Query 034273
Match_columns 99
No_of_seqs 126 out of 1024
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:40:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034273.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034273hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 99.9 1.6E-24 3.5E-29 142.0 8.6 77 21-98 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 3.8E-22 8.1E-27 128.9 8.2 74 22-96 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.8 1.3E-20 2.9E-25 120.6 8.5 66 21-97 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.8 1.1E-19 2.5E-24 114.7 7.3 63 20-96 2-72 (72)
5 cd01718 Sm_E The eukaryotic Sm 99.8 2.1E-19 4.5E-24 116.1 7.9 65 19-96 3-79 (79)
6 cd01717 Sm_B The eukaryotic Sm 99.8 1.4E-19 3E-24 116.0 6.7 71 19-96 8-78 (79)
7 cd01731 archaeal_Sm1 The archa 99.8 3E-19 6.4E-24 111.4 7.1 53 30-96 16-68 (68)
8 cd01729 LSm7 The eukaryotic Sm 99.8 2.4E-19 5.3E-24 115.8 6.8 71 18-97 9-79 (81)
9 PTZ00138 small nuclear ribonuc 99.7 6.2E-18 1.4E-22 111.4 8.1 69 16-97 8-88 (89)
10 cd01728 LSm1 The eukaryotic Sm 99.7 6.2E-18 1.3E-22 107.8 6.8 64 19-96 10-73 (74)
11 cd01726 LSm6 The eukaryotic Sm 99.7 9.5E-18 2.1E-22 104.5 7.3 59 23-95 1-67 (67)
12 cd01719 Sm_G The eukaryotic Sm 99.7 7.5E-18 1.6E-22 106.7 6.1 65 16-97 5-69 (72)
13 cd01727 LSm8 The eukaryotic Sm 99.7 1.4E-17 2.9E-22 105.6 6.5 59 30-98 15-73 (74)
14 KOG3460 Small nuclear ribonucl 99.7 9.7E-19 2.1E-23 113.7 0.1 77 20-97 3-87 (91)
15 KOG3459 Small nuclear ribonucl 99.7 1.1E-18 2.3E-23 118.3 0.1 95 3-98 5-109 (114)
16 cd01722 Sm_F The eukaryotic Sm 99.7 4.5E-17 9.7E-22 101.8 6.8 52 30-95 17-68 (68)
17 cd06168 LSm9 The eukaryotic Sm 99.7 4.3E-17 9.3E-22 104.2 6.7 66 20-96 9-74 (75)
18 COG1958 LSM1 Small nuclear rib 99.7 2.1E-16 4.6E-21 101.0 8.2 67 20-96 5-79 (79)
19 smart00651 Sm snRNP Sm protein 99.7 1.7E-16 3.6E-21 97.6 5.7 56 28-96 12-67 (67)
20 PF01423 LSM: LSM domain ; In 99.7 2E-16 4.3E-21 97.3 5.2 54 30-96 14-67 (67)
21 cd01723 LSm4 The eukaryotic Sm 99.6 3.6E-15 7.9E-20 95.0 7.0 61 23-96 2-70 (76)
22 cd01721 Sm_D3 The eukaryotic S 99.6 5.1E-15 1.1E-19 93.0 7.3 53 30-96 16-68 (70)
23 cd00600 Sm_like The eukaryotic 99.6 5.3E-15 1.1E-19 89.6 5.7 52 30-95 12-63 (63)
24 KOG1780 Small Nuclear ribonucl 99.5 1E-14 2.2E-19 93.0 3.4 66 15-97 8-73 (77)
25 cd01724 Sm_D1 The eukaryotic S 99.5 2E-13 4.4E-18 89.8 7.4 53 30-96 17-69 (90)
26 cd01733 LSm10 The eukaryotic S 99.5 2.9E-13 6.3E-18 86.9 6.9 53 30-96 25-77 (78)
27 KOG1781 Small Nuclear ribonucl 99.4 6.1E-15 1.3E-19 98.5 -2.3 64 28-97 31-94 (108)
28 KOG3168 U1 snRNP component [Tr 99.4 1.3E-14 2.9E-19 104.7 -2.1 63 30-96 20-82 (177)
29 cd01725 LSm2 The eukaryotic Sm 99.4 1.2E-12 2.6E-17 84.4 7.1 56 30-97 17-72 (81)
30 KOG3482 Small nuclear ribonucl 99.4 2.4E-13 5.1E-18 86.6 3.3 56 29-98 23-78 (79)
31 KOG1774 Small nuclear ribonucl 99.3 9.6E-13 2.1E-17 85.4 4.1 67 18-97 8-86 (88)
32 KOG1775 U6 snRNA-associated Sm 99.3 5.5E-13 1.2E-17 85.7 2.4 66 21-97 6-79 (84)
33 KOG1782 Small Nuclear ribonucl 99.2 1E-12 2.2E-17 90.8 -2.6 58 30-98 25-82 (129)
34 KOG1783 Small nuclear ribonucl 99.1 3.2E-12 6.8E-17 81.4 -2.3 54 30-97 22-75 (77)
35 KOG1784 Small Nuclear ribonucl 99.1 5.1E-11 1.1E-15 78.7 1.3 67 18-97 7-73 (96)
36 cd01739 LSm11_C The eukaryotic 98.9 5.7E-10 1.2E-14 69.7 1.3 27 35-61 23-49 (66)
37 KOG3293 Small nuclear ribonucl 98.5 1.8E-07 4E-12 64.9 4.2 61 22-95 2-70 (134)
38 KOG3448 Predicted snRNP core p 98.1 1E-05 2.2E-10 53.5 5.6 56 30-97 18-73 (96)
39 KOG3172 Small nuclear ribonucl 97.7 9.6E-05 2.1E-09 50.5 5.3 60 22-95 5-72 (119)
40 KOG3428 Small nuclear ribonucl 96.8 0.0035 7.6E-08 42.7 5.1 51 30-95 18-68 (109)
41 cd01716 Hfq Hfq, an abundant, 90.4 0.3 6.4E-06 30.1 2.5 25 30-54 17-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 89.3 0.4 8.6E-06 29.6 2.5 25 30-54 21-45 (61)
43 PRK00395 hfq RNA-binding prote 88.8 0.44 9.5E-06 30.8 2.5 26 30-55 25-50 (79)
44 cd01736 LSm14_N LSm14 (also kn 87.0 2.3 5E-05 27.2 5.0 68 18-92 3-71 (74)
45 PF12701 LSM14: Scd6-like Sm d 85.2 3.6 7.8E-05 27.3 5.5 70 18-95 5-75 (96)
46 PF14438 SM-ATX: Ataxin 2 SM d 77.6 2.9 6.3E-05 25.8 2.8 56 30-92 18-76 (77)
47 PRK14091 RNA-binding protein H 72.9 3.4 7.4E-05 30.1 2.5 26 31-56 111-136 (165)
48 PRK14091 RNA-binding protein H 69.7 4.5 9.7E-05 29.5 2.5 26 30-55 30-55 (165)
49 PF14563 DUF4444: Domain of un 69.3 4.8 0.0001 23.1 2.0 22 37-58 10-31 (42)
50 COG1923 Hfq Uncharacterized ho 67.5 5.2 0.00011 25.8 2.2 24 30-53 25-48 (77)
51 PF02237 BPL_C: Biotin protein 67.0 14 0.00031 20.8 3.8 25 33-57 11-35 (48)
52 KOG3382 NADH:ubiquinone oxidor 62.7 5.5 0.00012 28.4 1.7 31 26-56 34-64 (151)
53 cd01735 LSm12_N LSm12 belongs 62.2 11 0.00023 23.1 2.8 25 32-56 14-38 (61)
54 PF03614 Flag1_repress: Repres 39.9 24 0.00052 25.7 2.0 27 30-56 35-61 (165)
55 PF05071 NDUFA12: NADH ubiquin 38.5 13 0.00027 24.7 0.4 17 39-55 1-17 (105)
56 PF07355 GRDB: Glycine/sarcosi 30.5 69 0.0015 26.0 3.5 49 9-57 22-70 (349)
57 TIGR02038 protease_degS peripl 29.3 43 0.00093 26.4 2.1 30 27-56 104-133 (351)
58 cd08057 MPN_euk_non_mb Mpr1p, 28.8 99 0.0022 21.3 3.7 27 34-60 22-48 (157)
59 PRK10898 serine endoprotease; 25.8 56 0.0012 25.8 2.2 29 28-56 105-133 (353)
60 PF09196 DUF1953: Domain of un 25.8 80 0.0017 19.4 2.4 14 84-97 13-26 (66)
61 PF01398 JAB: JAB1/Mov34/MPN/P 25.1 92 0.002 19.9 2.8 26 34-59 25-51 (114)
62 PF11743 DUF3301: Protein of u 24.8 83 0.0018 20.5 2.5 21 78-98 76-96 (97)
63 TIGR01918 various_sel_PB selen 22.9 1.1E+02 0.0023 25.7 3.3 48 9-56 18-65 (431)
64 PRK14633 hypothetical protein; 22.9 56 0.0012 23.0 1.5 20 32-52 106-125 (150)
65 PRK10942 serine endoprotease; 22.8 65 0.0014 26.6 2.1 27 29-55 140-166 (473)
66 PRK14638 hypothetical protein; 21.3 62 0.0014 22.8 1.5 20 32-52 108-127 (150)
No 1
>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=99.91 E-value=1.6e-24 Score=142.05 Aligned_cols=77 Identities=84% Similarity=1.347 Sum_probs=62.0
Q ss_pred CCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 034273 21 TGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 90 (99)
Q Consensus 21 ~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdn 90 (99)
+||+++|+.++ ++|+.+.|+|+|||+||||+|+||+|++...++++.+. +..+..++|++|.+||||||
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~ 79 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDS 79 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCE
Confidence 48999998884 78999999999999999999999999987654432211 11123456889999999999
Q ss_pred EEEEEeCC
Q 034273 91 VIIVLRNP 98 (99)
Q Consensus 91 Vv~V~~~p 98 (99)
|++|+++|
T Consensus 80 Vv~Is~~~ 87 (87)
T cd01720 80 VILVLRNP 87 (87)
T ss_pred EEEEecCC
Confidence 99999987
No 2
>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=99.87 E-value=3.8e-22 Score=128.89 Aligned_cols=74 Identities=34% Similarity=0.579 Sum_probs=56.0
Q ss_pred CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273 22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 93 (99)
Q Consensus 22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 93 (99)
.|+++|+.+ +++||++.|+|+|||+||||+|+||+|++....++.+.. ........|.+|.+|||||||++
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~Vv~ 79 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSVIL 79 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEEEE
Confidence 367777665 489999999999999999999999999987543322110 00112246889999999999999
Q ss_pred EEe
Q 034273 94 VLR 96 (99)
Q Consensus 94 V~~ 96 (99)
|+|
T Consensus 80 i~~ 82 (82)
T cd01730 80 VSP 82 (82)
T ss_pred ECC
Confidence 985
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=99.84 E-value=1.3e-20 Score=120.60 Aligned_cols=66 Identities=26% Similarity=0.492 Sum_probs=54.6
Q ss_pred CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273 21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92 (99)
Q Consensus 21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 92 (99)
..|+++|.+++ ++|+++.|+|+|||+||||+|+||+|++.. ++. . ..+++|.+|||||||+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~~~---~-------~~~~lg~v~iRG~nV~ 70 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PEG---R-------KITKLDQILLNGNNIC 70 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CCC---c-------eeeEcCeEEEeCCeEE
Confidence 36888887765 899999999999999999999999999842 111 1 1367999999999999
Q ss_pred EEEeC
Q 034273 93 IVLRN 97 (99)
Q Consensus 93 ~V~~~ 97 (99)
+|+|.
T Consensus 71 ~i~p~ 75 (76)
T cd01732 71 MLVPG 75 (76)
T ss_pred EEECC
Confidence 99974
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.81 E-value=1.1e-19 Score=114.74 Aligned_cols=63 Identities=32% Similarity=0.535 Sum_probs=52.9
Q ss_pred cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273 20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91 (99)
Q Consensus 20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 91 (99)
...|+.+|..++ ++|+.+.|+|+|||+||||+|+||.|++.. . ..+.+|.+||||+||
T Consensus 2 ~~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~-------~~~~lg~v~iRG~~V 67 (72)
T PRK00737 2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-------E-------VVRKLGKVVIRGDNV 67 (72)
T ss_pred CcchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-------C-------eEeEcCcEEEeCCEE
Confidence 357888887765 899999999999999999999999997531 1 136799999999999
Q ss_pred EEEEe
Q 034273 92 IIVLR 96 (99)
Q Consensus 92 v~V~~ 96 (99)
++|+|
T Consensus 68 ~~i~~ 72 (72)
T PRK00737 68 VYVSP 72 (72)
T ss_pred EEEcC
Confidence 99975
No 5
>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=99.80 E-value=2.1e-19 Score=116.10 Aligned_cols=65 Identities=18% Similarity=0.472 Sum_probs=54.2
Q ss_pred ccCCChhhhhhhh------------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEE
Q 034273 19 FNTGPLSVLMMSV------------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFL 86 (99)
Q Consensus 19 ~~~~Pl~vL~~~l------------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~I 86 (99)
.+..|+.+|...+ ++|++++|+|.|||+||||+|+||+|+... +. ..+.+|.++|
T Consensus 3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------~~-------~~~~lG~ili 69 (79)
T cd01718 3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------TK-------TRKPLGRILL 69 (79)
T ss_pred cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------Cc-------eEeEcCcEEE
Confidence 4678888887765 388999999999999999999999998742 11 1367999999
Q ss_pred eCCcEEEEEe
Q 034273 87 RGDSVIIVLR 96 (99)
Q Consensus 87 RGdnVv~V~~ 96 (99)
|||||++|+|
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999985
No 6
>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=99.80 E-value=1.4e-19 Score=115.96 Aligned_cols=71 Identities=25% Similarity=0.440 Sum_probs=53.6
Q ss_pred ccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 19 FNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 19 ~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
+.+.++.+ .+++||.+.|+|+|||+||||+|+||+|++...++.+.. ......|++|++||||+||++|+-
T Consensus 8 ~l~~~V~V---~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 8 LINYRLRV---TLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred HcCCEEEE---EECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEEE
Confidence 34444444 678999999999999999999999999998654321100 012245889999999999999974
No 7
>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=99.79 E-value=3e-19 Score=111.37 Aligned_cols=53 Identities=28% Similarity=0.562 Sum_probs=46.0
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.+++|+.+.|+|.|||+||||+|+||+|++.. + ..+.+|.+||||+||++|+|
T Consensus 16 ~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 16 KLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG------E--------PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EECCCCEEEEEEEEECCcceEEEeeEEEEecC------C--------eEeEcCcEEEeCCEEEEEcC
Confidence 45899999999999999999999999998642 1 13679999999999999986
No 8
>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=99.79 E-value=2.4e-19 Score=115.79 Aligned_cols=71 Identities=18% Similarity=0.334 Sum_probs=53.4
Q ss_pred cccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
.+.+.++.+ .+++||++.|+|+|||+||||+|+||+|+........ ......+.+|.++|||+||++|++.
T Consensus 9 ~~i~k~V~V---~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~------~~~~~~~~lG~v~iRG~nV~~i~~~ 79 (81)
T cd01729 9 KYVDKKIRV---KFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDKTRQLGLVVCRGTSVVLISPV 79 (81)
T ss_pred HhcCCeEEE---EECCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc------ccccceeEccEEEEcCCEEEEEecC
Confidence 344555544 5689999999999999999999999999975322110 0011347899999999999999875
No 9
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.75 E-value=6.2e-18 Score=111.39 Aligned_cols=69 Identities=22% Similarity=0.507 Sum_probs=56.5
Q ss_pred cccccCCChhhhhhhh------------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeece
Q 034273 16 EEEFNTGPLSVLMMSV------------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISK 83 (99)
Q Consensus 16 ~~~~~~~Pl~vL~~~l------------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~ 83 (99)
....+..|+.++...+ +++++++|+|+|||+||||+|+||+|++.. + . ..+.+|.
T Consensus 8 ~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~------~-~------~~~~lG~ 74 (89)
T PTZ00138 8 LQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK------K-N------TRKDLGR 74 (89)
T ss_pred cceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC------C-c------eeeEcCe
Confidence 3456788999988776 346899999999999999999999998642 0 0 1367999
Q ss_pred EEEeCCcEEEEEeC
Q 034273 84 MFLRGDSVIIVLRN 97 (99)
Q Consensus 84 i~IRGdnVv~V~~~ 97 (99)
+|||||||++|++.
T Consensus 75 ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 75 ILLKGDNITLIMAA 88 (89)
T ss_pred EEEcCCEEEEEEcC
Confidence 99999999999875
No 10
>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=99.74 E-value=6.2e-18 Score=107.82 Aligned_cols=64 Identities=23% Similarity=0.330 Sum_probs=50.5
Q ss_pred ccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 19 FNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 19 ~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
+.+.++.+ .+++||++.|+|+|||+||||+|+||.|+.....+ ..++.+|.++|||+||++|+.
T Consensus 10 ~l~k~v~V---~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~-----------~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 10 DLDKKVVV---LLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDK-----------YGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred hcCCEEEE---EEcCCeEEEEEEEEECCcccEEecceEEEEecCCc-----------cceeEeeEEEEECCEEEEEEc
Confidence 34444444 56899999999999999999999999998753211 113679999999999999975
No 11
>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=99.74 E-value=9.5e-18 Score=104.48 Aligned_cols=59 Identities=20% Similarity=0.339 Sum_probs=48.1
Q ss_pred Chhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273 23 PLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 94 (99)
Q Consensus 23 Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V 94 (99)
|+.+|+.+ |++|+++.|+|.|||+||||+|+||+|.... . ..+.+|.+||||+||++|
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-------~-------~~~~~~~v~IRG~~I~~I 66 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-------Q-------LKNKYGDAFIRGNNVLYI 66 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-------c-------eeeEeCCEEEECCEEEEE
Confidence 55666555 4899999999999999999999999986421 1 135799999999999998
Q ss_pred E
Q 034273 95 L 95 (99)
Q Consensus 95 ~ 95 (99)
+
T Consensus 67 ~ 67 (67)
T cd01726 67 S 67 (67)
T ss_pred C
Confidence 5
No 12
>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=99.73 E-value=7.5e-18 Score=106.70 Aligned_cols=65 Identities=23% Similarity=0.422 Sum_probs=52.7
Q ss_pred cccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273 16 EEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 95 (99)
Q Consensus 16 ~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~ 95 (99)
-..+.+.++.+ .|++|+.+.|+|.|||+||||+|+||+|++.. . ..+.+|.++|||+||++|+
T Consensus 5 L~~~i~k~V~V---~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-------~-------~~~~lg~v~IRG~~I~~i~ 67 (72)
T cd01719 5 LKKYMDKKLSL---KLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-------G-------EKNNIGMVVIRGNSIVMLE 67 (72)
T ss_pred hHHhCCCeEEE---EECCCeEEEEEEEEEcccccEEeccEEEEccC-------C-------ceeEeceEEECCCEEEEEE
Confidence 34455666655 57899999999999999999999999998631 1 1367999999999999998
Q ss_pred eC
Q 034273 96 RN 97 (99)
Q Consensus 96 ~~ 97 (99)
+.
T Consensus 68 ~~ 69 (72)
T cd01719 68 AL 69 (72)
T ss_pred cc
Confidence 75
No 13
>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=99.72 E-value=1.4e-17 Score=105.65 Aligned_cols=59 Identities=19% Similarity=0.383 Sum_probs=48.4
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p 98 (99)
.+++||.+.|+|+|||+||||+|++|+|+....+. +. .++.+|.++|||+||++|++..
T Consensus 15 ~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~---~~-------~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 15 ITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE---GV-------EQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred EECCCcEEEEEEEEEccccCEEccceEEEEecCCC---Cc-------eeeEeceEEECCCEEEEEEccC
Confidence 56899999999999999999999999998642211 11 2467999999999999999864
No 14
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.71 E-value=9.7e-19 Score=113.70 Aligned_cols=77 Identities=32% Similarity=0.512 Sum_probs=60.6
Q ss_pred cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273 20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91 (99)
Q Consensus 20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 91 (99)
+..||++|+.+| +++|++.|+|+|||+|.||+|.|++|+++....+....++. ....+|.+..+|+|||+|
T Consensus 3 v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~-~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEI-VKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred ccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHH-HhhhhcceeEEEEeCCeE
Confidence 567999999886 89999999999999999999999999987643322111111 123457899999999999
Q ss_pred EEEEeC
Q 034273 92 IIVLRN 97 (99)
Q Consensus 92 v~V~~~ 97 (99)
++|+|-
T Consensus 82 ilvspp 87 (91)
T KOG3460|consen 82 ILVSPP 87 (91)
T ss_pred EEEcCc
Confidence 999974
No 15
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.71 E-value=1.1e-18 Score=118.27 Aligned_cols=95 Identities=77% Similarity=1.177 Sum_probs=81.2
Q ss_pred CcccccccCCccccccccCCChhhhhhhh----------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCcccc
Q 034273 3 RAMDEDTTGGKTEEEEFNTGPLSVLMMSV----------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKA 72 (99)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~Pl~vL~~~l----------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~ 72 (99)
.-..|+|.-+..|+.++..||++++..+. ++++.+-|.+.|||.|+|++|+++.|.|++.++.+++.. +
T Consensus 5 ~pk~e~t~~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~ 83 (114)
T KOG3459|consen 5 KPKEECTPLEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-A 83 (114)
T ss_pred chhhhcCccccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-C
Confidence 34456665455599999999999998876 778889999999999999999999999998887766654 5
Q ss_pred ccCcceeeeceEEEeCCcEEEEEeCC
Q 034273 73 LPVNKDRFISKMFLRGDSVIIVLRNP 98 (99)
Q Consensus 73 ~~~~~~r~lg~i~IRGdnVv~V~~~p 98 (99)
+++.+.|++|.+|||||+|++|..+|
T Consensus 84 ~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 84 KPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred CccchhhhhheeeecCCeEEEEEecc
Confidence 66777899999999999999998776
No 16
>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=99.70 E-value=4.5e-17 Score=101.78 Aligned_cols=52 Identities=19% Similarity=0.296 Sum_probs=43.8
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 95 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~ 95 (99)
.|++|+.+.|+|.|||+|||++|+||+|+... .. ...+|.+||||+||++|+
T Consensus 17 ~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-------~~-------~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 17 KLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-------KS-------TGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-------cc-------ccCcCcEEEECCEEEEEC
Confidence 45899999999999999999999999987421 11 246899999999999984
No 17
>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=99.70 E-value=4.3e-17 Score=104.17 Aligned_cols=66 Identities=15% Similarity=0.325 Sum_probs=52.0
Q ss_pred cCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 20 NTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 20 ~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
...++.+ .+++||.+.|+|.|||+||||+|+||.|++...++.. ....|++|+++|||++|++|+.
T Consensus 9 l~~~v~V---~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 9 LGRTMRI---HMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred cCCeEEE---EEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEEEE
Confidence 4444444 6789999999999999999999999999986433211 1135899999999999999874
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.68 E-value=2.1e-16 Score=100.99 Aligned_cols=67 Identities=30% Similarity=0.547 Sum_probs=51.9
Q ss_pred cCCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 034273 20 NTGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 91 (99)
Q Consensus 20 ~~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnV 91 (99)
...|+++|+.++ ++|+++.|+|+|||+||||+|+||+|.+.. + +... ..+..+.++|||+||
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--~---~~~~-----~~~~~~~~~IRG~~I 74 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH--D---GEKN-----VRRLGGEVLIRGDNI 74 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc--C---Cccc-----cceeccEEEEECCcE
Confidence 346788887765 899999999999999999999999998741 1 1110 124455999999999
Q ss_pred EEEEe
Q 034273 92 IIVLR 96 (99)
Q Consensus 92 v~V~~ 96 (99)
++|++
T Consensus 75 ~~I~~ 79 (79)
T COG1958 75 VLISP 79 (79)
T ss_pred EEEeC
Confidence 99974
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.66 E-value=1.7e-16 Score=97.56 Aligned_cols=56 Identities=29% Similarity=0.603 Sum_probs=47.5
Q ss_pred hhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 28 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 28 ~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.+.+++|+.+.|+|.+||+||||+|+||+|++... ...+++|.+||||++|++|++
T Consensus 12 ~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 12 LVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEeC
Confidence 34678999999999999999999999999987521 124789999999999999974
No 20
>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=99.65 E-value=2e-16 Score=97.31 Aligned_cols=54 Identities=28% Similarity=0.489 Sum_probs=47.1
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.+++|+.++|+|.+||+||||+|+||.|.+...+ ..+++|.+||||++|++|++
T Consensus 14 ~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 14 ELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEEEE
T ss_pred EEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEEEC
Confidence 6689999999999999999999999999875210 24789999999999999985
No 21
>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=99.60 E-value=3.6e-15 Score=94.98 Aligned_cols=61 Identities=25% Similarity=0.359 Sum_probs=49.3
Q ss_pred Chhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273 23 PLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 94 (99)
Q Consensus 23 Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V 94 (99)
|+.+|+.+ |++|+.+.|+|.+||.|||++|+||+|.... +.. ...++.+||||++|.+|
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------g~~-------~~~~~~v~IRG~~I~~i 68 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD------GDK-------FWKMPECYIRGNTIKYL 68 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC------CcE-------eeeCCcEEEeCCEEEEE
Confidence 77777766 4899999999999999999999999986321 111 13578999999999999
Q ss_pred Ee
Q 034273 95 LR 96 (99)
Q Consensus 95 ~~ 96 (99)
+.
T Consensus 69 ~~ 70 (76)
T cd01723 69 RV 70 (76)
T ss_pred Ec
Confidence 74
No 22
>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=99.59 E-value=5.1e-15 Score=93.04 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=43.7
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.|++|..+.|+|.+||.|||++|+||+|.... +. ...++.+||||+||.+|.-
T Consensus 16 eLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~------g~--------~~~~~~v~IRG~nI~~v~l 68 (70)
T cd01721 16 ELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD------GR--------VSQLEQVYIRGSKIRFFIL 68 (70)
T ss_pred EECCCcEEEEEEEEEcCCceeEEEEEEEECCC------Cc--------EeEcCcEEEeCCEEEEEEe
Confidence 35899999999999999999999999875321 11 1457999999999999863
No 23
>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=99.57 E-value=5.3e-15 Score=89.57 Aligned_cols=52 Identities=38% Similarity=0.631 Sum_probs=45.5
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 95 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~ 95 (99)
.+++|+.+.|+|.|||+|||++|.||.|++.. . ..+.+|.+||||++|.+|.
T Consensus 12 ~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~------~--------~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 12 ELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE------G--------KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred EECCCcEEEEEEEEECCCCCEEECCEEEEecC------C--------cEEECCeEEEECCEEEEEC
Confidence 67899999999999999999999999998752 0 1367999999999999874
No 24
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.51 E-value=1e-14 Score=93.01 Aligned_cols=66 Identities=21% Similarity=0.408 Sum_probs=51.5
Q ss_pred ccccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 034273 15 EEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 94 (99)
Q Consensus 15 ~~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V 94 (99)
|=-.|+++.+.+ .|++||.+.|+|+|||.|||+||+|+.|.... +. +..+|..+|||++|+++
T Consensus 8 eLkkymdKki~l---klnG~r~v~GiLrGyD~FmNiVlde~vE~~~~------~~--------~~~ig~~vIrgnsiv~~ 70 (77)
T KOG1780|consen 8 ELKKYMDKKIVL---KLNGGRKVTGILRGYDPFMNIVLDETVEPNGD------GD--------KNNIGMVVIRGNSIVMV 70 (77)
T ss_pred hHHHhhhheEEE---EeCCCcEEEEEEeccchHHhhhhhhceeecCc------CC--------cceeeeEEEeccEEEEE
Confidence 444455554444 67899999999999999999999999997431 11 24689999999999998
Q ss_pred EeC
Q 034273 95 LRN 97 (99)
Q Consensus 95 ~~~ 97 (99)
.+.
T Consensus 71 eaL 73 (77)
T KOG1780|consen 71 EAL 73 (77)
T ss_pred eec
Confidence 765
No 25
>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=99.47 E-value=2e-13 Score=89.80 Aligned_cols=53 Identities=21% Similarity=0.307 Sum_probs=44.8
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.|++|..+.|+|.++|.|||++|+||+|+... + . ...++.++|||+||.+|..
T Consensus 17 eLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~------~-~-------~~~~~~v~IRG~nI~yi~l 69 (90)
T cd01724 17 ELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG------R-N-------PVPLDTLSIRGNNIRYFIL 69 (90)
T ss_pred EECCCCEEEEEEEEEcCceeEEEEEEEEEcCC------C-c-------eeEcceEEEeCCEEEEEEc
Confidence 46999999999999999999999999987431 1 1 2468999999999999874
No 26
>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=99.45 E-value=2.9e-13 Score=86.92 Aligned_cols=53 Identities=23% Similarity=0.383 Sum_probs=43.8
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.||+|..+.|+|.++|.|||++|+||++.... + . ...+|.+||||+||.+|.-
T Consensus 25 eLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~------~-~-------~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 25 ELRNETTVTGRIASVDAFMNIRLAKVTIIDRN------G-K-------QVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred EECCCCEEEEEEEEEcCCceeEEEEEEEEcCC------C-c-------eeECCcEEEECCEEEEEEc
Confidence 46899999999999999999999999876321 1 1 2368999999999999863
No 27
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.43 E-value=6.1e-15 Score=98.53 Aligned_cols=64 Identities=16% Similarity=0.308 Sum_probs=51.7
Q ss_pred hhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 28 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 28 ~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
++.+.+||+++|+|+|||+.|||||+|++|+...++... + .....|.||++++||..+++|+|.
T Consensus 31 rvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~---~---~~~~tR~LGLvV~RGTalvlisp~ 94 (108)
T KOG1781|consen 31 RVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY---K---LTDETRKLGLVVCRGTALVLISPA 94 (108)
T ss_pred EEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc---c---hhhhhheeeeEEEcccEEEEEcCC
Confidence 445689999999999999999999999999976543321 1 123348999999999999999985
No 28
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.40 E-value=1.3e-14 Score=104.72 Aligned_cols=63 Identities=25% Similarity=0.516 Sum_probs=50.3
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 96 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~ 96 (99)
.+++||.+.|.+.+||+||||+|.||+|+....++..+. +. .+++|-+|++++||+|||+.+.
T Consensus 20 ~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~---~~-~eEkr~lgLvllRgenIvs~tV 82 (177)
T KOG3168|consen 20 RLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKM---TD-GEEKRVLGLVLLRGENIVSMTV 82 (177)
T ss_pred EeccCceeechhhhhHHHHHHHHHHHHHHhccccccccc---cc-cceeeEEEEEEecCCcEEEEec
Confidence 457899999999999999999999999987655443311 11 2346889999999999999764
No 29
>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=99.40 E-value=1.2e-12 Score=84.43 Aligned_cols=56 Identities=25% Similarity=0.300 Sum_probs=44.1
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
.|++|..+.|+|.++|.|||++|+||++.... . .. ....++.++|||++|.+|+..
T Consensus 17 eLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~--~----~~------~~~~~~~v~IRG~~I~~I~lp 72 (81)
T cd01725 17 ELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE--K----YP------HMLSVKNCFIRGSVVRYVQLP 72 (81)
T ss_pred EECCCcEEEEEEEEECCCcccEEEEEEEEcCC--C----cc------cccccCeEEEECCEEEEEEeC
Confidence 46899999999999999999999999876321 0 00 013579999999999999854
No 30
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.39 E-value=2.4e-13 Score=86.60 Aligned_cols=56 Identities=18% Similarity=0.294 Sum_probs=48.4
Q ss_pred hhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273 29 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98 (99)
Q Consensus 29 ~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p 98 (99)
.+|++|.++.|+|++.|.||||.|.+|+|++.. .. ...+|.++||++||++|..-|
T Consensus 23 vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------~~-------~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 23 VKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------VS-------TGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred EEEecCcEEEEEEEEecchhheehhhhhhhhcc-------cc-------cccceeEEEEeccEEEEecCC
Confidence 367999999999999999999999999998752 21 247999999999999998765
No 31
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.35 E-value=9.6e-13 Score=85.39 Aligned_cols=67 Identities=21% Similarity=0.515 Sum_probs=53.2
Q ss_pred cccCCChhhhhhhhcC------------CeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEE
Q 034273 18 EFNTGPLSVLMMSVKN------------NTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 85 (99)
Q Consensus 18 ~~~~~Pl~vL~~~lk~------------gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~ 85 (99)
..+..|+.+|-..|++ +-.+.|.++|||+|||+||+||+|..... + ..+.+|.++
T Consensus 8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~--------~-----~rk~lGRil 74 (88)
T KOG1774|consen 8 KVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT--------K-----SRKELGRIL 74 (88)
T ss_pred ceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc--------c-----CCCccccEE
Confidence 4567899998887743 45699999999999999999999975321 0 123799999
Q ss_pred EeCCcEEEEEeC
Q 034273 86 LRGDSVIIVLRN 97 (99)
Q Consensus 86 IRGdnVv~V~~~ 97 (99)
++||||.+|...
T Consensus 75 LKGDnItli~~~ 86 (88)
T KOG1774|consen 75 LKGDNITLIQSA 86 (88)
T ss_pred EcCCcEEEEeec
Confidence 999999999764
No 32
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.33 E-value=5.5e-13 Score=85.66 Aligned_cols=66 Identities=24% Similarity=0.488 Sum_probs=54.3
Q ss_pred CCChhhhhhhh--------cCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273 21 TGPLSVLMMSV--------KNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92 (99)
Q Consensus 21 ~~Pl~vL~~~l--------k~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 92 (99)
--|+.++.+++ ++.+++.|+|+|||.|.|++|+||+|+-..+. ++ +-.+++++++.|+||.
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e----gr-------~~tk~~~iLLnGNni~ 74 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE----GR-------RMTKLDQILLNGNNIT 74 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC----cc-------eeeeeeeeeecCCcEE
Confidence 36888888886 88999999999999999999999999865421 11 1246899999999999
Q ss_pred EEEeC
Q 034273 93 IVLRN 97 (99)
Q Consensus 93 ~V~~~ 97 (99)
++.|.
T Consensus 75 mLvPG 79 (84)
T KOG1775|consen 75 MLVPG 79 (84)
T ss_pred EEecC
Confidence 98774
No 33
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.18 E-value=1e-12 Score=90.76 Aligned_cols=58 Identities=26% Similarity=0.369 Sum_probs=48.9
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeCC
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 98 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~p 98 (99)
.|++||.+.|+|++||||-|++|++|.|.+....+ .+.+..|.++|||+||+++...+
T Consensus 25 lLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-----------Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 25 LLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-----------YCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred EEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-----------ecccCceEEEEecCcEEEEecCC
Confidence 46899999999999999999999999999875322 23456799999999999997654
No 34
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.12 E-value=3.2e-12 Score=81.40 Aligned_cols=54 Identities=20% Similarity=0.389 Sum_probs=46.9
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
.|.+|..+.|+|.+.|.|||+.|+.++|+.. ++. .+.+|..||||+||++|+..
T Consensus 22 Kl~sgvdyrG~l~~lDgymNiaLe~tee~~n-------gql-------~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 22 KLNSGVDYRGTLVCLDGYMNIALESTEEYVN-------GQL-------KNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred EecCCccccceehhhhhHHHHHHHHHHHHhc-------Ccc-------cccccceeeccccEEEEEec
Confidence 5688999999999999999999999999864 333 36789999999999999875
No 35
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.05 E-value=5.1e-11 Score=78.72 Aligned_cols=67 Identities=16% Similarity=0.397 Sum_probs=52.1
Q ss_pred cccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
.|+++-+++++. +||.+.|.|+|||+-.||+|+++.|++..... +.+ ...+|..+|||+||.+|.+.
T Consensus 7 ~y~n~~V~vIt~---DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~---gv~-------q~~lGlyiirgeNva~ig~i 73 (96)
T KOG1784|consen 7 DYMNQRVSVITN---DGRVIVGSLKGFDQTTNLIIDESHERIFSETE---GVE-------QIVLGLYIIRGENVAVIGEI 73 (96)
T ss_pred HHhhceEEEEec---CCeEEEEEeccccccceeeehhhHhhhhhhhc---chh-------heeeEEEEEecCccceeeec
Confidence 355555666555 69999999999999999999999998764221 222 35789999999999998763
No 36
>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=98.88 E-value=5.7e-10 Score=69.74 Aligned_cols=27 Identities=33% Similarity=0.450 Sum_probs=25.1
Q ss_pred eEEEEEEEEecCeeceEeeceEEEeec
Q 034273 35 TQLLGRVRAFDRHCNMVLENVREMWTE 61 (99)
Q Consensus 35 r~i~G~L~afD~hmNLvL~d~~E~~~~ 61 (99)
..++|.|.|||+||||+|.||+|.|..
T Consensus 23 G~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 23 GVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEEeeeeehhheehhhhhhhcc
Confidence 479999999999999999999999864
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.48 E-value=1.8e-07 Score=64.94 Aligned_cols=61 Identities=25% Similarity=0.326 Sum_probs=49.7
Q ss_pred CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273 22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 93 (99)
Q Consensus 22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 93 (99)
.||++|+.+ |++|-.|.|.|+..|.+|||.|.+|+++... +.+ --.+..+.|||.+|-+
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D------gdk-------f~r~pEcYirGttIky 68 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED------GDK-------FFRMPECYIRGTTIKY 68 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccC------CCc-------eeecceeEEecceeEE
Confidence 588888877 4899999999999999999999999987542 111 1236889999999988
Q ss_pred EE
Q 034273 94 VL 95 (99)
Q Consensus 94 V~ 95 (99)
|.
T Consensus 69 lr 70 (134)
T KOG3293|consen 69 LR 70 (134)
T ss_pred Ee
Confidence 75
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.09 E-value=1e-05 Score=53.52 Aligned_cols=56 Identities=23% Similarity=0.342 Sum_probs=42.6
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEeC
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 97 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~~~ 97 (99)
.|+++-.+.|+|.+.|+|.||-|.|+.-.-.. + .|.. -.+..+||||..|-+|...
T Consensus 18 eLKnd~~i~GtL~svDqyLNlkL~di~v~d~~--k--------yPhm--~Sv~ncfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 18 ELKNDLSICGTLHSVDQYLNLKLTDISVTDPD--K--------YPHM--LSVKNCFIRGSVVRYVQLP 73 (96)
T ss_pred EEcCCcEEEEEecccchhheeEEeeeEeeCcc--c--------CCCe--eeeeeEEEeccEEEEEEeC
Confidence 46889999999999999999999997654211 1 1111 3567899999999988654
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=97.71 E-value=9.6e-05 Score=50.46 Aligned_cols=60 Identities=17% Similarity=0.358 Sum_probs=45.7
Q ss_pred CChhhhhhh--------hcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 034273 22 GPLSVLMMS--------VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 93 (99)
Q Consensus 22 ~Pl~vL~~~--------lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~ 93 (99)
-|+.+|..+ +..|..|.|.|.-.+.+||++|+|++-+... +. .-++.++||||+.|-+
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d------g~--------vs~le~V~IRGS~IRF 70 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD------GR--------VSQLEQVFIRGSKIRF 70 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC------Cc--------ceeeeeEEEecCeEEE
Confidence 355555444 3778899999999999999999998865431 11 1368999999999977
Q ss_pred EE
Q 034273 94 VL 95 (99)
Q Consensus 94 V~ 95 (99)
+.
T Consensus 71 lv 72 (119)
T KOG3172|consen 71 LV 72 (119)
T ss_pred EE
Confidence 64
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=96.80 E-value=0.0035 Score=42.75 Aligned_cols=51 Identities=22% Similarity=0.368 Sum_probs=40.7
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 95 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~ 95 (99)
.|++|+.+.|++.+.|.+||..|.++.=+.. +. ...+..++|||+||-++.
T Consensus 18 eLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-------~~--------pv~l~~lsirgnniRy~~ 68 (109)
T KOG3428|consen 18 ELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-------GE--------PVRLDTLSIRGNNIRYYI 68 (109)
T ss_pred EecCCcEEeeeEEEEEhhheeEEEEEEEecC-------CC--------ceeEEEEEeecceEEEEE
Confidence 4589999999999999999999999874432 11 125788999999998764
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=90.41 E-value=0.3 Score=30.12 Aligned_cols=25 Identities=24% Similarity=0.442 Sum_probs=21.2
Q ss_pred hhcCCeEEEEEEEEecCeeceEeec
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLEN 54 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d 54 (99)
.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 17 ~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 17 YLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred EEeCCcEEEEEEEEEcceEEEEEEC
Confidence 5678999999999999999666554
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=89.32 E-value=0.4 Score=29.60 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=21.1
Q ss_pred hhcCCeEEEEEEEEecCeeceEeec
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLEN 54 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d 54 (99)
.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 21 ~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 21 FLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred EEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 5678999999999999999766544
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=88.84 E-value=0.44 Score=30.85 Aligned_cols=26 Identities=19% Similarity=0.368 Sum_probs=22.0
Q ss_pred hhcCCeEEEEEEEEecCeeceEeece
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENV 55 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~ 55 (99)
.|.+|-.+.|.+.|||+|+=|+-.+-
T Consensus 25 fL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 25 YLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred EEeCCcEEEEEEEEEccEEEEEEECC
Confidence 56789999999999999997776554
No 44
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=87.02 E-value=2.3 Score=27.16 Aligned_cols=68 Identities=21% Similarity=0.296 Sum_probs=46.0
Q ss_pred cccCCChhhhhhhhcCCeEEEEEEEEecCee-ceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273 18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92 (99)
Q Consensus 18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hm-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 92 (99)
.+...+++++.+. +-.++|.|..+|..- -+.|.||..+-++..+.... .. +. ...-+..++.||..|-
T Consensus 3 ~~IG~~isLISk~---~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~--~i-pp-~~~vyd~IvFrgsDIk 71 (74)
T cd01736 3 PYIGSKISLISKS---DIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGP--EI-PP-SDEVYDYIVFRGSDIK 71 (74)
T ss_pred cccCceEEEEecC---CcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCC--cc-CC-CCcceeEEEEcCCccc
Confidence 4667777777765 788999999999887 56799998876653322111 00 01 1234688999998874
No 45
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=85.24 E-value=3.6 Score=27.27 Aligned_cols=70 Identities=20% Similarity=0.273 Sum_probs=47.0
Q ss_pred cccCCChhhhhhhhcCCeEEEEEEEEecC-eeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 034273 18 EFNTGPLSVLMMSVKNNTQLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 95 (99)
Q Consensus 18 ~~~~~Pl~vL~~~lk~gr~i~G~L~afD~-hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv~V~ 95 (99)
.|....++++.+. +-.|+|+|...|. -.++.|.+|.-+-++.++...... -....+..+.+||..|--+.
T Consensus 5 ~~IGs~ISlisk~---~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ip-----p~~~v~~~I~Fr~sDIkdL~ 75 (96)
T PF12701_consen 5 PYIGSKISLISKS---DIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIP-----PSDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCTTCEEEEEETT---TEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS--------C-CSSSSEEEEETTTEEEEE
T ss_pred cccCCEEEEEECC---CcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccC-----CCCceeeEEEEEccccceEE
Confidence 4556666776654 7899999999998 679999999987664322111000 11234689999999886554
No 46
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=77.64 E-value=2.9 Score=25.84 Aligned_cols=56 Identities=13% Similarity=0.201 Sum_probs=28.3
Q ss_pred hhcCCeEEEEEEEEecC---eeceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 034273 30 SVKNNTQLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 92 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~---hmNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGdnVv 92 (99)
.+++|..|+|.|.+++. -+.++|.-+...-....++ .. .........++|.++.|+
T Consensus 18 ~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~---~~----~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 18 TTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN---SD----PLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EETTS-EEEEEEEEE-T---T--EEEEEEEETTS---------E----EEEEEE-GGGEEE-----
T ss_pred EECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc---CC----ccCCCCCceEEEeccccC
Confidence 35899999999999999 8899998777643211000 00 112234567888887765
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=72.90 E-value=3.4 Score=30.15 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=21.3
Q ss_pred hcCCeEEEEEEEEecCeeceEeeceE
Q 034273 31 VKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 31 lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
|.+|-.+.|.+.|||+|+=|+-.+..
T Consensus 111 L~NG~~l~G~I~~fD~ftvlL~~~gk 136 (165)
T PRK14091 111 LVNGVMLQGEIAAFDLFCMLLERDGY 136 (165)
T ss_pred EecCcEEEEEEEEEcceEEEEEeCCc
Confidence 46788999999999999977766643
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=69.69 E-value=4.5 Score=29.54 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=21.2
Q ss_pred hhcCCeEEEEEEEEecCeeceEeece
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENV 55 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~ 55 (99)
.|.+|-.+.|.+.+||+|.=|+-.+.
T Consensus 30 fL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 30 FLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred EEecCcEEEEEEEEEcceEEEEEeCC
Confidence 45678999999999999986666554
No 49
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=69.26 E-value=4.8 Score=23.10 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=15.3
Q ss_pred EEEEEEEecCeeceEeeceEEE
Q 034273 37 LLGRVRAFDRHCNMVLENVREM 58 (99)
Q Consensus 37 i~G~L~afD~hmNLvL~d~~E~ 58 (99)
.+|+.+|.|+-+.|+|++...+
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 6899999999999999987654
No 50
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=67.52 E-value=5.2 Score=25.79 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=19.5
Q ss_pred hhcCCeEEEEEEEEecCeeceEee
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLE 53 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~ 53 (99)
.|.+|-++.|.+.+||+|.=|+=.
T Consensus 25 fLvNG~~L~G~V~sfD~f~VlL~~ 48 (77)
T COG1923 25 FLVNGFKLQGQVESFDNFVVLLKN 48 (77)
T ss_pred EEEcCEEEEEEEEeeeeEEEEEEc
Confidence 567899999999999999854433
No 51
>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=67.04 E-value=14 Score=20.84 Aligned_cols=25 Identities=8% Similarity=0.218 Sum_probs=21.4
Q ss_pred CCeEEEEEEEEecCeeceEeeceEE
Q 034273 33 NNTQLLGRVRAFDRHCNMVLENVRE 57 (99)
Q Consensus 33 ~gr~i~G~L~afD~hmNLvL~d~~E 57 (99)
++..++|+..+.|..-.|+++....
T Consensus 11 ~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCeEEEEEEEEECCCCEEEEEECCC
Confidence 5788899999999999999986444
No 52
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=62.70 E-value=5.5 Score=28.43 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=23.1
Q ss_pred hhhhhhcCCeEEEEEEEEecCeeceEeeceE
Q 034273 26 VLMMSVKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 26 vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
++.+.++.+-.=+|+|+|.|+|-|=--+|-.
T Consensus 34 ~~~k~yrtd~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 34 LLDKLYRTDDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred HHHHHHhcccccceeeeeecccccchhcccc
Confidence 3444556666778999999999997776653
No 53
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=62.20 E-value=11 Score=23.13 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=20.3
Q ss_pred cCCeEEEEEEEEecCeeceEeeceE
Q 034273 32 KNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 32 k~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
-.|.+++|.+.|||.-.+|++=.+.
T Consensus 14 c~g~~ieGEV~afD~~tk~lIlk~~ 38 (61)
T cd01735 14 CFEQRLQGEVVAFDYPSKMLILKCP 38 (61)
T ss_pred cCCceEEEEEEEecCCCcEEEEECc
Confidence 3588999999999999988755433
No 54
>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=39.95 E-value=24 Score=25.68 Aligned_cols=27 Identities=19% Similarity=0.089 Sum_probs=23.3
Q ss_pred hhcCCeEEEEEEEEecCeeceEeeceE
Q 034273 30 SVKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 30 ~lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
.+.+|..|.|++.+|+.--|++|..+.
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 447899999999999999999997543
No 55
>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=38.53 E-value=13 Score=24.74 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=14.6
Q ss_pred EEEEEecCeeceEeece
Q 034273 39 GRVRAFDRHCNMVLENV 55 (99)
Q Consensus 39 G~L~afD~hmNLvL~d~ 55 (99)
|+|+|.|.|-|-=-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999877665
No 56
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=30.46 E-value=69 Score=26.00 Aligned_cols=49 Identities=18% Similarity=0.175 Sum_probs=38.3
Q ss_pred ccCCccccccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceEE
Q 034273 9 TTGGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVRE 57 (99)
Q Consensus 9 ~~~~~~~~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~E 57 (99)
...-+.+-.+-.-||-..|...|+++-+++|++.+=|.|+|=-.++|.+
T Consensus 22 ~Ad~~p~~~~g~vGp~~~l~~~l~~~~eIv~TiiCGDnyf~en~eea~~ 70 (349)
T PF07355_consen 22 KADTPPEVREGPVGPGLMLEKALKDDAEIVATIICGDNYFNENKEEALK 70 (349)
T ss_pred cCCCCCccccCCCChHHHHHHHhcCCCEEEEEEEECcchhhhCHHHHHH
Confidence 3334456667788999999999999999999999999999944444443
No 57
>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=29.27 E-value=43 Score=26.38 Aligned_cols=30 Identities=3% Similarity=0.243 Sum_probs=24.5
Q ss_pred hhhhhcCCeEEEEEEEEecCeeceEeeceE
Q 034273 27 LMMSVKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 27 L~~~lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
+.+.+.+|+.+.++++++|...+|.|=.+.
T Consensus 104 i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 104 IVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred EEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 344457899999999999999999986554
No 58
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=28.78 E-value=99 Score=21.27 Aligned_cols=27 Identities=11% Similarity=0.092 Sum_probs=23.1
Q ss_pred CeEEEEEEEEecCeeceEeeceEEEee
Q 034273 34 NTQLLGRVRAFDRHCNMVLENVREMWT 60 (99)
Q Consensus 34 gr~i~G~L~afD~hmNLvL~d~~E~~~ 60 (99)
...+.|.|.|+..=-.+.+.||.+.-.
T Consensus 22 ~~~v~G~LlG~~~~~~veV~nsF~lp~ 48 (157)
T cd08057 22 IKRVIGVLLGYVDGDKIEVTNSFELPF 48 (157)
T ss_pred CCeEEEEEEeEEeCCEEEEEEeEEccc
Confidence 368999999999877999999998754
No 59
>PRK10898 serine endoprotease; Provisional
Probab=25.79 E-value=56 Score=25.83 Aligned_cols=29 Identities=3% Similarity=0.172 Sum_probs=24.0
Q ss_pred hhhhcCCeEEEEEEEEecCeeceEeeceE
Q 034273 28 MMSVKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 28 ~~~lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
.+.+.+|+.+.+.++++|...+|.|=.+.
T Consensus 105 ~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 105 IVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred EEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 44457889999999999999999886654
No 60
>PF09196 DUF1953: Domain of unknown function (DUF1953); InterPro: IPR015279 This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. ; PDB: 3HJE_A 1IV8_A.
Probab=25.77 E-value=80 Score=19.44 Aligned_cols=14 Identities=14% Similarity=0.624 Sum_probs=11.7
Q ss_pred EEEeCCcEEEEEeC
Q 034273 84 MFLRGDSVIIVLRN 97 (99)
Q Consensus 84 i~IRGdnVv~V~~~ 97 (99)
-|+|||.|+.|...
T Consensus 13 gf~r~~kilviikt 26 (66)
T PF09196_consen 13 GFIRFNKILVIIKT 26 (66)
T ss_dssp EEEETTTEEEEEES
T ss_pred eEEecCEEEEEEec
Confidence 49999999988764
No 61
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=25.10 E-value=92 Score=19.90 Aligned_cols=26 Identities=8% Similarity=0.038 Sum_probs=22.2
Q ss_pred CeEEEEEEEEecCee-ceEeeceEEEe
Q 034273 34 NTQLLGRVRAFDRHC-NMVLENVREMW 59 (99)
Q Consensus 34 gr~i~G~L~afD~hm-NLvL~d~~E~~ 59 (99)
..++.|.|.|+..-- .+.+.|+.+.-
T Consensus 25 ~~~v~G~LlG~~~~~~~v~I~~~f~~p 51 (114)
T PF01398_consen 25 PNEVIGLLLGTQDGDNTVEITNSFPVP 51 (114)
T ss_dssp CTEEEEEEEEEEETT-EEEEEEEEEES
T ss_pred CCEEEEEEEEEecCceEEEEEEEEEee
Confidence 348999999998888 89999999864
No 62
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=24.76 E-value=83 Score=20.49 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=18.6
Q ss_pred eeeeceEEEeCCcEEEEEeCC
Q 034273 78 DRFISKMFLRGDSVIIVLRNP 98 (99)
Q Consensus 78 ~r~lg~i~IRGdnVv~V~~~p 98 (99)
.|+-|.+.++|..+..|...|
T Consensus 76 ~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hcceEEEEEECCeeeEEEcCC
Confidence 378899999999999998777
No 63
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=22.91 E-value=1.1e+02 Score=25.67 Aligned_cols=48 Identities=15% Similarity=0.041 Sum_probs=37.3
Q ss_pred ccCCccccccccCCChhhhhhhhcCCeEEEEEEEEecCeeceEeeceE
Q 034273 9 TTGGKTEEEEFNTGPLSVLMMSVKNNTQLLGRVRAFDRHCNMVLENVR 56 (99)
Q Consensus 9 ~~~~~~~~~~~~~~Pl~vL~~~lk~gr~i~G~L~afD~hmNLvL~d~~ 56 (99)
...-+.+-.+-.-||-..|...|+++-++++++.+=|.|+|=-++.|.
T Consensus 18 ~Ad~~p~~~~g~vGp~~~l~~~l~~~~eVvaTiiCGDnYf~en~eea~ 65 (431)
T TIGR01918 18 KADYEPEIAEGQPPISQMLNKLLEEDAEVVHTVVCGDSFFGENLEEAV 65 (431)
T ss_pred ccCCCCccccCCCChHHHHHHHhccCCEEEEEEEECchhhhhCHHHHH
Confidence 333344666666789999999999999999999999999995455443
No 64
>PRK14633 hypothetical protein; Provisional
Probab=22.85 E-value=56 Score=22.97 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=15.5
Q ss_pred cCCeEEEEEEEEecCeeceEe
Q 034273 32 KNNTQLLGRVRAFDRHCNMVL 52 (99)
Q Consensus 32 k~gr~i~G~L~afD~hmNLvL 52 (99)
.+.+.++|+|.+++.. ++.|
T Consensus 106 ~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 106 GSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CCcEEEEEEEEEEeCC-EEEE
Confidence 4678899999999884 4444
No 65
>PRK10942 serine endoprotease; Provisional
Probab=22.77 E-value=65 Score=26.62 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=22.8
Q ss_pred hhhcCCeEEEEEEEEecCeeceEeece
Q 034273 29 MSVKNNTQLLGRVRAFDRHCNMVLENV 55 (99)
Q Consensus 29 ~~lk~gr~i~G~L~afD~hmNLvL~d~ 55 (99)
+.+.+|+.+.+.++++|...+|.|=.+
T Consensus 140 V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 140 VQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred EEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 345788999999999999999988754
No 66
>PRK14638 hypothetical protein; Provisional
Probab=21.25 E-value=62 Score=22.76 Aligned_cols=20 Identities=20% Similarity=0.581 Sum_probs=15.4
Q ss_pred cCCeEEEEEEEEecCeeceEe
Q 034273 32 KNNTQLLGRVRAFDRHCNMVL 52 (99)
Q Consensus 32 k~gr~i~G~L~afD~hmNLvL 52 (99)
++++.++|+|.++|.- ++.|
T Consensus 108 ~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 108 KDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred CCCcEEEEEEEEEeCC-EEEE
Confidence 5788999999999963 3444
Done!