Query psy10748
Match_columns 98
No_of_seqs 110 out of 1084
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 17:31:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10748.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10748hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01718 Sm_E The eukaryotic Sm 99.9 1.5E-26 3.2E-31 148.1 10.3 79 12-90 1-79 (79)
2 PTZ00138 small nuclear ribonuc 99.9 5.9E-25 1.3E-29 143.5 11.5 83 9-91 6-88 (89)
3 cd01732 LSm5 The eukaryotic Sm 99.9 1.4E-23 3.1E-28 133.3 9.6 72 16-91 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.9 2.1E-23 4.5E-28 130.8 9.2 70 16-90 3-72 (72)
5 KOG1774|consensus 99.9 1.4E-23 3E-28 134.3 6.6 85 8-92 3-87 (88)
6 cd01731 archaeal_Sm1 The archa 99.9 6.1E-23 1.3E-27 127.1 9.3 68 18-90 1-68 (68)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.4E-22 3.1E-27 125.3 9.1 67 18-89 1-67 (67)
8 cd01730 LSm3 The eukaryotic Sm 99.9 1.5E-22 3.3E-27 129.7 8.9 70 17-90 1-82 (82)
9 cd01719 Sm_G The eukaryotic Sm 99.9 2.9E-22 6.3E-27 125.9 9.3 71 18-93 1-71 (72)
10 cd01720 Sm_D2 The eukaryotic S 99.9 5.1E-22 1.1E-26 129.1 9.7 74 16-91 1-86 (87)
11 cd01722 Sm_F The eukaryotic Sm 99.9 9.2E-22 2E-26 122.1 8.2 68 17-89 1-68 (68)
12 cd01729 LSm7 The eukaryotic Sm 99.9 2.1E-21 4.5E-26 124.5 9.8 69 20-92 5-80 (81)
13 cd01723 LSm4 The eukaryotic Sm 99.9 2.9E-21 6.3E-26 122.2 9.1 73 17-93 1-73 (76)
14 cd01721 Sm_D3 The eukaryotic S 99.9 4.5E-21 9.7E-26 119.7 9.4 70 18-92 1-70 (70)
15 COG1958 LSM1 Small nuclear rib 99.8 1.2E-20 2.7E-25 119.7 9.3 73 14-90 4-79 (79)
16 cd01728 LSm1 The eukaryotic Sm 99.8 4E-20 8.7E-25 116.9 10.0 69 18-90 3-73 (74)
17 cd01727 LSm8 The eukaryotic Sm 99.8 3.4E-20 7.4E-25 116.7 9.4 69 21-93 3-74 (74)
18 smart00651 Sm snRNP Sm protein 99.8 6.4E-20 1.4E-24 112.1 9.1 66 21-90 2-67 (67)
19 PF01423 LSM: LSM domain ; In 99.8 5.7E-20 1.2E-24 112.4 8.7 67 20-90 1-67 (67)
20 cd01717 Sm_B The eukaryotic Sm 99.8 9.5E-20 2.1E-24 115.8 9.0 66 21-90 4-78 (79)
21 cd01724 Sm_D1 The eukaryotic S 99.8 2.1E-19 4.7E-24 117.3 9.5 74 17-95 1-74 (90)
22 cd01725 LSm2 The eukaryotic Sm 99.8 2.1E-18 4.6E-23 110.4 8.9 73 17-93 1-74 (81)
23 KOG1780|consensus 99.8 7.3E-19 1.6E-23 110.7 6.2 71 17-94 6-76 (77)
24 cd01733 LSm10 The eukaryotic S 99.8 3.7E-18 8E-23 108.8 9.1 70 17-91 9-78 (78)
25 cd00600 Sm_like The eukaryotic 99.8 5.2E-18 1.1E-22 102.2 8.6 63 22-89 1-63 (63)
26 cd06168 LSm9 The eukaryotic Sm 99.8 6.7E-18 1.5E-22 107.0 9.3 67 20-90 3-74 (75)
27 KOG3460|consensus 99.7 1.1E-18 2.3E-23 112.3 1.6 75 15-93 3-89 (91)
28 KOG1775|consensus 99.7 6.3E-18 1.4E-22 107.2 3.6 74 15-92 5-80 (84)
29 KOG3482|consensus 99.7 3.1E-17 6.6E-22 103.2 5.8 74 14-92 5-78 (79)
30 KOG1781|consensus 99.6 2.4E-17 5.2E-22 108.9 -0.8 74 19-96 19-99 (108)
31 KOG1783|consensus 99.6 4.2E-16 9.1E-21 98.0 1.0 72 16-92 5-76 (77)
32 KOG3293|consensus 99.5 1.3E-14 2.7E-19 99.3 4.1 76 16-95 1-76 (134)
33 KOG1784|consensus 99.4 1.7E-13 3.7E-18 89.5 4.3 72 21-96 4-78 (96)
34 KOG1782|consensus 99.2 1.8E-12 3.9E-17 88.7 -0.4 68 22-93 14-83 (129)
35 KOG3172|consensus 99.2 5.7E-11 1.2E-15 79.8 6.2 74 15-93 3-76 (119)
36 KOG3448|consensus 99.2 1.7E-10 3.8E-15 75.1 7.9 71 19-93 4-75 (96)
37 KOG3168|consensus 99.2 2.8E-12 6E-17 91.8 -0.8 68 21-92 8-84 (177)
38 KOG3428|consensus 99.0 5.3E-09 1.1E-13 70.3 8.8 72 18-95 3-74 (109)
39 cd01739 LSm11_C The eukaryotic 99.0 3.4E-10 7.4E-15 70.0 2.8 47 22-68 1-49 (66)
40 KOG3459|consensus 98.7 2.4E-09 5.1E-14 72.1 0.2 75 16-92 23-109 (114)
41 cd01716 Hfq Hfq, an abundant, 97.5 0.00031 6.8E-09 43.0 4.8 37 21-60 3-39 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.4 0.0005 1.1E-08 42.1 5.1 38 20-60 6-43 (61)
43 PRK00395 hfq RNA-binding prote 96.7 0.005 1.1E-07 39.5 4.8 37 20-58 10-46 (79)
44 COG1923 Hfq Uncharacterized ho 96.5 0.008 1.7E-07 38.3 5.0 39 20-61 10-48 (77)
45 PF12701 LSM14: Scd6-like Sm d 96.3 0.027 5.8E-07 37.2 6.6 66 24-93 5-79 (96)
46 PF14438 SM-ATX: Ataxin 2 SM d 96.2 0.024 5.3E-07 35.2 6.0 63 20-86 5-76 (77)
47 PRK14091 RNA-binding protein H 96.1 0.014 3E-07 42.1 5.0 38 20-60 15-52 (165)
48 PRK14091 RNA-binding protein H 96.0 0.016 3.5E-07 41.8 5.0 38 20-60 95-132 (165)
49 cd01736 LSm14_N LSm14 (also kn 94.3 0.31 6.6E-06 30.9 6.4 60 24-87 3-72 (74)
50 PF02237 BPL_C: Biotin protein 93.2 0.51 1.1E-05 26.8 5.5 34 26-64 2-35 (48)
51 cd01735 LSm12_N LSm12 belongs 89.0 1.1 2.5E-05 27.2 4.3 35 25-63 4-38 (61)
52 PRK14638 hypothetical protein; 88.0 1.3 2.8E-05 31.1 4.7 36 20-60 93-128 (150)
53 PRK14633 hypothetical protein; 87.9 1.3 2.7E-05 31.1 4.6 40 20-60 87-126 (150)
54 PRK14640 hypothetical protein; 85.3 2 4.4E-05 30.1 4.6 40 20-60 90-129 (152)
55 PRK14639 hypothetical protein; 85.0 2.3 5E-05 29.5 4.7 36 20-60 81-116 (140)
56 PRK02001 hypothetical protein; 84.6 2.3 4.9E-05 30.1 4.5 36 20-60 83-118 (152)
57 cd01734 YlxS_C YxlS is a Bacil 84.6 2.8 6E-05 26.3 4.5 40 20-60 18-57 (83)
58 PRK14643 hypothetical protein; 84.0 2.3 5E-05 30.4 4.4 35 20-54 97-131 (164)
59 PRK14636 hypothetical protein; 82.5 2.8 6.1E-05 30.2 4.4 40 20-60 91-130 (176)
60 PRK14634 hypothetical protein; 81.4 3.4 7.4E-05 29.1 4.4 40 20-60 93-132 (155)
61 PF11095 Gemin7: Gem-associate 81.2 12 0.00025 24.0 6.8 62 19-90 16-78 (80)
62 PRK00092 ribosome maturation p 80.9 4 8.7E-05 28.4 4.6 35 19-53 90-124 (154)
63 COG0779 Uncharacterized protei 80.8 4 8.6E-05 29.0 4.6 40 20-60 92-131 (153)
64 PF14563 DUF4444: Domain of un 80.7 2 4.4E-05 24.4 2.4 22 44-65 10-31 (42)
65 PRK14646 hypothetical protein; 79.8 3.9 8.5E-05 28.8 4.3 40 20-60 93-132 (155)
66 PRK14631 hypothetical protein; 77.9 5.2 0.00011 28.8 4.5 34 19-52 109-142 (174)
67 PF02576 DUF150: Uncharacteris 77.0 2.5 5.4E-05 28.9 2.5 39 20-59 80-118 (141)
68 PRK14642 hypothetical protein; 77.0 6 0.00013 29.2 4.7 39 20-59 93-140 (197)
69 PRK14644 hypothetical protein; 74.5 5.4 0.00012 27.6 3.7 35 21-60 79-117 (136)
70 PRK14645 hypothetical protein; 73.8 8.1 0.00018 27.3 4.5 35 20-60 95-129 (154)
71 PRK14647 hypothetical protein; 71.3 10 0.00022 26.7 4.6 34 20-53 92-130 (159)
72 KOG1073|consensus 67.4 17 0.00037 29.3 5.5 66 23-92 5-80 (361)
73 PRK14632 hypothetical protein; 66.2 15 0.00033 26.3 4.7 38 20-60 91-133 (172)
74 PRK14641 hypothetical protein; 64.8 14 0.00031 26.6 4.3 33 20-52 97-129 (173)
75 PRK14637 hypothetical protein; 63.9 17 0.00036 25.6 4.4 37 19-60 90-127 (151)
76 PF10842 DUF2642: Protein of u 63.8 32 0.00069 21.2 6.5 54 19-90 13-66 (66)
77 PF06372 Gemin6: Gemin6 protei 62.6 11 0.00024 27.2 3.3 65 17-94 8-73 (166)
78 PRK06955 biotin--protein ligas 52.4 70 0.0015 24.5 6.5 24 38-61 256-279 (300)
79 TIGR02038 protease_degS peripl 51.3 34 0.00074 26.7 4.7 30 34-63 104-133 (351)
80 PRK10898 serine endoprotease; 50.5 37 0.0008 26.7 4.8 30 34-63 104-133 (353)
81 cd04479 RPA3 RPA3: A subfamily 50.4 33 0.00072 22.2 3.8 14 20-33 8-21 (101)
82 KOG3382|consensus 50.1 9.3 0.0002 27.0 1.2 20 45-64 46-65 (151)
83 PRK11886 bifunctional biotin-- 49.7 64 0.0014 24.6 5.9 22 39-60 279-300 (319)
84 PF05071 NDUFA12: NADH ubiquin 48.0 12 0.00027 24.6 1.5 17 46-62 1-17 (105)
85 PF14153 Spore_coat_CotO: Spor 46.4 33 0.00071 25.1 3.6 36 19-55 123-158 (185)
86 PF03614 Flag1_repress: Repres 46.0 38 0.00082 24.4 3.8 32 21-54 112-143 (165)
87 PRK14635 hypothetical protein; 45.8 55 0.0012 23.1 4.7 38 20-60 92-132 (162)
88 PRK10942 serine endoprotease; 43.8 49 0.0011 27.1 4.7 29 34-62 138-166 (473)
89 TIGR02037 degP_htrA_DO peripla 42.9 53 0.0011 26.2 4.7 30 34-63 84-113 (428)
90 PRK13325 bifunctional biotin-- 42.5 97 0.0021 26.3 6.3 23 39-61 286-308 (592)
91 PRK10139 serine endoprotease; 42.1 57 0.0012 26.6 4.8 56 35-92 118-175 (455)
92 PF03614 Flag1_repress: Repres 39.9 74 0.0016 22.9 4.5 27 37-63 35-61 (165)
93 PHA00672 hypothetical protein 38.0 1.4E+02 0.0031 21.0 5.8 44 36-87 52-95 (152)
94 PRK14630 hypothetical protein; 37.7 77 0.0017 22.0 4.3 35 20-60 90-124 (143)
95 PF11607 DUF3247: Protein of u 33.7 1E+02 0.0022 20.5 4.1 29 19-49 18-46 (101)
96 PRK08330 biotin--protein ligas 30.9 2E+02 0.0043 21.0 5.8 23 39-61 195-218 (236)
97 PF08863 YolD: YolD-like prote 30.5 1.3E+02 0.0028 18.2 6.5 39 21-60 34-74 (92)
98 PTZ00275 biotin-acetyl-CoA-car 28.9 1.9E+02 0.0041 22.1 5.5 23 39-61 244-266 (285)
99 TIGR00121 birA_ligase birA, bi 28.0 2.1E+02 0.0045 20.9 5.5 22 39-60 200-221 (237)
100 PRK06630 hypothetical protein; 26.7 36 0.00079 22.6 1.1 19 45-63 12-30 (99)
101 PF14485 DUF4431: Domain of un 25.2 89 0.0019 17.8 2.4 14 19-32 11-24 (48)
102 PF11684 DUF3280: Protein of u 24.4 70 0.0015 22.2 2.2 38 42-84 83-123 (140)
103 PRK08477 biotin--protein ligas 21.4 2.7E+02 0.0058 20.4 4.9 28 38-65 181-208 (211)
No 1
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.94 E-value=1.5e-26 Score=148.14 Aligned_cols=79 Identities=77% Similarity=1.222 Sum_probs=72.9
Q ss_pred eeeeeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 12 QKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 12 ~~~~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
++.|++|+..+.+|++++.+|+||++.++|++++|+|.|||+|||++|+||+|+...+++.+.+|.++|||+||++|++
T Consensus 1 ~~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 1 QKVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 5789999999999999999999998888999999999999999999999999997444567889999999999999974
No 2
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.93 E-value=5.9e-25 Score=143.47 Aligned_cols=83 Identities=66% Similarity=1.063 Sum_probs=76.6
Q ss_pred ccceeeeeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEE
Q psy10748 9 PKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88 (98)
Q Consensus 9 ~~~~~~~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I 88 (98)
++-|+.|.+|+.++.+|+.++.+|.||+...++++++|+|.|||+|||++|+||+|...+++..+.+|.++||||||.+|
T Consensus 6 ~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I 85 (89)
T PTZ00138 6 RKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLI 85 (89)
T ss_pred cccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEE
Confidence 48899999999999999999999999998888999999999999999999999999875455678999999999999999
Q ss_pred Eec
Q psy10748 89 QNL 91 (98)
Q Consensus 89 ~~~ 91 (98)
++.
T Consensus 86 ~~~ 88 (89)
T PTZ00138 86 MAA 88 (89)
T ss_pred EcC
Confidence 864
No 3
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=1.4e-23 Score=133.26 Aligned_cols=72 Identities=35% Similarity=0.696 Sum_probs=63.8
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec--CceeeeeCeEEEeCCcEEEEEec
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK--SKTRKALGTIMLKGDNITLIQNL 91 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~--~~~~~~lg~vliRG~~I~~I~~~ 91 (98)
..|+++|.++++++ |++++++|+++.|+|+|||+|||++|+||+|++.+ +++.+++|.++|||+||.+|+|.
T Consensus 2 ~~P~~~L~~~~~~~----V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSR----IWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCE----EEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 47999999999999 45689999999999999999999999999999732 33567899999999999999963
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.90 E-value=2.1e-23 Score=130.84 Aligned_cols=70 Identities=24% Similarity=0.500 Sum_probs=62.7
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
..|+++|.+++++++ .+++++|++|+|+|.|||+|||++|+||+|.. +++..+.+|.++|||+||++|++
T Consensus 3 ~~P~~~L~~~~~k~V----~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSPV----LVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCEE----EEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEcC
Confidence 579999999999994 34789999999999999999999999999986 45567889999999999999974
No 5
>KOG1774|consensus
Probab=99.89 E-value=1.4e-23 Score=134.32 Aligned_cols=85 Identities=74% Similarity=1.146 Sum_probs=78.7
Q ss_pred cccceeeeeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEE
Q psy10748 8 APKVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITL 87 (98)
Q Consensus 8 ~~~~~~~~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~ 87 (98)
.+++|+.|++|++++.+|+..+.||.||+.-.-|..++|.++|||+|||+||+||+|...+....+.+|.++++||||.+
T Consensus 3 ~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItl 82 (88)
T KOG1774|consen 3 REKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITL 82 (88)
T ss_pred cccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEE
Confidence 36999999999999999999999999999999999999999999999999999999998666666699999999999999
Q ss_pred EEecC
Q psy10748 88 IQNLN 92 (98)
Q Consensus 88 I~~~~ 92 (98)
|....
T Consensus 83 i~~~~ 87 (88)
T KOG1774|consen 83 IQSAG 87 (88)
T ss_pred EeecC
Confidence 98654
No 6
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.89 E-value=6.1e-23 Score=127.11 Aligned_cols=68 Identities=25% Similarity=0.483 Sum_probs=61.4
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
|+++|.+++++++ ++++++|++|+|+|.|||+|||++|+||+|++. +...+.+|.++|||+||++|++
T Consensus 1 p~~~L~~~~~~~V----~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~-~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPV----LVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDD-GEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEE----EEEECCCCEEEEEEEEECCcceEEEeeEEEEec-CCeEeEcCcEEEeCCEEEEEcC
Confidence 8999999999994 447899999999999999999999999999874 4467889999999999999975
No 7
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=1.4e-22 Score=125.32 Aligned_cols=67 Identities=25% Similarity=0.472 Sum_probs=60.4
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEE
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~ 89 (98)
|+++|++++++++ .+++++|++|+|+|.|||+|||++|+||+|.. .+...+.++.++|||++|.+|+
T Consensus 1 p~~~L~~~~~~~V----~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPV----VVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeE----EEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCceeeEeCCEEEECCEEEEEC
Confidence 8999999999994 44789999999999999999999999999875 4556788999999999999984
No 8
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=1.5e-22 Score=129.67 Aligned_cols=70 Identities=21% Similarity=0.469 Sum_probs=61.5
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC------------ceeeeeCeEEEeCCc
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS------------KTRKALGTIMLKGDN 84 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~------------~~~~~lg~vliRG~~ 84 (98)
.|+++|.+++++++ .+++++|+++.|+|.|||+||||+|+||+|.+... ...+.+|.++|||+|
T Consensus 1 ~pl~~l~~~~~k~V----~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~ 76 (82)
T cd01730 1 EPLDLIRLSLDERV----YVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDS 76 (82)
T ss_pred CchHHHHHhCCCEE----EEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCE
Confidence 49999999999994 44789999999999999999999999999997421 246789999999999
Q ss_pred EEEEEe
Q psy10748 85 ITLIQN 90 (98)
Q Consensus 85 I~~I~~ 90 (98)
|++|++
T Consensus 77 Vv~i~~ 82 (82)
T cd01730 77 VILVSP 82 (82)
T ss_pred EEEECC
Confidence 999874
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=2.9e-22 Score=125.91 Aligned_cols=71 Identities=25% Similarity=0.523 Sum_probs=63.0
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCC
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
|-..|.+++++++ ++++++|++++|+|.|||+||||+|+||+|+. ++...+.+|.++|||+||++|++.|+
T Consensus 1 ~~~~L~~~i~k~V----~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 1 HPPELKKYMDKKL----SLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeE----EEEECCCeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCCEEEEEEcccc
Confidence 4568999999994 44789999999999999999999999999987 44567889999999999999998865
No 10
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=5.1e-22 Score=129.10 Aligned_cols=74 Identities=23% Similarity=0.439 Sum_probs=61.5
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC------------ceeeeeCeEEEeCC
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS------------KTRKALGTIMLKGD 83 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~------------~~~~~lg~vliRG~ 83 (98)
+.|+++|.+++...-+| .+++++|+++.|+|.|||+||||+|+||+|.+... ...+.+|.+||||+
T Consensus 1 ~gPl~~L~~~~~~~~~V--~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd 78 (87)
T cd01720 1 TGPLSLLTQAVKNNTQV--LINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGD 78 (87)
T ss_pred CChHHHHHHHHcCCCEE--EEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCC
Confidence 47999999998433334 44789999999999999999999999999987532 13567899999999
Q ss_pred cEEEEEec
Q psy10748 84 NITLIQNL 91 (98)
Q Consensus 84 ~I~~I~~~ 91 (98)
+|++|++.
T Consensus 79 ~Vv~Is~~ 86 (87)
T cd01720 79 SVILVLRN 86 (87)
T ss_pred EEEEEecC
Confidence 99999875
No 11
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.87 E-value=9.2e-22 Score=122.08 Aligned_cols=68 Identities=22% Similarity=0.448 Sum_probs=60.6
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEE
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~ 89 (98)
.|+.+|++++++++ .+++++|++|+|+|.|||+|||++|+||+|+. ++.....+|.++|||++|.+|+
T Consensus 1 ~p~~~L~~~~g~~V----~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPV----IVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEE----EEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCccccCcCcEEEECCEEEEEC
Confidence 49999999999994 44789999999999999999999999999985 4556678999999999999983
No 12
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.1e-21 Score=124.48 Aligned_cols=69 Identities=22% Similarity=0.460 Sum_probs=60.2
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC-------ceeeeeCeEEEeCCcEEEEEecC
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS-------KTRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~-------~~~~~lg~vliRG~~I~~I~~~~ 92 (98)
--|.++++++++| ++++|+++.|+|.|||+||||+|+||+|+...+ ...+.+|.++|||+||++|++.+
T Consensus 5 ~~L~~~i~k~V~V----~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRV----KFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEE----EECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 3499999999544 789999999999999999999999999987532 25688999999999999999876
No 13
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=2.9e-21 Score=122.20 Aligned_cols=73 Identities=15% Similarity=0.219 Sum_probs=64.2
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCC
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
.|+++|+++.++++ .+++++|++++|+|.+||+|||++|+||++...+++....++.++|||++|.+|..++.
T Consensus 1 ~Pl~~L~~~~g~~V----~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~ 73 (76)
T cd01723 1 LPLSLLKTAQNHPM----LVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDE 73 (76)
T ss_pred CchHHHHhcCCCEE----EEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHH
Confidence 49999999999993 44789999999999999999999999999986555555678999999999999998764
No 14
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=4.5e-21 Score=119.74 Aligned_cols=70 Identities=14% Similarity=0.204 Sum_probs=62.3
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecC
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~ 92 (98)
|+++|.++.+++ |++++++|.+|+|+|.++|+|||++|+||++...++ +...++.++|||+||.+|..||
T Consensus 1 P~~~L~~~~g~~----V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g-~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHI----VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG-RVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCE----EEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCC-cEeEcCcEEEeCCEEEEEEeCC
Confidence 899999999999 345889999999999999999999999999875443 4567899999999999999886
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.84 E-value=1.2e-20 Score=119.72 Aligned_cols=73 Identities=30% Similarity=0.583 Sum_probs=61.0
Q ss_pred eeeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEe-cCce-eeee-CeEEEeCCcEEEEEe
Q psy10748 14 VMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNI-KSKT-RKAL-GTIMLKGDNITLIQN 90 (98)
Q Consensus 14 ~~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~-~~~~-~~~l-g~vliRG~~I~~I~~ 90 (98)
....|+.+|.+++++++ .+++++|++|.|+|+|||+|||++|+||+|+.. ++.. .+.+ +.++|||+||.+|.+
T Consensus 4 ~~~~~~~~l~~~~~~~V----~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 4 LGPLPLSFLKKLLNKRV----LVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred ccCCcHHHHHHhhCCEE----EEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 45578999999999883 447899999999999999999999999999874 3333 3344 499999999999863
No 16
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=4e-20 Score=116.92 Aligned_cols=69 Identities=17% Similarity=0.297 Sum_probs=60.1
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC--ceeeeeCeEEEeCCcEEEEEe
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS--KTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~--~~~~~lg~vliRG~~I~~I~~ 90 (98)
++..|.+++++++ .+++++|+++.|+|.|||+|||++|+||.|....+ ...+.+|.+++||+||+++..
T Consensus 3 ~~~~L~~~l~k~v----~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKV----VVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEE----EEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 5678999999994 44789999999999999999999999999986533 236789999999999999975
No 17
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=3.4e-20 Score=116.69 Aligned_cols=69 Identities=22% Similarity=0.418 Sum_probs=59.9
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec---CceeeeeCeEEEeCCcEEEEEecCC
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK---SKTRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~---~~~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
-|.+|++++++ +++++|+.+.|+|.|||+|||++|+||+|+... +.+.+.+|.+++||+||++|.+.|.
T Consensus 3 ~L~~~l~~~V~----V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 3 TLEDYLNKTVS----VITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hHHHhcCCEEE----EEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 57899999944 478999999999999999999999999998642 2356789999999999999998763
No 18
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.83 E-value=6.4e-20 Score=112.07 Aligned_cols=66 Identities=27% Similarity=0.521 Sum_probs=59.0
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
+|.+++++++ ++.+++|+++.|+|.+||+|||++|+||+|+..++.+.+.++.++|||++|.+|.+
T Consensus 2 ~L~~~~~~~V----~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRV----LVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEE----EEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 6889999993 45789999999999999999999999999998543678899999999999999864
No 19
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.83 E-value=5.7e-20 Score=112.43 Aligned_cols=67 Identities=24% Similarity=0.479 Sum_probs=59.7
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
++|++++++++ ++.+++|++++|+|.+||+|||++|+||.+....+.+.++++.++|||++|++|.+
T Consensus 1 ~~L~~~~g~~V----~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRV----RVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEE----EEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEE----EEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 47899999994 44789999999999999999999999999998543388899999999999999975
No 20
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=9.5e-20 Score=115.84 Aligned_cols=66 Identities=27% Similarity=0.535 Sum_probs=57.1
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC---------ceeeeeCeEEEeCCcEEEEEe
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS---------KTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~---------~~~~~lg~vliRG~~I~~I~~ 90 (98)
-|.+|++++++ +++++|+++.|+|.|||+||||+|+||+|++... .+.+.+|.++|||++|++|+.
T Consensus 4 ~l~~~l~~~V~----V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLR----VTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEE----EEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 47899999944 4689999999999999999999999999987421 356889999999999999973
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=99.81 E-value=2.1e-19 Score=117.27 Aligned_cols=74 Identities=18% Similarity=0.255 Sum_probs=65.4
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCCCc
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPDE 95 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~~~ 95 (98)
.|+.+|+++.++++ .+++++|.+|+|+|.++|.|||++|+||+++. +++....++.++|||+||.+|..||..+
T Consensus 1 ~~~~fL~~l~g~~V----~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~-~~~~~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 1 KLVRFLMKLTNETV----TIELKNGTIVHGTITGVDPSMNTHLKNVKLTL-KGRNPVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred CHhHHHHhCCCCEE----EEEECCCCEEEEEEEEEcCceeEEEEEEEEEc-CCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence 37899999999994 34789999999999999999999999999986 4456778999999999999999998763
No 22
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=2.1e-18 Score=110.42 Aligned_cols=73 Identities=14% Similarity=0.195 Sum_probs=61.5
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCc-eeeeeCeEEEeCCcEEEEEecCC
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSK-TRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~-~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
.|+.+|.+..++++ .+++++|..|+|+|.++|.|||++|+||++...+.. ....++.++|||++|.+|..|+.
T Consensus 1 l~~~fL~~l~g~~V----~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~ 74 (81)
T cd01725 1 LFFSFFKTLVGKEV----TVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPAD 74 (81)
T ss_pred ChhHHHHhCCCCEE----EEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChh
Confidence 48899999999993 347899999999999999999999999988753221 23456899999999999998865
No 23
>KOG1780|consensus
Probab=99.77 E-value=7.3e-19 Score=110.73 Aligned_cols=71 Identities=25% Similarity=0.545 Sum_probs=62.9
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCCC
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPD 94 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~~ 94 (98)
.| -|.+|++|+ +.+++++||..+|+|+|||.|||+||+|+.|... ...+..++.++|||++|+++++.++.
T Consensus 6 ~P--eLkkymdKk----i~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~-~~~~~~ig~~vIrgnsiv~~eaL~~~ 76 (77)
T KOG1780|consen 6 HP--ELKKYMDKK----IVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG-DGDKNNIGMVVIRGNSIVMVEALERV 76 (77)
T ss_pred Cc--hHHHhhhhe----EEEEeCCCcEEEEEEeccchHHhhhhhhceeecC-cCCcceeeeEEEeccEEEEEeecccc
Confidence 46 799999999 4568899999999999999999999999999874 34577899999999999999998764
No 24
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.77 E-value=3.7e-18 Score=108.80 Aligned_cols=70 Identities=20% Similarity=0.270 Sum_probs=60.2
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEec
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNL 91 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~ 91 (98)
.+..+|+...++. |.+++++|.+|+|+|.++|.|||++|+||++.. .+.....++.++|||++|.+|..|
T Consensus 9 tl~~~L~~l~g~~----V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKV----VTVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCE----EEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCCceeECCcEEEECCEEEEEEcC
Confidence 4578899999998 344789999999999999999999999999875 344556799999999999999865
No 25
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=5.2e-18 Score=102.21 Aligned_cols=63 Identities=27% Similarity=0.534 Sum_probs=55.3
Q ss_pred HHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEE
Q psy10748 22 IFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89 (98)
Q Consensus 22 L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~ 89 (98)
|++++++++ ++.+++|++|.|+|.+||+|||++|+||.+.... ...+.++.++|||++|.+|.
T Consensus 1 l~~~~g~~V----~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTV----RVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE-GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEE----EEEECCCcEEEEEEEEECCCCCEEECCEEEEecC-CcEEECCeEEEECCEEEEEC
Confidence 467899984 4478999999999999999999999999998743 56788999999999999874
No 26
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=6.7e-18 Score=106.99 Aligned_cols=67 Identities=27% Similarity=0.361 Sum_probs=58.9
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec-----CceeeeeCeEEEeCCcEEEEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK-----SKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~-----~~~~~~lg~vliRG~~I~~I~~ 90 (98)
..|.++++++++| ++++||.+.|+|.+||+||||+|+||.|+... ..+.+.+|.++|||++|++++.
T Consensus 3 ~~L~~~l~~~v~V----~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRI----HMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEE----EEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 4588999999554 68999999999999999999999999999853 2468899999999999999873
No 27
>KOG3460|consensus
Probab=99.72 E-value=1.1e-18 Score=112.31 Aligned_cols=75 Identities=23% Similarity=0.444 Sum_probs=66.2
Q ss_pred eeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec--C----------ceeeeeCeEEEeC
Q psy10748 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK--S----------KTRKALGTIMLKG 82 (98)
Q Consensus 15 ~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~--~----------~~~~~lg~vliRG 82 (98)
|..|+++|.-+++++ |++|++++++++|+|.+||+|+|++|.|++|+... . ...|....+|+||
T Consensus 3 v~ePldllrlsLdEr----VyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRG 78 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDER----VYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRG 78 (91)
T ss_pred ccccHHHHhhcccce----EEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeC
Confidence 678999999999999 56699999999999999999999999999998751 1 2357788999999
Q ss_pred CcEEEEEecCC
Q psy10748 83 DNITLIQNLNP 93 (98)
Q Consensus 83 ~~I~~I~~~~~ 93 (98)
++|.+|+++-.
T Consensus 79 d~Vilvspp~~ 89 (91)
T KOG3460|consen 79 DGVILVSPPLR 89 (91)
T ss_pred CeEEEEcCccc
Confidence 99999999854
No 28
>KOG1775|consensus
Probab=99.71 E-value=6.3e-18 Score=107.22 Aligned_cols=74 Identities=31% Similarity=0.656 Sum_probs=66.8
Q ss_pred eeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCc--eeeeeCeEEEeCCcEEEEEecC
Q psy10748 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSK--TRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 15 ~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~--~~~~lg~vliRG~~I~~I~~~~ 92 (98)
...|++++.+|++.+ ||+.+++.+++.|+|+|||.|.|++|+|++|+...++ ...+++++++.|+||.+..+.-
T Consensus 5 ~llPlEliDkcIgsk----i~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSK----IWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred hcccHHHHHHhcCce----EEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 357999999999999 6889999999999999999999999999999986543 5678999999999999988764
No 29
>KOG3482|consensus
Probab=99.70 E-value=3.1e-17 Score=103.20 Aligned_cols=74 Identities=23% Similarity=0.384 Sum_probs=66.0
Q ss_pred eeeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecC
Q psy10748 14 VMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 14 ~~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~ 92 (98)
+...|-.||+...++++. +++|-|.+|+|+|++.|.|||+.|.+|+|+. ++...-.+|.++||++||.+|...+
T Consensus 5 ~PvNPKpFL~~l~gk~V~----vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i-dG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 5 QPVNPKPFLNGLTGKPVL----VKLKWGQEYKGTLVSVDNYMNLQLANAEEYI-DGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred ccCCchHHHhhccCCeEE----EEEecCcEEEEEEEEecchhheehhhhhhhh-cccccccceeEEEEeccEEEEecCC
Confidence 345899999999999954 4789999999999999999999999999986 6777889999999999999997654
No 30
>KOG1781|consensus
Probab=99.63 E-value=2.4e-17 Score=108.90 Aligned_cols=74 Identities=24% Similarity=0.421 Sum_probs=65.9
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC-------ceeeeeCeEEEeCCcEEEEEec
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS-------KTRKALGTIMLKGDNITLIQNL 91 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~-------~~~~~lg~vliRG~~I~~I~~~ 91 (98)
+-.|.+|+++++|| ++.+||+.+|+|.|||+.||+||+|+.|+-.++ ++.|++|.+++||..+++|++.
T Consensus 19 ilDLsky~Dk~Irv----kf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~ 94 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRV----KFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPA 94 (108)
T ss_pred HhhHHHhhccceEE----EeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCC
Confidence 55788999999665 679999999999999999999999999987643 3569999999999999999999
Q ss_pred CCCcc
Q psy10748 92 NPDEV 96 (98)
Q Consensus 92 ~~~~~ 96 (98)
|..|.
T Consensus 95 dG~e~ 99 (108)
T KOG1781|consen 95 DGSEE 99 (108)
T ss_pred cchhh
Confidence 98873
No 31
>KOG1783|consensus
Probab=99.57 E-value=4.2e-16 Score=98.02 Aligned_cols=72 Identities=25% Similarity=0.451 Sum_probs=65.5
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecC
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~ 92 (98)
.-|-+||.++++++| .+++.+|-.|+|+|...|.||||.|+.++|+. .++.++..+.+||||++|.+|+...
T Consensus 5 ~~~~~fl~~iiGr~V----~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTV----VVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCeE----EEEecCCccccceehhhhhHHHHHHHHHHHHh-cCcccccccceeeccccEEEEEecc
Confidence 468999999999994 44889999999999999999999999999986 6888999999999999999998753
No 32
>KOG3293|consensus
Probab=99.51 E-value=1.3e-14 Score=99.33 Aligned_cols=76 Identities=13% Similarity=0.186 Sum_probs=69.0
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCCCc
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPDE 95 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~~~ 95 (98)
+.||.+|..+-++. +.|+||||..|.|.|+.+|.||||.|.+++++..++.....++.+.|||++|.++..+|..-
T Consensus 1 mlPLsLL~~aq~~p----mlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~ii 76 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHP----MLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEII 76 (134)
T ss_pred CcchhHHHhcCCCe----EEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHH
Confidence 37999999999999 45688999999999999999999999999999988888888999999999999999887643
No 33
>KOG1784|consensus
Probab=99.42 E-value=1.7e-13 Score=89.50 Aligned_cols=72 Identities=21% Similarity=0.428 Sum_probs=61.9
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec---CceeeeeCeEEEeCCcEEEEEecCCCcc
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK---SKTRKALGTIMLKGDNITLIQNLNPDEV 96 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~---~~~~~~lg~vliRG~~I~~I~~~~~~~~ 96 (98)
-|..|+++++.| ...+||.+.|.|.|||+..||+|+++.|+..+ +.+...+|.++|||+||.+|.++|..-+
T Consensus 4 ~L~~y~n~~V~v----It~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d 78 (96)
T KOG1784|consen 4 TLEDYMNQRVSV----ITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD 78 (96)
T ss_pred hHHHHhhceEEE----EecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence 477999999543 68999999999999999999999999998753 2356788999999999999999986543
No 34
>KOG1782|consensus
Probab=99.20 E-value=1.8e-12 Score=88.66 Aligned_cols=68 Identities=18% Similarity=0.408 Sum_probs=58.7
Q ss_pred HHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCc--eeeeeCeEEEeCCcEEEEEecCC
Q psy10748 22 IFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSK--TRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 22 L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~--~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
+.+++++++ .|-+++||.+-|.|++||||-|++|+++.|.+..+. -....|..+|||+||+++...|.
T Consensus 14 l~~~~dkKl----lVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~ 83 (129)
T KOG1782|consen 14 LVEYLDKKL----LVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDL 83 (129)
T ss_pred HHHHhcceE----EEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCc
Confidence 778999994 346899999999999999999999999999986543 24567999999999999998865
No 35
>KOG3172|consensus
Probab=99.19 E-value=5.7e-11 Score=79.82 Aligned_cols=74 Identities=14% Similarity=0.196 Sum_probs=64.1
Q ss_pred eeCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCC
Q psy10748 15 MVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 15 ~~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
+..|+.+|++.-++= |.+++.+|..|+|.|...|.+||++|+|.+.+..++ ....+.+++|||+.|.++..||-
T Consensus 3 ~gvpiKlLhEaqGhI----Vt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg-~vs~le~V~IRGS~IRFlvlPdm 76 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHI----VTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDG-RVSQLEQVFIRGSKIRFLVLPDM 76 (119)
T ss_pred cccceeeeecccCcE----EEEEecCCceeeeeeEEeccccccEEEEEEEEccCC-cceeeeeEEEecCeEEEEECchH
Confidence 457999999999988 345789999999999999999999999999887543 56678999999999999988863
No 36
>KOG3448|consensus
Probab=99.18 E-value=1.7e-10 Score=75.13 Aligned_cols=71 Identities=13% Similarity=0.210 Sum_probs=58.1
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecC-ceeeeeCeEEEeCCcEEEEEecCC
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS-KTRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~-~~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
.+|+...+++++. +.+||+-.+.|+|.|+|+|+|+-|.|......+. ..--.+..+||||+.|.+|..+..
T Consensus 4 ysfFkslvg~~V~----VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 4 YSFFKSLVGKEVV----VELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred HHHHHHhcCCeEE----EEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence 4688899999943 3789999999999999999999999998775321 134567889999999999987643
No 37
>KOG3168|consensus
Probab=99.17 E-value=2.8e-12 Score=91.82 Aligned_cols=68 Identities=26% Similarity=0.484 Sum_probs=57.2
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEe---------cCceeeeeCeEEEeCCcEEEEEec
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNI---------KSKTRKALGTIMLKGDNITLIQNL 91 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~---------~~~~~~~lg~vliRG~~I~~I~~~ 91 (98)
-+-+.++.+.+| .+.+|+.+.|.+.+||+|||++|.||+|.-. +.++.|-++++++||+||++.+..
T Consensus 8 kml~~iNyr~rv----~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 8 KMLQHINYRMRV----RLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred HHHHhhcceEEE----EeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence 355677888665 5799999999999999999999999998753 235789999999999999998765
Q ss_pred C
Q psy10748 92 N 92 (98)
Q Consensus 92 ~ 92 (98)
+
T Consensus 84 g 84 (177)
T KOG3168|consen 84 G 84 (177)
T ss_pred C
Confidence 3
No 38
>KOG3428|consensus
Probab=98.98 E-value=5.3e-09 Score=70.28 Aligned_cols=72 Identities=19% Similarity=0.224 Sum_probs=62.4
Q ss_pred cHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCCCc
Q psy10748 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPDE 95 (98)
Q Consensus 18 Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~~~ 95 (98)
.+.+|.++.++++. +.+++|...+|++.+.|.+||..|.++.... .+ ++.++..+.+||+||.++..+|...
T Consensus 3 lvr~L~kl~~e~vt----IeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~-~~-~pv~l~~lsirgnniRy~~lpD~l~ 74 (109)
T KOG3428|consen 3 LVRFLKKLLNERVT----IELKNGTIVHGTIDSVDVQMNTHLKHVKMTV-KG-EPVRLDTLSIRGNNIRYYILPDSLN 74 (109)
T ss_pred HHHHHHHhhCCeEE----EEecCCcEEeeeEEEEEhhheeEEEEEEEec-CC-CceeEEEEEeecceEEEEEccCCcC
Confidence 36789999999933 3789999999999999999999999998765 33 6778899999999999999998764
No 39
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.98 E-value=3.4e-10 Score=69.99 Aligned_cols=47 Identities=26% Similarity=0.409 Sum_probs=41.4
Q ss_pred HHHHhcCcceEEEEEEecCC--eEEEEEEEEEcccCCeEEeceEEEEec
Q psy10748 22 IFRFLQNRSRVQIWLYENVN--LRIEGHILGFDEYMNIVLESAEEYNIK 68 (98)
Q Consensus 22 L~~~i~k~vrV~V~v~l~~g--~~i~G~L~gfD~~mNlvL~d~~e~~~~ 68 (98)
|.+++..+.||.|+++..+| ..++|.|++||+||||+|.|++|.+..
T Consensus 1 ~~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 1 LHRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CchhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 35788888899999988888 489999999999999999999998854
No 40
>KOG3459|consensus
Probab=98.72 E-value=2.4e-09 Score=72.14 Aligned_cols=75 Identities=21% Similarity=0.426 Sum_probs=64.3
Q ss_pred eCcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEec------C------ceeeeeCeEEEeCC
Q psy10748 16 VQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIK------S------KTRKALGTIMLKGD 83 (98)
Q Consensus 16 ~~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~------~------~~~~~lg~vliRG~ 83 (98)
.+|+..+.....+...| .+-++|++.+-|.+.|||.|-|++|+++.|.+.+ + ...|+++.+|||||
T Consensus 23 ~Gpls~~~~~~~~~~~v--Li~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGd 100 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQV--LINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGD 100 (114)
T ss_pred cCchhhhHHHhhcCcee--EEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCC
Confidence 38999999999999776 4468999999999999999999999999998852 1 12678999999999
Q ss_pred cEEEEEecC
Q psy10748 84 NITLIQNLN 92 (98)
Q Consensus 84 ~I~~I~~~~ 92 (98)
+|+.+...+
T Consensus 101 svI~v~r~p 109 (114)
T KOG3459|consen 101 SVILVLRNP 109 (114)
T ss_pred eEEEEEecc
Confidence 999998554
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=97.48 E-value=0.00031 Score=42.97 Aligned_cols=37 Identities=24% Similarity=0.485 Sum_probs=31.5
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
+|+.+..++..|+| .|.||..++|.+.|||+|+ +.|+
T Consensus 3 fln~~r~~~~~Vtv--~L~NG~~l~G~I~~fD~ft-Vll~ 39 (61)
T cd01716 3 FLNAARKEKIPVTI--YLVNGVQLKGQIESFDNFT-VLLE 39 (61)
T ss_pred HHHHHHHcCCcEEE--EEeCCcEEEEEEEEEcceE-EEEE
Confidence 67888888988765 7899999999999999999 4444
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=97.40 E-value=0.0005 Score=42.08 Aligned_cols=38 Identities=21% Similarity=0.477 Sum_probs=31.6
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
.+|+.+..++..|+| .|.||..++|.+.|||+|+ +.|+
T Consensus 6 ~fln~~r~~~~~Vti--~L~nG~~l~G~I~~fD~ft-Vll~ 43 (61)
T TIGR02383 6 QFLNTLRKERIPVTV--FLVNGVQLKGVIESFDNFT-VLLE 43 (61)
T ss_pred HHHHHHHHcCCcEEE--EEeCCcEEEEEEEEEeeeE-EEEE
Confidence 477888888888765 7899999999999999998 4443
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.66 E-value=0.005 Score=39.48 Aligned_cols=37 Identities=22% Similarity=0.494 Sum_probs=31.0
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeE
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIV 58 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlv 58 (98)
.+|+.+..++..|+| .|.||..+.|.+.|||+|.=+.
T Consensus 10 ~fLn~lr~~~~~Vti--fL~NG~~l~G~I~~fD~ftVll 46 (79)
T PRK00395 10 PFLNALRKERVPVTI--YLVNGIKLQGQIESFDNFVVLL 46 (79)
T ss_pred HHHHHHHHcCCCEEE--EEeCCcEEEEEEEEEccEEEEE
Confidence 477888888888765 7899999999999999998443
No 44
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.51 E-value=0.008 Score=38.33 Aligned_cols=39 Identities=15% Similarity=0.480 Sum_probs=31.8
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEec
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLES 61 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d 61 (98)
.+|+....+++.|+| .+.||..+.|.+.|||+|. +.|++
T Consensus 10 ~fLn~~Rk~~i~VtI--fLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 10 PFLNALRKEKIPVTI--FLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred HHHHHHHhcCCeEEE--EEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 367777778877765 7899999999999999998 55655
No 45
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.25 E-value=0.027 Score=37.19 Aligned_cols=66 Identities=18% Similarity=0.453 Sum_probs=50.7
Q ss_pred HHhcCcceEEEEEEecCCeEEEEEEEEEcc-cCCeEEeceEEEEecCc--------eeeeeCeEEEeCCcEEEEEecCC
Q psy10748 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDE-YMNIVLESAEEYNIKSK--------TRKALGTIMLKGDNITLIQNLNP 93 (98)
Q Consensus 24 ~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~-~mNlvL~d~~e~~~~~~--------~~~~lg~vliRG~~I~~I~~~~~ 93 (98)
.|+|++ |.+..+.+..|+|+|..+|. --+|.|.++..+-.++. .......+..||+.|.-+...+.
T Consensus 5 ~~IGs~----ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~ 79 (96)
T PF12701_consen 5 PYIGSK----ISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEP 79 (96)
T ss_dssp CCTTCE----EEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-
T ss_pred cccCCE----EEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcC
Confidence 578999 45578999999999999998 67799999887654321 12346889999999988776543
No 46
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.21 E-value=0.024 Score=35.16 Aligned_cols=63 Identities=11% Similarity=0.194 Sum_probs=37.0
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcc---cCCeEEeceEEEEecC---c---eeeeeCeEEEeCCcEE
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDE---YMNIVLESAEEYNIKS---K---TRKALGTIMLKGDNIT 86 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~---~mNlvL~d~~e~~~~~---~---~~~~lg~vliRG~~I~ 86 (98)
-++..++|+++. +.++||..|+|+|.+++. -+.++|+-+....... . .......+++.++.|+
T Consensus 5 ~l~~~lvG~~V~----V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 5 YLLTNLVGQTVE----VTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHTTTTSEEE----EEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHhCcCCEEE----EEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 356778899944 367999999999999999 8999998887653211 1 1233455666666654
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=96.12 E-value=0.014 Score=42.11 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=31.9
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
.+|+.+..+++.|+| .|.||-.++|.+.|||+|. +.|+
T Consensus 15 ~fLn~~Rk~k~~Vtv--fL~nG~rl~G~I~~fD~ft-VlL~ 52 (165)
T PRK14091 15 IFLNSLRKTKTPVTM--FLVKGVKLQGIITWFDNFS-ILLR 52 (165)
T ss_pred HHHHHHHhcCCcEEE--EEecCcEEEEEEEEEcceE-EEEE
Confidence 478888889988765 6799999999999999998 4444
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=96.04 E-value=0.016 Score=41.78 Aligned_cols=38 Identities=18% Similarity=0.363 Sum_probs=31.9
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
.+|+.+..+++.|+| .|.||-.++|.+.|||+|. +.|+
T Consensus 95 ~fLn~~rk~k~~Vtv--fL~NG~~l~G~I~~fD~ft-vlL~ 132 (165)
T PRK14091 95 VFLSAVRDSGEPVTM--FLVNGVMLQGEIAAFDLFC-MLLE 132 (165)
T ss_pred HHHHHHHhcCCcEEE--EEecCcEEEEEEEEEcceE-EEEE
Confidence 478888889988765 7899999999999999998 4443
No 49
>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=94.30 E-value=0.31 Score=30.90 Aligned_cols=60 Identities=17% Similarity=0.396 Sum_probs=44.1
Q ss_pred HHhcCcceEEEEEEecCCeEEEEEEEEEcccCC-eEEeceEEEEecCc---------eeeeeCeEEEeCCcEEE
Q psy10748 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDEYMN-IVLESAEEYNIKSK---------TRKALGTIMLKGDNITL 87 (98)
Q Consensus 24 ~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mN-lvL~d~~e~~~~~~---------~~~~lg~vliRG~~I~~ 87 (98)
.|++++ |.+..+.+..|+|+|.++|..=+ +.|+|+..+-.++. ...-.+.++.||+.|--
T Consensus 3 ~~IG~~----isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSK----ISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCce----EEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 578888 45678999999999999998665 55888876654321 12345678899988754
No 50
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=93.19 E-value=0.51 Score=26.81 Aligned_cols=34 Identities=24% Similarity=0.299 Sum_probs=26.2
Q ss_pred hcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEE
Q psy10748 26 LQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEE 64 (98)
Q Consensus 26 i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e 64 (98)
++++++| .. ++..++|+..|+|+.=.|+++....
T Consensus 2 lG~~V~v----~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 2 LGQEVRV----ET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TTSEEEE----EE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCEEEE----EE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 5677443 34 7788899999999999999976443
No 51
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=89.03 E-value=1.1 Score=27.22 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=26.9
Q ss_pred HhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceE
Q psy10748 25 FLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 25 ~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~ 63 (98)
++|.. |.+++..|.+++|.+.+||.-.++++=.+.
T Consensus 4 ~iGs~----V~~kTc~g~~ieGEV~afD~~tk~lIlk~~ 38 (61)
T cd01735 4 SVGSQ----VSCRTCFEQRLQGEVVAFDYPSKMLILKCP 38 (61)
T ss_pred ccccE----EEEEecCCceEEEEEEEecCCCcEEEEECc
Confidence 34556 345789999999999999999988754433
No 52
>PRK14638 hypothetical protein; Provisional
Probab=87.95 E-value=1.3 Score=31.14 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=27.6
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++| ++++++.++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~v~V----~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKI----VTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEE----EECCCcEEEEEEEEEeCC-EEEEE
Confidence 4677888999544 568999999999999974 35554
No 53
>PRK14633 hypothetical protein; Provisional
Probab=87.93 E-value=1.3 Score=31.14 Aligned_cols=40 Identities=8% Similarity=0.062 Sum_probs=28.8
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+|+|++++|+..-...++++++|+|.++|+- ++.|.
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 46778999996664322235779999999999985 45554
No 54
>PRK14640 hypothetical protein; Provisional
Probab=85.33 E-value=2 Score=30.11 Aligned_cols=40 Identities=15% Similarity=0.212 Sum_probs=28.5
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++|+..-...+.++++|+|.++|+- ++.|.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 46778999996654322236779999999999984 35554
No 55
>PRK14639 hypothetical protein; Provisional
Probab=85.02 E-value=2.3 Score=29.51 Aligned_cols=36 Identities=25% Similarity=0.387 Sum_probs=28.1
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++| ++.+++.++|+|.++|+- ++.|+
T Consensus 81 ~~f~r~~G~~v~v----~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 81 EHFAKSIGELVKI----TTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHHHHhCCCEEEE----EECCCcEEEEEEEEEeCC-EEEEE
Confidence 4677899999554 567899999999999984 45553
No 56
>PRK02001 hypothetical protein; Validated
Probab=84.64 E-value=2.3 Score=30.12 Aligned_cols=36 Identities=25% Similarity=0.299 Sum_probs=28.1
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
....+++|+.++| ++.++++++|+|.++|+- ++.|.
T Consensus 83 ~~f~r~~G~~v~V----~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 83 RQYKKNIGRELEV----LTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred HHHHHhCCCEEEE----EECCCCEEEEEEEEEeCC-EEEEE
Confidence 4667899999554 567899999999999985 45554
No 57
>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=84.59 E-value=2.8 Score=26.29 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=25.3
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.+.|...-...+.++++|.|.++|+- ++.|.
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 45678888985543211112346999999999984 34443
No 58
>PRK14643 hypothetical protein; Provisional
Probab=83.98 E-value=2.3 Score=30.36 Aligned_cols=35 Identities=14% Similarity=0.080 Sum_probs=26.1
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEccc
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEY 54 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~ 54 (98)
..+.+|+|+.++|+..-...+.++++|+|.++|.-
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 46779999997664433334568999999999864
No 59
>PRK14636 hypothetical protein; Provisional
Probab=82.54 E-value=2.8 Score=30.24 Aligned_cols=40 Identities=10% Similarity=0.173 Sum_probs=27.0
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+|+|+.++|+..-...+.++++|+|.++|.- ++.|.
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 46778999996653322223447999999999883 35553
No 60
>PRK14634 hypothetical protein; Provisional
Probab=81.45 E-value=3.4 Score=29.14 Aligned_cols=40 Identities=18% Similarity=0.135 Sum_probs=27.0
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++|+..-...+.++++|+|.++|.- ++.|.
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 46778999996654321123448999999999984 35553
No 61
>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=81.24 E-value=12 Score=23.99 Aligned_cols=62 Identities=8% Similarity=0.079 Sum_probs=42.6
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccC-CeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYM-NIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~m-NlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
|.+|....++++ .+.+..+.+.+|+..++|..- |+..++-. .+ .-..+..++|++-|+++..
T Consensus 16 Lr~l~~~~gk~v----~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TP--lGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 16 LRSLLAMVGKPV----EFTLHENTTVSARFGACDIDVSNFQVSNLQ----TP--LGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHCTTSEE----EEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TT--TTEEEEEEEEGGGEEEEEE
T ss_pred HHHHHHhcCCce----EEEEeCCeEEEEEEEEecCchheEEhhhcC----CC--cccChhheeecCCEEEEEe
Confidence 566777788883 446899999999999999764 44444422 11 1224778999999999875
No 62
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=80.91 E-value=4 Score=28.45 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=26.0
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcc
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDE 53 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~ 53 (98)
...+.+++|+.++|+..-...++++++|+|.++|.
T Consensus 90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 35678899999665432223677899999999998
No 63
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.80 E-value=4 Score=29.01 Aligned_cols=40 Identities=25% Similarity=0.408 Sum_probs=30.7
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
+-+.+|+|+.+.|.......+++.++|+|.++|.-. +.+.
T Consensus 92 ~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 92 EHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred HHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEEE
Confidence 467889999966644444478899999999999987 5543
No 64
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=80.69 E-value=2 Score=24.37 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=14.8
Q ss_pred EEEEEEEEcccCCeEEeceEEE
Q psy10748 44 IEGHILGFDEYMNIVLESAEEY 65 (98)
Q Consensus 44 i~G~L~gfD~~mNlvL~d~~e~ 65 (98)
.+|+..|+|+.+.+.|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6799999999999999986643
No 65
>PRK14646 hypothetical protein; Provisional
Probab=79.75 E-value=3.9 Score=28.82 Aligned_cols=40 Identities=8% Similarity=-0.024 Sum_probs=27.4
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+|+|+.++|+..-...+.+.++|+|.++|+- ++.|+
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 46789999996654321122337899999999985 46654
No 66
>PRK14631 hypothetical protein; Provisional
Probab=77.92 E-value=5.2 Score=28.84 Aligned_cols=34 Identities=6% Similarity=0.229 Sum_probs=24.6
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEc
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFD 52 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD 52 (98)
...+.+|+|+.++|+..-...+.+.++|+|.++|
T Consensus 109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 3567889999966533222246699999999998
No 67
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=77.01 E-value=2.5 Score=28.93 Aligned_cols=39 Identities=28% Similarity=0.347 Sum_probs=24.6
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEE
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVL 59 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL 59 (98)
+.+.+++|+.++|+..-...+.++++|+|.++|. =+++|
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 5788999999554211011455799999999999 23444
No 68
>PRK14642 hypothetical protein; Provisional
Probab=77.01 E-value=6 Score=29.25 Aligned_cols=39 Identities=8% Similarity=-0.016 Sum_probs=26.2
Q ss_pred HHHHHHhcCcceEEEEEEec---------CCeEEEEEEEEEcccCCeEE
Q psy10748 20 NLIFRFLQNRSRVQIWLYEN---------VNLRIEGHILGFDEYMNIVL 59 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~---------~g~~i~G~L~gfD~~mNlvL 59 (98)
..+.+|+|+.+.|+...-.. +.+.++|+|.++|.. ++.|
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 46778888885543211111 679999999999984 4555
No 69
>PRK14644 hypothetical protein; Provisional
Probab=74.48 E-value=5.4 Score=27.63 Aligned_cols=35 Identities=20% Similarity=0.112 Sum_probs=26.2
Q ss_pred HHHHHhcCcceEEEEEEecCC----eEEEEEEEEEcccCCeEEe
Q psy10748 21 LIFRFLQNRSRVQIWLYENVN----LRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g----~~i~G~L~gfD~~mNlvL~ 60 (98)
.+.+++|+.++| ++++. ++++|+|.++|.. ++.|+
T Consensus 79 ~f~r~~G~~v~V----~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDV----SLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEE----EEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 578999999655 44444 8999999999984 35554
No 70
>PRK14645 hypothetical protein; Provisional
Probab=73.77 E-value=8.1 Score=27.29 Aligned_cols=35 Identities=14% Similarity=0.201 Sum_probs=25.7
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++| + .++++++|+|.++|+-. +.|.
T Consensus 95 ~df~r~~G~~v~v----~-~~~k~~~G~L~~~~d~~-i~l~ 129 (154)
T PRK14645 95 RHFERFAGLKAKV----R-GPGENFTGRIKAVSGDQ-VTFD 129 (154)
T ss_pred HHHHHhCCCEEEE----E-cCCeEEEEEEEEEeCCE-EEEE
Confidence 4667888888544 3 37899999999999853 5553
No 71
>PRK14647 hypothetical protein; Provisional
Probab=71.34 E-value=10 Score=26.72 Aligned_cols=34 Identities=12% Similarity=0.130 Sum_probs=23.7
Q ss_pred HHHHHHhcCcceEEEEEEec-----CCeEEEEEEEEEcc
Q psy10748 20 NLIFRFLQNRSRVQIWLYEN-----VNLRIEGHILGFDE 53 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~-----~g~~i~G~L~gfD~ 53 (98)
..+.+++|+.++|+..-... +.++++|+|.++|+
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 46778899996653211111 45899999999997
No 72
>KOG1073|consensus
Probab=67.39 E-value=17 Score=29.33 Aligned_cols=66 Identities=15% Similarity=0.287 Sum_probs=45.3
Q ss_pred HHHhcCcceEEEEEEecCCeEEEEEEEEEcc-cCCeEEeceEEEEecCc---------eeeeeCeEEEeCCcEEEEEecC
Q psy10748 23 FRFLQNRSRVQIWLYENVNLRIEGHILGFDE-YMNIVLESAEEYNIKSK---------TRKALGTIMLKGDNITLIQNLN 92 (98)
Q Consensus 23 ~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~-~mNlvL~d~~e~~~~~~---------~~~~lg~vliRG~~I~~I~~~~ 92 (98)
..||+++ |.|..|+..+|+|+|--+|- ---|-|.++..+-+++. ...-...++.||+.|..+...+
T Consensus 5 t~yIGS~----ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSF----ISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccce----eEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 4689999 45678999999999987763 23366677644433211 1125688999999999666554
No 73
>PRK14632 hypothetical protein; Provisional
Probab=66.16 E-value=15 Score=26.28 Aligned_cols=38 Identities=11% Similarity=0.299 Sum_probs=26.6
Q ss_pred HHHHHHhcCcceEEEEEEe-----cCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYE-----NVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l-----~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|+.++|+. +- .+.++++|+|.++|.- ++.|+
T Consensus 91 ~~f~r~iG~~V~V~l--~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTL--IDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEE--eccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 467789999966532 22 1368999999999974 45554
No 74
>PRK14641 hypothetical protein; Provisional
Probab=64.80 E-value=14 Score=26.60 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=22.2
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEc
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFD 52 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD 52 (98)
..+.+++|+.++|+..-...+.++++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 467788899965532111123568999999995
No 75
>PRK14637 hypothetical protein; Provisional
Probab=63.88 E-value=17 Score=25.57 Aligned_cols=37 Identities=22% Similarity=0.193 Sum_probs=25.6
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEE-EEEEEEEcccCCeEEe
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRI-EGHILGFDEYMNIVLE 60 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i-~G~L~gfD~~mNlvL~ 60 (98)
...+.+++|+.++| ++.+..++ +|+|.++|+- ++.|.
T Consensus 90 ~~~f~r~~G~~V~V----~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 90 AAEFSIFVGETVKV----WFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHHhCCCEEEE----EECCCCcEEEEEEEEEeCC-EEEEE
Confidence 34677889999554 45444556 7999999985 45554
No 76
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=63.76 E-value=32 Score=21.16 Aligned_cols=54 Identities=15% Similarity=0.180 Sum_probs=36.3
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEe
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQN 90 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~ 90 (98)
...|++.+|+++.| .+ ....++|+|.+...-- ++|+.. -...+||=..|++|.|
T Consensus 13 yq~lq~liG~~vvV----~T-~~g~v~G~L~~V~pDh-Ivl~~~------------~~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 13 YQTLQSLIGQRVVV----QT-TRGSVRGILVDVKPDH-IVLEEN------------GTPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCEEEE----EE-cCCcEEEEEEeecCCE-EEEEeC------------CcEEEEEeeeEEEEcC
Confidence 56899999999543 34 4456699999875432 344332 1557888888888753
No 77
>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=62.55 E-value=11 Score=27.20 Aligned_cols=65 Identities=15% Similarity=0.305 Sum_probs=39.5
Q ss_pred CcHHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEccc-CCeEEeceEEEEecCceeeeeCeEEEeCCcEEEEEecCCC
Q psy10748 17 QPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEY-MNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQNLNPD 94 (98)
Q Consensus 17 ~Pl~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~-mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~I~~~~~~ 94 (98)
.|++ +..|++|.|+| .+.+ +++.|.|-.+|.- -|++|-+-.| ++ .. ..-+|=|.+|..+...+..
T Consensus 8 ~p~~-~~~yv~K~VkV----~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~--~~--sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 8 SPLE-WQDYVGKEVKV----TLSD-KEYKGWVYTIDPVSASIVLVNFQE---DG--KR--SVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp -HHH-HHCTTT-EEEE----EETT-EEEEEEEEEE-TTT--EEEEEE-T---TS---E--EEEEE-GGGEEEEEEEE--
T ss_pred CHHH-HHHhhCcEEEE----EEec-cEEEEEEEEeCCCCCeEEEEEccc---CC--ce--eEEEEEccceEEEEEccCC
Confidence 3444 56899999665 4688 9999999999974 5778775443 11 22 2466778888888776543
No 78
>PRK06955 biotin--protein ligase; Provisional
Probab=52.35 E-value=70 Score=24.51 Aligned_cols=24 Identities=25% Similarity=0.317 Sum_probs=20.3
Q ss_pred ecCCeEEEEEEEEEcccCCeEEec
Q psy10748 38 ENVNLRIEGHILGFDEYMNIVLES 61 (98)
Q Consensus 38 l~~g~~i~G~L~gfD~~mNlvL~d 61 (98)
..+++.++|+..|+|+.=.|++++
T Consensus 256 ~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 256 EDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred ECCCcEEEEEEeeECCCceEEEEe
Confidence 345677999999999999999964
No 79
>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=51.34 E-value=34 Score=26.74 Aligned_cols=30 Identities=17% Similarity=0.240 Sum_probs=25.1
Q ss_pred EEEEecCCeEEEEEEEEEcccCCeEEeceE
Q psy10748 34 IWLYENVNLRIEGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 34 V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~ 63 (98)
+.+.+.+|+++.++++++|...+|.|=...
T Consensus 104 i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 104 IVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred EEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 345789999999999999999999885443
No 80
>PRK10898 serine endoprotease; Provisional
Probab=50.53 E-value=37 Score=26.65 Aligned_cols=30 Identities=13% Similarity=0.149 Sum_probs=24.8
Q ss_pred EEEEecCCeEEEEEEEEEcccCCeEEeceE
Q psy10748 34 IWLYENVNLRIEGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 34 V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~ 63 (98)
+.+.+.+|+++.+.++++|....|.+=...
T Consensus 104 i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 104 IIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred EEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 345779999999999999999999775543
No 81
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=50.35 E-value=33 Score=22.16 Aligned_cols=14 Identities=14% Similarity=0.423 Sum_probs=11.4
Q ss_pred HHHHHHhcCcceEE
Q psy10748 20 NLIFRFLQNRSRVQ 33 (98)
Q Consensus 20 ~~L~~~i~k~vrV~ 33 (98)
..|.+|.++.||+.
T Consensus 8 ~~L~~f~gk~V~iv 21 (101)
T cd04479 8 AMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHhhCCCEEEEE
Confidence 47889999997763
No 82
>KOG3382|consensus
Probab=50.12 E-value=9.3 Score=26.99 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=17.0
Q ss_pred EEEEEEEcccCCeEEeceEE
Q psy10748 45 EGHILGFDEYMNIVLESAEE 64 (98)
Q Consensus 45 ~G~L~gfD~~mNlvL~d~~e 64 (98)
.|||+|.|+|=|=.-+|-.-
T Consensus 46 iGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 46 IGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred ceeeeeecccccchhcccce
Confidence 49999999999998887643
No 83
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=49.67 E-value=64 Score=24.61 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=19.5
Q ss_pred cCCeEEEEEEEEEcccCCeEEe
Q psy10748 39 NVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 39 ~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
.++..++|++.|+|..-.|+++
T Consensus 279 ~~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 279 IGDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred eCCcEEEEEEEEECCCceEEEE
Confidence 4567899999999999999996
No 84
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=47.99 E-value=12 Score=24.57 Aligned_cols=17 Identities=35% Similarity=0.600 Sum_probs=15.7
Q ss_pred EEEEEEcccCCeEEece
Q psy10748 46 GHILGFDEYMNIVLESA 62 (98)
Q Consensus 46 G~L~gfD~~mNlvL~d~ 62 (98)
|+|+|.|.|=|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998876
No 85
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=46.37 E-value=33 Score=25.07 Aligned_cols=36 Identities=19% Similarity=0.316 Sum_probs=25.1
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccC
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYM 55 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~m 55 (98)
|+||.++-+.--+|. +....++..|+|+++++|+--
T Consensus 123 I~fL~~~P~~lp~i~-C~i~t~~~~Y~G~I~~~~~~~ 158 (185)
T PF14153_consen 123 IDFLINLPHHLPPIK-CEIETKDKSYRGIILSYDEGE 158 (185)
T ss_pred HHHHHhCcccCCCCc-eEEEeCCceEEEEEEeccCCE
Confidence 677777666544442 233567899999999999863
No 86
>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=45.95 E-value=38 Score=24.40 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=23.6
Q ss_pred HHHHHhcCcceEEEEEEecCCeEEEEEEEEEccc
Q psy10748 21 LIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEY 54 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~ 54 (98)
..+++..+.+.| .+.+.+||+++|.-.|.|.-
T Consensus 112 Icrka~qqg~sI--rVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 112 ICRKAHQQGKSI--RVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred HHHHHHHCCCeE--EEEEcCCcEEEeeecccceE
Confidence 445666666444 44789999999999998863
No 87
>PRK14635 hypothetical protein; Provisional
Probab=45.83 E-value=55 Score=23.07 Aligned_cols=38 Identities=16% Similarity=0.145 Sum_probs=26.5
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEE---EEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEG---HILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G---~L~gfD~~mNlvL~ 60 (98)
..+.+|.|+.++|+ +...++..+.| +|.++|.- ++.|.
T Consensus 92 ~~~~r~~G~~v~v~--~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 92 EDLDRFRGIPVRLV--FRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred HHHHHhCCCEEEEE--EecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 45678899996653 33446778888 99999884 45443
No 88
>PRK10942 serine endoprotease; Provisional
Probab=43.82 E-value=49 Score=27.11 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=24.4
Q ss_pred EEEEecCCeEEEEEEEEEcccCCeEEece
Q psy10748 34 IWLYENVNLRIEGHILGFDEYMNIVLESA 62 (98)
Q Consensus 34 V~v~l~~g~~i~G~L~gfD~~mNlvL~d~ 62 (98)
|.+.+.+|+++.+.++++|...+|-|=..
T Consensus 138 i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 138 IKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred EEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 34567999999999999999999977543
No 89
>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=42.95 E-value=53 Score=26.16 Aligned_cols=30 Identities=13% Similarity=0.163 Sum_probs=24.9
Q ss_pred EEEEecCCeEEEEEEEEEcccCCeEEeceE
Q psy10748 34 IWLYENVNLRIEGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 34 V~v~l~~g~~i~G~L~gfD~~mNlvL~d~~ 63 (98)
+.+.+.+|+++.+.++++|...+|.|=...
T Consensus 84 i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 84 ITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred EEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 344678999999999999999999875543
No 90
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=42.52 E-value=97 Score=26.33 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=20.0
Q ss_pred cCCeEEEEEEEEEcccCCeEEec
Q psy10748 39 NVNLRIEGHILGFDEYMNIVLES 61 (98)
Q Consensus 39 ~~g~~i~G~L~gfD~~mNlvL~d 61 (98)
.++.+++|+..|+|+.=.|+|+.
T Consensus 286 ~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 286 DGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCCcEEEEEEEEECCCCEEEEEE
Confidence 55667999999999999999974
No 91
>PRK10139 serine endoprotease; Provisional
Probab=42.07 E-value=57 Score=26.63 Aligned_cols=56 Identities=18% Similarity=0.172 Sum_probs=35.4
Q ss_pred EEEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCe--EEEeCCcEEEEEecC
Q psy10748 35 WLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGT--IMLKGDNITLIQNLN 92 (98)
Q Consensus 35 ~v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~--vliRG~~I~~I~~~~ 92 (98)
.+.+.+|+++.++++|+|....|-+=..... ++-..-.++. -+-.|+.|..|..|.
T Consensus 118 ~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~--~~l~~~~lg~s~~~~~G~~V~aiG~P~ 175 (455)
T PRK10139 118 SIQLNDGREFDAKLIGSDDQSDIALLQIQNP--SKLTQIAIADSDKLRVGDFAVAVGNPF 175 (455)
T ss_pred EEEECCCCEEEEEEEEEcCCCCEEEEEecCC--CCCceeEecCccccCCCCEEEEEecCC
Confidence 4467999999999999999999987544311 0111112221 233477777777654
No 92
>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=39.88 E-value=74 Score=22.94 Aligned_cols=27 Identities=15% Similarity=0.039 Sum_probs=24.7
Q ss_pred EecCCeEEEEEEEEEcccCCeEEeceE
Q psy10748 37 YENVNLRIEGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 37 ~l~~g~~i~G~L~gfD~~mNlvL~d~~ 63 (98)
.+.||..+.|++.||+.-=|.+|..+.
T Consensus 35 v~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 35 VSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred EecCCcEEEEEEeccCcccCEEeccCC
Confidence 689999999999999999999997655
No 93
>PHA00672 hypothetical protein
Probab=38.02 E-value=1.4e+02 Score=21.01 Aligned_cols=44 Identities=9% Similarity=0.237 Sum_probs=29.0
Q ss_pred EEecCCeEEEEEEEEEcccCCeEEeceEEEEecCceeeeeCeEEEeCCcEEE
Q psy10748 36 LYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITL 87 (98)
Q Consensus 36 v~l~~g~~i~G~L~gfD~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~I~~ 87 (98)
+...-|.-++|.+.-||.+ |+++.-.-...+++..+ +||-+++-
T Consensus 52 i~IPkGt~LtG~~hkf~~~--ii~sG~itV~tdge~~r------l~g~~~i~ 95 (152)
T PHA00672 52 IRIPAGVALTGALIKVSTV--LIFSGHATVFIGGEAVE------LRGYHVIP 95 (152)
T ss_pred EeccCceeeeeeeeEeeEE--EEecccEEEEeCCcEEE------Eecceeee
Confidence 4558899999999999998 66654333333443333 67766653
No 94
>PRK14630 hypothetical protein; Provisional
Probab=37.75 E-value=77 Score=21.96 Aligned_cols=35 Identities=14% Similarity=0.077 Sum_probs=24.0
Q ss_pred HHHHHHhcCcceEEEEEEecCCeEEEEEEEEEcccCCeEEe
Q psy10748 20 NLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 20 ~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
..+.+++|++++| ++.. ...+|+|.++|.-. +.|+
T Consensus 90 ~df~r~~G~~v~V----~l~~-~~~~G~L~~~~d~~-i~l~ 124 (143)
T PRK14630 90 REFKIFEGKKIKL----MLDN-DFEEGFILEAKADS-FIFK 124 (143)
T ss_pred HHHHHhCCCEEEE----EEcC-cceEEEEEEEeCCE-EEEE
Confidence 4677899999554 4443 34599999999843 5553
No 95
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=33.74 E-value=1e+02 Score=20.53 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=19.7
Q ss_pred HHHHHHHhcCcceEEEEEEecCCeEEEEEEE
Q psy10748 19 INLIFRFLQNRSRVQIWLYENVNLRIEGHIL 49 (98)
Q Consensus 19 l~~L~~~i~k~vrV~V~v~l~~g~~i~G~L~ 49 (98)
|+-|-..++...+| .+.+++|+.+.|++.
T Consensus 18 LE~lv~~L~ge~~V--~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 18 LEHLVSELDGEERV--ELELDDGSMLRGTVA 46 (101)
T ss_dssp HHHHHHCTTTT-EE--EEEETTS-EEEEEEC
T ss_pred HHHHHhhcCCcceE--EEEEcCCCeeeeeec
Confidence 45555666677676 457899999999974
No 96
>PRK08330 biotin--protein ligase; Provisional
Probab=30.87 E-value=2e+02 Score=21.01 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=18.8
Q ss_pred cCCeEE-EEEEEEEcccCCeEEec
Q psy10748 39 NVNLRI-EGHILGFDEYMNIVLES 61 (98)
Q Consensus 39 ~~g~~i-~G~L~gfD~~mNlvL~d 61 (98)
.++..+ +|+..|+|..=.|+++.
T Consensus 195 ~~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 195 GDGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred ECCcEEEEEEEEEECCCCEEEEEE
Confidence 355664 79999999999999874
No 97
>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=30.47 E-value=1.3e+02 Score=18.24 Aligned_cols=39 Identities=18% Similarity=0.090 Sum_probs=28.8
Q ss_pred HHHHHhcCcceEEEEEEecCC--eEEEEEEEEEcccCCeEEe
Q psy10748 21 LIFRFLQNRSRVQIWLYENVN--LRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 21 ~L~~~i~k~vrV~V~v~l~~g--~~i~G~L~gfD~~mNlvL~ 60 (98)
.|..++.....|+|.. ..+| ..++|++..+|..-+.+.-
T Consensus 34 ~l~~a~~~~~~v~ity-~~~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 34 KLSEAYQENQPVTITY-YEDGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HHHHHhcCCCEEEEEE-EECCeeEEEEEEEEEEcCCCCEEEE
Confidence 5666776666666653 5666 6999999999999886653
No 98
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=28.90 E-value=1.9e+02 Score=22.06 Aligned_cols=23 Identities=22% Similarity=0.140 Sum_probs=20.2
Q ss_pred cCCeEEEEEEEEEcccCCeEEec
Q psy10748 39 NVNLRIEGHILGFDEYMNIVLES 61 (98)
Q Consensus 39 ~~g~~i~G~L~gfD~~mNlvL~d 61 (98)
.++..++|++.|+|..=.|+++.
T Consensus 244 ~~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 244 QDNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred eCCCEEEEEEEEECCCCeEEEEe
Confidence 46789999999999999999864
No 99
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=27.97 E-value=2.1e+02 Score=20.85 Aligned_cols=22 Identities=36% Similarity=0.382 Sum_probs=19.3
Q ss_pred cCCeEEEEEEEEEcccCCeEEe
Q psy10748 39 NVNLRIEGHILGFDEYMNIVLE 60 (98)
Q Consensus 39 ~~g~~i~G~L~gfD~~mNlvL~ 60 (98)
.++.+++|+..|+|+.=.|+++
T Consensus 200 ~~~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 200 TGNGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred eCCcEEEEEEEeECCCceEEEE
Confidence 3557799999999999999997
No 100
>PRK06630 hypothetical protein; Provisional
Probab=26.68 E-value=36 Score=22.65 Aligned_cols=19 Identities=32% Similarity=0.366 Sum_probs=16.6
Q ss_pred EEEEEEEcccCCeEEeceE
Q psy10748 45 EGHILGFDEYMNIVLESAE 63 (98)
Q Consensus 45 ~G~L~gfD~~mNlvL~d~~ 63 (98)
.|+|+|-|+|=|-.-++..
T Consensus 12 ~G~lVG~D~~GNkYYE~~~ 30 (99)
T PRK06630 12 FHKKVGEDEFLNQYYESRN 30 (99)
T ss_pred cCeEeEEeCCCChhcccCC
Confidence 5999999999999988743
No 101
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=25.20 E-value=89 Score=17.81 Aligned_cols=14 Identities=21% Similarity=0.292 Sum_probs=11.7
Q ss_pred HHHHHHHhcCcceE
Q psy10748 19 INLIFRFLQNRSRV 32 (98)
Q Consensus 19 l~~L~~~i~k~vrV 32 (98)
.+.+++++||+|+|
T Consensus 11 ~~~~~~~~Gk~V~V 24 (48)
T PF14485_consen 11 YSYLKSLLGKRVSV 24 (48)
T ss_pred hHHHHHhcCCeEEE
Confidence 67888899999765
No 102
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=24.43 E-value=70 Score=22.24 Aligned_cols=38 Identities=13% Similarity=0.196 Sum_probs=24.4
Q ss_pred eEEEEEEEEE---cccCCeEEeceEEEEecCceeeeeCeEEEeCCc
Q psy10748 42 LRIEGHILGF---DEYMNIVLESAEEYNIKSKTRKALGTIMLKGDN 84 (98)
Q Consensus 42 ~~i~G~L~gf---D~~mNlvL~d~~e~~~~~~~~~~lg~vliRG~~ 84 (98)
..+.|.+.=. =-+||+.+.|+. ..+...-+.+=||||+
T Consensus 83 ~~lvG~VqKvS~Lil~~~~~v~Dv~-----tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 83 YVLVGEVQKVSNLILNMNVYVRDVE-----TGKVVRGRSVDIRGNT 123 (140)
T ss_pred EEEEEEEechhhhheeeeEEEEECC-----CCCEEeeeeeeEecCc
Confidence 4455655422 347888888875 3345556788899986
No 103
>PRK08477 biotin--protein ligase; Provisional
Probab=21.38 E-value=2.7e+02 Score=20.44 Aligned_cols=28 Identities=11% Similarity=-0.030 Sum_probs=22.9
Q ss_pred ecCCeEEEEEEEEEcccCCeEEeceEEE
Q psy10748 38 ENVNLRIEGHILGFDEYMNIVLESAEEY 65 (98)
Q Consensus 38 l~~g~~i~G~L~gfD~~mNlvL~d~~e~ 65 (98)
..+++.++|+..++|+.--|+++....+
T Consensus 181 ~~~~~~~~g~a~~I~~~G~L~v~~~~~~ 208 (211)
T PRK08477 181 HIDGKLVSLKDAELLEDGSILINGKKVY 208 (211)
T ss_pred EECCEEEEEEEeeECCCCeEEECCEEee
Confidence 3678999999999999988888765543
Done!