Query 035338
Match_columns 67
No_of_seqs 109 out of 1065
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 11:04:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035338.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035338hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.8 9.6E-20 2.1E-24 106.9 6.7 62 5-66 6-80 (81)
2 cd01719 Sm_G The eukaryotic Sm 99.8 1.4E-19 2.9E-24 104.3 6.5 62 5-67 4-71 (72)
3 cd01732 LSm5 The eukaryotic Sm 99.8 2E-19 4.3E-24 104.7 7.0 60 6-65 8-75 (76)
4 PRK00737 small nuclear ribonuc 99.8 3.8E-19 8.3E-24 102.1 6.4 59 5-64 8-72 (72)
5 cd01727 LSm8 The eukaryotic Sm 99.8 6.2E-19 1.3E-23 101.6 6.7 64 1-66 1-73 (74)
6 PTZ00138 small nuclear ribonuc 99.8 1.2E-19 2.6E-24 108.6 2.6 43 24-66 47-89 (89)
7 cd01731 archaeal_Sm1 The archa 99.8 1.5E-18 3.2E-23 98.4 6.3 59 5-64 4-68 (68)
8 cd01730 LSm3 The eukaryotic Sm 99.8 1.4E-18 3E-23 101.9 6.3 59 6-64 6-82 (82)
9 KOG1780 Small Nuclear ribonucl 99.8 1E-18 2.2E-23 101.2 4.0 62 5-67 8-75 (77)
10 cd01717 Sm_B The eukaryotic Sm 99.7 4E-18 8.7E-23 99.2 6.3 60 5-64 4-78 (79)
11 cd01718 Sm_E The eukaryotic Sm 99.7 5.5E-18 1.2E-22 99.4 6.2 60 5-64 10-79 (79)
12 cd01726 LSm6 The eukaryotic Sm 99.7 9.4E-18 2E-22 95.0 6.3 57 6-63 5-67 (67)
13 cd01720 Sm_D2 The eukaryotic S 99.7 9.6E-18 2.1E-22 99.9 6.6 60 6-65 7-86 (87)
14 cd01728 LSm1 The eukaryotic Sm 99.7 1.2E-17 2.5E-22 96.9 6.8 60 5-64 6-73 (74)
15 cd01722 Sm_F The eukaryotic Sm 99.7 1.6E-17 3.4E-22 94.4 5.8 58 5-63 5-68 (68)
16 KOG1774 Small nuclear ribonucl 99.7 4.6E-19 1E-23 104.4 -1.5 66 1-66 1-87 (88)
17 PF01423 LSM: LSM domain ; In 99.7 3.3E-17 7.2E-22 91.7 6.1 61 4-64 1-67 (67)
18 smart00651 Sm snRNP Sm protein 99.7 1E-16 2.3E-21 89.6 6.5 60 5-64 2-67 (67)
19 cd01723 LSm4 The eukaryotic Sm 99.7 3.9E-16 8.4E-21 90.4 6.1 61 6-66 6-72 (76)
20 COG1958 LSM1 Small nuclear rib 99.7 4.3E-16 9.4E-21 90.5 6.2 60 5-64 11-79 (79)
21 cd01721 Sm_D3 The eukaryotic S 99.6 8.2E-16 1.8E-20 87.9 6.8 60 6-66 5-70 (70)
22 cd06168 LSm9 The eukaryotic Sm 99.6 8.6E-16 1.9E-20 89.2 6.6 61 4-64 3-74 (75)
23 cd01724 Sm_D1 The eukaryotic S 99.6 1.9E-15 4.1E-20 90.3 6.8 60 6-66 6-71 (90)
24 cd00600 Sm_like The eukaryotic 99.6 2.8E-15 6.1E-20 82.7 6.3 57 6-63 1-63 (63)
25 cd01733 LSm10 The eukaryotic S 99.6 1.4E-14 3.1E-19 84.5 6.4 58 6-64 14-77 (78)
26 KOG3482 Small nuclear ribonucl 99.5 1.1E-14 2.4E-19 84.3 3.4 60 6-66 13-78 (79)
27 cd01725 LSm2 The eukaryotic Sm 99.5 7.6E-14 1.7E-18 81.8 6.1 61 6-66 6-73 (81)
28 KOG1783 Small nuclear ribonucl 99.5 5.3E-15 1.1E-19 85.6 0.2 61 5-66 10-76 (77)
29 KOG1781 Small Nuclear ribonucl 99.3 7E-14 1.5E-18 84.9 -1.6 62 5-66 21-95 (108)
30 KOG1784 Small Nuclear ribonucl 99.3 1.1E-12 2.3E-17 78.8 2.5 62 5-66 4-74 (96)
31 KOG3460 Small nuclear ribonucl 99.2 3.7E-12 8E-17 75.5 2.1 56 10-65 14-87 (91)
32 KOG1782 Small Nuclear ribonucl 99.1 1.7E-11 3.8E-16 76.9 0.9 62 5-66 13-82 (129)
33 KOG1775 U6 snRNA-associated Sm 99.1 6.4E-11 1.4E-15 69.3 2.1 60 7-66 13-80 (84)
34 KOG3168 U1 snRNP component [Tr 99.1 1.9E-11 4.1E-16 80.2 -0.4 62 5-66 8-84 (177)
35 KOG3293 Small nuclear ribonucl 98.8 7.6E-09 1.6E-13 65.2 4.2 60 7-66 8-73 (134)
36 KOG3172 Small nuclear ribonucl 98.7 3.7E-08 8.1E-13 60.9 5.0 56 10-66 3-75 (119)
37 KOG3459 Small nuclear ribonucl 98.5 4.4E-08 9.4E-13 60.6 0.8 57 8-64 31-107 (114)
38 KOG3448 Predicted snRNP core p 98.0 2.2E-05 4.8E-10 47.2 5.6 58 7-64 8-72 (96)
39 cd01739 LSm11_C The eukaryotic 97.7 8.9E-06 1.9E-10 46.3 0.6 29 12-40 9-47 (66)
40 KOG3428 Small nuclear ribonucl 97.4 0.00052 1.1E-08 42.4 5.5 59 6-66 7-71 (109)
41 PF02237 BPL_C: Biotin protein 50.3 35 0.00075 17.4 3.3 42 10-55 2-48 (48)
42 PF11684 DUF3280: Protein of u 42.9 31 0.00066 22.0 2.7 28 26-58 96-123 (140)
43 PF11743 DUF3301: Protein of u 41.8 44 0.00095 19.8 3.1 23 43-65 73-95 (97)
44 PF14438 SM-ATX: Ataxin 2 SM d 36.4 42 0.00091 18.5 2.3 55 6-60 7-76 (77)
45 PF12701 LSM14: Scd6-like Sm d 32.4 1.1E+02 0.0025 18.2 4.0 59 7-65 4-77 (96)
46 PRK07228 N-ethylammeline chlor 32.2 1.1E+02 0.0024 22.0 4.4 36 29-64 1-36 (445)
47 cd01716 Hfq Hfq, an abundant, 29.2 87 0.0019 17.3 2.8 25 11-35 11-41 (61)
48 PF09196 DUF1953: Domain of un 28.7 79 0.0017 17.7 2.5 13 52-64 13-25 (66)
49 TIGR02383 Hfq RNA chaperone Hf 26.7 1E+02 0.0022 17.1 2.8 25 11-35 15-45 (61)
50 PF10894 DUF2689: Protein of u 23.9 11 0.00024 20.9 -1.5 18 24-41 19-36 (61)
51 PRK00395 hfq RNA-binding prote 20.7 1.5E+02 0.0033 17.3 2.8 26 11-36 19-50 (79)
No 1
>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=9.6e-20 Score=106.92 Aligned_cols=62 Identities=24% Similarity=0.473 Sum_probs=55.3
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecC-------ceeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-------NTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-------~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
+|.+++++++.|.+++++. |||+||||+|+||+|+.... .+.+.+|.++|||+||++|++.+
T Consensus 6 ~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 5899999999999999887 99999999999999996432 25788999999999999999876
No 2
>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=99.80 E-value=1.4e-19 Score=104.28 Aligned_cols=62 Identities=29% Similarity=0.598 Sum_probs=56.7
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK 67 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~ 67 (67)
.|++++++++.|.+++++. |||+|||++|+||+|+. .+.+.+.+|.++|||+||++|++.|+
T Consensus 4 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~-~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 4 ELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN-SGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred hhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc-cCCceeEeceEEECCCEEEEEEcccc
Confidence 5889999999999999877 99999999999999985 56678899999999999999999874
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=99.80 E-value=2e-19 Score=104.69 Aligned_cols=60 Identities=30% Similarity=0.593 Sum_probs=53.6
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEec--CceeeecCeEEEeCCcEEEEEEc
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK--KNTRKPLGRILLKGDNITLMMNT 65 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~--~~~~~~~g~~~iRG~nV~~i~~~ 65 (67)
|++++++++.|.+++++. |||+|||++|+||+|++.+ +++.+.+|.++||||||++|+|.
T Consensus 8 L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 8 IDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred HHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 688899999999999987 9999999999999999632 34678899999999999999985
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.79 E-value=3.8e-19 Score=102.13 Aligned_cols=59 Identities=29% Similarity=0.572 Sum_probs=53.3
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
-|++++++++.|.+++++. |||+|||++|+||+|.. +++..+.+|.++|||+||++|+|
T Consensus 8 ~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 8 VLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred HHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEcC
Confidence 4789999999999999877 99999999999999984 66677899999999999999974
No 5
>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=6.2e-19 Score=101.64 Aligned_cols=64 Identities=25% Similarity=0.409 Sum_probs=56.5
Q ss_pred CChhhhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---CceeeecCeEEEeCCcEEEEEEcC
Q 035338 1 MASTKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 1 ms~~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
||. |++++++++.|++++++. |||+|||++|+||+|+... +.+++.+|.+++||+||++|++.|
T Consensus 1 ~~~--L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 1 SST--LEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred Chh--HHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 455 999999999999999887 9999999999999998642 335778999999999999999876
No 6
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.77 E-value=1.2e-19 Score=108.58 Aligned_cols=43 Identities=81% Similarity=1.158 Sum_probs=38.3
Q ss_pred cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 24 GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 24 ~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|||+|||++|+||+|+..++++.+.+|.++||||||++|++.+
T Consensus 47 gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~~ 89 (89)
T PTZ00138 47 GFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK 89 (89)
T ss_pred EEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcCC
Confidence 9999999999999998644567889999999999999998763
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=99.77 E-value=1.5e-18 Score=98.44 Aligned_cols=59 Identities=27% Similarity=0.563 Sum_probs=53.2
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
-|++++++++.|.+++++. +||+|||++|+||+|++ .+.+++.+|.++|||+||++|+|
T Consensus 4 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 4 VLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred HHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCCEEEEEcC
Confidence 3788999999999999877 99999999999999985 55578899999999999999975
No 8
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=1.4e-18 Score=101.91 Aligned_cols=59 Identities=19% Similarity=0.414 Sum_probs=51.5
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecC------------ceeeecCeEEEeCCcEEEEEE
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~------------~~~~~~g~~~iRG~nV~~i~~ 64 (67)
|++.+++++.|.+++++. |||+||||+|+||+|++... ..++.+|.++|||+||++|++
T Consensus 6 l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 6 IRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEECC
Confidence 577799999999999988 99999999999999997421 247789999999999999874
No 9
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.75 E-value=1e-18 Score=101.24 Aligned_cols=62 Identities=23% Similarity=0.512 Sum_probs=56.4
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcCC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK 67 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~~ 67 (67)
+|.|||.+++.+.+++.+. |||.|||+||+|++|.. ..+.+..+|.++|||++|+++++.++
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~-~~~~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPN-GDGDKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeec-CcCCcceeeeEEEeccEEEEEeeccc
Confidence 7999999999999999888 99999999999999985 44568889999999999999998764
No 10
>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=99.75 E-value=4e-18 Score=99.20 Aligned_cols=60 Identities=32% Similarity=0.538 Sum_probs=53.4
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------CceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
+|.+++++++.|.+++++. |||+|||++|+||+|++.. +.+++.+|.++|||++|++|+.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 6999999999999999988 9999999999999998642 2356889999999999999974
No 11
>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=99.74 E-value=5.5e-18 Score=99.44 Aligned_cols=60 Identities=62% Similarity=0.928 Sum_probs=48.5
Q ss_pred hhhccccC--cEEEEEc--cccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQ--PINLIFR--FLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~--pi~v~~~--~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
.+.+++.. |+.|.++ +++. |||+|||++|+||+|+...+++.+.+|.++||||||++|+|
T Consensus 10 ~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 10 LIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred HHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 46777877 5666555 4444 99999999999999996435677889999999999999975
No 12
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.73 E-value=9.4e-18 Score=95.04 Aligned_cols=57 Identities=21% Similarity=0.454 Sum_probs=51.9
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~ 63 (67)
|++++++++.|.+++++. +||+|||++|+||+|.. .+++++.+|.++|||++|++|+
T Consensus 5 L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 5 LKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCceeeEeCCEEEECCEEEEEC
Confidence 688999999999999877 99999999999999974 6667889999999999999985
No 13
>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=99.73 E-value=9.6e-18 Score=99.87 Aligned_cols=60 Identities=20% Similarity=0.448 Sum_probs=50.5
Q ss_pred hhccc--cCcEEEEEccccc------cccceecEEEccEEEEEecC------------ceeeecCeEEEeCCcEEEEEEc
Q 035338 6 VQRIM--TQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK------------NTRKPLGRILLKGDNITLMMNT 65 (67)
Q Consensus 6 l~~~m--~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~------------~~~~~~g~~~iRG~nV~~i~~~ 65 (67)
|++.+ ++|+.|.+++.+. |||+|||++|+||+|++... .+++.+|.+||||+||++|++.
T Consensus 7 L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is~~ 86 (87)
T cd01720 7 LTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVLRN 86 (87)
T ss_pred HHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEecC
Confidence 45565 7899999999888 99999999999999986431 2366789999999999999874
No 14
>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=99.73 E-value=1.2e-17 Score=96.85 Aligned_cols=60 Identities=23% Similarity=0.406 Sum_probs=53.3
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecC--ceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK--NTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~--~~~~~~g~~~iRG~nV~~i~~ 64 (67)
.|.+++++++.|.+++++. |||+|||++|+||.|+...+ ..++.+|.+++||+||++|++
T Consensus 6 ~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 6 SLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred HHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 6899999999999999888 99999999999999986443 246789999999999999986
No 15
>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=99.72 E-value=1.6e-17 Score=94.43 Aligned_cols=58 Identities=22% Similarity=0.438 Sum_probs=52.1
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~ 63 (67)
-|++++++++.|.+++++. +||+|||++|+||+|+. .+.+...+|.++|||+||.+|+
T Consensus 5 ~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 5 FLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCccccCcCcEEEECCEEEEEC
Confidence 4788999999999999877 99999999999999984 6667788999999999999984
No 16
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.71 E-value=4.6e-19 Score=104.41 Aligned_cols=66 Identities=76% Similarity=1.167 Sum_probs=57.9
Q ss_pred CChhhhhccccCcEEEEEccccc---------------------cccceecEEEccEEEEEecCceeeecCeEEEeCCcE
Q 035338 1 MASTKVQRIMTQPINLIFRFLQS---------------------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI 59 (67)
Q Consensus 1 ms~~~l~~~m~~pi~v~~~~~~~---------------------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV 59 (67)
||..++++.|.+|++++++..+. |||+|||+||+||+|...+....+++|.+++.|+||
T Consensus 1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnI 80 (88)
T KOG1774|consen 1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNI 80 (88)
T ss_pred CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcE
Confidence 78888999999999999977654 999999999999999976655566999999999999
Q ss_pred EEEEEcC
Q 035338 60 TLMMNTG 66 (67)
Q Consensus 60 ~~i~~~~ 66 (67)
.+|...+
T Consensus 81 tli~~~~ 87 (88)
T KOG1774|consen 81 TLIQSAG 87 (88)
T ss_pred EEEeecC
Confidence 9998765
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=99.71 E-value=3.3e-17 Score=91.74 Aligned_cols=61 Identities=25% Similarity=0.499 Sum_probs=54.5
Q ss_pred hhhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 4 TKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 4 ~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
+.|++++++|+.|.++++.. +||+|||++|+||.|....+.+.+.+|.++|||++|.+|.+
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 35899999999999999877 99999999999999996333388999999999999999975
No 18
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.69 E-value=1e-16 Score=89.58 Aligned_cols=60 Identities=27% Similarity=0.576 Sum_probs=53.6
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
.|++++++++.|.+++++. +||+|||++|+||+|+..++.+.+.+|.++|||++|.+|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 3788999999999999877 99999999999999996443688999999999999999874
No 19
>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=99.65 E-value=3.9e-16 Score=90.40 Aligned_cols=61 Identities=11% Similarity=0.216 Sum_probs=52.8
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|++..+++|.|.++++.. +||+|||++|+||+|...+++.....+.++|||++|.+|...+
T Consensus 6 L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 6 LKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred HHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCH
Confidence 578899999999999877 9999999999999998544555567899999999999998764
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.65 E-value=4.3e-16 Score=90.47 Aligned_cols=60 Identities=35% Similarity=0.658 Sum_probs=50.8
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEe-cCce-eeecC-eEEEeCCcEEEEEE
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHI-KKNT-RKPLG-RILLKGDNITLMMN 64 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~-~~~~-~~~~g-~~~iRG~nV~~i~~ 64 (67)
-|++++++++.|.+++++. |||+|||++|+||+|+.. ++.. .+.++ .++|||+||++|.+
T Consensus 11 ~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 11 FLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred HHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 4788999999999999877 999999999999999963 3433 35555 99999999999864
No 21
>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=99.64 E-value=8.2e-16 Score=87.90 Aligned_cols=60 Identities=12% Similarity=0.233 Sum_probs=52.2
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|++..++++.|.++++.. +||+|||++|+||.+.. .+++...+|.++|||+||.+|...|
T Consensus 5 L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~-~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 5 LHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA-RDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred HhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC-CCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 678889999999999866 99999999999999874 3445677899999999999998765
No 22
>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=99.64 E-value=8.6e-16 Score=89.19 Aligned_cols=61 Identities=16% Similarity=0.283 Sum_probs=54.6
Q ss_pred hhhhccccCcEEEEEccccc------cccceecEEEccEEEEEec-----CceeeecCeEEEeCCcEEEEEE
Q 035338 4 TKVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK-----KNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 4 ~~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~-----~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
.+|++++++++.|.+++++. +||+|||++|+||.|+... +.+.+.+|+++|||++|++|+.
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 36899999999999999988 9999999999999999743 2578899999999999999873
No 23
>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=99.62 E-value=1.9e-15 Score=90.30 Aligned_cols=60 Identities=18% Similarity=0.334 Sum_probs=53.7
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|+++.+++|.|.++++.. ++|+|||++|+||+++. +++....+|.++|||+||.+|...+
T Consensus 6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~-~~~~~~~~~~v~IRG~nI~yi~lPd 71 (90)
T cd01724 6 LMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL-KGRNPVPLDTLSIRGNNIRYFILPD 71 (90)
T ss_pred HHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc-CCCceeEcceEEEeCCEEEEEEcCC
Confidence 578899999999999866 99999999999999984 5667788999999999999998765
No 24
>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=99.61 E-value=2.8e-15 Score=82.65 Aligned_cols=57 Identities=35% Similarity=0.669 Sum_probs=51.2
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEE
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMM 63 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~ 63 (67)
|++++++++.|.+++++. +||+|||++|+||.|.. ...+.+.+|.++|||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~-~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETI-KEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEe-cCCcEEECCeEEEECCEEEEEC
Confidence 578899999999998877 99999999999999986 4467889999999999999874
No 25
>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=99.56 E-value=1.4e-14 Score=84.49 Aligned_cols=58 Identities=17% Similarity=0.336 Sum_probs=50.4
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
|+...+++|.|.++++.. ++|+|||++|+||++.. .++....+|.++|||+||.+|..
T Consensus 14 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 14 LQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNGKQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred HHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCCceeECCcEEEECCEEEEEEc
Confidence 577889999999998866 99999999999999874 45566689999999999999975
No 26
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.51 E-value=1.1e-14 Score=84.30 Aligned_cols=60 Identities=28% Similarity=0.488 Sum_probs=54.9
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|+.+.++|+.|.++++.+ +.|.|||+.|.+|+|+ +++.....+|.++||+|||.+|...+
T Consensus 13 L~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 13 LNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred HhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEecCC
Confidence 678899999999999977 9999999999999999 48888899999999999999997654
No 27
>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=99.50 E-value=7.6e-14 Score=81.78 Aligned_cols=61 Identities=11% Similarity=0.241 Sum_probs=50.2
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecC-ceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-NTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|+++.+++|.|.++++.. ++|+|||++|+||++...++ .....++.++|||++|.+|...+
T Consensus 6 L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~ 73 (81)
T cd01725 6 FKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPA 73 (81)
T ss_pred HHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeCh
Confidence 578889999999998766 99999999999998874222 23456689999999999998764
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.48 E-value=5.3e-15 Score=85.60 Aligned_cols=61 Identities=18% Similarity=0.388 Sum_probs=55.4
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
=|++++++|+.|++.++.. +.|.|||+.|+.++|+ .++..++.+|.+||||+||.+|+...
T Consensus 10 fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred HHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccccEEEEEecc
Confidence 4788999999999988755 9999999999999999 58889999999999999999998753
No 29
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.33 E-value=7e-14 Score=84.95 Aligned_cols=62 Identities=24% Similarity=0.466 Sum_probs=55.4
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec-------CceeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK-------KNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~-------~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
+|.+|.++.|.|.+.++++ |||+.|||||+|++|+.-+ +.+.|++|.+++||..+++|++.|
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~d 95 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPAD 95 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCc
Confidence 5899999999999999988 9999999999999998533 235699999999999999999875
No 30
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.31 E-value=1.1e-12 Score=78.78 Aligned_cols=62 Identities=23% Similarity=0.418 Sum_probs=55.8
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---CceeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---KNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
-|..||++.+.|++.+++- |||+..||+|+|+-|++.+ +.+...+|..+|||+||.+|.+.|
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD 74 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID 74 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence 3899999999999999877 9999999999999999754 456788999999999999999875
No 31
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.24 E-value=3.7e-12 Score=75.50 Aligned_cols=56 Identities=27% Similarity=0.503 Sum_probs=46.7
Q ss_pred ccCcEEEEEccccc------cccceecEEEccEEEEEec------------CceeeecCeEEEeCCcEEEEEEc
Q 035338 10 MTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK------------KNTRKPLGRILLKGDNITLMMNT 65 (67)
Q Consensus 10 m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~------------~~~~~~~g~~~iRG~nV~~i~~~ 65 (67)
..-.+.|++++.++ +||+|+|++|.||+|+... ...++.+.++|+||++|++|+|.
T Consensus 14 LdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp 87 (91)
T KOG3460|consen 14 LDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP 87 (91)
T ss_pred ccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence 35668888888766 9999999999999998642 13478889999999999999985
No 32
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.11 E-value=1.7e-11 Score=76.88 Aligned_cols=62 Identities=23% Similarity=0.415 Sum_probs=54.6
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEecCc--eeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKN--TRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~--~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
.+.++..+++-|++++++. +||+|-|++|++|.|++.-+. ...+.|..+|||.||+++...|
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 5788899999999999988 999999999999999976443 4667799999999999998765
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.07 E-value=6.4e-11 Score=69.28 Aligned_cols=60 Identities=33% Similarity=0.623 Sum_probs=51.8
Q ss_pred hccccCcEEEEEccccc------cccceecEEEccEEEEEec--CceeeecCeEEEeCCcEEEEEEcC
Q 035338 7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK--KNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~--~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
-|-+++++-+++++.++ |||.|.|++|+|++||-.. +....+.+.+++.||||.+..|..
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 46688999999999877 9999999999999999654 346778899999999999988764
No 34
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.06 E-value=1.9e-11 Score=80.19 Aligned_cols=62 Identities=32% Similarity=0.494 Sum_probs=52.3
Q ss_pred hhhccccCcEEEEEccccc------cccceecEEEccEEEEEec---------CceeeecCeEEEeCCcEEEEEEcC
Q 035338 5 KVQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIK---------KNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 5 ~l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~---------~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
++-..++-.+++++++++. +||.|||++|.||+|+-.. +++++.+|+|++||.||++.+.-+
T Consensus 8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 5666778888899988877 9999999999999998531 468999999999999999987644
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.80 E-value=7.6e-09 Score=65.19 Aligned_cols=60 Identities=13% Similarity=0.197 Sum_probs=52.2
Q ss_pred hccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
.-.-+.|+.|.++.+.. .+|.+|||.|.+++++..++.+...+..|+|||++|.++...|
T Consensus 8 ~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 8 KTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred HhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccH
Confidence 34457899999988765 9999999999999999877888888999999999999987654
No 36
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.70 E-value=3.7e-08 Score=60.89 Aligned_cols=56 Identities=18% Similarity=0.335 Sum_probs=47.7
Q ss_pred ccCcEEEEEccccc-----------------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 10 MTQPINLIFRFLQS-----------------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 10 m~~pi~v~~~~~~~-----------------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
++.||++++.+..+ ..|++||+.|+|.+-+. .......+..+||||+.|.++...|
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~-~dg~vs~le~V~IRGS~IRFlvlPd 75 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA-RDGRVSQLEQVFIRGSKIRFLVLPD 75 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc-cCCcceeeeeEEEecCeEEEEECch
Confidence 47899999988766 89999999999998884 5567888999999999999987654
No 37
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.47 E-value=4.4e-08 Score=60.61 Aligned_cols=57 Identities=19% Similarity=0.472 Sum_probs=43.2
Q ss_pred ccccCcEEEEEccccc--------cccceecEEEccEEEEEec------C------ceeeecCeEEEeCCcEEEEEE
Q 035338 8 RIMTQPINLIFRFLQS--------GFDEYMNLVLDDAEEVHIK------K------NTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 8 ~~m~~pi~v~~~~~~~--------~~D~~mNlvL~da~e~~~~------~------~~~~~~g~~~iRG~nV~~i~~ 64 (67)
.-+..-..+++.|... +||-|.|++|+++.|.+.. + ...+.+|.+||||++|+.+..
T Consensus 31 ~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r 107 (114)
T KOG3459|consen 31 ASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLR 107 (114)
T ss_pred HHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEe
Confidence 3344455666666544 9999999999999998742 1 136789999999999998764
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.02 E-value=2.2e-05 Score=47.16 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=43.9
Q ss_pred hccccCcEEEEEccccc------cccceecEEEccEEEEEecC-ceeeecCeEEEeCCcEEEEEE
Q 035338 7 QRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKK-NTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 7 ~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~-~~~~~~g~~~iRG~nV~~i~~ 64 (67)
+.++++.+.|.+++... +.|+|+|+-|+|..-...+. .--..+..|||||+.|.++..
T Consensus 8 kslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l 72 (96)
T KOG3448|consen 8 KSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQL 72 (96)
T ss_pred HHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEe
Confidence 45788999999988654 99999999999987764211 122334579999999999865
No 39
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.74 E-value=8.9e-06 Score=46.31 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=23.5
Q ss_pred CcEEEEEccccc----------cccceecEEEccEEEEE
Q 035338 12 QPINLIFRFLQS----------GFDEYMNLVLDDAEEVH 40 (67)
Q Consensus 12 ~pi~v~~~~~~~----------~~D~~mNlvL~da~e~~ 40 (67)
.+|.|.++.... +||+|||++|.|+.|.+
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y 47 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY 47 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence 566776665433 99999999999999987
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.44 E-value=0.00052 Score=42.45 Aligned_cols=59 Identities=15% Similarity=0.256 Sum_probs=47.6
Q ss_pred hhccccCcEEEEEccccc------cccceecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEEcC
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTG 66 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~~~ 66 (67)
|+++..-.+.|-++.+.. +.|.+||..|.++.-.. ++ +........+||+||-++...|
T Consensus 7 L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~-~~-~pv~l~~lsirgnniRy~~lpD 71 (109)
T KOG3428|consen 7 LKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV-KG-EPVRLDTLSIRGNNIRYYILPD 71 (109)
T ss_pred HHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec-CC-CceeEEEEEeecceEEEEEccC
Confidence 456666778888888755 99999999999987763 55 6677889999999999987654
No 41
>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=50.32 E-value=35 Score=17.40 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=26.6
Q ss_pred ccCcEEEEEccccc-----cccceecEEEccEEEEEecCceeeecCeEEEe
Q 035338 10 MTQPINLIFRFLQS-----GFDEYMNLVLDDAEEVHIKKNTRKPLGRILLK 55 (67)
Q Consensus 10 m~~pi~v~~~~~~~-----~~D~~mNlvL~da~e~~~~~~~~~~~g~~~iR 55 (67)
++++|.+....... +.|+.=.|+++...... ..-..|.+++|
T Consensus 2 lG~~V~v~~~~~~~~G~~~gId~~G~L~v~~~~g~~----~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQEVRVETGDGEIEGIAEGIDDDGALLVRTEDGSI----RTISSGDVSLR 48 (48)
T ss_dssp TTSEEEEEETSCEEEEEEEEEETTSEEEEEETTEEE----EEESSSEEEEE
T ss_pred CCCEEEEEECCeEEEEEEEEECCCCEEEEEECCCCE----EEEEEEEEEeC
Confidence 57888888855433 88888888886543311 23344666665
No 42
>PF11684 DUF3280: Protein of unknown function (DUF2380); InterPro: IPR021698 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=42.88 E-value=31 Score=21.96 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=20.2
Q ss_pred cceecEEEccEEEEEecCceeeecCeEEEeCCc
Q 035338 26 DEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDN 58 (67)
Q Consensus 26 D~~mNlvL~da~e~~~~~~~~~~~g~~~iRG~n 58 (67)
=-+||+.+.|+ +.++...-+.+=||||+
T Consensus 96 il~~~~~v~Dv-----~tg~~v~~~~~diRgnt 123 (140)
T PF11684_consen 96 ILNMNVYVRDV-----ETGKVVRGRSVDIRGNT 123 (140)
T ss_pred heeeeEEEEEC-----CCCCEEeeeeeeEecCc
Confidence 34788888875 23466666889999986
No 43
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=41.79 E-value=44 Score=19.77 Aligned_cols=23 Identities=9% Similarity=0.208 Sum_probs=19.6
Q ss_pred CceeeecCeEEEeCCcEEEEEEc
Q 035338 43 KNTRKPLGRILLKGDNITLMMNT 65 (67)
Q Consensus 43 ~~~~~~~g~~~iRG~nV~~i~~~ 65 (67)
.++.+.-|.+.++|..+..+...
T Consensus 73 ~G~~ry~G~l~m~G~~l~~v~lp 95 (97)
T PF11743_consen 73 DGEDRYQGELVMLGRRLISVELP 95 (97)
T ss_pred CChhcceEEEEEECCeeeEEEcC
Confidence 45788889999999999988764
No 44
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=36.38 E-value=42 Score=18.54 Aligned_cols=55 Identities=9% Similarity=0.172 Sum_probs=30.3
Q ss_pred hhccccCcEEEEEccccc------cccc---eecEEEccEEEEEecC------ceeeecCeEEEeCCcEE
Q 035338 6 VQRIMTQPINLIFRFLQS------GFDE---YMNLVLDDAEEVHIKK------NTRKPLGRILLKGDNIT 60 (67)
Q Consensus 6 l~~~m~~pi~v~~~~~~~------~~D~---~mNlvL~da~e~~~~~------~~~~~~g~~~iRG~nV~ 60 (67)
+..++++++.|.++++.. +++. -+-++|.-|....... ........+++.++.|+
T Consensus 7 ~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 356789999999999866 5555 8899998877753111 12334456777776654
No 45
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=32.35 E-value=1.1e+02 Score=18.17 Aligned_cols=59 Identities=14% Similarity=0.179 Sum_probs=40.1
Q ss_pred hccccCcEEEEEccccc------cccc-eecEEEccEEEEEecC--------ceeeecCeEEEeCCcEEEEEEc
Q 035338 7 QRIMTQPINLIFRFLQS------GFDE-YMNLVLDDAEEVHIKK--------NTRKPLGRILLKGDNITLMMNT 65 (67)
Q Consensus 7 ~~~m~~pi~v~~~~~~~------~~D~-~mNlvL~da~e~~~~~--------~~~~~~g~~~iRG~nV~~i~~~ 65 (67)
.+++++.+.++.+..-. ..|. -=.+.|.++.-+...+ .....++.+..||..|.-+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~ 77 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVI 77 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEEC
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEE
Confidence 47899999999987533 5554 4467888877653221 1133578899999999877643
No 46
>PRK07228 N-ethylammeline chlorohydrolase; Provisional
Probab=32.23 E-value=1.1e+02 Score=21.95 Aligned_cols=36 Identities=19% Similarity=0.363 Sum_probs=24.4
Q ss_pred ecEEEccEEEEEecCceeeecCeEEEeCCcEEEEEE
Q 035338 29 MNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN 64 (67)
Q Consensus 29 mNlvL~da~e~~~~~~~~~~~g~~~iRG~nV~~i~~ 64 (67)
|.+++.++.-+..++.....-|.++|+|+-|..|.+
T Consensus 1 ~~~~i~~~~vi~~~~~~~~~~g~V~I~dg~I~~vg~ 36 (445)
T PRK07228 1 MTILIKNAGIVTMNAKREIVDGDVLIEDDRIAAVGD 36 (445)
T ss_pred CeEEEEccEEEecCCCcEecccEEEEECCEEEEecC
Confidence 567788776553333234455789999999988864
No 47
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=29.17 E-value=87 Score=17.31 Aligned_cols=25 Identities=20% Similarity=0.351 Sum_probs=18.6
Q ss_pred cCcEEEEEccccc------cccceecEEEcc
Q 035338 11 TQPINLIFRFLQS------GFDEYMNLVLDD 35 (67)
Q Consensus 11 ~~pi~v~~~~~~~------~~D~~mNlvL~d 35 (67)
..|+.+.+.++-. +||+|+=+.-.+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 5688888877644 999998666544
No 48
>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=28.70 E-value=79 Score=17.66 Aligned_cols=13 Identities=8% Similarity=0.286 Sum_probs=10.7
Q ss_pred EEEeCCcEEEEEE
Q 035338 52 ILLKGDNITLMMN 64 (67)
Q Consensus 52 ~~iRG~nV~~i~~ 64 (67)
-|+|||.|+.|..
T Consensus 13 gf~r~~kilviik 25 (66)
T PF09196_consen 13 GFIRFNKILVIIK 25 (66)
T ss_dssp EEEETTTEEEEEE
T ss_pred eEEecCEEEEEEe
Confidence 3899999988765
No 49
>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=26.67 E-value=1e+02 Score=17.07 Aligned_cols=25 Identities=16% Similarity=0.305 Sum_probs=18.4
Q ss_pred cCcEEEEEccccc------cccceecEEEcc
Q 035338 11 TQPINLIFRFLQS------GFDEYMNLVLDD 35 (67)
Q Consensus 11 ~~pi~v~~~~~~~------~~D~~mNlvL~d 35 (67)
..|+.+.+.++-. +||+|+=++-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 5678888777644 999998666544
No 50
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=23.85 E-value=11 Score=20.95 Aligned_cols=18 Identities=22% Similarity=0.372 Sum_probs=15.5
Q ss_pred cccceecEEEccEEEEEe
Q 035338 24 GFDEYMNLVLDDAEEVHI 41 (67)
Q Consensus 24 ~~D~~mNlvL~da~e~~~ 41 (67)
--|+||+-||++|+-.++
T Consensus 19 vsDDFmhaVlSNCtTrIv 36 (61)
T PF10894_consen 19 VSDDFMHAVLSNCTTRIV 36 (61)
T ss_pred ccHHHHHHHHhcCceeEE
Confidence 569999999999988764
No 51
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=20.67 E-value=1.5e+02 Score=17.29 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=19.3
Q ss_pred cCcEEEEEccccc------cccceecEEEccE
Q 035338 11 TQPINLIFRFLQS------GFDEYMNLVLDDA 36 (67)
Q Consensus 11 ~~pi~v~~~~~~~------~~D~~mNlvL~da 36 (67)
..|+.+.+.++-. |||+|+=++-.+.
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 5678887777644 9999997776553
Done!