identities=18% Similarity=0.234 Sum_probs=26.3
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
.+.+|..|.+...+|.-+.|.|..+++.....|.
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~ 35 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLYEVF 35 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEE
Confidence 4678988888876788999999999986333333
No 122
>PF03088 Str_synth: Strictosidine synthase; InterPro: IPR018119 This entry represents a conserved region found in strictosidine synthase (4.3.3.2 from EC), a key enzyme in alkaloid biosynthesis. It catalyses the Pictet-Spengler stereospecific condensation of tryptamine with secologanin to form strictosidine []. The structure of the native enzyme from the Indian medicinal plant Rauvolfia serpentina (Serpentwood) (Devilpepper) represents the first example of a six-bladed four-stranded beta-propeller fold from the plant kingdom [].; GO: 0016844 strictosidine synthase activity, 0009058 biosynthetic process; PDB: 2FPB_A 2V91_B 2FP8_A 3V1S_B 2FPC_A 2VAQ_A 2FP9_B.
Probab=26.06 E-value=93 Score=21.90 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=14.5
Q ss_pred CEEEEEEEEEeCCCCeE-EEEe
Q 030131 26 DEFDGQVMAFDRFTNML-VIQE 46 (182)
Q Consensus 26 ~~~~G~V~~~D~~~~~l-vL~~ 46 (182)
..-.|.++.|||.++.+ +|..
T Consensus 33 ~~~~GRll~ydp~t~~~~vl~~ 54 (89)
T PF03088_consen 33 GRPTGRLLRYDPSTKETTVLLD 54 (89)
T ss_dssp T---EEEEEEETTTTEEEEEEE
T ss_pred CCCCcCEEEEECCCCeEEEehh
Confidence 45579999999999976 5544
No 123
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=25.92 E-value=1.3e+02 Score=18.86 Aligned_cols=29 Identities=17% Similarity=0.291 Sum_probs=23.4
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCC
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTN 40 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~ 40 (182)
|.+|.+|.|.=..|..++++|.......+
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~ 29 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNG 29 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCC
Confidence 46899999998888999999999887543
No 124
>CHL00132 psaF photosystem I subunit III; Validated
Probab=25.90 E-value=1.6e+02 Score=23.78 Aligned_cols=39 Identities=15% Similarity=0.264 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCH---------HHHHHHHHHhhh
Q 030131 87 SRLQAREHLAVRQAEADAQRIGVGVTT---------EAQNIFDALSKT 125 (182)
Q Consensus 87 ~~l~~r~~~ai~~~~~~~~~~g~gvs~---------egQ~lFd~L~Kt 125 (182)
.+.++|+++++++.+.++..+..+.+| .+|+=|+..++.
T Consensus 36 ~aF~kR~~~~~k~Le~rlk~Y~~~s~p~lal~~qi~~tk~RFe~Y~~~ 83 (185)
T CHL00132 36 PAFQKRLNNSVKKLENRLAKYEANSPPALALQQQIDKTKARFDKYGRS 83 (185)
T ss_pred HHHHHHHHHHHHHHHhhhhccCCCCChHHHHHHHHHHHHHHHHHhccc
Confidence 478899999999999999999999888 788888888885
No 125
>PF02393 US22: US22 like; InterPro: IPR003360 Herpesviruses are large and complex DNA viruses, widely found in nature. Human cytomegalovirus (HCMV), an important human pathogen, defines the betaherpesvirus family. Mouse cytomegalovirus (MCMV) and rat cytomegalovirus serve as biological model systems for HCMV. HCMV, MCMV, and rat CMV display the largest genomes among the herpesviruses and are essentially co-linear over the central 180 kb of the 230-kb genomes. Betaherpesviruses, which include the CMVs as well as human herpesviruses 6 and 7, differ from alpha- and gammaherpesviruses by the presence of additional gene families such as the US22 gene family, which are mainly clustered at the ends of the genome. The US22 family was first described in HCMV. This gene family comprises 12 members in both HCMV and MCMV and 11 in rat CMV []. Members of the US22 gene family are characterised by stretches of hydrophobic and charged residues as well as up to four conserved sequence motifs which are specific for betaherpesviruses. Motif I differs between the HCMV US and UL family members []. Motifs I and II have consensus sequences, while motifs III and IV are less well defined but have stretches of non-polar residues [, ]. Members of this gene family are widely divergent in function and their involvement in viral replication []. This entry contains US22 family members from the Cytomegalovirus, Muromegalovirus and the Roseolovirus taxonomic groups. The name sake of this family US22 is an early nuclear protein that is secreted from cells []. The US22 family may have a role in virus replication and pathogenesis [].
Probab=24.90 E-value=65 Score=23.16 Aligned_cols=18 Identities=28% Similarity=0.346 Sum_probs=15.1
Q ss_pred EEEEEEEeCCCCeEEEEe
Q 030131 29 DGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 29 ~G~V~~~D~~~~~lvL~~ 46 (182)
.|.||+||+..+.|.+..
T Consensus 90 ~G~Vy~yd~~~~~l~~lA 107 (125)
T PF02393_consen 90 SGRVYAYDPEDDRLYRLA 107 (125)
T ss_pred CCeEEEEEcCCCEEEEEe
Confidence 499999999988877654
No 126
>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=24.88 E-value=1.6e+02 Score=21.88 Aligned_cols=35 Identities=14% Similarity=0.067 Sum_probs=29.9
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
..--|..|.|.+-.+.-.+|.|...++..+.+++.
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Ve 75 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVE 75 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEc
Confidence 45679999999998888999999999888877664
No 127
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=24.85 E-value=1.3e+02 Score=20.89 Aligned_cols=37 Identities=22% Similarity=0.527 Sum_probs=25.5
Q ss_pred HHHHHHhhhcc---eEEcCCcEEEeeeEEEcCCCCCCCccCCChhHHHHHHHHHHHHHHHHh
Q 030131 117 NIFDALSKTLP---VRWDKTVIVVMNEVRVSSPYLPESVSGGTAAANERVKKVLEFERKRLQ 175 (182)
Q Consensus 117 ~lFd~L~Kt~p---v~W~~~~IvV~d~V~I~pPY~~~n~~~~~~~~l~rV~kIl~~~~~~~~ 175 (182)
.||..++|+|| -.|.+. -+.+.+-|+.+++...+--+
T Consensus 35 ~lYshiaKsMPpL~kHWN~~----------------------~PeaK~~ik~li~~Ik~lNe 74 (82)
T PF10835_consen 35 ALYSHIAKSMPPLAKHWNGT----------------------YPEAKEEIKELIEEIKQLNE 74 (82)
T ss_pred HHHHHHHHhCcHHHHhhccc----------------------CchHHHHHHHHHHHHHHHHH
Confidence 57999999998 489753 23466677777766554443
No 128
>cd07933 RHD-n_c-Rel N-terminal sub-domain of the Rel homology domain (RHD) of c-Rel. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the c-Rel family of transcription factors, categorized as a class II member of the NF-kappa B family. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B
Probab=24.62 E-value=63 Score=25.80 Aligned_cols=28 Identities=25% Similarity=0.465 Sum_probs=23.8
Q ss_pred hhhcc----eEEcCCcEEEeeeEEEcCCCCCC
Q 030131 123 SKTLP----VRWDKTVIVVMNEVRVSSPYLPE 150 (182)
Q Consensus 123 ~Kt~p----v~W~~~~IvV~d~V~I~pPY~~~ 150 (182)
.|||| +.|+|..+|+..=|+-.+||.+-
T Consensus 37 ~KT~Ptv~i~nY~G~a~I~VslVT~d~P~rpH 68 (172)
T cd07933 37 NRTYPSIQILNYTGKGKVRITLVTKNEPYKPH 68 (172)
T ss_pred CCcCCeEEEEcCcCCEEEEEEEEeCCCCCCCC
Confidence 38998 57789988888899999999884
No 129
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=24.46 E-value=2e+02 Score=19.97 Aligned_cols=35 Identities=14% Similarity=0.232 Sum_probs=31.1
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
.+..|..|.|..-.+.--+|.|...|+..+.+++.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 56789999999988888889999999999988774
No 130
>cd07887 RHD-n_Dorsal_Dif N-terminal sub-domain of the Rel homology domain (RHD) of the arthropod protein Dorsal. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the arthropod Dorsal and Dif (Dorsal-related immunity factor), and similar proteins. Dorsal and Dif are Rel-like transcription factors, which play roles in mediating innate immunity in Drosophila. They are activated via the Toll pathway. Cytoplasmic Dorsal/Dif are inactivated via forming a complex with Cactus, the Drosophila homologue of mammalian I-kappa B proteins. In response to signals, Cactus is degraded and Dorsal/Dif can be transported into the nucleus, where they act as transcription factors. Dorsal is also an essential gene in establishing the proper dorsal/ventral polarity in the developing embryo.
Probab=24.40 E-value=64 Score=25.75 Aligned_cols=27 Identities=37% Similarity=0.700 Sum_probs=23.5
Q ss_pred hhhcc----eEEcCCcEEEeeeEEEcCCCCC
Q 030131 123 SKTLP----VRWDKTVIVVMNEVRVSSPYLP 149 (182)
Q Consensus 123 ~Kt~p----v~W~~~~IvV~d~V~I~pPY~~ 149 (182)
.|||| +.|+|..+|+..=|+-.+||.+
T Consensus 37 ~KT~PtVki~nY~G~a~I~vslVT~d~p~rp 67 (173)
T cd07887 37 GKTFPTIQVVNYDGRAVVVVSCVTKDEPFRP 67 (173)
T ss_pred CCcCCeEEEecccCCEEEEEEEEeCCCCCCC
Confidence 48998 5788999888888999999987
No 131
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: 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 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.25 E-value=1.3e+02 Score=19.38 Aligned_cols=22 Identities=14% Similarity=0.286 Sum_probs=16.6
Q ss_pred cCCCEEEEEEEEEeCCCCeEEE
Q 030131 23 TLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 23 ~~~~~~~G~V~~~D~~~~~lvL 44 (182)
.-|+.+...|..+|+..+.|.|
T Consensus 44 ~~G~~i~~kVi~id~~~~~i~L 65 (66)
T cd05695 44 KEGQKVRARILYVDPSTKVVGL 65 (66)
T ss_pred CCCCEEEEEEEEEeCCCCEEec
Confidence 3467777888899988877665
No 132
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=24.23 E-value=73 Score=23.21 Aligned_cols=29 Identities=10% Similarity=0.052 Sum_probs=22.9
Q ss_pred EEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 18 LSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 18 V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
=+|--|.+..++|+.|||=+. +.+=+.|.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~ 31 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECF 31 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHH
Confidence 467889999999999999876 66665554
No 133
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=24.10 E-value=1.2e+02 Score=23.05 Aligned_cols=37 Identities=8% Similarity=-0.076 Sum_probs=30.8
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
.+..|.+|+|+--.=.-++|.|..+|.....+++...
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~ 145 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNL 145 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehh
Confidence 4678999999977778999999999988887766543
No 134
>PF05735 TSP_C: Thrombospondin C-terminal region; InterPro: IPR008859 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. The globular C-terminal domain is a beta sandwich of two curved antiparallel beta-sheets []. The fold is an elaboration of the jelly role topology, with strand B3-B7, B11 and B14-B15 forming the eight-stranded jelly roll motif. The function of the C-terminal domain is not yet known.; GO: 0005509 calcium ion binding, 0007155 cell adhesion, 0005576 extracellular region; PDB: 1UX6_A 1YO8_A 2RHP_A 3FBY_C.
Probab=23.61 E-value=1.2e+02 Score=24.76 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=19.7
Q ss_pred EEEEecCCCEEEEEEEEEeCCCCeEEE
Q 030131 18 LSIKTTLGDEFDGQVMAFDRFTNMLVI 44 (182)
Q Consensus 18 V~vtt~~~~~~~G~V~~~D~~~~~lvL 44 (182)
..|.|..|+-+-|.||+|.++.++.++
T Consensus 41 ~~Vnt~~DDDyiGFVFGYQsn~~FYvv 67 (201)
T PF05735_consen 41 FFVNTTSDDDYIGFVFGYQSNRKFYVV 67 (201)
T ss_dssp EEE--SS---EEEEEEEEEETTEEEEE
T ss_pred EEEecCCCCCEEEEEEEecCCCeEEEE
Confidence 356688899999999999999999988
No 135
>PRK14630 hypothetical protein; Provisional
Probab=23.36 E-value=3.4e+02 Score=20.68 Aligned_cols=47 Identities=9% Similarity=0.052 Sum_probs=30.5
Q ss_pred eccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCCCCCcceEEEEecCCeeEEEE
Q 030131 14 VGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLKSGPRRNIRLLNANYIKDFSF 69 (182)
Q Consensus 14 vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~~~~~~~~~iIn~~~Ik~i~v 69 (182)
+|.+|+|++ .+...+|.+..+|. +.++|.... ...-|+.+.|+...+
T Consensus 96 ~G~~v~V~l-~~~~~~G~L~~~~d--~~i~l~~~~------~~~~i~~~~I~ka~l 142 (143)
T PRK14630 96 EGKKIKLML-DNDFEEGFILEAKA--DSFIFKTDS------KEVNVLYSDVKKAKL 142 (143)
T ss_pred CCCEEEEEE-cCcceEEEEEEEeC--CEEEEEECC------EEEEEEhHhcceEEE
Confidence 899999988 34456899999986 566665421 123345566655543
No 136
>cd07935 RHD-n_NFkB1 N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 family of transcription factors, a class I member of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex
Probab=23.26 E-value=67 Score=26.28 Aligned_cols=27 Identities=15% Similarity=0.158 Sum_probs=23.2
Q ss_pred hhhcc----eEEcCCcEEEeeeEEEcCCCCC
Q 030131 123 SKTLP----VRWDKTVIVVMNEVRVSSPYLP 149 (182)
Q Consensus 123 ~Kt~p----v~W~~~~IvV~d~V~I~pPY~~ 149 (182)
.|||| +.|+|..+|+..=|+-.+||.+
T Consensus 37 ~KT~Ptv~i~nY~G~a~I~VsLVT~d~p~rp 67 (202)
T cd07935 37 KKSYPQVKICNYVGPAKVIVQLVTNGKNIHL 67 (202)
T ss_pred CCcCCeEEEecCcCCEEEEEEEEeCCCCCCC
Confidence 38998 5789999888889999999966
No 137
>PLN02150 terpene synthase/cyclase family protein
Probab=23.08 E-value=1.1e+02 Score=21.78 Aligned_cols=20 Identities=20% Similarity=0.170 Sum_probs=18.0
Q ss_pred ChhHHHHHHHHHHHHHHHHh
Q 030131 156 TAAANERVKKVLEFERKRLQ 175 (182)
Q Consensus 156 ~~~~l~rV~kIl~~~~~~~~ 175 (182)
.+.|.+++++.++..|+++.
T Consensus 21 eeeA~~~i~~li~~~WK~iN 40 (96)
T PLN02150 21 KEEAVSELKKMIRDNYKIVM 40 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999986
No 138
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=22.99 E-value=2.2e+02 Score=20.32 Aligned_cols=35 Identities=26% Similarity=0.408 Sum_probs=24.9
Q ss_pred ccEEEEEecCCCEEEEEEEEEeCCCCeEEEEecCC
Q 030131 15 GCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEGLK 49 (182)
Q Consensus 15 G~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~~~ 49 (182)
+..|.+....|+.+.=.|...|+..+.++|..+..
T Consensus 21 ~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD~~~~ 55 (108)
T PF07317_consen 21 RSPLTVRHPRGQSFITSILAVDPDRGTLVLDEGSD 55 (108)
T ss_dssp T--EEEETT-SSEEEE-EEEEETTTTEEEEE--BS
T ss_pred CCeEEEEeCCCCEEEEEEEEEeCCCCEEEEEcCCC
Confidence 34677887778889999999999999999987643
No 139
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=22.96 E-value=2.4e+02 Score=19.24 Aligned_cols=35 Identities=14% Similarity=0.200 Sum_probs=31.1
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
.+..|.+|.|.+-.+.=-+|+|...|+..+.+++.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 67789999999988888889999999999988775
No 140
>COG3553 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.80 E-value=2.6e+02 Score=20.07 Aligned_cols=60 Identities=17% Similarity=0.279 Sum_probs=38.9
Q ss_pred HHHHHHHhhhcceEEcCC----cEEEeeeEEEcCCCCCCC--ccCCChhHHHHHHHHHHHHHHHHh
Q 030131 116 QNIFDALSKTLPVRWDKT----VIVVMNEVRVSSPYLPES--VSGGTAAANERVKKVLEFERKRLQ 175 (182)
Q Consensus 116 Q~lFd~L~Kt~pv~W~~~----~IvV~d~V~I~pPY~~~n--~~~~~~~~l~rV~kIl~~~~~~~~ 175 (182)
|+|-.+...-+|++|+.. +.=+++-++...|=..=. |.++.+..|.|.+.||..+-.+..
T Consensus 18 ~qLckHwahKf~ve~~p~~g~idl~~~~~~~l~a~a~~L~i~v~~d~e~~lA~le~VVa~Hi~rfa 83 (96)
T COG3553 18 QQLCKHWAHKFPVEFDPTHGTIDLPVLGTLTLDADAQTLTIVVEADEEQNLARLEDVVASHIDRFA 83 (96)
T ss_pred HHHHHHhhccCCceECCCcceeecCccceEEeecCCCEEEEEeccchhhhHHHHHHHHHHHHHHHH
Confidence 445556666779999864 223345555655544333 345666789999999998877664
No 141
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=22.32 E-value=1.4e+02 Score=22.32 Aligned_cols=28 Identities=21% Similarity=0.288 Sum_probs=22.7
Q ss_pred eeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 12 FAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 12 ~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
...|.+||+ -|+|..||+.++.|+|...
T Consensus 22 ~~~g~KVRf--------LgcV~~Y~~~~~~L~l~h~ 49 (124)
T PF12658_consen 22 CSPGDKVRF--------LGCVSSYDTSTGTLTLEHN 49 (124)
T ss_dssp TTCTEEEEE--------EEEEEEEECCCTEEEEEET
T ss_pred CCCCCEEEE--------EEEEeEEecCccEEEEeec
Confidence 346777765 4899999999999999873
No 142
>PRK06955 biotin--protein ligase; Provisional
Probab=22.26 E-value=1.6e+02 Score=25.09 Aligned_cols=35 Identities=11% Similarity=0.093 Sum_probs=27.0
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEe
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQE 46 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~ 46 (182)
+...|..|++....++.++|.+..+|+. +.|+|+.
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~-G~L~v~~ 279 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGIDET-GQLLLDT 279 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeECCC-ceEEEEe
Confidence 4568999999766667799999999965 5555664
No 143
>KOG3350 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.07 E-value=52 Score=26.79 Aligned_cols=25 Identities=20% Similarity=0.384 Sum_probs=17.3
Q ss_pred eeeEEEcCCCCCCCccCCChhHHHH
Q 030131 138 MNEVRVSSPYLPESVSGGTAAANER 162 (182)
Q Consensus 138 ~d~V~I~pPY~~~n~~~~~~~~l~r 162 (182)
+|-|.+.|||-.+.|.+..+....+
T Consensus 136 fdiivaDPPfL~~eCl~Kts~tik~ 160 (217)
T KOG3350|consen 136 FDIIVADPPFLSEECLAKTSETIKR 160 (217)
T ss_pred ccEEEeCCccccchhhhhhHHHHHH
Confidence 4566777999999997655444333
No 144
>PF14208 DUF4320: Domain of unknown function (DUF4320)
Probab=22.00 E-value=3.3e+02 Score=20.07 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=21.0
Q ss_pred cCCCCCHHHHHHHHHHhhhc---c-eEEc
Q 030131 107 IGVGVTTEAQNIFDALSKTL---P-VRWD 131 (182)
Q Consensus 107 ~g~gvs~egQ~lFd~L~Kt~---p-v~W~ 131 (182)
+.-|++.++.+.|..|++.+ | +.|+
T Consensus 38 ~~Gg~~~e~~~~~~~l~~k~g~~~~i~w~ 66 (116)
T PF14208_consen 38 REGGVTSETVDRIEDLSEKTGLDPMISWS 66 (116)
T ss_pred HhCCCcHHHHHHHHHHHHHhCCCCCceEe
Confidence 35788999999999999865 5 8997
No 145
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=21.93 E-value=2.2e+02 Score=21.32 Aligned_cols=35 Identities=11% Similarity=0.082 Sum_probs=30.4
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEE
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQ 45 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~ 45 (182)
....|..|.|.+-.+.--+|.|..+|+..+.+++.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 45689999999988888889999999999987775
No 146
>PF06094 AIG2: AIG2-like family; InterPro: IPR009288 AIG2 is an Arabidopsis protein that exhibit RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2 []. Its structure consists of a five-stranded beta-barrel surrounded by two alpha-helices and a small beta-sheet. A long flexible alpha-helix protrudes from the structure at the C-terminal end. Conserved residues in a hydrophilic cavity, which are able to bind small ligands, may act as an active site in AIG2-like proteins [].; PDB: 1XHS_A 2KL2_A 1VKB_A 3JUD_A 3JUB_A 3JUC_A 2JQV_A 2QIK_A 2G0Q_A 1V30_A.
Probab=21.81 E-value=1.5e+02 Score=20.20 Aligned_cols=20 Identities=15% Similarity=0.343 Sum_probs=15.3
Q ss_pred EEEEEecCCCEEEEEEEEEe
Q 030131 17 LLSIKTTLGDEFDGQVMAFD 36 (182)
Q Consensus 17 ~V~vtt~~~~~~~G~V~~~D 36 (182)
.|.|.+.+|+.++++||.+.
T Consensus 83 ~v~v~~~~g~~~~a~vYv~~ 102 (102)
T PF06094_consen 83 RVPVELGDGEEVEAWVYVWN 102 (102)
T ss_dssp EEEEECCTSSEEEEEEEEE-
T ss_pred EEEEEeCCCCEeEEEEEEEC
Confidence 56667778888899999873
No 147
>COG4806 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism]
Probab=21.48 E-value=45 Score=29.14 Aligned_cols=14 Identities=43% Similarity=1.158 Sum_probs=12.8
Q ss_pred ceEEcCCcEEEeee
Q 030131 127 PVRWDKTVIVVMNE 140 (182)
Q Consensus 127 pv~W~~~~IvV~d~ 140 (182)
||||+.+..+++|+
T Consensus 290 PVRWDSDHVV~~DD 303 (419)
T COG4806 290 PVRWDSDHVVLLDD 303 (419)
T ss_pred cccccCCeEEEech
Confidence 79999999999983
No 148
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=21.42 E-value=1.8e+02 Score=24.17 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=28.9
Q ss_pred ceeeccEEEEEecCCCEEEEEEEEEeCCCCeEEEEec
Q 030131 11 EFAVGCLLSIKTTLGDEFDGQVMAFDRFTNMLVIQEG 47 (182)
Q Consensus 11 ~~~vG~~V~vtt~~~~~~~G~V~~~D~~~~~lvL~~~ 47 (182)
...+|..|++++-.+..+.|.+...|..- -|+|.+.
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G-~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDG-ALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCc-eEEEEeC
Confidence 45689999999999999999999999654 4555543
No 149
>PF00447 HSF_DNA-bind: HSF-type DNA-binding; InterPro: IPR000232 Heat shock factor (HSF) is a transcriptional activator of heat shock genes []: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs []. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus []. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats []. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear []. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus []. The DNA-binding component of HSF lies to the N terminus of the first NLS region, and is referred to as the HSF domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1FBQ_B 1FYL_B 1FBS_A 1FYM_B 3HTS_B 2HTS_A 3HSF_A 1FBU_B 1FYK_A 2LDU_A ....
Probab=20.49 E-value=1e+02 Score=21.77 Aligned_cols=24 Identities=13% Similarity=0.567 Sum_probs=16.7
Q ss_pred HHHHHHHhh-hc-c-eEEcC--CcEEEee
Q 030131 116 QNIFDALSK-TL-P-VRWDK--TVIVVMN 139 (182)
Q Consensus 116 Q~lFd~L~K-t~-p-v~W~~--~~IvV~d 139 (182)
+.||+.|.. .. + ++|.+ +.++|.|
T Consensus 4 ~kL~~~l~~~~~~~~I~W~~~G~~fiI~d 32 (103)
T PF00447_consen 4 SKLYEMLEDPENSDIIRWSPDGDSFIIHD 32 (103)
T ss_dssp HHHHHHHCTTTTTTTCEECTTSSEEEES-
T ss_pred HHHHHHHcCCCCCCEEEEeCCCCEEEEee
Confidence 568888885 44 4 89965 4788866
Done!