Query 034463
Match_columns 94
No_of_seqs 105 out of 1045
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:08:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034463hhsearch_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 8.4E-25 1.8E-29 140.5 6.2 72 4-91 8-79 (79)
2 PTZ00138 small nuclear ribonuc 99.9 2.7E-24 5.9E-29 140.9 6.5 73 4-92 16-88 (89)
3 KOG1774 Small nuclear ribonucl 99.9 1.4E-24 3.1E-29 139.9 1.3 74 3-92 13-86 (88)
4 cd01720 Sm_D2 The eukaryotic S 99.9 3.7E-22 8E-27 130.1 9.4 75 13-93 13-87 (87)
5 cd01730 LSm3 The eukaryotic Sm 99.8 6.2E-21 1.4E-25 122.4 8.9 66 25-91 17-82 (82)
6 cd01732 LSm5 The eukaryotic Sm 99.8 1.5E-20 3.2E-25 119.7 9.4 61 21-92 15-75 (76)
7 cd01729 LSm7 The eukaryotic Sm 99.8 1.6E-19 3.5E-24 116.0 9.1 61 27-93 20-80 (81)
8 cd01717 Sm_B The eukaryotic Sm 99.8 5.3E-19 1.2E-23 112.5 9.1 64 21-90 14-77 (79)
9 KOG3460 Small nuclear ribonucl 99.8 2.9E-20 6.2E-25 120.5 0.8 71 21-93 17-88 (91)
10 cd01727 LSm8 The eukaryotic Sm 99.8 1.8E-18 4E-23 109.0 9.0 62 22-93 12-73 (74)
11 PRK00737 small nuclear ribonuc 99.8 1.3E-18 2.8E-23 109.2 8.0 55 21-91 18-72 (72)
12 cd01731 archaeal_Sm1 The archa 99.8 1.4E-18 3.1E-23 107.6 8.0 55 23-91 14-68 (68)
13 cd01728 LSm1 The eukaryotic Sm 99.8 3.9E-18 8.4E-23 108.2 9.2 59 22-91 15-73 (74)
14 cd01719 Sm_G The eukaryotic Sm 99.8 5.5E-18 1.2E-22 106.7 8.6 57 23-93 14-70 (72)
15 smart00651 Sm snRNP Sm protein 99.7 5.7E-17 1.2E-21 98.9 7.8 58 21-91 10-67 (67)
16 cd06168 LSm9 The eukaryotic Sm 99.7 1.1E-16 2.5E-21 101.6 9.0 57 27-91 18-74 (75)
17 PF01423 LSM: LSM domain ; In 99.7 1.8E-16 4E-21 96.8 8.3 58 21-91 10-67 (67)
18 cd01726 LSm6 The eukaryotic Sm 99.7 2.7E-16 5.9E-21 97.3 7.9 53 24-90 15-67 (67)
19 cd01722 Sm_F The eukaryotic Sm 99.7 4.8E-16 1E-20 96.5 7.4 54 23-90 15-68 (68)
20 COG1958 LSM1 Small nuclear rib 99.6 1.1E-15 2.5E-20 96.9 8.0 59 21-91 21-79 (79)
21 cd00600 Sm_like The eukaryotic 99.6 7.5E-15 1.6E-19 88.3 8.1 54 23-90 10-63 (63)
22 KOG1780 Small Nuclear ribonucl 99.6 3.7E-15 8.1E-20 94.7 5.0 57 22-92 17-73 (77)
23 cd01723 LSm4 The eukaryotic Sm 99.5 7.2E-14 1.6E-18 88.4 8.0 60 21-93 13-72 (76)
24 KOG1781 Small Nuclear ribonucl 99.5 1.4E-15 3E-20 101.3 -0.5 61 27-93 35-95 (108)
25 cd01721 Sm_D3 The eukaryotic S 99.5 1.8E-13 4E-18 85.4 8.5 58 21-92 12-69 (70)
26 cd01724 Sm_D1 The eukaryotic S 99.4 5.9E-13 1.3E-17 87.1 7.1 53 27-93 19-71 (90)
27 KOG1775 U6 snRNA-associated Sm 99.4 9.8E-14 2.1E-18 88.8 3.2 61 21-92 19-79 (84)
28 KOG3168 U1 snRNP component [Tr 99.4 2.4E-14 5.2E-19 102.9 0.0 66 23-92 18-83 (177)
29 cd01725 LSm2 The eukaryotic Sm 99.4 1.3E-12 2.7E-17 83.8 6.5 70 7-93 2-73 (81)
30 cd01733 LSm10 The eukaryotic S 99.4 4.2E-12 9E-17 81.1 8.0 52 27-92 27-78 (78)
31 KOG3459 Small nuclear ribonucl 99.3 1.8E-13 3.9E-18 92.6 -0.4 69 24-93 41-109 (114)
32 KOG1782 Small Nuclear ribonucl 99.2 6.9E-13 1.5E-17 91.2 -2.2 56 27-93 27-82 (129)
33 cd01739 LSm11_C The eukaryotic 99.2 5.7E-12 1.2E-16 78.4 2.1 46 8-56 2-49 (66)
34 KOG1784 Small Nuclear ribonucl 99.1 1.1E-10 2.4E-15 76.8 4.0 62 21-92 12-73 (96)
35 KOG3482 Small nuclear ribonucl 98.8 9.9E-09 2.2E-13 65.3 4.8 53 27-93 26-78 (79)
36 KOG1783 Small nuclear ribonucl 98.6 5.8E-09 1.3E-13 66.3 0.1 53 27-93 24-76 (77)
37 KOG3448 Predicted snRNP core p 97.7 8.3E-05 1.8E-09 49.0 5.3 69 6-91 2-72 (96)
38 KOG3172 Small nuclear ribonucl 96.9 0.0065 1.4E-07 41.4 6.8 57 22-92 18-74 (119)
39 KOG3293 Small nuclear ribonucl 96.5 0.0052 1.1E-07 42.7 4.6 53 27-92 20-72 (134)
40 cd01716 Hfq Hfq, an abundant, 95.8 0.01 2.2E-07 36.5 2.8 36 9-49 6-41 (61)
41 TIGR02383 Hfq RNA chaperone Hf 95.6 0.032 6.9E-07 34.3 4.5 35 10-49 11-45 (61)
42 KOG3428 Small nuclear ribonucl 95.4 0.13 2.8E-06 35.0 7.2 53 25-92 18-70 (109)
43 PRK00395 hfq RNA-binding prote 95.3 0.034 7.4E-07 35.8 4.0 36 10-50 15-50 (79)
44 COG1923 Hfq Uncharacterized ho 95.1 0.012 2.6E-07 37.8 1.5 38 7-49 12-49 (77)
45 PRK14091 RNA-binding protein H 92.1 0.25 5.3E-06 35.9 3.9 38 10-52 100-137 (165)
46 PRK14091 RNA-binding protein H 91.7 0.3 6.5E-06 35.4 3.9 37 9-50 19-55 (165)
47 PF14438 SM-ATX: Ataxin 2 SM d 86.2 2.7 5.9E-05 25.8 5.0 58 21-87 16-76 (77)
48 cd01735 LSm12_N LSm12 belongs 71.7 10 0.00023 23.1 4.1 30 23-52 10-39 (61)
49 PF14563 DUF4444: Domain of un 67.5 5.8 0.00013 22.7 2.1 23 32-54 10-32 (42)
50 PF12701 LSM14: Scd6-like Sm d 54.5 59 0.0013 21.3 6.9 62 21-87 10-72 (96)
51 PF02237 BPL_C: Biotin protein 48.6 48 0.001 18.5 4.9 25 28-52 11-35 (48)
52 cd01736 LSm14_N LSm14 (also kn 38.5 1E+02 0.0022 19.5 7.1 63 21-87 8-71 (74)
53 PF08863 YolD: YolD-like prote 30.0 1.3E+02 0.0029 18.2 4.8 36 10-48 38-74 (92)
54 PF11743 DUF3301: Protein of u 29.4 62 0.0013 21.0 2.6 22 72-93 75-96 (97)
55 PF03614 Flag1_repress: Repres 28.9 76 0.0016 23.0 3.1 31 21-51 31-61 (165)
56 PRK14633 hypothetical protein; 27.2 84 0.0018 21.9 3.1 20 27-47 106-125 (150)
57 PRK14643 hypothetical protein; 23.2 1E+02 0.0023 21.9 3.0 27 21-47 108-137 (164)
58 cd01734 YlxS_C YxlS is a Bacil 22.8 1.2E+02 0.0027 18.7 3.0 22 21-42 29-52 (83)
59 TIGR02038 protease_degS peripl 22.4 1.5E+02 0.0033 23.1 4.1 25 27-51 109-133 (351)
60 PRK10898 serine endoprotease; 21.8 1.6E+02 0.0035 23.0 4.1 25 27-51 109-133 (353)
61 PRK14646 hypothetical protein; 21.7 1.1E+02 0.0024 21.4 2.9 26 21-47 104-131 (155)
62 PF05071 NDUFA12: NADH ubiquin 20.5 39 0.00086 22.2 0.3 17 34-50 1-17 (105)
63 COG0779 Uncharacterized protei 20.4 1.3E+02 0.0029 21.3 3.0 25 22-47 106-130 (153)
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=99.91 E-value=8.4e-25 Score=140.52 Aligned_cols=72 Identities=25% Similarity=0.529 Sum_probs=64.5
Q ss_pred EEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 4 IQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 4 ~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
++.+|+||+++.++ ++|+.++.+++++|+|+|||+||||+|+||+|+... . ++++.+|.+++||
T Consensus 8 ~~~l~~~l~~~~~V---~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~---~----------~~~~~lG~iliRG 71 (79)
T cd01718 8 INLIFRFLQSKQRV---QIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK---T----------KTRKPLGRILLKG 71 (79)
T ss_pred HHHHHHHHccCcEE---EEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC---C----------ceEeEcCcEEEeC
Confidence 56789999999999 999999999999999999999999999999998642 0 1356899999999
Q ss_pred CeEEEEEe
Q 034463 84 DSVIIVLR 91 (94)
Q Consensus 84 dnVv~I~~ 91 (94)
|||++|+|
T Consensus 72 nnV~~I~p 79 (79)
T cd01718 72 DNITLIQN 79 (79)
T ss_pred CEEEEEcC
Confidence 99999996
No 2
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.90 E-value=2.7e-24 Score=140.88 Aligned_cols=73 Identities=26% Similarity=0.582 Sum_probs=65.7
Q ss_pred EEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 4 IQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 4 ~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
||++|+|++++++| .+|+.++.+++++|+|+|||+|||+||+||+|.+.. . +.++.+|.+++||
T Consensus 16 ~~~~~~~~~~~~~V---~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~---~----------~~~~~lG~ilIRG 79 (89)
T PTZ00138 16 INQIFRFFTEKTRV---QIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK---K----------NTRKDLGRILLKG 79 (89)
T ss_pred HHHHHHHhcCCcEE---EEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC---C----------ceeeEcCeEEEcC
Confidence 67899999999999 999999999999999999999999999999997642 0 1357899999999
Q ss_pred CeEEEEEeC
Q 034463 84 DSVIIVLRN 92 (94)
Q Consensus 84 dnVv~I~~~ 92 (94)
|||++|+|.
T Consensus 80 nnV~~I~~~ 88 (89)
T PTZ00138 80 DNITLIMAA 88 (89)
T ss_pred CEEEEEEcC
Confidence 999999875
No 3
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.89 E-value=1.4e-24 Score=139.95 Aligned_cols=74 Identities=24% Similarity=0.560 Sum_probs=65.6
Q ss_pred eEEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEe
Q 034463 3 VIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLR 82 (94)
Q Consensus 3 ~~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iR 82 (94)
-||++|+|||+++|+ ++|+.|+.+.+++|.+.|||+|||+||+||+|..... ..++.+|.++++
T Consensus 13 Pin~Ifr~Lq~~t~V---qIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~-------------~~rk~lGRilLK 76 (88)
T KOG1774|consen 13 PINLIFRFLQNRTRV---QIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT-------------KSRKELGRILLK 76 (88)
T ss_pred cHHHHHHHHhcCCce---EEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc-------------cCCCccccEEEc
Confidence 379999999999999 9999999999999999999999999999999985420 123479999999
Q ss_pred CCeEEEEEeC
Q 034463 83 GDSVIIVLRN 92 (94)
Q Consensus 83 GdnVv~I~~~ 92 (94)
||||.+|...
T Consensus 77 GDnItli~~~ 86 (88)
T KOG1774|consen 77 GDNITLIQSA 86 (88)
T ss_pred CCcEEEEeec
Confidence 9999999764
No 4
>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=3.7e-22 Score=130.15 Aligned_cols=75 Identities=76% Similarity=1.161 Sum_probs=57.8
Q ss_pred CcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 13 SQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 13 ~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
.+.++ .+.+ +.++++.|+|+|||+||||+|+||+|.+...+++..+.+ ....+++|++|++|+|||||++|+|.
T Consensus 13 ~~~~V---~V~l--r~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~-~~~~~~~r~lg~v~iRGd~Vv~Is~~ 86 (87)
T cd01720 13 NNTQV---LINC--RNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKK-AKPVNKDRFISKMFLRGDSVILVLRN 86 (87)
T ss_pred CCCEE---EEEE--cCCCEEEEEEEEecCccEEEEcceEEEeecccccccccc-ccceeeeeEcccEEEeCCEEEEEecC
Confidence 35566 6666 889999999999999999999999999876443221111 11123567899999999999999997
Q ss_pred C
Q 034463 93 P 93 (94)
Q Consensus 93 ~ 93 (94)
|
T Consensus 87 ~ 87 (87)
T cd01720 87 P 87 (87)
T ss_pred C
Confidence 6
No 5
>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=99.85 E-value=6.2e-21 Score=122.40 Aligned_cols=66 Identities=33% Similarity=0.429 Sum_probs=50.8
Q ss_pred EecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 25 LEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 25 ~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
.-++||++.|+|+|||+||||+|+||+|.+....++.+..+ ......+|.+|+++||||||++|+|
T Consensus 17 ~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~-~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 17 KLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYE-EIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred EECCCCEEEEEEEEEccceEEeccceEEEeecccccccccc-cccceeEEEcCeEEEeCCEEEEECC
Confidence 33889999999999999999999999999875433221100 0112346899999999999999986
No 6
>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=1.5e-20 Score=119.73 Aligned_cols=61 Identities=23% Similarity=0.389 Sum_probs=51.2
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
++|+.-+.+|++.|+|+|||+||||+|+||+|++... ++ .+.+++|.+++|||||++|+|.
T Consensus 15 ~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~-~~----------~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 15 RIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP-EG----------RKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC-CC----------ceeeEcCeEEEeCCeEEEEECC
Confidence 4566669999999999999999999999999997431 11 1357899999999999999985
No 7
>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=99.81 E-value=1.6e-19 Score=115.95 Aligned_cols=61 Identities=20% Similarity=0.257 Sum_probs=49.1
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++||++.|+|+|||+||||||+||+|+......+. +....++.+|+++|||+||++|+|..
T Consensus 20 ~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~------~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 20 QGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred CCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc------ccccceeEccEEEEcCCEEEEEecCC
Confidence 78999999999999999999999999876422110 01124678999999999999999864
No 8
>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=5.3e-19 Score=112.53 Aligned_cols=64 Identities=25% Similarity=0.350 Sum_probs=50.1
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEE
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~ 90 (94)
.+.+ ++||++.|+|.|||+||||||+||+|++...+.+.. .....++|++|++++|||||++|+
T Consensus 14 ~V~l--~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~----~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 14 RVTL--QDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK----NSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred EEEE--CCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc----cccCcceeEeeeEEEcCCEEEEEE
Confidence 4444 789999999999999999999999999865332110 011235689999999999999997
No 9
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.78 E-value=2.9e-20 Score=120.46 Aligned_cols=71 Identities=30% Similarity=0.358 Sum_probs=58.0
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCcc-ccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKK-KALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~-~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++|+..|++|++.|+|+|||+|+||+|+||+|++++...++...+ ..|. .+|.+.++|+|||+|++|+|+.
T Consensus 17 rVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~--~~r~~emlFvRGd~Vilvspp~ 88 (91)
T KOG3460|consen 17 RVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKT--TKRTVEMLFVRGDGVILVSPPL 88 (91)
T ss_pred eEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhh--hhcceeEEEEeCCeEEEEcCcc
Confidence 567777788999999999999999999999999988765543322 2332 3688999999999999999985
No 10
>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=99.78 E-value=1.8e-18 Score=108.95 Aligned_cols=62 Identities=18% Similarity=0.309 Sum_probs=50.3
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+++..+++|.+.|+|+|||+|||++|+||+|...... . + .+++.+|.+++||+||++++|..
T Consensus 12 V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~-~--~-------~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 12 VSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD-E--G-------VEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred EEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC-C--C-------ceeeEeceEEECCCEEEEEEccC
Confidence 3445588999999999999999999999999864311 1 1 13578999999999999999865
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.78 E-value=1.3e-18 Score=109.22 Aligned_cols=55 Identities=27% Similarity=0.381 Sum_probs=47.3
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
.+.+ +.|+.+.|+|.|||+|||++|+||+|.+.. +..+.+|.+++||+||++|+|
T Consensus 18 ~V~l--k~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 18 LVRL--KGGREFRGELQGYDIHMNLVLDNAEEIQDG--------------EVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEEE--CCCCEEEEEEEEEcccceeEEeeEEEEcCC--------------CeEeEcCcEEEeCCEEEEEcC
Confidence 5666 779999999999999999999999997521 135689999999999999986
No 12
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.78 E-value=1.4e-18 Score=107.60 Aligned_cols=55 Identities=25% Similarity=0.402 Sum_probs=47.2
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
++.-+.|+++.|+|.|||+|||++|+||+|.+.. .+++.+|.+++||+||++|+|
T Consensus 14 ~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~--------------~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 14 LVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG--------------EPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEEECCCCEEEEEEEEECCcceEEEeeEEEEecC--------------CeEeEcCcEEEeCCEEEEEcC
Confidence 3444889999999999999999999999998642 135789999999999999987
No 13
>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=99.77 E-value=3.9e-18 Score=108.15 Aligned_cols=59 Identities=25% Similarity=0.286 Sum_probs=48.8
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
+++.-+++|++.|+|+|||+|||++|+||+|..... + + ..++.+|.+++|||||++++.
T Consensus 15 v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~--~-~--------~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 15 VVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG--D-K--------YGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred EEEEEcCCeEEEEEEEEECCcccEEecceEEEEecC--C-c--------cceeEeeEEEEECCEEEEEEc
Confidence 444558899999999999999999999999987532 1 0 125789999999999999985
No 14
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.76 E-value=5.5e-18 Score=106.71 Aligned_cols=57 Identities=21% Similarity=0.272 Sum_probs=48.2
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++.-++|+++.|+|.|||+||||+|+||+|.... ...+.+|.++|||+||++|+|..
T Consensus 14 ~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~--------------~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 14 SLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG--------------GEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred EEEECCCeEEEEEEEEEcccccEEeccEEEEccC--------------CceeEeceEEECCCEEEEEEccc
Confidence 3344889999999999999999999999998621 13578999999999999999853
No 15
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.71 E-value=5.7e-17 Score=98.93 Aligned_cols=58 Identities=24% Similarity=0.390 Sum_probs=49.2
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
++++.-++++.+.|+|.|||+|||++|+||+|.+... .+.+++|.++|||++|++|++
T Consensus 10 ~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 10 RVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEeC
Confidence 4555558899999999999999999999999986531 136789999999999999975
No 16
>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=99.71 E-value=1.1e-16 Score=101.65 Aligned_cols=57 Identities=18% Similarity=0.282 Sum_probs=48.0
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
++||.+.|+|.|||+|||+||+||+|++...++.. ..+.|.+|++++||++|++++-
T Consensus 18 ~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 18 TDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred cCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEEEE
Confidence 78999999999999999999999999986533211 1246899999999999999863
No 17
>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=99.69 E-value=1.8e-16 Score=96.81 Aligned_cols=58 Identities=21% Similarity=0.235 Sum_probs=49.7
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
++++.-+.|+.++|+|.|||+|||++|+||.|..... .+++++|.+++||++|.+|+|
T Consensus 10 ~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~-------------~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 10 RVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG-------------PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE-------------SEEEEEEEEEEEGGGEEEEEE
T ss_pred EEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC-------------CcEeECcEEEEECCEEEEEEC
Confidence 4455568999999999999999999999999986531 046789999999999999986
No 18
>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=99.68 E-value=2.7e-16 Score=97.26 Aligned_cols=53 Identities=19% Similarity=0.240 Sum_probs=44.5
Q ss_pred EEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEE
Q 034463 24 ALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90 (94)
Q Consensus 24 l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~ 90 (94)
+.-+.|+++.|+|.|||+|||++|+||+|.... .+++.+|.++|||++|++||
T Consensus 15 V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~--------------~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 15 VKLNSGVDYRGILACLDGYMNIALEQTEEYVNG--------------QLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred EEECCCCEEEEEEEEEccceeeEEeeEEEEeCC--------------ceeeEeCCEEEECCEEEEEC
Confidence 333889999999999999999999999986421 13567999999999999985
No 19
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.66 E-value=4.8e-16 Score=96.52 Aligned_cols=54 Identities=15% Similarity=0.188 Sum_probs=44.7
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEE
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~ 90 (94)
++.-+.|+.+.|+|.|||+|||++|+||+|.... .+.+.+|.+++||+||++|+
T Consensus 15 ~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~--------------~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 15 IVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG--------------KSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC--------------ccccCcCcEEEECCEEEEEC
Confidence 3444889999999999999999999999987421 12457999999999999874
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.64 E-value=1.1e-15 Score=96.95 Aligned_cols=59 Identities=24% Similarity=0.381 Sum_probs=45.9
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEe
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~ 91 (94)
.+++ +.|+++.|+|+|||+|||++|+||+|.... +... ...+..|.++|||+||++|++
T Consensus 21 ~V~l--k~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--~~~~--------~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 21 LVKL--KNGREYRGTLVGFDQYMNLVLDDVEEIISH--DGEK--------NVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEEE--CCCCEEEEEEEEEccceeEEEeceEEEecc--CCcc--------ccceeccEEEEECCcEEEEeC
Confidence 4555 889999999999999999999999998751 1100 013445599999999999975
No 21
>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=99.60 E-value=7.5e-15 Score=88.28 Aligned_cols=54 Identities=33% Similarity=0.402 Sum_probs=46.1
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEE
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~ 90 (94)
++.-++++.+.|+|.|||+|||++|+||.|.+.. .+.+++|.+++||++|.+|.
T Consensus 10 ~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------------~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 10 RVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------------GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred EEEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------------CcEEECCeEEEECCEEEEEC
Confidence 3444789999999999999999999999998753 13578999999999999873
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.57 E-value=3.7e-15 Score=94.66 Aligned_cols=57 Identities=21% Similarity=0.249 Sum_probs=46.6
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
+.+.-.++|+++|.|+|||.|||+||+|+.|.... ..+..+|.++|||++|+++.+-
T Consensus 17 i~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~--------------~~~~~ig~~vIrgnsiv~~eaL 73 (77)
T KOG1780|consen 17 IVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD--------------GDKNNIGMVVIRGNSIVMVEAL 73 (77)
T ss_pred EEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc--------------CCcceeeeEEEeccEEEEEeec
Confidence 33444779999999999999999999999996432 1245799999999999999864
No 23
>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=99.52 E-value=7.2e-14 Score=88.43 Aligned_cols=60 Identities=15% Similarity=0.101 Sum_probs=47.3
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++++.-+.++++.|+|.+||.|||++|+||+|.... + +....+|.+++||++|.+|+.++
T Consensus 13 ~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~------g-------~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 13 PMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD------G-------DKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred EEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC------C-------cEeeeCCcEEEeCCEEEEEEcCH
Confidence 344455889999999999999999999999986321 1 11245799999999999998654
No 24
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.51 E-value=1.4e-15 Score=101.28 Aligned_cols=61 Identities=15% Similarity=0.220 Sum_probs=50.9
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
.+||+.+|+|+|||+.|||||+|++|+...++++. +...+.|++|++++||..+++|||..
T Consensus 35 ~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~------~~~~~tR~LGLvV~RGTalvlisp~d 95 (108)
T KOG1781|consen 35 TGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDETRKLGLVVCRGTALVLISPAD 95 (108)
T ss_pred ecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc------chhhhhheeeeEEEcccEEEEEcCCc
Confidence 56899999999999999999999999887644322 22345699999999999999999964
No 25
>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=99.50 E-value=1.8e-13 Score=85.44 Aligned_cols=58 Identities=12% Similarity=0.145 Sum_probs=46.7
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
.+++.-+.|.++.|+|.+||.|||++|+||+|.... + +..++|.++|||+||.++.-|
T Consensus 12 ~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~------g--------~~~~~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 12 IVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD------G--------RVSQLEQVYIRGSKIRFFILP 69 (70)
T ss_pred EEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC------C--------cEeEcCcEEEeCCEEEEEEeC
Confidence 344445889999999999999999999999885321 1 134689999999999998765
No 26
>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=99.43 E-value=5.9e-13 Score=87.11 Aligned_cols=53 Identities=15% Similarity=0.155 Sum_probs=45.3
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+.|..++|+|.++|.|||++|+||+|.... + ....+|.++|||+||.+|.-|+
T Consensus 19 Kng~~~~G~L~~vD~~MNl~L~~a~~~~~~------~--------~~~~~~~v~IRG~nI~yi~lPd 71 (90)
T cd01724 19 KNGTIVHGTITGVDPSMNTHLKNVKLTLKG------R--------NPVPLDTLSIRGNNIRYFILPD 71 (90)
T ss_pred CCCCEEEEEEEEEcCceeEEEEEEEEEcCC------C--------ceeEcceEEEeCCEEEEEEcCC
Confidence 889999999999999999999999887431 1 2357999999999999998764
No 27
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.42 E-value=9.8e-14 Score=88.82 Aligned_cols=61 Identities=23% Similarity=0.453 Sum_probs=52.0
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
++|+..+..|++.|+|.|||.|.|+||+|++|.-.+++ ++ .-.+++++++.|+||.++.|.
T Consensus 19 ki~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e----gr-------~~tk~~~iLLnGNni~mLvPG 79 (84)
T KOG1775|consen 19 KIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE----GR-------RMTKLDQILLNGNNITMLVPG 79 (84)
T ss_pred eEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC----cc-------eeeeeeeeeecCCcEEEEecC
Confidence 67999999999999999999999999999999865421 10 224699999999999999885
No 28
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.42 E-value=2.4e-14 Score=102.94 Aligned_cols=66 Identities=24% Similarity=0.384 Sum_probs=51.7
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
.+.-+++|.+.|++.+||+||||||.||+|....+....+. ...+++|-+|++++||+|||+.+-.
T Consensus 18 rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~----~~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 18 RVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKM----TDGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred EEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccc----cccceeeEEEEEEecCCcEEEEecc
Confidence 33448899999999999999999999999987654433211 1124678999999999999998743
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=99.39 E-value=1.3e-12 Score=83.84 Aligned_cols=70 Identities=21% Similarity=0.183 Sum_probs=50.2
Q ss_pred EeeeeeC--cceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCC
Q 034463 7 RFSFRNS--QTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 84 (94)
Q Consensus 7 ~~~~~~~--~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGd 84 (94)
+|+||++ +.+| .+-+ +.|..+.|+|.++|.|||++|+||++.... .. .....+|.++|||+
T Consensus 2 ~~~fL~~l~g~~V---~VeL--Kng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~~--------~~~~~~~~v~IRG~ 64 (81)
T cd01725 2 FFSFFKTLVGKEV---TVEL--KNDLSIRGTLHSVDQYLNIKLTNISVTDPE----KY--------PHMLSVKNCFIRGS 64 (81)
T ss_pred hhHHHHhCCCCEE---EEEE--CCCcEEEEEEEEECCCcccEEEEEEEEcCC----Cc--------ccccccCeEEEECC
Confidence 3455443 3344 4444 789999999999999999999999875321 00 01235799999999
Q ss_pred eEEEEEeCC
Q 034463 85 SVIIVLRNP 93 (94)
Q Consensus 85 nVv~I~~~~ 93 (94)
+|..|.-|+
T Consensus 65 ~I~~I~lp~ 73 (81)
T cd01725 65 VVRYVQLPA 73 (81)
T ss_pred EEEEEEeCh
Confidence 999888664
No 30
>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=99.37 E-value=4.2e-12 Score=81.09 Aligned_cols=52 Identities=19% Similarity=0.250 Sum_probs=43.5
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
+.|..+.|+|.++|.|||++|+||++.... + ...++|.++|||+||..|.-|
T Consensus 27 Kng~~~~G~L~~vD~~MNl~L~~~~~~~~~------~--------~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 27 RNETTVTGRIASVDAFMNIRLAKVTIIDRN------G--------KQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred CCCCEEEEEEEEEcCCceeEEEEEEEEcCC------C--------ceeECCcEEEECCEEEEEEcC
Confidence 889999999999999999999999876321 1 234699999999999998743
No 31
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.32 E-value=1.8e-13 Score=92.55 Aligned_cols=69 Identities=78% Similarity=1.225 Sum_probs=59.0
Q ss_pred EEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 24 ALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 24 l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
++=|..+++-|.+.|||.|+||+|+++.|.|+..+..+++.+ .++....|.+|.+|||||+||++...|
T Consensus 41 i~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 41 INCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred EEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhheeeecCCeEEEEEecc
Confidence 344889999999999999999999999999998877666654 556666899999999999999998655
No 32
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.21 E-value=6.9e-13 Score=91.25 Aligned_cols=56 Identities=25% Similarity=0.250 Sum_probs=48.2
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
|+||++.|+|++||+|-|++|++|.|++..-. ..+.+..|..+|||+||+++...+
T Consensus 27 RDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----------~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 27 RDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----------KYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred ecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----------eecccCceEEEEecCcEEEEecCC
Confidence 89999999999999999999999999887521 135677999999999999997543
No 33
>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=99.21 E-value=5.7e-12 Score=78.43 Aligned_cols=46 Identities=24% Similarity=0.273 Sum_probs=40.1
Q ss_pred eeeeeCcceEEEEEEEEEecCCE--EEEEEEeeecCeeceEeeceEEeeee
Q 034463 8 FSFRNSQTTLMLFCFWALEFIVL--QLLGRVRAFDRHCNMVLENVREMWTE 56 (94)
Q Consensus 8 ~~~~~~~~~i~~l~~~l~~~~~r--~~~G~L~gfD~hmNLVL~d~~E~~~~ 56 (94)
.+.+.++.+| ++|+....+. .++|.|.|||+||||+|.|++|.|..
T Consensus 2 ~~~~~er~RV---rV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 2 HRCVQERIRV---RVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred chhhhCCcEE---EEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 4567789999 9999777654 49999999999999999999999875
No 34
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.09 E-value=1.1e-10 Score=76.83 Aligned_cols=62 Identities=16% Similarity=0.300 Sum_probs=50.5
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
++.+...+||-+.|.|.|||+-.||+|+|+.|++.+... + . +...+|+.++|||||.+|.+.
T Consensus 12 ~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~---g------v-~q~~lGlyiirgeNva~ig~i 73 (96)
T KOG1784|consen 12 RVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE---G------V-EQIVLGLYIIRGENVAVIGEI 73 (96)
T ss_pred eEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc---c------h-hheeeEEEEEecCccceeeec
Confidence 345567889999999999999999999999998764221 1 1 245799999999999999875
No 35
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=98.80 E-value=9.9e-09 Score=65.29 Aligned_cols=53 Identities=17% Similarity=0.248 Sum_probs=45.3
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
+-|.++.|+|.+-|.||||-|.+|+|.+... ..-.+|-++||.+||..|.-.|
T Consensus 26 Kwg~eYkG~LvsvD~YmNlqL~~~eE~idG~--------------~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 26 KWGQEYKGTLVSVDNYMNLQLANAEEYIDGV--------------STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred ecCcEEEEEEEEecchhheehhhhhhhhccc--------------ccccceeEEEEeccEEEEecCC
Confidence 6689999999999999999999999986431 2357999999999999997655
No 36
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=98.63 E-value=5.8e-09 Score=66.30 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=45.5
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeCC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
..|..+.|+|.+.|.|||+.|+.++|.... ..++..|..||||+||..||...
T Consensus 24 ~sgvdyrG~l~~lDgymNiaLe~tee~~ng--------------ql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 24 NSGVDYRGTLVCLDGYMNIALESTEEYVNG--------------QLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCCccccceehhhhhHHHHHHHHHHHHhcC--------------cccccccceeeccccEEEEEecc
Confidence 668999999999999999999999997532 13577999999999999998753
No 37
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=97.75 E-value=8.3e-05 Score=49.02 Aligned_cols=69 Identities=20% Similarity=0.210 Sum_probs=46.4
Q ss_pred EEeeeeeC--cceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463 6 IRFSFRNS--QTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 83 (94)
Q Consensus 6 ~~~~~~~~--~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG 83 (94)
++|||+++ ++.+ .+-| +.+..+.|+|+|-|+|+|+-|.|..-.-.+ +- + .--.+..+||||
T Consensus 2 LFysfFkslvg~~V---~VeL--Knd~~i~GtL~svDqyLNlkL~di~v~d~~--ky--P--------hm~Sv~ncfIRG 64 (96)
T KOG3448|consen 2 LFYSFFKSLVGKEV---VVEL--KNDLSICGTLHSVDQYLNLKLTDISVTDPD--KY--P--------HMLSVKNCFIRG 64 (96)
T ss_pred chHHHHHHhcCCeE---EEEE--cCCcEEEEEecccchhheeEEeeeEeeCcc--cC--C--------CeeeeeeEEEec
Confidence 35667664 2333 3333 789999999999999999999997654211 00 0 112466899999
Q ss_pred CeEEEEEe
Q 034463 84 DSVIIVLR 91 (94)
Q Consensus 84 dnVv~I~~ 91 (94)
..|=.|.-
T Consensus 65 SvvrYv~l 72 (96)
T KOG3448|consen 65 SVVRYVQL 72 (96)
T ss_pred cEEEEEEe
Confidence 98866643
No 38
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=96.87 E-value=0.0065 Score=41.43 Aligned_cols=57 Identities=12% Similarity=0.178 Sum_probs=44.0
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
+.+-...|-.+.|+|+--|.+||..|+|+.-+..+ + .--++.+++|||.+|=++.-|
T Consensus 18 Vt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d------g--------~vs~le~V~IRGS~IRFlvlP 74 (119)
T KOG3172|consen 18 VTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD------G--------RVSQLEQVFIRGSKIRFLVLP 74 (119)
T ss_pred EEEEecCCceeeeeeEEeccccccEEEEEEEEccC------C--------cceeeeeEEEecCeEEEEECc
Confidence 44455668889999999999999999998765432 1 124688999999999776544
No 39
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=96.54 E-value=0.0052 Score=42.73 Aligned_cols=53 Identities=17% Similarity=0.131 Sum_probs=41.3
Q ss_pred cCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
+.+-.+.|.|...|.+|||-|.+++++..+ +. +--.+.-+.|||.+|=++--+
T Consensus 20 KNget~nGhL~~cD~wMNl~L~~Vi~ts~D------gd-------kf~r~pEcYirGttIkylri~ 72 (134)
T KOG3293|consen 20 KNGETYNGHLVNCDNWMNLHLREVICTSED------GD-------KFFRMPECYIRGTTIKYLRIP 72 (134)
T ss_pred cCCCEecceeecchhhhhcchheeEEeccC------CC-------ceeecceeEEecceeEEEecc
Confidence 778899999999999999999999987432 11 112467899999999877543
No 40
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.81 E-value=0.01 Score=36.52 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=29.2
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
...+++.++ .++| ..|.++.|.+.|||+|+=++-.+
T Consensus 6 ~~r~~~~~V---tv~L--~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 6 AARKEKIPV---TIYL--VNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHcCCcE---EEEE--eCCcEEEEEEEEEcceEEEEEEC
Confidence 345678888 8888 66999999999999999777444
No 41
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.62 E-value=0.032 Score=34.33 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=28.4
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
..+++.++ .++| ..|.++.|.+.|||+|+=|+-.+
T Consensus 11 ~r~~~~~V---ti~L--~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 11 LRKERIPV---TVFL--VNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHcCCcE---EEEE--eCCcEEEEEEEEEeeeEEEEEEC
Confidence 34677888 8888 56999999999999999777443
No 42
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=95.41 E-value=0.13 Score=35.02 Aligned_cols=53 Identities=15% Similarity=0.158 Sum_probs=41.1
Q ss_pred EecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEEEEEeC
Q 034463 25 LEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 92 (94)
Q Consensus 25 ~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv~I~~~ 92 (94)
.-+.+....|++.+-|.+||..|.++.=... + +..++..+.+||+||=.+..|
T Consensus 18 eLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-------~--------~pv~l~~lsirgnniRy~~lp 70 (109)
T KOG3428|consen 18 ELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-------G--------EPVRLDTLSIRGNNIRYYILP 70 (109)
T ss_pred EecCCcEEeeeEEEEEhhheeEEEEEEEecC-------C--------CceeEEEEEeecceEEEEEcc
Confidence 3378999999999999999999998875432 1 123577899999999776554
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.28 E-value=0.034 Score=35.85 Aligned_cols=36 Identities=14% Similarity=0.354 Sum_probs=29.6
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeece
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENV 50 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~ 50 (94)
+.+++.++ .++| ..|.++.|.+.|||+|+=|+-.+.
T Consensus 15 lr~~~~~V---tifL--~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 15 LRKERVPV---TIYL--VNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHcCCCE---EEEE--eCCcEEEEEEEEEccEEEEEEECC
Confidence 34677888 8888 569999999999999997776554
No 44
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.14 E-value=0.012 Score=37.76 Aligned_cols=38 Identities=16% Similarity=0.315 Sum_probs=30.4
Q ss_pred EeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeec
Q 034463 7 RFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLEN 49 (94)
Q Consensus 7 ~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d 49 (94)
+.+..+++.++ .+|| ..|.++.|.+.|||+|.=|+=.+
T Consensus 12 Ln~~Rk~~i~V---tIfL--vNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 12 LNALRKEKIPV---TIFL--VNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred HHHHHhcCCeE---EEEE--EcCEEEEEEEEeeeeEEEEEEcC
Confidence 34556788888 8999 56999999999999998665444
No 45
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=92.11 E-value=0.25 Score=35.86 Aligned_cols=38 Identities=21% Similarity=0.341 Sum_probs=30.4
Q ss_pred eeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEE
Q 034463 10 FRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVRE 52 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E 52 (94)
..+++.++ .+|| ..|.++.|.+.|||+|+=|+-.+...
T Consensus 100 ~rk~k~~V---tvfL--~NG~~l~G~I~~fD~ftvlL~~~gkq 137 (165)
T PRK14091 100 VRDSGEPV---TMFL--VNGVMLQGEIAAFDLFCMLLERDGYV 137 (165)
T ss_pred HHhcCCcE---EEEE--ecCcEEEEEEEEEcceEEEEEeCCcE
Confidence 34677888 8888 55999999999999999777666433
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.67 E-value=0.3 Score=35.40 Aligned_cols=37 Identities=19% Similarity=0.320 Sum_probs=30.0
Q ss_pred eeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeece
Q 034463 9 SFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENV 50 (94)
Q Consensus 9 ~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~ 50 (94)
.+.+++.++ .+|| -.|.++.|.+.|||+|.=|+-.+.
T Consensus 19 ~~Rk~k~~V---tvfL--~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 19 SLRKTKTPV---TMFL--VKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHhcCCcE---EEEE--ecCcEEEEEEEEEcceEEEEEeCC
Confidence 345678888 8888 559999999999999997776554
No 47
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=86.21 E-value=2.7 Score=25.82 Aligned_cols=58 Identities=9% Similarity=0.033 Sum_probs=30.0
Q ss_pred EEEEEecCCEEEEEEEeeecC---eeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEE
Q 034463 21 CFWALEFIVLQLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 87 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~---hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv 87 (94)
.+.+ ++|.+++|.|.+++. -+-++|.-|...-....++ .. .........+++.++.|+
T Consensus 16 ~V~~--~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~~------~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 16 EVTT--KNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-SD------PLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEEE--TTS-EEEEEEEEE-T---T--EEEEEEEETTS-------E------EEEEEE-GGGEEE-----
T ss_pred EEEE--CCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-CC------ccCCCCCceEEEeccccC
Confidence 4554 889999999999999 8999998887753321110 00 112334567777777665
No 48
>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=71.65 E-value=10 Score=23.07 Aligned_cols=30 Identities=23% Similarity=0.248 Sum_probs=22.9
Q ss_pred EEEecCCEEEEEEEeeecCeeceEeeceEE
Q 034463 23 WALEFIVLQLLGRVRAFDRHCNMVLENVRE 52 (94)
Q Consensus 23 ~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E 52 (94)
+...-.|-+++|.+.|||.-.+|+.=.+.+
T Consensus 10 ~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 10 SCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 344455889999999999999998655444
No 49
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=67.52 E-value=5.8 Score=22.68 Aligned_cols=23 Identities=22% Similarity=0.302 Sum_probs=15.8
Q ss_pred EEEEEeeecCeeceEeeceEEee
Q 034463 32 LLGRVRAFDRHCNMVLENVREMW 54 (94)
Q Consensus 32 ~~G~L~gfD~hmNLVL~d~~E~~ 54 (94)
.+|++.|-|+-..|.|.|..+..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~ 32 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTH 32 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EE
T ss_pred cceeEEeeccccceEEEeCCccE
Confidence 68999999999999999877654
No 50
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=54.46 E-value=59 Score=21.31 Aligned_cols=62 Identities=21% Similarity=0.278 Sum_probs=41.2
Q ss_pred EEEEEecCCEEEEEEEeeecC-eeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEE
Q 034463 21 CFWALEFIVLQLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 87 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~-hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv 87 (94)
.+.|.-+.+.+++|+|...|. --.+.|.+|.-.-++-..... ...+ .......+..||.-|-
T Consensus 10 ~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~---~ipp--~~~v~~~I~Fr~sDIk 72 (96)
T PF12701_consen 10 KISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR---EIPP--SDEVYDYIVFRGSDIK 72 (96)
T ss_dssp EEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS------C---CSSSSEEEEETTTEE
T ss_pred EEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc---ccCC--CCceeeEEEEEccccc
Confidence 356677889999999999998 688999998876543211110 0111 1224678999998774
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=48.64 E-value=48 Score=18.51 Aligned_cols=25 Identities=8% Similarity=0.041 Sum_probs=21.2
Q ss_pred CCEEEEEEEeeecCeeceEeeceEE
Q 034463 28 IVLQLLGRVRAFDRHCNMVLENVRE 52 (94)
Q Consensus 28 ~~r~~~G~L~gfD~hmNLVL~d~~E 52 (94)
.+..++|+..|.|..=.|+++....
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 4567799999999999999976555
No 52
>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=38.47 E-value=1e+02 Score=19.50 Aligned_cols=63 Identities=19% Similarity=0.215 Sum_probs=39.4
Q ss_pred EEEEEecCCEEEEEEEeeecCeec-eEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCeEE
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCN-MVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 87 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmN-LVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdnVv 87 (94)
++.|..+.+.+++|.|...|..=. +.|.++..+-++-...... ...+ ...-.+.++.||..|-
T Consensus 8 ~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~--~ipp--~~~vyd~IvFrgsDIk 71 (74)
T cd01736 8 KISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGP--EIPP--SDEVYDYIVFRGSDIK 71 (74)
T ss_pred eEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCC--ccCC--CCcceeEEEEcCCccc
Confidence 346667888999999999998755 4478877765532211100 0111 1234678999998763
No 53
>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=29.99 E-value=1.3e+02 Score=18.21 Aligned_cols=36 Identities=8% Similarity=-0.042 Sum_probs=26.5
Q ss_pred eeeCcceEEEEEEEEEecCC-EEEEEEEeeecCeeceEee
Q 034463 10 FRNSQTTLMLFCFWALEFIV-LQLLGRVRAFDRHCNMVLE 48 (94)
Q Consensus 10 ~~~~~~~i~~l~~~l~~~~~-r~~~G~L~gfD~hmNLVL~ 48 (94)
-++.+.++ ++...+.+. ..++|++..+|..-+.+.-
T Consensus 38 a~~~~~~v---~ity~~~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 38 AYQENQPV---TITYYEDGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HhcCCCEE---EEEEEECCeeEEEEEEEEEEcCCCCEEEE
Confidence 34566777 777766553 5699999999999887753
No 54
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=29.39 E-value=62 Score=20.98 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=19.7
Q ss_pred eeEeeCeEEEeCCeEEEEEeCC
Q 034463 72 KDRFISKMFLRGDSVIIVLRNP 93 (94)
Q Consensus 72 ~~r~lG~v~iRGdnVv~I~~~~ 93 (94)
..|.-|.+.++|..+..+.-||
T Consensus 75 ~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 75 EDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hhcceEEEEEECCeeeEEEcCC
Confidence 3578999999999999999887
No 55
>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=28.91 E-value=76 Score=23.00 Aligned_cols=31 Identities=13% Similarity=-0.110 Sum_probs=25.2
Q ss_pred EEEEEecCCEEEEEEEeeecCeeceEeeceE
Q 034463 21 CFWALEFIVLQLLGRVRAFDRHCNMVLENVR 51 (94)
Q Consensus 21 ~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~ 51 (94)
.+-+....|..+.|++.||+.--|+||+.+.
T Consensus 31 pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 31 PVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred ceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 3444457799999999999999999997654
No 56
>PRK14633 hypothetical protein; Provisional
Probab=27.25 E-value=84 Score=21.93 Aligned_cols=20 Identities=15% Similarity=0.223 Sum_probs=15.6
Q ss_pred cCCEEEEEEEeeecCeeceEe
Q 034463 27 FIVLQLLGRVRAFDRHCNMVL 47 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL 47 (94)
.++++++|+|.++|.- ++.|
T Consensus 106 ~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 106 GSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CCcEEEEEEEEEEeCC-EEEE
Confidence 4678999999999984 3444
No 57
>PRK14643 hypothetical protein; Provisional
Probab=23.15 E-value=1e+02 Score=21.89 Aligned_cols=27 Identities=11% Similarity=0.062 Sum_probs=18.1
Q ss_pred EEEEEe--cCCEEEEEEEeeecCe-eceEe
Q 034463 21 CFWALE--FIVLQLLGRVRAFDRH-CNMVL 47 (94)
Q Consensus 21 ~~~l~~--~~~r~~~G~L~gfD~h-mNLVL 47 (94)
.+.+.+ .+.++++|+|.++|.- ..+.|
T Consensus 108 ~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 108 YVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred EEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 455544 3468899999999864 44443
No 58
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=22.79 E-value=1.2e+02 Score=18.67 Aligned_cols=22 Identities=9% Similarity=-0.065 Sum_probs=15.5
Q ss_pred EEEEEe--cCCEEEEEEEeeecCe
Q 034463 21 CFWALE--FIVLQLLGRVRAFDRH 42 (94)
Q Consensus 21 ~~~l~~--~~~r~~~G~L~gfD~h 42 (94)
.+.+.. .+.++++|.|.++|.-
T Consensus 29 ~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 29 HVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred EEEEEcccCCeEEEEEEEEeEeCC
Confidence 444433 3457899999999983
No 59
>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=22.41 E-value=1.5e+02 Score=23.06 Aligned_cols=25 Identities=4% Similarity=-0.037 Sum_probs=21.7
Q ss_pred cCCEEEEEEEeeecCeeceEeeceE
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVR 51 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~ 51 (94)
.+++++.+++.++|...+|.+=.+.
T Consensus 109 ~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 109 QDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCCCEEEEEEEEecCCCCEEEEEec
Confidence 5689999999999999999986554
No 60
>PRK10898 serine endoprotease; Provisional
Probab=21.84 E-value=1.6e+02 Score=23.01 Aligned_cols=25 Identities=4% Similarity=-0.104 Sum_probs=21.6
Q ss_pred cCCEEEEEEEeeecCeeceEeeceE
Q 034463 27 FIVLQLLGRVRAFDRHCNMVLENVR 51 (94)
Q Consensus 27 ~~~r~~~G~L~gfD~hmNLVL~d~~ 51 (94)
.+++++.+++.|+|....|.+=.+.
T Consensus 109 ~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 109 QDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 5688999999999999999876654
No 61
>PRK14646 hypothetical protein; Provisional
Probab=21.73 E-value=1.1e+02 Score=21.43 Aligned_cols=26 Identities=8% Similarity=-0.068 Sum_probs=17.2
Q ss_pred EEEEEec--CCEEEEEEEeeecCeeceEe
Q 034463 21 CFWALEF--IVLQLLGRVRAFDRHCNMVL 47 (94)
Q Consensus 21 ~~~l~~~--~~r~~~G~L~gfD~hmNLVL 47 (94)
++.+.+. ..++++|+|.++|.- ++.|
T Consensus 104 ~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 104 NVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred EEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 4444443 346799999999984 4444
No 62
>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=20.53 E-value=39 Score=22.19 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=13.6
Q ss_pred EEEeeecCeeceEeece
Q 034463 34 GRVRAFDRHCNMVLENV 50 (94)
Q Consensus 34 G~L~gfD~hmNLVL~d~ 50 (94)
|+|+|.|.|=|-=-+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999998765554
No 63
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.38 E-value=1.3e+02 Score=21.33 Aligned_cols=25 Identities=16% Similarity=0.062 Sum_probs=18.5
Q ss_pred EEEEecCCEEEEEEEeeecCeeceEe
Q 034463 22 FWALEFIVLQLLGRVRAFDRHCNMVL 47 (94)
Q Consensus 22 ~~l~~~~~r~~~G~L~gfD~hmNLVL 47 (94)
.+.--.+++.++|+|.++|.-+ +++
T Consensus 106 l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 106 LRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred EecccCCceEEEEEEEEEcCCe-EEE
Confidence 3334466788999999999987 444
Done!