Query 034407
Match_columns 95
No_of_seqs 134 out of 1079
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 02:32:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034407.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034407hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1782 Small Nuclear ribonucl 99.9 1.4E-23 3E-28 146.3 2.3 93 1-95 33-129 (129)
2 cd01727 LSm8 The eukaryotic Sm 99.7 1.8E-17 3.9E-22 105.6 5.8 51 1-51 23-74 (74)
3 cd01728 LSm1 The eukaryotic Sm 99.7 2.3E-17 5E-22 106.0 5.9 49 1-49 26-74 (74)
4 cd01729 LSm7 The eukaryotic Sm 99.7 3.5E-17 7.5E-22 106.4 5.9 50 1-50 26-80 (81)
5 cd01732 LSm5 The eukaryotic Sm 99.7 1.2E-16 2.5E-21 103.1 5.9 49 1-49 27-75 (76)
6 cd01718 Sm_E The eukaryotic Sm 99.7 9.5E-17 2.1E-21 104.6 5.4 46 1-48 34-79 (79)
7 cd01719 Sm_G The eukaryotic Sm 99.6 5E-16 1.1E-20 99.0 5.4 48 1-51 24-71 (72)
8 cd01730 LSm3 The eukaryotic Sm 99.6 5.8E-16 1.3E-20 100.4 5.4 48 1-48 25-82 (82)
9 PTZ00138 small nuclear ribonuc 99.6 1E-15 2.2E-20 101.8 6.0 47 1-49 42-88 (89)
10 KOG1784 Small Nuclear ribonucl 99.6 8E-17 1.7E-21 107.7 -1.4 69 1-70 24-93 (96)
11 cd01731 archaeal_Sm1 The archa 99.6 5.1E-15 1.1E-19 92.6 5.4 45 1-48 24-68 (68)
12 cd01717 Sm_B The eukaryotic Sm 99.6 6.8E-15 1.5E-19 94.6 5.5 47 1-47 24-77 (79)
13 cd01720 Sm_D2 The eukaryotic S 99.5 1.2E-14 2.5E-19 96.1 5.6 49 1-49 28-86 (87)
14 PRK00737 small nuclear ribonuc 99.5 1.4E-14 2.9E-19 92.0 5.1 45 1-48 28-72 (72)
15 cd01722 Sm_F The eukaryotic Sm 99.5 1.3E-13 2.8E-18 86.6 5.2 44 1-47 25-68 (68)
16 KOG1780 Small Nuclear ribonucl 99.4 5.3E-14 1.2E-18 91.0 3.0 48 1-51 28-75 (77)
17 smart00651 Sm snRNP Sm protein 99.4 2.3E-13 4.9E-18 83.7 5.4 46 1-48 22-67 (67)
18 cd01726 LSm6 The eukaryotic Sm 99.4 2E-13 4.3E-18 85.4 5.0 44 1-47 24-67 (67)
19 cd06168 LSm9 The eukaryotic Sm 99.4 2.9E-13 6.2E-18 87.1 5.6 47 1-47 24-73 (75)
20 COG1958 LSM1 Small nuclear rib 99.4 4.2E-13 9.2E-18 86.1 5.7 48 1-48 31-79 (79)
21 PF01423 LSM: LSM domain ; In 99.4 1E-12 2.3E-17 80.8 5.2 46 1-48 22-67 (67)
22 KOG1774 Small nuclear ribonucl 99.3 3.9E-13 8.4E-18 88.5 2.1 47 2-50 41-87 (88)
23 cd00600 Sm_like The eukaryotic 99.3 1.5E-11 3.2E-16 74.5 6.0 43 1-46 20-62 (63)
24 KOG1781 Small Nuclear ribonucl 99.2 2.5E-13 5.4E-18 92.2 -2.8 54 1-54 41-99 (108)
25 cd01721 Sm_D3 The eukaryotic S 99.2 1.8E-11 3.9E-16 77.4 5.6 47 1-50 24-70 (70)
26 cd01723 LSm4 The eukaryotic Sm 99.2 1.5E-11 3.3E-16 78.7 5.2 48 1-50 25-72 (76)
27 cd01724 Sm_D1 The eukaryotic S 99.2 5.9E-11 1.3E-15 78.6 5.7 50 1-53 25-74 (90)
28 cd01733 LSm10 The eukaryotic S 99.1 3.2E-10 7E-15 73.3 5.3 45 1-48 33-77 (78)
29 cd01725 LSm2 The eukaryotic Sm 99.0 5.3E-10 1.1E-14 72.5 5.5 52 1-54 25-77 (81)
30 KOG3460 Small nuclear ribonucl 98.9 2.8E-10 6.1E-15 75.3 0.2 50 1-50 29-88 (91)
31 KOG3482 Small nuclear ribonucl 98.8 2.8E-09 6E-14 69.1 3.1 46 2-50 33-78 (79)
32 KOG1775 U6 snRNA-associated Sm 98.7 3.8E-09 8.2E-14 69.0 1.0 50 1-50 31-80 (84)
33 KOG1783 Small nuclear ribonucl 98.7 1.2E-09 2.6E-14 70.6 -1.5 46 2-50 31-76 (77)
34 KOG3168 U1 snRNP component [Tr 98.5 6.1E-09 1.3E-13 76.4 -2.4 53 1-53 28-87 (177)
35 cd01739 LSm11_C The eukaryotic 97.1 0.00014 3.1E-09 46.1 0.4 21 1-21 26-46 (66)
36 KOG3448 Predicted snRNP core p 97.1 0.00095 2.1E-08 44.9 4.1 50 2-53 27-77 (96)
37 KOG3459 Small nuclear ribonucl 96.9 0.00015 3.3E-09 50.2 -1.1 46 2-47 51-106 (114)
38 KOG3293 Small nuclear ribonucl 95.8 0.0072 1.6E-07 42.8 2.2 51 2-54 27-77 (134)
39 KOG3172 Small nuclear ribonucl 94.6 0.085 1.8E-06 36.7 4.7 50 2-54 30-79 (119)
40 KOG3428 Small nuclear ribonucl 92.0 0.4 8.6E-06 33.2 4.7 48 2-53 27-74 (109)
41 KOG3382 NADH:ubiquinone oxidor 65.0 3.4 7.3E-05 29.9 1.0 18 1-18 46-63 (151)
42 PF05071 NDUFA12: NADH ubiquin 60.0 4.5 9.8E-05 27.1 0.9 17 2-18 1-17 (105)
43 cd01716 Hfq Hfq, an abundant, 53.3 13 0.00027 23.1 2.1 16 2-17 26-41 (61)
44 TIGR02383 Hfq RNA chaperone Hf 50.3 15 0.00032 22.9 2.0 17 1-17 29-45 (61)
45 PRK00395 hfq RNA-binding prote 45.0 20 0.00043 23.5 2.1 18 1-18 33-50 (79)
46 PF02237 BPL_C: Biotin protein 39.2 60 0.0013 18.4 3.4 19 2-20 17-35 (48)
47 PF10894 DUF2689: Protein of u 35.5 6.2 0.00013 24.5 -1.3 18 8-25 21-38 (61)
48 PRK06630 hypothetical protein; 33.1 25 0.00054 24.0 1.2 17 2-18 13-29 (99)
49 PLN03095 NADH:ubiquinone oxido 30.5 31 0.00066 24.0 1.3 18 1-18 9-26 (115)
50 COG1923 Hfq Uncharacterized ho 23.7 58 0.0013 21.2 1.6 13 2-14 34-46 (77)
51 PF14438 SM-ATX: Ataxin 2 SM d 23.6 80 0.0017 19.3 2.2 42 2-44 27-76 (77)
52 PRK08183 NADH dehydrogenase; V 22.7 48 0.001 23.5 1.1 18 1-18 25-42 (133)
53 PF05413 Peptidase_C34: Putati 22.1 49 0.0011 22.1 1.0 17 30-46 75-91 (92)
54 PRK14091 RNA-binding protein H 20.3 85 0.0018 23.2 2.1 18 1-18 38-55 (165)
No 1
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.88 E-value=1.4e-23 Score=146.34 Aligned_cols=93 Identities=55% Similarity=0.935 Sum_probs=80.5
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCcccCCCCCCceecHHHHHHHHHHHH----
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAER---- 76 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~e~~~~~~~~v~~~ei~~~~~~~~---- 76 (95)
+|+|+|||||.|+||++|+||++.++.|...+.|.++|||+||+++|++|.++| ..++.++|+++++..++.++
T Consensus 33 ~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE--~~~l~~i~~~e~~~~~~~~q~~k~ 110 (129)
T KOG1782|consen 33 IGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE--EEPLEQISFEEALNEIKREQEAKK 110 (129)
T ss_pred hhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh--hccceeCCHHHHHHHHHHHHHHhh
Confidence 599999999999999999999999999999999999999999999999999998 47999999998865444444
Q ss_pred HHhhhhhhhhhhcccccCC
Q 034407 77 EASDLKGSMRKRMEFLDLD 95 (95)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~ 95 (95)
+++..+..++.+++|+|.+
T Consensus 111 e~~~lkg~m~~rg~~~D~~ 129 (129)
T KOG1782|consen 111 EEERLKGTMAERGEFLDFD 129 (129)
T ss_pred hHHHHHHHHHHhcccccCC
Confidence 4444455677889999875
No 2
>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=99.71 E-value=1.8e-17 Score=105.61 Aligned_cols=51 Identities=45% Similarity=0.761 Sum_probs=44.2
Q ss_pred CeeEEEeccccceEecceEEEEecCc-ccceeccceEEEecCcEEEEeeeCC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGD-LYCDIPLGLYVIRGENVVLIGELDL 51 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~-~~~~~~lG~~lIRGdnIv~I~~~d~ 51 (95)
+|+|+|||+||||||++|.|++...+ ......+|++++||+||++|+++|+
T Consensus 23 ~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 23 VGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred EEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 59999999999999999999876432 2346789999999999999999884
No 3
>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=99.71 E-value=2.3e-17 Score=105.97 Aligned_cols=49 Identities=63% Similarity=1.079 Sum_probs=43.5
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 49 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~ 49 (95)
.|+|+|||+||||+|++|.|+++.++.+.++.+|++++||+||++||++
T Consensus 26 ~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 26 IGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred EEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 4999999999999999999988765545578899999999999999974
No 4
>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=99.70 E-value=3.5e-17 Score=106.40 Aligned_cols=50 Identities=40% Similarity=0.481 Sum_probs=42.8
Q ss_pred CeeEEEeccccceEecceEEEEecCcc-----cceeccceEEEecCcEEEEeeeC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDL-----YCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~-----~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
+|+|+|||+||||||++|+|+++.++. ...+.+|+++|||+||++|++.+
T Consensus 26 ~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 26 TGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred EEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 499999999999999999998865321 23678999999999999999876
No 5
>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=99.67 E-value=1.2e-16 Score=103.09 Aligned_cols=49 Identities=29% Similarity=0.373 Sum_probs=41.7
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 49 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~ 49 (95)
.|+|+|||+||||||++|.|+.+.++....+.+|.++|||+||++|++.
T Consensus 27 ~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 27 VGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 4999999999999999999987554432357899999999999999863
No 6
>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=99.67 E-value=9.5e-17 Score=104.60 Aligned_cols=46 Identities=33% Similarity=0.585 Sum_probs=40.0
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|+|||+||||||+||+|++..++ ....+|.++||||||++|++
T Consensus 34 ~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 34 EGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred EEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 49999999999999999999875332 36789999999999999874
No 7
>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=99.63 E-value=5e-16 Score=99.01 Aligned_cols=48 Identities=38% Similarity=0.593 Sum_probs=41.9
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 51 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~ 51 (95)
.|+|.|||+||||+|++|+|++. +. ..+.+|.++|||+||++|+++|.
T Consensus 24 ~G~L~~~D~~mNlvL~~~~E~~~-~~--~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 24 SGILRGFDPFMNLVLDDAVEVNS-GG--EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred EEEEEEEcccccEEeccEEEEcc-CC--ceeEeceEEECCCEEEEEEcccc
Confidence 49999999999999999999763 22 36789999999999999999875
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=99.62 E-value=5.8e-16 Score=100.44 Aligned_cols=48 Identities=23% Similarity=0.417 Sum_probs=40.0
Q ss_pred CeeEEEeccccceEecceEEEEecCc----------ccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGD----------LYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~----------~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
+|+|+|||+||||||++|+|++.... ....+.+|+++|||+||++|++
T Consensus 25 ~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 25 RGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred EEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEECC
Confidence 49999999999999999999875421 1135689999999999999874
No 9
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.62 E-value=1e-15 Score=101.79 Aligned_cols=47 Identities=30% Similarity=0.477 Sum_probs=40.5
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 49 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~ 49 (95)
.|+|+|||+||||||+||+|++..+. ..+.+|+++||||||++|++.
T Consensus 42 ~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 42 EGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred EEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEcC
Confidence 49999999999999999999764332 367899999999999999874
No 10
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.59 E-value=8e-17 Score=107.65 Aligned_cols=69 Identities=39% Similarity=0.624 Sum_probs=61.6
Q ss_pred CeeEEEeccccceEecceEEEEecCcc-cceeccceEEEecCcEEEEeeeCCcccCCCCCCceecHHHHHH
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDL-YCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKR 70 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~-~~~~~lG~~lIRGdnIv~I~~~d~~~e~~~~~~~~v~~~ei~~ 70 (95)
+|.|.||||..||+|+++.||+++... .+...+|+++|||+||.+||++|++.+. ..+|++++.+++.+
T Consensus 24 vgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~-~ld~tkir~epl~~ 93 (96)
T KOG1784|consen 24 VGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDS-RLDLTKIRAEPLHP 93 (96)
T ss_pred EEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhh-hhhhhhcccCCCCC
Confidence 599999999999999999999987653 5688999999999999999999999996 88888888877654
No 11
>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=99.57 E-value=5.1e-15 Score=92.62 Aligned_cols=45 Identities=42% Similarity=0.400 Sum_probs=39.3
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|+|||+||||+|++|+|+...+ ....+|.++|||+||++|++
T Consensus 24 ~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 24 RGRLKSYDQHMNLVLEDAEEIDDGE---PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEEEEEECCcceEEEeeEEEEecCC---eEeEcCcEEEeCCEEEEEcC
Confidence 4999999999999999999976433 36789999999999999975
No 12
>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=99.56 E-value=6.8e-15 Score=94.64 Aligned_cols=47 Identities=34% Similarity=0.441 Sum_probs=39.4
Q ss_pred CeeEEEeccccceEecceEEEEecCc-------ccceeccceEEEecCcEEEEe
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGD-------LYCDIPLGLYVIRGENVVLIG 47 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~-------~~~~~~lG~~lIRGdnIv~I~ 47 (95)
.|+|+|||+||||||++|+|+..... ....+.+|+++|||+||++|+
T Consensus 24 ~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 24 VGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred EEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 49999999999999999999764321 123578999999999999987
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=99.54 E-value=1.2e-14 Score=96.09 Aligned_cols=49 Identities=27% Similarity=0.308 Sum_probs=39.4
Q ss_pred CeeEEEeccccceEecceEEEEecCcc----------cceeccceEEEecCcEEEEeee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDL----------YCDIPLGLYVIRGENVVLIGEL 49 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~----------~~~~~lG~~lIRGdnIv~I~~~ 49 (95)
+|+|+|||+||||||+||+|......+ ...+.+|+++||||||++|++.
T Consensus 28 ~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is~~ 86 (87)
T cd01720 28 LGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVLRN 86 (87)
T ss_pred EEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEecC
Confidence 499999999999999999996543211 1245789999999999999763
No 14
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.53 E-value=1.4e-14 Score=92.00 Aligned_cols=45 Identities=40% Similarity=0.512 Sum_probs=38.3
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|+|||+||||+|++|.|.. .++ ..+.+|.++|||+||++|++
T Consensus 28 ~G~L~~~D~~mNlvL~d~~e~~-~~~--~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 28 RGELQGYDIHMNLVLDNAEEIQ-DGE--VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEEEEEEcccceeEEeeEEEEc-CCC--eEeEcCcEEEeCCEEEEEcC
Confidence 4999999999999999999954 222 35689999999999999864
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=99.45 E-value=1.3e-13 Score=86.58 Aligned_cols=44 Identities=34% Similarity=0.349 Sum_probs=37.4
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEe
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 47 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~ 47 (95)
.|+|.|||+||||+|++|+|+.... ....+|.++|||+||.+|.
T Consensus 25 ~G~L~~~D~~mNi~L~~~~e~~~~~---~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 25 KGTLVSVDSYMNLQLANTEEYIDGK---STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EEEEEEECCCEEEEEeeEEEEeCCc---cccCcCcEEEECCEEEEEC
Confidence 4999999999999999999975322 2567999999999999873
No 16
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.44 E-value=5.3e-14 Score=90.99 Aligned_cols=48 Identities=33% Similarity=0.538 Sum_probs=40.8
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 51 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~ 51 (95)
.|+|+|||+||||||++|+|.-..+ ....+|..+|||++|+++.+++.
T Consensus 28 ~GiLrGyD~FmNiVlde~vE~~~~~---~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 28 TGILRGYDPFMNIVLDETVEPNGDG---DKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred EEEEeccchHHhhhhhhceeecCcC---CcceeeeEEEeccEEEEEeeccc
Confidence 4999999999999999999964333 26789999999999999988763
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.44 E-value=2.3e-13 Score=83.71 Aligned_cols=46 Identities=50% Similarity=0.603 Sum_probs=39.6
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|.|||+||||+|++|.|+...+. ....+|.++|||++|.+|++
T Consensus 22 ~G~L~~~D~~~NlvL~~~~e~~~~~~--~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 22 RGTLKGFDQFMNLVLEDVEETVKDGE--KKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEEEEECccccEEEccEEEEecCCc--EEeEeCCEEEcCCEEEEEeC
Confidence 49999999999999999999764322 37789999999999999874
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=99.43 E-value=2e-13 Score=85.39 Aligned_cols=44 Identities=36% Similarity=0.470 Sum_probs=37.2
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEe
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 47 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~ 47 (95)
.|+|.|||+||||+|++|+|... +. ....+|.++|||+||.+|+
T Consensus 24 ~G~L~~~D~~mNlvL~~~~~~~~-~~--~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 24 RGILACLDGYMNIALEQTEEYVN-GQ--LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred EEEEEEEccceeeEEeeEEEEeC-Cc--eeeEeCCEEEECCEEEEEC
Confidence 49999999999999999988542 22 2568999999999999884
No 19
>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=99.43 E-value=2.9e-13 Score=87.13 Aligned_cols=47 Identities=30% Similarity=0.277 Sum_probs=40.5
Q ss_pred CeeEEEeccccceEecceEEEEecCc---ccceeccceEEEecCcEEEEe
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGD---LYCDIPLGLYVIRGENVVLIG 47 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~---~~~~~~lG~~lIRGdnIv~I~ 47 (95)
+|+|.|||+||||||++|.|+...+. ....+.+|+++|||++|++|.
T Consensus 24 ~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 24 VGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred EEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 59999999999999999999875432 235779999999999999986
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.41 E-value=4.2e-13 Score=86.06 Aligned_cols=48 Identities=38% Similarity=0.470 Sum_probs=37.3
Q ss_pred CeeEEEeccccceEecceEEEEecCccc-ceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLY-CDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~-~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|+|||+||||+|++|.|+....... .....|.++|||+||++|++
T Consensus 31 ~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 31 RGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 4999999999999999999976422221 12334599999999999864
No 21
>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=99.37 E-value=1e-12 Score=80.85 Aligned_cols=46 Identities=46% Similarity=0.605 Sum_probs=39.7
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|.+||+||||+|++|.|....+. ....+|.++|||++|++|++
T Consensus 22 ~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 22 RGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred EEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence 49999999999999999999754332 37789999999999999975
No 22
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.34 E-value=3.9e-13 Score=88.52 Aligned_cols=47 Identities=32% Similarity=0.531 Sum_probs=39.3
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
|.+.|||+|||+||++|+| ++..+. ..+++|.++++||||++|...+
T Consensus 41 G~IvGFDEyMNvVlD~aee-v~~k~~-~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 41 GRIVGFDEYMNLVLDDAEE-VHSKTK-SRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred EEEechHHhhhhhhcchhh-cccccc-CCCccccEEEcCCcEEEEeecC
Confidence 8999999999999999999 444332 2558999999999999997653
No 23
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.27 E-value=1.5e-11 Score=74.49 Aligned_cols=43 Identities=42% Similarity=0.662 Sum_probs=37.5
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEE
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLI 46 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I 46 (95)
.|+|.+||+|||++|++|.|..... ...++|.++|||++|.+|
T Consensus 20 ~G~L~~~D~~~Ni~L~~~~~~~~~~---~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 20 EGVLVAFDKYMNLVLDDVEETIKEG---KKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred EEEEEEECCCCCEEECCEEEEecCC---cEEECCeEEEECCEEEEE
Confidence 4999999999999999999965432 367899999999999987
No 24
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.25 E-value=2.5e-13 Score=92.15 Aligned_cols=54 Identities=35% Similarity=0.394 Sum_probs=47.2
Q ss_pred CeeEEEeccccceEecceEEEEecCcc-----cceeccceEEEecCcEEEEeeeCCccc
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDL-----YCDIPLGLYVIRGENVVLIGELDLERD 54 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~-----~~~~~lG~~lIRGdnIv~I~~~d~~~e 54 (95)
+|+|+||||.|||||++|+|+...++. ...+++|++++||..+++|++.|..++
T Consensus 41 sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~ 99 (108)
T KOG1781|consen 41 SGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEE 99 (108)
T ss_pred eeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhh
Confidence 599999999999999999998765541 235899999999999999999998876
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=99.24 E-value=1.8e-11 Score=77.35 Aligned_cols=47 Identities=21% Similarity=0.160 Sum_probs=38.4
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
.|+|.++|+|||++|++|.+....++ ...+|.++|||+||.++...|
T Consensus 24 ~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 24 RGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred EEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence 49999999999999999987432222 457899999999999987654
No 26
>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=99.24 E-value=1.5e-11 Score=78.67 Aligned_cols=48 Identities=23% Similarity=0.213 Sum_probs=38.7
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
.|+|.+||+|||++|++|+|...+++. ...+|.++|||+||.++...+
T Consensus 25 ~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 25 NGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred EEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCH
Confidence 499999999999999999985333321 345789999999999997654
No 27
>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=99.17 E-value=5.9e-11 Score=78.64 Aligned_cols=50 Identities=24% Similarity=0.215 Sum_probs=41.9
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCcc
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 53 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~ 53 (95)
.|+|.++|+|||++|++|++....+ ....+|.++|||+||.+|...|.-.
T Consensus 25 ~G~L~~vD~~MNl~L~~a~~~~~~~---~~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 25 HGTITGVDPSMNTHLKNVKLTLKGR---NPVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred EEEEEEEcCceeEEEEEEEEEcCCC---ceeEcceEEEeCCEEEEEEcCCcCC
Confidence 4999999999999999998864332 2567899999999999999877653
No 28
>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=99.06 E-value=3.2e-10 Score=73.29 Aligned_cols=45 Identities=18% Similarity=0.225 Sum_probs=36.7
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEee
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 48 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~ 48 (95)
.|+|.++|+|||++|++|.+.. .+. ....+|.++|||+||.+|..
T Consensus 33 ~G~L~~vD~~MNl~L~~~~~~~-~~~--~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 33 TGRIASVDAFMNIRLAKVTIID-RNG--KQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred EEEEEEEcCCceeEEEEEEEEc-CCC--ceeECCcEEEECCEEEEEEc
Confidence 4999999999999999998742 222 24578999999999999863
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=99.03 E-value=5.3e-10 Score=72.54 Aligned_cols=52 Identities=27% Similarity=0.190 Sum_probs=40.8
Q ss_pred CeeEEEeccccceEecceEEEEecCcc-cceeccceEEEecCcEEEEeeeCCccc
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDL-YCDIPLGLYVIRGENVVLIGELDLERD 54 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~-~~~~~lG~~lIRGdnIv~I~~~d~~~e 54 (95)
.|+|.++|+|||++|++|.+.. ++. .....+|.++|||+||.+|...|...+
T Consensus 25 ~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 25 RGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred EEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence 4999999999999999997642 222 123457899999999999998776654
No 30
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=98.90 E-value=2.8e-10 Score=75.33 Aligned_cols=50 Identities=26% Similarity=0.392 Sum_probs=40.3
Q ss_pred CeeEEEeccccceEecceEEEEecCc----c------cceeccceEEEecCcEEEEeeeC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGD----L------YCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~----~------~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
.|+|++||+|.|+||.+++|.+..-+ . ..++.+.++++||++|+++++.-
T Consensus 29 ~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp~ 88 (91)
T KOG3460|consen 29 RGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPPL 88 (91)
T ss_pred hcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCcc
Confidence 49999999999999999999765421 1 23556789999999999999853
No 31
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=98.83 E-value=2.8e-09 Score=69.07 Aligned_cols=46 Identities=35% Similarity=0.350 Sum_probs=40.4
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
|+|.+.|.||||-|.+|+|++... ....+|.++||++||..|..++
T Consensus 33 G~LvsvD~YmNlqL~~~eE~idG~---~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 33 GTLVSVDNYMNLQLANAEEYIDGV---STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred EEEEEecchhheehhhhhhhhccc---ccccceeEEEEeccEEEEecCC
Confidence 899999999999999999976422 3678999999999999998765
No 32
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=98.71 E-value=3.8e-09 Score=69.03 Aligned_cols=50 Identities=30% Similarity=0.399 Sum_probs=42.4
Q ss_pred CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
+|+|.|||.|-|+||+|++|+-..++.-.-..++.+++.|+||+++-+.-
T Consensus 31 ~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 31 VGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred eeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 59999999999999999999876655323568899999999999987654
No 33
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=98.70 E-value=1.2e-09 Score=70.65 Aligned_cols=46 Identities=37% Similarity=0.482 Sum_probs=39.8
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 50 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d 50 (95)
|+|.+.|.||||.|+.+.|+.. ++ ....+|..+|||+||..|+...
T Consensus 31 G~l~~lDgymNiaLe~tee~~n-gq--l~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 31 GTLVCLDGYMNIALESTEEYVN-GQ--LKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred ceehhhhhHHHHHHHHHHHHhc-Cc--ccccccceeeccccEEEEEecc
Confidence 8999999999999999999763 32 2678999999999999998753
No 34
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.52 E-value=6.1e-09 Score=76.39 Aligned_cols=53 Identities=28% Similarity=0.285 Sum_probs=41.4
Q ss_pred CeeEEEeccccceEecceEEEEe-cCc------ccceeccceEEEecCcEEEEeeeCCcc
Q 034407 1 MGTLCSFDQFANAVLEGACERVI-VGD------LYCDIPLGLYVIRGENVVLIGELDLER 53 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Eri~-~~~------~~~~~~lG~~lIRGdnIv~I~~~d~~~ 53 (95)
+|.+..||.||||||.+|+|... ..+ ..+.+-+|++++||.||++.+..+.-.
T Consensus 28 ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp 87 (177)
T KOG3168|consen 28 IGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPP 87 (177)
T ss_pred echhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCC
Confidence 58899999999999999999432 111 245778999999999999987655443
No 35
>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=97.10 E-value=0.00014 Score=46.14 Aligned_cols=21 Identities=38% Similarity=0.483 Sum_probs=19.4
Q ss_pred CeeEEEeccccceEecceEEE
Q 034407 1 MGTLCSFDQFANAVLEGACER 21 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~~Er 21 (95)
+|.|.+||.|+||+|.|+.|.
T Consensus 26 ~G~lvAFDK~wNm~L~DV~E~ 46 (66)
T cd01739 26 SGFLVAFDKFWNMALVDVDET 46 (66)
T ss_pred EEEEEeeeeehhheehhhhhh
Confidence 489999999999999999994
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=97.07 E-value=0.00095 Score=44.85 Aligned_cols=50 Identities=30% Similarity=0.259 Sum_probs=36.4
Q ss_pred eeEEEeccccceEecceEEEEecCcccc-eeccceEEEecCcEEEEeeeCCcc
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYC-DIPLGLYVIRGENVVLIGELDLER 53 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~-~~~lG~~lIRGdnIv~I~~~d~~~ 53 (95)
|+|.|.|||.|+-|.|. ++.++++|. -.....++|||..|-++.......
T Consensus 27 GtL~svDqyLNlkL~di--~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~v 77 (96)
T KOG3448|consen 27 GTLHSVDQYLNLKLTDI--SVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAV 77 (96)
T ss_pred EEecccchhheeEEeee--EeeCcccCCCeeeeeeEEEeccEEEEEEeChhHH
Confidence 99999999999999997 444444431 223457899999998886644433
No 37
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=96.86 E-value=0.00015 Score=50.15 Aligned_cols=46 Identities=28% Similarity=0.333 Sum_probs=35.8
Q ss_pred eeEEEeccccceEecceEEEEecC----c--c---c-ceeccceEEEecCcEEEEe
Q 034407 2 GTLCSFDQFANAVLEGACERVIVG----D--L---Y-CDIPLGLYVIRGENVVLIG 47 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~----~--~---~-~~~~lG~~lIRGdnIv~I~ 47 (95)
|...|||-|.|++|+++.|....- + + . ..+.+|.++||||+|+++.
T Consensus 51 ~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 51 GRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred hhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 678899999999999999843221 1 1 1 1568899999999999876
No 38
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=95.75 E-value=0.0072 Score=42.80 Aligned_cols=51 Identities=24% Similarity=0.192 Sum_probs=39.3
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCccc
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 54 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~e 54 (95)
|.|...|.+|||-|.++++....+++ --.+-.+-|||++|-++-..|+..+
T Consensus 27 GhL~~cD~wMNl~L~~Vi~ts~Dgdk--f~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 27 GHLVNCDNWMNLHLREVICTSEDGDK--FFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred ceeecchhhhhcchheeEEeccCCCc--eeecceeEEecceeEEEeccHHHHH
Confidence 78999999999999999886543332 2244578899999999877766554
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=94.60 E-value=0.085 Score=36.67 Aligned_cols=50 Identities=18% Similarity=0.172 Sum_probs=38.6
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCccc
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 54 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~e 54 (95)
|.|+--+.+||+.|+|.+=. +.+. ...++..++|||+.|-++-..|-=+.
T Consensus 30 GkliEaeDnmNcql~di~vT-~~dg--~vs~le~V~IRGS~IRFlvlPdmLKn 79 (119)
T KOG3172|consen 30 GKLIEAEDNMNCQLRDITVT-ARDG--RVSQLEQVFIRGSKIRFLVLPDMLKN 79 (119)
T ss_pred eeeEEeccccccEEEEEEEE-ccCC--cceeeeeEEEecCeEEEEECchHhhc
Confidence 78899999999999998653 2222 25678889999999998877665544
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=92.03 E-value=0.4 Score=33.17 Aligned_cols=48 Identities=29% Similarity=0.219 Sum_probs=37.0
Q ss_pred eeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCcc
Q 034407 2 GTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 53 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~ 53 (95)
|++.+.|-+||..|-++.=... + +...+-...+||+||=++-..|.-.
T Consensus 27 G~I~~Vd~~Mn~~l~~v~~t~~-~---~pv~l~~lsirgnniRy~~lpD~l~ 74 (109)
T KOG3428|consen 27 GTIDSVDVQMNTHLKHVKMTVK-G---EPVRLDTLSIRGNNIRYYILPDSLN 74 (109)
T ss_pred eeEEEEEhhheeEEEEEEEecC-C---CceeEEEEEeecceEEEEEccCCcC
Confidence 8999999999999998754322 2 2456778999999999987766543
No 41
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=64.99 E-value=3.4 Score=29.89 Aligned_cols=18 Identities=39% Similarity=0.663 Sum_probs=15.4
Q ss_pred CeeEEEeccccceEecce
Q 034407 1 MGTLCSFDQFANAVLEGA 18 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~ 18 (95)
||+|.|.|.|.|=.-++-
T Consensus 46 iGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 46 IGTLVGVDKFGNKYYENN 63 (151)
T ss_pred ceeeeeecccccchhccc
Confidence 699999999999776654
No 42
>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=59.96 E-value=4.5 Score=27.10 Aligned_cols=17 Identities=41% Similarity=0.624 Sum_probs=15.1
Q ss_pred eeEEEeccccceEecce
Q 034407 2 GTLCSFDQFANAVLEGA 18 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~ 18 (95)
|+|.|.|.|+|..-+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999987665
No 43
>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=53.32 E-value=13 Score=23.13 Aligned_cols=16 Identities=31% Similarity=0.511 Sum_probs=12.7
Q ss_pred eeEEEeccccceEecc
Q 034407 2 GTLCSFDQFANAVLEG 17 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d 17 (95)
|.+.|||+|+=|+-.+
T Consensus 26 G~I~~fD~ftVll~~~ 41 (61)
T cd01716 26 GQIESFDNFTVLLESD 41 (61)
T ss_pred EEEEEEcceEEEEEEC
Confidence 8999999999555444
No 44
>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=50.25 E-value=15 Score=22.89 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=12.8
Q ss_pred CeeEEEeccccceEecc
Q 034407 1 MGTLCSFDQFANAVLEG 17 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d 17 (95)
.|.+.|||+|+=|+-.+
T Consensus 29 ~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 29 KGVIESFDNFTVLLESQ 45 (61)
T ss_pred EEEEEEEeeeEEEEEEC
Confidence 38999999999555433
No 45
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=44.96 E-value=20 Score=23.46 Aligned_cols=18 Identities=28% Similarity=0.438 Sum_probs=13.6
Q ss_pred CeeEEEeccccceEecce
Q 034407 1 MGTLCSFDQFANAVLEGA 18 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~ 18 (95)
.|.+.|||+|+=|+-.+.
T Consensus 33 ~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 33 QGQIESFDNFVVLLRNTG 50 (79)
T ss_pred EEEEEEEccEEEEEEECC
Confidence 389999999996664443
No 46
>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=39.23 E-value=60 Score=18.36 Aligned_cols=19 Identities=11% Similarity=0.041 Sum_probs=14.9
Q ss_pred eeEEEeccccceEecceEE
Q 034407 2 GTLCSFDQFANAVLEGACE 20 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~~E 20 (95)
|+..|+|....|++.....
T Consensus 17 G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 17 GIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp EEEEEEETTSEEEEEETTE
T ss_pred EEEEEECCCCEEEEEECCC
Confidence 8889999999999865433
No 47
>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=35.55 E-value=6.2 Score=24.54 Aligned_cols=18 Identities=33% Similarity=0.639 Sum_probs=15.7
Q ss_pred ccccceEecceEEEEecC
Q 034407 8 DQFANAVLEGACERVIVG 25 (95)
Q Consensus 8 Dq~mNLVL~d~~Eri~~~ 25 (95)
|.||+-||++|.-||.-+
T Consensus 21 DDFmhaVlSNCtTrIvLp 38 (61)
T PF10894_consen 21 DDFMHAVLSNCTTRIVLP 38 (61)
T ss_pred HHHHHHHHhcCceeEEec
Confidence 889999999999988654
No 48
>PRK06630 hypothetical protein; Provisional
Probab=33.10 E-value=25 Score=23.96 Aligned_cols=17 Identities=24% Similarity=0.221 Sum_probs=15.0
Q ss_pred eeEEEeccccceEecce
Q 034407 2 GTLCSFDQFANAVLEGA 18 (95)
Q Consensus 2 G~L~gfDq~mNLVL~d~ 18 (95)
|+|.|-|+|+|-.-++.
T Consensus 13 G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 13 HKKVGEDEFLNQYYESR 29 (99)
T ss_pred CeEeEEeCCCChhcccC
Confidence 89999999999987764
No 49
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=30.49 E-value=31 Score=23.99 Aligned_cols=18 Identities=33% Similarity=0.495 Sum_probs=15.3
Q ss_pred CeeEEEeccccceEecce
Q 034407 1 MGTLCSFDQFANAVLEGA 18 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~ 18 (95)
.|.|.|-|+|+|-.-++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 489999999999887754
No 50
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=23.71 E-value=58 Score=21.24 Aligned_cols=13 Identities=38% Similarity=0.654 Sum_probs=10.6
Q ss_pred eeEEEeccccceE
Q 034407 2 GTLCSFDQFANAV 14 (95)
Q Consensus 2 G~L~gfDq~mNLV 14 (95)
|.+.|||+|.=|+
T Consensus 34 G~V~sfD~f~VlL 46 (77)
T COG1923 34 GQVESFDNFVVLL 46 (77)
T ss_pred EEEEeeeeEEEEE
Confidence 8899999998443
No 51
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=23.57 E-value=80 Score=19.34 Aligned_cols=42 Identities=21% Similarity=0.140 Sum_probs=20.1
Q ss_pred eeEEEecc---ccceEecceEEEEecC----cc-cceeccceEEEecCcEE
Q 034407 2 GTLCSFDQ---FANAVLEGACERVIVG----DL-YCDIPLGLYVIRGENVV 44 (95)
Q Consensus 2 G~L~gfDq---~mNLVL~d~~Eri~~~----~~-~~~~~lG~~lIRGdnIv 44 (95)
|+|.+++. -+.++|.-+.. +..+ .. ........+++.++.|+
T Consensus 27 Gif~s~s~~~~~~~vvLk~a~~-~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 27 GIFHSASPESNEFDVVLKMARK-VPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEEEEE-T---T--EEEEEEEE-TTS------EEEEEEE-GGGEEE-----
T ss_pred EEEEeCCCcccceeEEEEeeee-ccccccccCCccCCCCCceEEEeccccC
Confidence 89999988 77899987766 3221 11 12234456777777665
No 52
>PRK08183 NADH dehydrogenase; Validated
Probab=22.66 E-value=48 Score=23.51 Aligned_cols=18 Identities=22% Similarity=0.279 Sum_probs=14.9
Q ss_pred CeeEEEeccccceEecce
Q 034407 1 MGTLCSFDQFANAVLEGA 18 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~ 18 (95)
.|.|.|-|+|.|-.-++.
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 389999999999886654
No 53
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=22.14 E-value=49 Score=22.07 Aligned_cols=17 Identities=29% Similarity=0.722 Sum_probs=13.5
Q ss_pred eeccceEEEecCcEEEE
Q 034407 30 DIPLGLYVIRGENVVLI 46 (95)
Q Consensus 30 ~~~lG~~lIRGdnIv~I 46 (95)
.-++|.+++|||...+.
T Consensus 75 Gl~~Gr~~LRGNHF~v~ 91 (92)
T PF05413_consen 75 GLPLGRMLLRGNHFSVA 91 (92)
T ss_pred cCchhheeecccceeec
Confidence 44789999999986654
No 54
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=20.26 E-value=85 Score=23.17 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=13.6
Q ss_pred CeeEEEeccccceEecce
Q 034407 1 MGTLCSFDQFANAVLEGA 18 (95)
Q Consensus 1 iG~L~gfDq~mNLVL~d~ 18 (95)
.|++.|||+|+=|+-.+.
T Consensus 38 ~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 38 QGIITWFDNFSILLRRDG 55 (165)
T ss_pred EEEEEEEcceEEEEEeCC
Confidence 389999999996554444
Done!