Query 035130
Match_columns 72
No_of_seqs 121 out of 1041
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 09:27:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035130hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 99.9 8.2E-26 1.8E-30 133.9 8.6 69 2-71 19-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 1.6E-24 3.4E-29 126.8 8.0 67 2-69 16-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 2.9E-23 6.2E-28 120.3 8.3 58 2-70 18-75 (76)
4 cd01729 LSm7 The eukaryotic Sm 99.9 6.2E-23 1.4E-27 120.0 8.3 63 2-70 17-79 (81)
5 cd01717 Sm_B The eukaryotic Sm 99.9 1.8E-22 3.8E-27 117.3 8.3 64 2-69 15-78 (79)
6 cd01728 LSm1 The eukaryotic Sm 99.9 1.1E-21 2.4E-26 113.2 8.2 57 2-69 17-73 (74)
7 cd01731 archaeal_Sm1 The archa 99.9 9.1E-22 2E-26 111.4 7.2 54 2-69 15-68 (68)
8 cd01718 Sm_E The eukaryotic Sm 99.9 1.2E-21 2.6E-26 114.4 7.8 55 2-69 23-79 (79)
9 PRK00737 small nuclear ribonuc 99.9 8.5E-22 1.8E-26 112.8 7.0 54 2-69 19-72 (72)
10 cd01727 LSm8 The eukaryotic Sm 99.9 1.9E-21 4.2E-26 111.8 8.0 60 2-71 14-73 (74)
11 cd01719 Sm_G The eukaryotic Sm 99.8 6.2E-21 1.3E-25 109.4 7.6 55 2-70 15-69 (72)
12 PTZ00138 small nuclear ribonuc 99.8 5.1E-20 1.1E-24 109.6 8.0 56 2-70 31-88 (89)
13 KOG3460 Small nuclear ribonucl 99.8 6.6E-22 1.4E-26 115.7 -0.1 68 2-70 20-87 (91)
14 cd06168 LSm9 The eukaryotic Sm 99.8 7.5E-20 1.6E-24 105.8 8.3 60 2-69 15-74 (75)
15 cd01726 LSm6 The eukaryotic Sm 99.8 6E-20 1.3E-24 103.8 7.3 53 2-68 15-67 (67)
16 smart00651 Sm snRNP Sm protein 99.8 2.3E-19 4.9E-24 100.4 7.6 55 2-69 13-67 (67)
17 cd01722 Sm_F The eukaryotic Sm 99.8 1.3E-19 2.8E-24 102.7 6.6 53 2-68 16-68 (68)
18 PF01423 LSM: LSM domain ; In 99.8 2.7E-19 5.9E-24 100.2 6.9 55 2-69 13-67 (67)
19 COG1958 LSM1 Small nuclear rib 99.8 3.7E-19 8E-24 103.2 7.6 58 2-69 22-79 (79)
20 cd00600 Sm_like The eukaryotic 99.7 1.6E-17 3.5E-22 91.7 7.8 53 2-68 11-63 (63)
21 cd01723 LSm4 The eukaryotic Sm 99.7 3.4E-17 7.5E-22 94.5 6.6 57 2-71 16-72 (76)
22 KOG1780 Small Nuclear ribonucl 99.7 1.2E-17 2.6E-22 95.8 4.5 55 1-69 18-72 (77)
23 cd01721 Sm_D3 The eukaryotic S 99.7 9.8E-17 2.1E-21 91.4 7.8 55 2-70 15-69 (70)
24 KOG1781 Small Nuclear ribonucl 99.7 1.4E-18 3E-23 104.4 -1.6 63 2-70 32-94 (108)
25 cd01724 Sm_D1 The eukaryotic S 99.7 6.9E-16 1.5E-20 91.8 8.0 56 2-71 16-71 (90)
26 cd01733 LSm10 The eukaryotic S 99.7 7.5E-16 1.6E-20 89.5 7.5 54 2-69 24-77 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.6 4.6E-15 1E-19 86.7 7.2 58 2-71 16-73 (81)
28 KOG3168 U1 snRNP component [Tr 99.6 7.2E-17 1.6E-21 104.7 -1.2 63 2-68 19-81 (177)
29 KOG1774 Small nuclear ribonucl 99.6 1.3E-15 2.8E-20 88.9 3.0 51 7-70 36-86 (88)
30 KOG3459 Small nuclear ribonucl 99.5 4.3E-16 9.4E-21 95.1 -0.9 69 2-71 41-109 (114)
31 KOG1782 Small Nuclear ribonucl 99.5 2.7E-16 5.9E-21 97.6 -1.8 60 1-71 23-82 (129)
32 KOG1775 U6 snRNA-associated Sm 99.5 2.2E-15 4.8E-20 87.1 2.0 58 2-70 22-79 (84)
33 KOG3482 Small nuclear ribonucl 99.5 8.6E-15 1.9E-19 83.9 4.2 57 1-71 22-78 (79)
34 KOG1784 Small Nuclear ribonucl 99.3 8.8E-13 1.9E-17 78.4 3.5 59 2-70 15-73 (96)
35 KOG1783 Small nuclear ribonucl 99.3 3.1E-13 6.8E-18 77.5 -0.9 55 2-70 21-75 (77)
36 cd01739 LSm11_C The eukaryotic 99.1 4.5E-11 9.7E-16 67.3 1.3 26 9-34 24-49 (66)
37 KOG3293 Small nuclear ribonucl 98.4 3.6E-07 7.8E-12 57.1 3.9 55 2-69 17-71 (134)
38 KOG3448 Predicted snRNP core p 98.3 2.9E-06 6.3E-11 50.4 6.4 57 2-70 17-73 (96)
39 KOG3172 Small nuclear ribonucl 98.0 4.4E-05 9.5E-10 46.9 6.3 53 3-69 21-73 (119)
40 KOG3428 Small nuclear ribonucl 97.6 0.00035 7.6E-09 42.9 6.6 53 2-69 17-69 (109)
41 cd01716 Hfq Hfq, an abundant, 96.0 0.019 4E-07 32.0 4.1 26 2-27 16-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 95.8 0.024 5.2E-07 31.6 4.1 26 2-27 20-45 (61)
43 PRK00395 hfq RNA-binding prote 95.6 0.029 6.2E-07 32.8 4.1 27 2-28 24-50 (79)
44 PF14438 SM-ATX: Ataxin 2 SM d 95.4 0.026 5.6E-07 32.0 3.4 57 2-65 17-76 (77)
45 COG1923 Hfq Uncharacterized ho 92.3 0.33 7.2E-06 28.2 3.8 26 2-27 24-49 (77)
46 PRK14091 RNA-binding protein H 92.0 0.33 7.2E-06 31.9 4.0 27 2-28 109-135 (165)
47 PRK14091 RNA-binding protein H 91.3 0.45 9.7E-06 31.3 4.1 27 2-28 29-55 (165)
48 PF02237 BPL_C: Biotin protein 86.6 2.3 5E-05 21.9 4.1 25 6-30 11-35 (48)
49 cd01735 LSm12_N LSm12 belongs 85.8 1.9 4E-05 23.9 3.6 26 2-27 11-36 (61)
50 PF14563 DUF4444: Domain of un 82.6 1.5 3.2E-05 22.7 2.1 24 10-33 10-33 (42)
51 TIGR02038 protease_degS peripl 73.6 5.4 0.00012 28.4 3.6 28 2-29 106-133 (351)
52 PF11095 Gemin7: Gem-associate 72.3 11 0.00025 21.9 4.1 50 2-70 29-79 (80)
53 PRK10898 serine endoprotease; 71.7 6.6 0.00014 28.1 3.7 28 2-29 106-133 (353)
54 PRK10942 serine endoprotease; 68.8 7.7 0.00017 28.9 3.6 27 2-28 140-166 (473)
55 PRK14638 hypothetical protein; 67.8 7.3 0.00016 24.9 2.9 18 2-19 105-122 (150)
56 PF03614 Flag1_repress: Repres 66.9 8.7 0.00019 25.1 3.1 28 2-29 34-61 (165)
57 KOG3382 NADH:ubiquinone oxidor 64.9 3.6 7.8E-05 26.4 1.0 21 9-29 44-64 (151)
58 PRK10139 serine endoprotease; 64.4 11 0.00024 28.0 3.7 28 2-29 119-146 (455)
59 PF05071 NDUFA12: NADH ubiquin 62.1 3.2 6.9E-05 25.0 0.4 17 12-28 1-17 (105)
60 TIGR02037 degP_htrA_DO peripla 61.6 13 0.00029 27.0 3.6 28 2-29 86-113 (428)
61 PRK02001 hypothetical protein; 61.3 11 0.00025 24.2 2.9 19 2-20 95-113 (152)
62 PRK14639 hypothetical protein; 57.4 15 0.00032 23.2 2.9 23 2-25 93-115 (140)
63 PF12701 LSM14: Scd6-like Sm d 48.4 57 0.0012 19.4 5.9 60 3-67 14-74 (96)
64 cd01734 YlxS_C YxlS is a Bacil 47.6 36 0.00077 19.2 3.2 15 6-20 37-52 (83)
65 PRK14642 hypothetical protein; 43.2 38 0.00082 22.8 3.2 15 6-20 122-136 (197)
66 TIGR02603 CxxCH_TIGR02603 puta 41.6 32 0.0007 21.0 2.6 24 2-25 62-86 (133)
67 PF02751 TFIIA_gamma_C: Transc 37.9 67 0.0014 17.1 3.5 28 5-32 3-33 (52)
68 PF07076 DUF1344: Protein of u 37.8 43 0.00094 18.5 2.4 23 9-31 4-27 (61)
69 PRK14644 hypothetical protein; 37.6 52 0.0011 20.7 3.1 23 2-25 90-116 (136)
70 PF11743 DUF3301: Protein of u 37.6 40 0.00087 19.9 2.5 21 51-71 76-96 (97)
71 PF11607 DUF3247: Protein of u 36.9 34 0.00074 20.7 2.0 14 2-15 33-46 (101)
72 PF03122 Herpes_MCP: Herpes vi 33.3 14 0.00031 31.4 0.0 51 4-66 254-304 (1354)
73 PRK14645 hypothetical protein; 33.0 49 0.0011 21.2 2.5 15 6-20 110-124 (154)
74 cd01736 LSm14_N LSm14 (also kn 32.9 1E+02 0.0022 17.7 6.4 57 5-65 14-71 (74)
75 PRK14633 hypothetical protein; 31.7 49 0.0011 21.0 2.3 16 5-20 106-121 (150)
76 PRK14640 hypothetical protein; 31.1 72 0.0016 20.3 3.0 16 5-20 109-124 (152)
77 PF09196 DUF1953: Domain of un 30.7 64 0.0014 17.8 2.3 13 57-69 13-25 (66)
78 PRK06630 hypothetical protein; 30.5 27 0.00059 21.2 0.9 19 10-28 11-29 (99)
79 PRK14636 hypothetical protein; 30.1 79 0.0017 20.7 3.1 19 6-25 111-129 (176)
80 PF01887 SAM_adeno_trans: S-ad 29.7 81 0.0018 21.8 3.3 22 9-30 169-190 (258)
81 PF05989 Chordopox_A35R: Chord 29.6 39 0.00084 22.5 1.6 22 10-31 93-114 (176)
82 COG0779 Uncharacterized protei 28.9 83 0.0018 20.3 3.0 21 4-25 110-130 (153)
83 PLN03095 NADH:ubiquinone oxido 27.8 34 0.00073 21.2 1.0 20 11-30 9-28 (115)
84 PRK14643 hypothetical protein; 27.1 64 0.0014 20.9 2.3 20 6-25 117-137 (164)
85 COG0265 DegQ Trypsin-like seri 26.3 1.1E+02 0.0023 21.5 3.5 28 2-29 100-127 (347)
86 COG5324 Uncharacterized conser 25.4 43 0.00093 26.3 1.4 16 8-23 73-88 (758)
87 PRK14632 hypothetical protein; 24.1 1.2E+02 0.0026 19.7 3.1 14 6-19 114-127 (172)
88 PF02576 DUF150: Uncharacteris 24.0 90 0.002 19.2 2.5 15 5-19 99-113 (141)
89 PRK14634 hypothetical protein; 23.9 1.3E+02 0.0028 19.2 3.2 15 6-20 113-127 (155)
90 PRK14646 hypothetical protein; 23.5 1.3E+02 0.0028 19.2 3.2 18 7-25 114-131 (155)
91 PRK08183 NADH dehydrogenase; V 22.3 46 0.00099 21.1 0.9 19 11-29 25-43 (133)
92 PF02707 MOSP_N: Major Outer S 21.3 96 0.0021 21.1 2.3 18 8-25 30-47 (204)
93 PF12869 tRNA_anti-like: tRNA_ 21.2 81 0.0018 19.0 1.8 21 9-29 124-144 (144)
94 PRK06955 biotin--protein ligas 21.1 1.6E+02 0.0035 20.5 3.5 22 6-27 258-279 (300)
95 PRK00092 ribosome maturation p 21.1 1.4E+02 0.0031 18.8 3.0 15 5-19 110-124 (154)
96 PF09511 RNA_lig_T4_1: RNA lig 20.7 70 0.0015 21.2 1.6 15 9-23 15-29 (221)
97 PF05413 Peptidase_C34: Putati 20.3 56 0.0012 19.3 0.9 15 52-66 76-90 (92)
No 1
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.93 E-value=8.2e-26 Score=133.93 Aligned_cols=69 Identities=84% Similarity=1.367 Sum_probs=56.0
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
|+|++||++.|+|+|||+||||+|+||+|++...++++++.+ .....+++.+|.+|||||||++|+++|
T Consensus 19 V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~-~~~~~~~r~lg~v~iRGd~Vv~Is~~~ 87 (87)
T cd01720 19 INCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKK-AKPVNKDRFISKMFLRGDSVILVLRNP 87 (87)
T ss_pred EEEcCCCEEEEEEEEecCccEEEEcceEEEeecccccccccc-ccceeeeeEcccEEEeCCEEEEEecCC
Confidence 789999999999999999999999999999876544332211 112335678999999999999999987
No 2
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=1.6e-24 Score=126.85 Aligned_cols=67 Identities=33% Similarity=0.553 Sum_probs=52.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|+|+|||++.|+|+|||+||||+|+||+|++...+++.+... .......|.+|.++||||||++|+|
T Consensus 16 V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~-~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 16 VKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYE-EIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred EEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccc-cccceeEEEcCeEEEeCCEEEEECC
Confidence 789999999999999999999999999999875443221110 0112246889999999999999985
No 3
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.90 E-value=2.9e-23 Score=120.33 Aligned_cols=58 Identities=28% Similarity=0.567 Sum_probs=49.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|++++||++.|+|+|||+||||+|+||+|++.. ++ ++ +.+++|.++||||||++|+|.
T Consensus 18 V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~~-~~---------~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 18 IVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PE-GR---------KITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CC-Cc---------eeeEcCeEEEeCCeEEEEECC
Confidence 689999999999999999999999999999842 21 11 247799999999999999975
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=99.89 E-value=6.2e-23 Score=120.04 Aligned_cols=63 Identities=21% Similarity=0.368 Sum_probs=50.7
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|+|+|||+++|+|+|||+||||+|+||+|+........+ .....+.+|.++|||+||++|+|.
T Consensus 17 V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~------~~~~~~~lG~v~iRG~nV~~i~~~ 79 (81)
T cd01729 17 VKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYK------LTDKTRQLGLVVCRGTSVVLISPV 79 (81)
T ss_pred EEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccc------cccceeEccEEEEcCCEEEEEecC
Confidence 789999999999999999999999999998753221100 011357799999999999999874
No 5
>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=99.88 E-value=1.8e-22 Score=117.32 Aligned_cols=64 Identities=25% Similarity=0.486 Sum_probs=51.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|+|+|||++.|+|+|||+||||||+||+|++...+..... ....+.|.+|++++||+||++|+-
T Consensus 15 V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 15 VTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred EEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEEE
Confidence 7899999999999999999999999999998654321100 011246889999999999999974
No 6
>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=99.87 E-value=1.1e-21 Score=113.22 Aligned_cols=57 Identities=23% Similarity=0.384 Sum_probs=48.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|+|+|||++.|+|+|||+||||+|+||.|+..... . ..++.+|.+++|||||++|++
T Consensus 17 V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~----~-------~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 17 VLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD----K-------YGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred EEEcCCeEEEEEEEEECCcccEEecceEEEEecCC----c-------cceeEeeEEEEECCEEEEEEc
Confidence 78999999999999999999999999999875321 0 124779999999999999985
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=99.86 E-value=9.1e-22 Score=111.38 Aligned_cols=54 Identities=28% Similarity=0.561 Sum_probs=47.9
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|++||++.|+|.|||+||||+|+||+|++.. + .++.+|.++|||+||++|+|
T Consensus 15 V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 15 VKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG------E--------PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEECCCCEEEEEEEEECCcceEEEeeEEEEecC------C--------eEeEcCcEEEeCCEEEEEcC
Confidence 789999999999999999999999999998642 0 14679999999999999986
No 8
>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=99.86 E-value=1.2e-21 Score=114.36 Aligned_cols=55 Identities=18% Similarity=0.456 Sum_probs=46.5
Q ss_pred eEEe--cCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVK--NNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~--~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|+ +||+++|+|+|||+||||+|+||+|+... + ...+.+|.++||||||++|+|
T Consensus 23 V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~------~-------~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 23 IWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK------T-------KTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred EEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC------C-------ceEeEcCcEEEeCCEEEEEcC
Confidence 4455 99999999999999999999999998641 0 024679999999999999985
No 9
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=8.5e-22 Score=112.83 Aligned_cols=54 Identities=30% Similarity=0.540 Sum_probs=47.3
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|+|||++.|+|+|||+|||++|+||+|.+.. + ..+.+|.++|||+||++|+|
T Consensus 19 V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-----~---------~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 19 VRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-----E---------VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-----C---------eEeEcCcEEEeCCEEEEEcC
Confidence 689999999999999999999999999997521 1 24679999999999999975
No 10
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.86 E-value=1.9e-21 Score=111.81 Aligned_cols=60 Identities=18% Similarity=0.382 Sum_probs=50.1
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
+++++||.+.|+|+|||+||||+|++|+|+....+. + ..++.+|.+++||+||++|++..
T Consensus 14 V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~---~-------~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 14 VITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE---G-------VEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred EEECCCcEEEEEEEEEccccCEEccceEEEEecCCC---C-------ceeeEeceEEECCCEEEEEEccC
Confidence 689999999999999999999999999998643211 1 12567999999999999999753
No 11
>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=99.85 E-value=6.2e-21 Score=109.45 Aligned_cols=55 Identities=24% Similarity=0.462 Sum_probs=48.0
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|+|++||++.|+|.|||+||||+|+||+|+... . ..+.+|.++|||+||++|++.
T Consensus 15 V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-----~---------~~~~lg~v~IRG~~I~~i~~~ 69 (72)
T cd01719 15 LKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-----G---------EKNNIGMVVIRGNSIVMLEAL 69 (72)
T ss_pred EEECCCeEEEEEEEEEcccccEEeccEEEEccC-----C---------ceeEeceEEECCCEEEEEEcc
Confidence 789999999999999999999999999998621 0 146799999999999999863
No 12
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.82 E-value=5.1e-20 Score=109.55 Aligned_cols=56 Identities=25% Similarity=0.584 Sum_probs=46.0
Q ss_pred eEEec--CeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKN--NTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~--gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|.+.+ +|+++|+|+|||+||||+|+||+|++... ...+.+|.+++|||||++|++.
T Consensus 31 i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~-------------~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 31 IWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK-------------NTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred EEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCC-------------ceeeEcCeEEEcCCEEEEEEcC
Confidence 34445 69999999999999999999999976420 0247799999999999999874
No 13
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.82 E-value=6.6e-22 Score=115.69 Aligned_cols=68 Identities=31% Similarity=0.522 Sum_probs=55.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|+++++|++.|+|.|||+|+||+|.||+|+++....+....++..+ ..+|.+..+|+|||+|++|+|.
T Consensus 20 VKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k-~~~r~~emlFvRGd~Vilvspp 87 (91)
T KOG3460|consen 20 VKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVK-TTKRTVEMLFVRGDGVILVSPP 87 (91)
T ss_pred EEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHh-hhhcceeEEEEeCCeEEEEcCc
Confidence 7899999999999999999999999999999876544443333222 2357899999999999999985
No 14
>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=99.82 E-value=7.5e-20 Score=105.78 Aligned_cols=60 Identities=17% Similarity=0.374 Sum_probs=50.3
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|+|||.+.|+|.|||+|||+||+||.|++...++... ...|.+|++++||++|++|.-
T Consensus 15 V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~--------~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 15 IHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSP--------TEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred EEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCC--------ccEEEeeeEEEeCCeEEEEEE
Confidence 789999999999999999999999999999864332111 136899999999999999864
No 15
>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=99.82 E-value=6e-20 Score=103.77 Aligned_cols=53 Identities=19% Similarity=0.350 Sum_probs=45.9
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 68 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~ 68 (72)
|.|++|+++.|+|.|||+|||++|+||+|.... . ..+.+|.++|||+||++|+
T Consensus 15 V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-----~---------~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 15 VKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-----Q---------LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred EEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-----c---------eeeEeCCEEEECCEEEEEC
Confidence 689999999999999999999999999986421 0 2467999999999999985
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.81 E-value=2.3e-19 Score=100.39 Aligned_cols=55 Identities=29% Similarity=0.597 Sum_probs=48.2
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|+||+++.|+|.|||+|||++|+||+|++... ...+++|.++|||++|.+|++
T Consensus 13 V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 13 VELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEeC
Confidence 6899999999999999999999999999986421 125789999999999999974
No 17
>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=99.81 E-value=1.3e-19 Score=102.75 Aligned_cols=53 Identities=19% Similarity=0.301 Sum_probs=45.5
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 68 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~ 68 (72)
|.|++|+++.|+|.|||+|||++|+||+|.... . ....+|.++|||+||++|+
T Consensus 16 V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-----~---------~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 16 VKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-----K---------STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-----c---------cccCcCcEEEECCEEEEEC
Confidence 789999999999999999999999999997421 0 1356899999999999984
No 18
>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=99.80 E-value=2.7e-19 Score=100.19 Aligned_cols=55 Identities=27% Similarity=0.490 Sum_probs=48.6
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|++|+.++|+|.+||+||||+|+||.|++...+ ..+++|.++|||++|++|++
T Consensus 13 V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 13 VELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEEEE
T ss_pred EEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEEEC
Confidence 68999999999999999999999999999864211 25789999999999999986
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.80 E-value=3.7e-19 Score=103.18 Aligned_cols=58 Identities=29% Similarity=0.603 Sum_probs=46.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|++|+++.|+|+|||+||||+|+||+|++.. ++. . ...+..+.++|||+||++|++
T Consensus 22 V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~--~-----~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 22 VKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGE--K-----NVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCc--c-----ccceeccEEEEECCcEEEEeC
Confidence 689999999999999999999999999998741 111 0 012445599999999999974
No 20
>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=99.74 E-value=1.6e-17 Score=91.67 Aligned_cols=53 Identities=36% Similarity=0.590 Sum_probs=46.9
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 68 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~ 68 (72)
|.|++|+.+.|+|.|||+|||++|+||.|++.. ...+.+|.+++||++|.+|.
T Consensus 11 V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~--------------~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 11 VELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE--------------GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred EEECCCcEEEEEEEEECCCCCEEECCEEEEecC--------------CcEEECCeEEEECCEEEEEC
Confidence 689999999999999999999999999998752 02577999999999999873
No 21
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.71 E-value=3.4e-17 Score=94.53 Aligned_cols=57 Identities=19% Similarity=0.260 Sum_probs=46.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
|.||+|+++.|+|.+||.|||++|+||+|... +++ ....++.++|||++|.+|+..+
T Consensus 16 VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g~---------~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 16 VELKNGETYNGHLVNCDNWMNIHLREVICTSK----DGD---------KFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred EEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CCc---------EeeeCCcEEEeCCEEEEEEcCH
Confidence 67999999999999999999999999998621 111 1244789999999999998543
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.71 E-value=1.2e-17 Score=95.83 Aligned_cols=55 Identities=24% Similarity=0.486 Sum_probs=46.6
Q ss_pred CeEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 1 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 1 ~i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
+++|.+||.++|.|+|||.|||+||+|+.|.... + .+..+|..+|||++|+++.+
T Consensus 18 ~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~----------~~~~ig~~vIrgnsiv~~ea 72 (77)
T KOG1780|consen 18 VLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----G----------DKNNIGMVVIRGNSIVMVEA 72 (77)
T ss_pred EEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----C----------CcceeeeEEEeccEEEEEee
Confidence 3689999999999999999999999999996431 1 13568999999999998865
No 23
>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=99.70 E-value=9.8e-17 Score=91.41 Aligned_cols=55 Identities=15% Similarity=0.303 Sum_probs=46.1
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|.||+|.+++|+|.+||.|||++|+||+|... +++ ...+|.++|||+||.+|...
T Consensus 15 VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~----~g~----------~~~~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 15 VELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR----DGR----------VSQLEQVYIRGSKIRFFILP 69 (70)
T ss_pred EEECCCcEEEEEEEEEcCCceeEEEEEEEECC----CCc----------EeEcCcEEEeCCEEEEEEeC
Confidence 68999999999999999999999999988532 111 24579999999999998753
No 24
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.69 E-value=1.4e-18 Score=104.39 Aligned_cols=63 Identities=16% Similarity=0.322 Sum_probs=52.3
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
+++.+||+++|+|+|||+.|||||+|++|+...+++..+ .....|.+|++++||..+++|+|.
T Consensus 32 vkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~------~~~~tR~LGLvV~RGTalvlisp~ 94 (108)
T KOG1781|consen 32 VKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYK------LTDETRKLGLVVCRGTALVLISPA 94 (108)
T ss_pred EEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccc------hhhhhheeeeEEEcccEEEEEcCC
Confidence 688999999999999999999999999998765433221 122358999999999999999974
No 25
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.66 E-value=6.9e-16 Score=91.85 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=47.6
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
|.|++|..++|+|.++|.|||++|+||+|+... + ....+|.++|||+||.+|....
T Consensus 16 VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~----~----------~~~~~~~v~IRG~nI~yi~lPd 71 (90)
T cd01724 16 IELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG----R----------NPVPLDTLSIRGNNIRYFILPD 71 (90)
T ss_pred EEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC----C----------ceeEcceEEEeCCEEEEEEcCC
Confidence 689999999999999999999999999987421 1 1356899999999999998653
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.65 E-value=7.5e-16 Score=89.55 Aligned_cols=54 Identities=22% Similarity=0.386 Sum_probs=45.7
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.||+|.++.|+|.++|.|||+.|+||++.... + ....+|.++|||+||.+|..
T Consensus 24 VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~----~----------~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 24 VELRNETTVTGRIASVDAFMNIRLAKVTIIDRN----G----------KQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred EEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC----C----------ceeECCcEEEECCEEEEEEc
Confidence 689999999999999999999999999876311 1 13468999999999999874
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=99.60 E-value=4.6e-15 Score=86.65 Aligned_cols=58 Identities=22% Similarity=0.271 Sum_probs=46.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
|.||+|..+.|+|.++|.|||++|+||++.... ..+ ....++.++|||++|.+|...+
T Consensus 16 VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~~~--------~~~~~~~v~IRG~~I~~I~lp~ 73 (81)
T cd01725 16 VELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----KYP--------HMLSVKNCFIRGSVVRYVQLPA 73 (81)
T ss_pred EEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----Ccc--------cccccCeEEEECCEEEEEEeCh
Confidence 689999999999999999999999999875311 100 1234689999999999998654
No 28
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.59 E-value=7.2e-17 Score=104.74 Aligned_cols=63 Identities=25% Similarity=0.556 Sum_probs=52.3
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 68 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~ 68 (72)
+.++|||.+.|.+.+||+||||+|.||+|+....+++.+..+ .+++|-+|++++||+||++.+
T Consensus 19 v~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~----~eEkr~lgLvllRgenIvs~t 81 (177)
T KOG3168|consen 19 VRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTD----GEEKRVLGLVLLRGENIVSMT 81 (177)
T ss_pred EEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccc----cceeeEEEEEEecCCcEEEEe
Confidence 678999999999999999999999999999876655442211 235789999999999999865
No 29
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.57 E-value=1.3e-15 Score=88.91 Aligned_cols=51 Identities=24% Similarity=0.558 Sum_probs=42.0
Q ss_pred CeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 7 NTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 7 gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|-.++|.++|||+|||+|||||+|.... ++ ..+++|.++++||||.+|...
T Consensus 36 ~~rieG~IvGFDEyMNvVlD~aeev~~k------~~-------~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 36 GLRIEGRIVGFDEYMNLVLDDAEEVHSK------TK-------SRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred CcEEeEEEechHHhhhhhhcchhhcccc------cc-------CCCccccEEEcCCcEEEEeec
Confidence 5579999999999999999999998542 11 124799999999999999754
No 30
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.54 E-value=4.3e-16 Score=95.11 Aligned_cols=69 Identities=81% Similarity=1.354 Sum_probs=61.1
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
|.+|+++.+-|.+.|||.|+|++|+++.|.|+..+..+++.. .++..+.|.+|.+|||||+|+++...|
T Consensus 41 i~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 41 INCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred EEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhheeeecCCeEEEEEecc
Confidence 678999999999999999999999999999998887766654 455666899999999999999998776
No 31
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.54 E-value=2.7e-16 Score=97.60 Aligned_cols=60 Identities=23% Similarity=0.354 Sum_probs=51.5
Q ss_pred CeEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 1 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 1 ~i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
++.|+|||.+.|.|++||||-|++|++|.|++.... ....+..|..+|||+||+++.+.+
T Consensus 23 lVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----------~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 23 LVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----------KYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred EEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----------eecccCceEEEEecCcEEEEecCC
Confidence 367999999999999999999999999999987421 124566899999999999998765
No 32
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.54 E-value=2.2e-15 Score=87.06 Aligned_cols=58 Identities=26% Similarity=0.552 Sum_probs=48.9
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|.+|++|++.|+|.|||.|.|++|+|++|+-.. |+ + + +..+++++++.|+||.++.|.
T Consensus 22 iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~-~e---g----r---~~tk~~~iLLnGNni~mLvPG 79 (84)
T KOG1775|consen 22 IIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEIT-PE---G----R---RMTKLDQILLNGNNITMLVPG 79 (84)
T ss_pred EEEccCceeeeEEechHHHHHHHHHhhhheeeC-CC---c----c---eeeeeeeeeecCCcEEEEecC
Confidence 679999999999999999999999999997653 22 1 1 245689999999999999875
No 33
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.54 E-value=8.6e-15 Score=83.90 Aligned_cols=57 Identities=18% Similarity=0.306 Sum_probs=49.2
Q ss_pred CeEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeCC
Q 035130 1 MMSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 1 ~i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~~ 71 (72)
+++||+|.++.|+|.+.|.||||.|.+|+|++.. . ....+|.++||.+||++|..-|
T Consensus 22 ~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-------~-------~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 22 LVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-------V-------STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred EEEEecCcEEEEEEEEecchhheehhhhhhhhcc-------c-------ccccceeEEEEeccEEEEecCC
Confidence 4789999999999999999999999999998642 1 1356999999999999997654
No 34
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.34 E-value=8.8e-13 Score=78.40 Aligned_cols=59 Identities=15% Similarity=0.388 Sum_probs=48.2
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|.-.|||.+.|.|.||||-.||+|+|+.|+...... +. ....+|..+|||+||.+|.+.
T Consensus 15 vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~---gv-------~q~~lGlyiirgeNva~ig~i 73 (96)
T KOG1784|consen 15 VITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE---GV-------EQIVLGLYIIRGENVAVIGEI 73 (96)
T ss_pred EEecCCeEEEEEeccccccceeeehhhHhhhhhhhc---ch-------hheeeEEEEEecCccceeeec
Confidence 345799999999999999999999999998764221 11 246689999999999999864
No 35
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.28 E-value=3.1e-13 Score=77.45 Aligned_cols=55 Identities=18% Similarity=0.347 Sum_probs=48.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
|+|.+|-.+.|+|.+.|.|||+.|+.++|.... + .++.+|..||||+||++|+..
T Consensus 21 VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ng-----q---------l~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 21 VKLNSGVDYRGTLVCLDGYMNIALESTEEYVNG-----Q---------LKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred EEecCCccccceehhhhhHHHHHHHHHHHHhcC-----c---------ccccccceeeccccEEEEEec
Confidence 689999999999999999999999999997632 1 246789999999999999975
No 36
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.07 E-value=4.5e-11 Score=67.33 Aligned_cols=26 Identities=35% Similarity=0.482 Sum_probs=24.3
Q ss_pred EEEEEEEEecCeeceEEccEEEeeec
Q 035130 9 QLLGRVRAFDRHCNMVLENVREMWTE 34 (72)
Q Consensus 9 ~~~G~L~~fD~~mNlvL~d~~E~~~~ 34 (72)
.++|.|+|||+||||+|.|++|.|..
T Consensus 24 ~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 24 VCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred EEEEEEEeeeeehhheehhhhhhhcc
Confidence 68999999999999999999999864
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.41 E-value=3.6e-07 Score=57.15 Aligned_cols=55 Identities=20% Similarity=0.271 Sum_probs=44.6
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.||+|-.|.|.|+..|.+|||-|.+++++... +. . --.++.+.|||.+|-++-.
T Consensus 17 vELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----gd--k-------f~r~pEcYirGttIkylri 71 (134)
T KOG3293|consen 17 VELKNGETYNGHLVNCDNWMNLHLREVICTSED----GD--K-------FFRMPECYIRGTTIKYLRI 71 (134)
T ss_pred EEecCCCEecceeecchhhhhcchheeEEeccC----CC--c-------eeecceeEEecceeEEEec
Confidence 679999999999999999999999999997532 11 1 1236789999999988753
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.34 E-value=2.9e-06 Score=50.44 Aligned_cols=57 Identities=23% Similarity=0.322 Sum_probs=43.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
+.||++-.+.|+|.+.|+|+||-|.|..-.- +++ .+ .--.+..++|||..|-+|...
T Consensus 17 VeLKnd~~i~GtL~svDqyLNlkL~di~v~d--~~k--------yP--hm~Sv~ncfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 17 VELKNDLSICGTLHSVDQYLNLKLTDISVTD--PDK--------YP--HMLSVKNCFIRGSVVRYVQLP 73 (96)
T ss_pred EEEcCCcEEEEEecccchhheeEEeeeEeeC--ccc--------CC--CeeeeeeEEEeccEEEEEEeC
Confidence 5689999999999999999999999977531 111 01 123456899999999888754
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=97.96 E-value=4.4e-05 Score=46.90 Aligned_cols=53 Identities=15% Similarity=0.325 Sum_probs=42.9
Q ss_pred EEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 3 SVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 3 ~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
.+..|-.|.|.|+--+.+||+.|+|++=+..+ + +.-++.+++|||..|-++..
T Consensus 21 Et~tGe~YRGkliEaeDnmNcql~di~vT~~d------g--------~vs~le~V~IRGS~IRFlvl 73 (119)
T KOG3172|consen 21 ETKTGEVYRGKLIEAEDNMNCQLRDITVTARD------G--------RVSQLEQVFIRGSKIRFLVL 73 (119)
T ss_pred EecCCceeeeeeEEeccccccEEEEEEEEccC------C--------cceeeeeEEEecCeEEEEEC
Confidence 46789999999999999999999998865431 1 13458899999999987754
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.65 E-value=0.00035 Score=42.88 Aligned_cols=53 Identities=21% Similarity=0.356 Sum_probs=42.8
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEe
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 69 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~ 69 (72)
|.|++|+.+.|++.+.|.+||..|.++.=... ++ ...+..+.+||+||=++..
T Consensus 17 IeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-----~~----------pv~l~~lsirgnniRy~~l 69 (109)
T KOG3428|consen 17 IELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-----GE----------PVRLDTLSIRGNNIRYYIL 69 (109)
T ss_pred EEecCCcEEeeeEEEEEhhheeEEEEEEEecC-----CC----------ceeEEEEEeecceEEEEEc
Confidence 78999999999999999999999999874321 11 2346789999999988754
No 41
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.00 E-value=0.019 Score=32.01 Aligned_cols=26 Identities=23% Similarity=0.457 Sum_probs=22.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEcc
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLEN 27 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d 27 (72)
|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 16 v~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 16 IYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred EEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 78999999999999999998666544
No 42
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.82 E-value=0.024 Score=31.59 Aligned_cols=26 Identities=23% Similarity=0.371 Sum_probs=22.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEcc
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLEN 27 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d 27 (72)
|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 20 i~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 20 VFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred EEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 68999999999999999998666544
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.65 E-value=0.029 Score=32.77 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=23.2
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENV 28 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~ 28 (72)
|.|.+|-.+.|.+.|||+|+=|+-.+.
T Consensus 24 ifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 24 IYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred EEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 689999999999999999986665553
No 44
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=95.41 E-value=0.026 Score=31.96 Aligned_cols=57 Identities=12% Similarity=0.207 Sum_probs=30.7
Q ss_pred eEEecCeEEEEEEEEecC---eeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEE
Q 035130 2 MSVKNNTQLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 65 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~---~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~ 65 (72)
|.+++|..|+|.|.+++. -+-++|.-|...-....++ . . .........+++.++.|+
T Consensus 17 V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~--~----~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 17 VTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-S--D----PLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEETTS-EEEEEEEEE-T---T--EEEEEEEETTS---------E----EEEEEE-GGGEEE-----
T ss_pred EEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-C--C----ccCCCCCceEEEeccccC
Confidence 689999999999999998 7899999888753211100 0 0 112344567777777664
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=92.26 E-value=0.33 Score=28.18 Aligned_cols=26 Identities=23% Similarity=0.415 Sum_probs=21.5
Q ss_pred eEEecCeEEEEEEEEecCeeceEEcc
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLEN 27 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d 27 (72)
|.|.+|=.+.|.+.|||+|.=|+=.+
T Consensus 24 IfLvNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 24 IFLVNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred EEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence 78999999999999999997544333
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=92.02 E-value=0.33 Score=31.89 Aligned_cols=27 Identities=30% Similarity=0.481 Sum_probs=23.1
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENV 28 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~ 28 (72)
|.|.+|-.++|.+.|||+|+=|+-.+.
T Consensus 109 vfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 109 MFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred EEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 679999999999999999986665554
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.30 E-value=0.45 Score=31.27 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=22.6
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENV 28 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~ 28 (72)
|.|.+|-.++|.+.|||+|.=|+-.+.
T Consensus 29 vfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 29 MFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred EEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 678999999999999999985555443
No 48
>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=86.55 E-value=2.3 Score=21.89 Aligned_cols=25 Identities=8% Similarity=0.218 Sum_probs=21.8
Q ss_pred cCeEEEEEEEEecCeeceEEccEEE
Q 035130 6 NNTQLLGRVRAFDRHCNMVLENVRE 30 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~mNlvL~d~~E 30 (72)
++..++|+..+.|..-.|+++....
T Consensus 11 ~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCeEEEEEEEEECCCCEEEEEECCC
Confidence 5888999999999999999976554
No 49
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=85.81 E-value=1.9 Score=23.91 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=21.1
Q ss_pred eEEecCeEEEEEEEEecCeeceEEcc
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLEN 27 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d 27 (72)
++...|-+++|.+.+||.-.+|+.=.
T Consensus 11 ~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 11 CRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred EEecCCceEEEEEEEecCCCcEEEEE
Confidence 45567899999999999998877544
No 50
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=82.55 E-value=1.5 Score=22.66 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=16.4
Q ss_pred EEEEEEEecCeeceEEccEEEeee
Q 035130 10 LLGRVRAFDRHCNMVLENVREMWT 33 (72)
Q Consensus 10 ~~G~L~~fD~~mNlvL~d~~E~~~ 33 (72)
.+|+..|.|+-+.|+|.+..++.-
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~L 33 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTHL 33 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EEE
T ss_pred cceeEEeeccccceEEEeCCccEE
Confidence 789999999999999998776543
No 51
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=73.60 E-value=5.4 Score=28.41 Aligned_cols=28 Identities=4% Similarity=0.208 Sum_probs=24.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
+.+.+|+.+.++++++|...+|.|=.+.
T Consensus 106 V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 106 VALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred EEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 5678999999999999999999985544
No 52
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=72.25 E-value=11 Score=21.89 Aligned_cols=50 Identities=24% Similarity=0.338 Sum_probs=34.6
Q ss_pred eEEecCeEEEEEEEEecCe-eceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEEEeC
Q 035130 2 MSVKNNTQLLGRVRAFDRH-CNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRN 70 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~-mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I~~~ 70 (72)
+.|.++.++.|+..|+|.. .|+..++-. + | -...+..+||..-|++++..
T Consensus 29 f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-T----P--------------lGv~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 29 FTLHENTTVSARFGACDIDVSNFQVSNLQ-T----P--------------LGVQPEALLRCSDVISISFD 79 (80)
T ss_dssp EEEGGG-EEEEEEEEE-TTS-EEEEEEEE-T----T--------------TTEEEEEEEEGGGEEEEEE-
T ss_pred EEEeCCeEEEEEEEEecCchheEEhhhcC-C----C--------------cccChhheeecCCEEEEEec
Confidence 6788999999999999987 477666532 1 1 12256889999999998864
No 53
>PRK10898 serine endoprotease; Provisional
Probab=71.67 E-value=6.6 Score=28.07 Aligned_cols=28 Identities=4% Similarity=0.149 Sum_probs=24.3
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
+.+.||+.+.+++.++|...+|.|=.+.
T Consensus 106 V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 106 VALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred EEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 5678999999999999999999876554
No 54
>PRK10942 serine endoprotease; Provisional
Probab=68.76 E-value=7.7 Score=28.93 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=24.0
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENV 28 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~ 28 (72)
|.+.||+++.++++++|...+|.|=.+
T Consensus 140 V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 140 VQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred EEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 678899999999999999999987644
No 55
>PRK14638 hypothetical protein; Provisional
Probab=67.82 E-value=7.3 Score=24.86 Aligned_cols=18 Identities=22% Similarity=0.591 Sum_probs=15.9
Q ss_pred eEEecCeEEEEEEEEecC
Q 035130 2 MSVKNNTQLLGRVRAFDR 19 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~ 19 (72)
|++++++.++|+|.++|.
T Consensus 105 V~~~~~k~~~G~L~~~~~ 122 (150)
T PRK14638 105 IVTKDGKTFIGRIESFVD 122 (150)
T ss_pred EEECCCcEEEEEEEEEeC
Confidence 567799999999999986
No 56
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=66.91 E-value=8.7 Score=25.15 Aligned_cols=28 Identities=18% Similarity=0.104 Sum_probs=24.7
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
+.+.||..+.|++.||+.--|+||..+.
T Consensus 34 vv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 34 VVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred EEecCCcEEEEEEeccCcccCEEeccCC
Confidence 4678999999999999999999987654
No 57
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=64.89 E-value=3.6 Score=26.43 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=16.7
Q ss_pred EEEEEEEEecCeeceEEccEE
Q 035130 9 QLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 9 ~~~G~L~~fD~~mNlvL~d~~ 29 (72)
.=.|+|+|.|+|-|=--++-.
T Consensus 44 ~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 44 HKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred ccceeeeeecccccchhcccc
Confidence 346999999999997776653
No 58
>PRK10139 serine endoprotease; Provisional
Probab=64.42 E-value=11 Score=27.98 Aligned_cols=28 Identities=7% Similarity=0.296 Sum_probs=24.6
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
|.+.||+++.++++|+|....|.+=.+.
T Consensus 119 V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 119 IQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred EEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 6789999999999999999999885543
No 59
>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=62.14 E-value=3.2 Score=24.98 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=14.6
Q ss_pred EEEEEecCeeceEEccE
Q 035130 12 GRVRAFDRHCNMVLENV 28 (72)
Q Consensus 12 G~L~~fD~~mNlvL~d~ 28 (72)
|+|+|.|.|-|---+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999877665
No 60
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=61.61 E-value=13 Score=26.96 Aligned_cols=28 Identities=4% Similarity=0.246 Sum_probs=24.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
|.+.+|+++.+++.++|.+.+|.|=.+.
T Consensus 86 V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 86 VTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred EEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 5678999999999999999999886554
No 61
>PRK02001 hypothetical protein; Validated
Probab=61.32 E-value=11 Score=24.15 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=16.3
Q ss_pred eEEecCeEEEEEEEEecCe
Q 035130 2 MSVKNNTQLLGRVRAFDRH 20 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~ 20 (72)
|.+.++++++|+|.++|.-
T Consensus 95 V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 95 VLTKNGKKIEGELKSADEN 113 (152)
T ss_pred EEECCCCEEEEEEEEEeCC
Confidence 5677999999999999864
No 62
>PRK14639 hypothetical protein; Provisional
Probab=57.36 E-value=15 Score=23.17 Aligned_cols=23 Identities=17% Similarity=0.491 Sum_probs=17.9
Q ss_pred eEEecCeEEEEEEEEecCeeceEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL 25 (72)
|.+++++.++|+|.++|.- ++.|
T Consensus 93 v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 93 ITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred EEECCCcEEEEEEEEEeCC-EEEE
Confidence 4567899999999999883 4444
No 63
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=48.38 E-value=57 Score=19.39 Aligned_cols=60 Identities=23% Similarity=0.340 Sum_probs=38.6
Q ss_pred EEecCeEEEEEEEEecCe-eceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEEE
Q 035130 3 SVKNNTQLLGRVRAFDRH-CNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 67 (72)
Q Consensus 3 ~l~~gr~~~G~L~~fD~~-mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~I 67 (72)
.-+.+-.|+|+|...|.. -.+.|.+|.-+-+....... ...+ .......+.+||..|--+
T Consensus 14 isk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~---~ipp--~~~v~~~I~Fr~sDIkdL 74 (96)
T PF12701_consen 14 ISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR---EIPP--SDEVYDYIVFRGSDIKDL 74 (96)
T ss_dssp EETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS------C---CSSSSEEEEETTTEEEE
T ss_pred EECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc---ccCC--CCceeeEEEEEccccceE
Confidence 346777899999999984 89999998876442111000 0001 123467999999988644
No 64
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=47.61 E-value=36 Score=19.24 Aligned_cols=15 Identities=13% Similarity=0.335 Sum_probs=12.3
Q ss_pred cC-eEEEEEEEEecCe
Q 035130 6 NN-TQLLGRVRAFDRH 20 (72)
Q Consensus 6 ~g-r~~~G~L~~fD~~ 20 (72)
+| ++++|.|.++|.-
T Consensus 37 ~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 37 DGQKEFEGTLLGVDDD 52 (83)
T ss_pred CCeEEEEEEEEeEeCC
Confidence 44 6899999999873
No 65
>PRK14642 hypothetical protein; Provisional
Probab=43.17 E-value=38 Score=22.80 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=13.1
Q ss_pred cCeEEEEEEEEecCe
Q 035130 6 NNTQLLGRVRAFDRH 20 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~ 20 (72)
+.+.++|+|.++|..
T Consensus 122 ~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 122 NRKKFRGTLERAESG 136 (197)
T ss_pred CceEEEEEEEEEcCC
Confidence 678999999999873
No 66
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=41.59 E-value=32 Score=21.04 Aligned_cols=24 Identities=17% Similarity=0.227 Sum_probs=17.9
Q ss_pred eEEecCeEEEEEEEEec-CeeceEE
Q 035130 2 MSVKNNTQLLGRVRAFD-RHCNMVL 25 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD-~~mNlvL 25 (72)
|.++||+.++|.+.+=| ....|..
T Consensus 62 v~~~dG~~~~G~~~~e~~~~~~l~~ 86 (133)
T TIGR02603 62 VTLKDGRILSGIVASETADGVTVKM 86 (133)
T ss_pred EEECCCCEEEEEEEecCCCeEEEEc
Confidence 68999999999999854 3344443
No 67
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=37.89 E-value=67 Score=17.14 Aligned_cols=28 Identities=25% Similarity=0.414 Sum_probs=21.5
Q ss_pred ecCeEEEEEEEEe---cCeeceEEccEEEee
Q 035130 5 KNNTQLLGRVRAF---DRHCNMVLENVREMW 32 (72)
Q Consensus 5 ~~gr~~~G~L~~f---D~~mNlvL~d~~E~~ 32 (72)
++.-.+.|.|..| |.-|=.+|.|++=..
T Consensus 3 k~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~ 33 (52)
T PF02751_consen 3 KNKLSFKGHLDTYRFCDNVWTFILKNVEFKM 33 (52)
T ss_dssp --EEEEEEEEEEEEEETTEEEEEEEEEEEEE
T ss_pred ceeEEEEEeeeEEEeeCcEEEEEEcCEEEEE
Confidence 3445688999998 999999999987443
No 68
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=37.78 E-value=43 Score=18.54 Aligned_cols=23 Identities=13% Similarity=0.419 Sum_probs=19.7
Q ss_pred EEEEEEEEecCe-eceEEccEEEe
Q 035130 9 QLLGRVRAFDRH-CNMVLENVREM 31 (72)
Q Consensus 9 ~~~G~L~~fD~~-mNlvL~d~~E~ 31 (72)
+.+|++.++|.. +-|.|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 579999999988 68999997754
No 69
>PRK14644 hypothetical protein; Provisional
Probab=37.58 E-value=52 Score=20.68 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=16.4
Q ss_pred eEEecC----eEEEEEEEEecCeeceEE
Q 035130 2 MSVKNN----TQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 2 i~l~~g----r~~~G~L~~fD~~mNlvL 25 (72)
|++++. ++++|+|.++|.. ++.|
T Consensus 90 V~l~~~~~~~~~~~G~L~~v~~~-~i~l 116 (136)
T PRK14644 90 VSLNKEVNKTDFITGELLENNPE-TITL 116 (136)
T ss_pred EEEccCcCCeEEEEEEEEEEeCC-EEEE
Confidence 445555 8899999999873 3444
No 70
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=37.58 E-value=40 Score=19.87 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=19.0
Q ss_pred eeeeCeEEEeCCcEEEEEeCC
Q 035130 51 DRFISKMFLRGDSVIIVLRNP 71 (72)
Q Consensus 51 ~r~lg~i~iRG~nV~~I~~~~ 71 (72)
.|.-|.+.++|..+..+..+|
T Consensus 76 ~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hcceEEEEEECCeeeEEEcCC
Confidence 577899999999999998887
No 71
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=36.89 E-value=34 Score=20.69 Aligned_cols=14 Identities=21% Similarity=0.463 Sum_probs=10.8
Q ss_pred eEEecCeEEEEEEE
Q 035130 2 MSVKNNTQLLGRVR 15 (72)
Q Consensus 2 i~l~~gr~~~G~L~ 15 (72)
+.|+||+.+.|++.
T Consensus 33 l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 33 LELDDGSMLRGTVA 46 (101)
T ss_dssp EEETTS-EEEEEEC
T ss_pred EEEcCCCeeeeeec
Confidence 56899999999963
No 72
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=33.31 E-value=14 Score=31.41 Aligned_cols=51 Identities=8% Similarity=0.190 Sum_probs=0.0
Q ss_pred EecCeEEEEEEEEecCeeceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEEE
Q 035130 4 VKNNTQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 66 (72)
Q Consensus 4 l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~~ 66 (72)
-.+|+.+.|.|+.-|.-|+-+|.-..+. ... . ......+|.++|||+|.|.
T Consensus 254 t~~G~~v~GVlvTT~~V~q~Ll~~l~~i-~~~-----~------v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 254 TSSGRPVDGVLVTTANVMQKLLNLLGQI-SDT-----S------VSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp ---------------------------------------------------------------
T ss_pred cCCCCEeceEEeccHHHHHHHHHHHhhh-ccc-----e------eecchhheeeeecCccHHH
Confidence 3689999999999999988777665552 110 0 0124568999999999874
No 73
>PRK14645 hypothetical protein; Provisional
Probab=32.97 E-value=49 Score=21.24 Aligned_cols=15 Identities=20% Similarity=0.452 Sum_probs=13.0
Q ss_pred cCeEEEEEEEEecCe
Q 035130 6 NNTQLLGRVRAFDRH 20 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~ 20 (72)
++++++|+|.++|.-
T Consensus 110 ~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 110 PGENFTGRIKAVSGD 124 (154)
T ss_pred CCeEEEEEEEEEeCC
Confidence 589999999999773
No 74
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=32.92 E-value=1e+02 Score=17.69 Aligned_cols=57 Identities=25% Similarity=0.388 Sum_probs=35.5
Q ss_pred ecCeEEEEEEEEecCe-eceEEccEEEeeeccCCCcCCccccccCceeeeeCeEEEeCCcEE
Q 035130 5 KNNTQLLGRVRAFDRH-CNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 65 (72)
Q Consensus 5 ~~gr~~~G~L~~fD~~-mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~iRG~nV~ 65 (72)
+.+-.++|+|...|.. --+.|.++..+-+.....+ +. +..+ ...-+..++.||..|-
T Consensus 14 k~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~-~~-~ipp--~~~vyd~IvFrgsDIk 71 (74)
T cd01736 14 KSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD-GP-EIPP--SDEVYDYIVFRGSDIK 71 (74)
T ss_pred cCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC-CC-ccCC--CCcceeEEEEcCCccc
Confidence 5666799999999988 4677899876654311100 00 0011 1234678999998874
No 75
>PRK14633 hypothetical protein; Provisional
Probab=31.68 E-value=49 Score=21.02 Aligned_cols=16 Identities=13% Similarity=0.285 Sum_probs=13.8
Q ss_pred ecCeEEEEEEEEecCe
Q 035130 5 KNNTQLLGRVRAFDRH 20 (72)
Q Consensus 5 ~~gr~~~G~L~~fD~~ 20 (72)
.+.++++|+|.+++.-
T Consensus 106 ~~~~~~~G~L~~v~~~ 121 (150)
T PRK14633 106 GSQTKFKGVLERVEGN 121 (150)
T ss_pred CCcEEEEEEEEEEeCC
Confidence 4789999999999874
No 76
>PRK14640 hypothetical protein; Provisional
Probab=31.06 E-value=72 Score=20.26 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=13.8
Q ss_pred ecCeEEEEEEEEecCe
Q 035130 5 KNNTQLLGRVRAFDRH 20 (72)
Q Consensus 5 ~~gr~~~G~L~~fD~~ 20 (72)
.+.++++|+|.++|.-
T Consensus 109 ~~~k~~~G~L~~v~~~ 124 (152)
T PRK14640 109 NNRRKFKGVIKAVQGD 124 (152)
T ss_pred CCceEEEEEEEEEeCC
Confidence 4779999999999874
No 77
>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=30.73 E-value=64 Score=17.84 Aligned_cols=13 Identities=15% Similarity=0.659 Sum_probs=10.9
Q ss_pred EEEeCCcEEEEEe
Q 035130 57 MFLRGDSVIIVLR 69 (72)
Q Consensus 57 i~iRG~nV~~I~~ 69 (72)
-|+|||.|+.|..
T Consensus 13 gf~r~~kilviik 25 (66)
T PF09196_consen 13 GFIRFNKILVIIK 25 (66)
T ss_dssp EEEETTTEEEEEE
T ss_pred eEEecCEEEEEEe
Confidence 4899999998865
No 78
>PRK06630 hypothetical protein; Provisional
Probab=30.46 E-value=27 Score=21.17 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=16.2
Q ss_pred EEEEEEEecCeeceEEccE
Q 035130 10 LLGRVRAFDRHCNMVLENV 28 (72)
Q Consensus 10 ~~G~L~~fD~~mNlvL~d~ 28 (72)
..|+|+|-|+|-|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4699999999999887764
No 79
>PRK14636 hypothetical protein; Provisional
Probab=30.13 E-value=79 Score=20.72 Aligned_cols=19 Identities=16% Similarity=0.445 Sum_probs=13.9
Q ss_pred cCeEEEEEEEEecCeeceEE
Q 035130 6 NNTQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~mNlvL 25 (72)
+.++++|+|.++|.- ++.|
T Consensus 111 g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 111 GRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CeEEEEEEEEEEeCC-EEEE
Confidence 446999999999773 3444
No 80
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=29.68 E-value=81 Score=21.82 Aligned_cols=22 Identities=27% Similarity=0.356 Sum_probs=18.6
Q ss_pred EEEEEEEEecCeeceEEccEEE
Q 035130 9 QLLGRVRAFDRHCNMVLENVRE 30 (72)
Q Consensus 9 ~~~G~L~~fD~~mNlvL~d~~E 30 (72)
.+.|.+.-.|.|-|+++.=..|
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~~ 190 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISRE 190 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEHH
T ss_pred eEEEEEEEECccCCeeeCCCHH
Confidence 7999999999999999864433
No 81
>PF05989 Chordopox_A35R: Chordopoxvirus A35R protein; InterPro: IPR009247 This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown.
Probab=29.58 E-value=39 Score=22.50 Aligned_cols=22 Identities=9% Similarity=0.055 Sum_probs=17.6
Q ss_pred EEEEEEEecCeeceEEccEEEe
Q 035130 10 LLGRVRAFDRHCNMVLENVREM 31 (72)
Q Consensus 10 ~~G~L~~fD~~mNlvL~d~~E~ 31 (72)
-.+.+..||++.+|.+++-.--
T Consensus 93 ~n~~iiccD~~~~l~i~~k~q~ 114 (176)
T PF05989_consen 93 KNSFIICCDKDPKLSIDNKFQP 114 (176)
T ss_pred CCcEEEEecCcceEEECCCccc
Confidence 3567899999999999885543
No 82
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.92 E-value=83 Score=20.30 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=17.1
Q ss_pred EecCeEEEEEEEEecCeeceEE
Q 035130 4 VKNNTQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 4 l~~gr~~~G~L~~fD~~mNlvL 25 (72)
+.+.+.++|+|.++|.-. +++
T Consensus 110 ~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 110 IEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred cCCceEEEEEEEEEcCCe-EEE
Confidence 378899999999999876 444
No 83
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=27.78 E-value=34 Score=21.23 Aligned_cols=20 Identities=30% Similarity=0.227 Sum_probs=16.3
Q ss_pred EEEEEEecCeeceEEccEEE
Q 035130 11 LGRVRAFDRHCNMVLENVRE 30 (72)
Q Consensus 11 ~G~L~~fD~~mNlvL~d~~E 30 (72)
.|.|+|-|+|-|---++..+
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred cceEeEEcCCCCeeeEcCCC
Confidence 68999999999987776443
No 84
>PRK14643 hypothetical protein; Provisional
Probab=27.13 E-value=64 Score=20.90 Aligned_cols=20 Identities=10% Similarity=0.235 Sum_probs=14.9
Q ss_pred cCeEEEEEEEEecCe-eceEE
Q 035130 6 NNTQLLGRVRAFDRH-CNMVL 25 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~-mNlvL 25 (72)
+.++++|+|.++|.- ..+.|
T Consensus 117 g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 117 KVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred CceEEEEEEEEEeCCcEEEEE
Confidence 468999999999854 44443
No 85
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.32 E-value=1.1e+02 Score=21.48 Aligned_cols=28 Identities=4% Similarity=0.213 Sum_probs=22.4
Q ss_pred eEEecCeEEEEEEEEecCeeceEEccEE
Q 035130 2 MSVKNNTQLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 2 i~l~~gr~~~G~L~~fD~~mNlvL~d~~ 29 (72)
+.+.+||++.+.+.|+|...-+.+-...
T Consensus 100 v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 100 VTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred EEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 3468999999999999999877664444
No 86
>COG5324 Uncharacterized conserved protein [Function unknown]
Probab=25.42 E-value=43 Score=26.32 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=12.4
Q ss_pred eEEEEEEEEecCeece
Q 035130 8 TQLLGRVRAFDRHCNM 23 (72)
Q Consensus 8 r~~~G~L~~fD~~mNl 23 (72)
.+..-.++|||+|+|.
T Consensus 73 ~~~~iviRgYdKFFN~ 88 (758)
T COG5324 73 GEVRIVIRGYDKFFNY 88 (758)
T ss_pred CceeEEEeechhhccc
Confidence 3445679999999985
No 87
>PRK14632 hypothetical protein; Provisional
Probab=24.07 E-value=1.2e+02 Score=19.74 Aligned_cols=14 Identities=14% Similarity=0.302 Sum_probs=12.2
Q ss_pred cCeEEEEEEEEecC
Q 035130 6 NNTQLLGRVRAFDR 19 (72)
Q Consensus 6 ~gr~~~G~L~~fD~ 19 (72)
+.++++|+|.++|.
T Consensus 114 g~k~~~G~L~~v~~ 127 (172)
T PRK14632 114 GRRKFRGELLAVEG 127 (172)
T ss_pred CceEEEEEEEEEeC
Confidence 46899999999975
No 88
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=23.97 E-value=90 Score=19.22 Aligned_cols=15 Identities=13% Similarity=0.370 Sum_probs=12.1
Q ss_pred ecCeEEEEEEEEecC
Q 035130 5 KNNTQLLGRVRAFDR 19 (72)
Q Consensus 5 ~~gr~~~G~L~~fD~ 19 (72)
.+.+++.|+|.++|.
T Consensus 99 ~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 99 NGRKEFEGKLLEVDE 113 (141)
T ss_dssp SS-SEEEEEEEEEET
T ss_pred CCcEEEEEEEEEEeC
Confidence 355789999999988
No 89
>PRK14634 hypothetical protein; Provisional
Probab=23.91 E-value=1.3e+02 Score=19.19 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=12.3
Q ss_pred cCeEEEEEEEEecCe
Q 035130 6 NNTQLLGRVRAFDRH 20 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~ 20 (72)
+.+.++|+|.++|.-
T Consensus 113 ~~k~~~G~L~~~~~~ 127 (155)
T PRK14634 113 SEQRLEGLLLERNED 127 (155)
T ss_pred CeEEEEEEEEEEeCC
Confidence 347899999999873
No 90
>PRK14646 hypothetical protein; Provisional
Probab=23.50 E-value=1.3e+02 Score=19.18 Aligned_cols=18 Identities=11% Similarity=0.089 Sum_probs=13.4
Q ss_pred CeEEEEEEEEecCeeceEE
Q 035130 7 NTQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 7 gr~~~G~L~~fD~~mNlvL 25 (72)
-+.++|+|.++|.- ++.|
T Consensus 114 ~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 114 IKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred eEEEEEEEEEEeCC-EEEE
Confidence 36789999999874 4444
No 91
>PRK08183 NADH dehydrogenase; Validated
Probab=22.28 E-value=46 Score=21.10 Aligned_cols=19 Identities=16% Similarity=0.055 Sum_probs=15.5
Q ss_pred EEEEEEecCeeceEEccEE
Q 035130 11 LGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 11 ~G~L~~fD~~mNlvL~d~~ 29 (72)
.|.|+|-|++-|---++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6899999999998776543
No 92
>PF02707 MOSP_N: Major Outer Sheath Protein N-terminal region; InterPro: IPR003857 This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [].
Probab=21.34 E-value=96 Score=21.14 Aligned_cols=18 Identities=0% Similarity=-0.003 Sum_probs=14.9
Q ss_pred eEEEEEEEEecCeeceEE
Q 035130 8 TQLLGRVRAFDRHCNMVL 25 (72)
Q Consensus 8 r~~~G~L~~fD~~mNlvL 25 (72)
-.++++|+.|+-||++==
T Consensus 30 ~s~eAtLh~ygaYltig~ 47 (204)
T PF02707_consen 30 FSIEATLHCYGAYLTIGK 47 (204)
T ss_pred eeEEEEEEEEeeEEEecc
Confidence 358999999999998743
No 93
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=21.17 E-value=81 Score=18.99 Aligned_cols=21 Identities=10% Similarity=0.267 Sum_probs=8.6
Q ss_pred EEEEEEEEecCeeceEEccEE
Q 035130 9 QLLGRVRAFDRHCNMVLENVR 29 (72)
Q Consensus 9 ~~~G~L~~fD~~mNlvL~d~~ 29 (72)
.+.|+..|||-.-++.|++|.
T Consensus 124 ti~G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 124 TIKGICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp EEEEE-----SSS-EEEE---
T ss_pred EEEEEEEeeecCCcEEeeccC
Confidence 478999999844577777763
No 94
>PRK06955 biotin--protein ligase; Provisional
Probab=21.13 E-value=1.6e+02 Score=20.51 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=18.8
Q ss_pred cCeEEEEEEEEecCeeceEEcc
Q 035130 6 NNTQLLGRVRAFDRHCNMVLEN 27 (72)
Q Consensus 6 ~gr~~~G~L~~fD~~mNlvL~d 27 (72)
+++.++|+++|.|..-.|++++
T Consensus 258 ~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 258 GAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred CCcEEEEEEeeECCCceEEEEe
Confidence 4567899999999999999863
No 95
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=21.10 E-value=1.4e+02 Score=18.77 Aligned_cols=15 Identities=20% Similarity=0.295 Sum_probs=13.2
Q ss_pred ecCeEEEEEEEEecC
Q 035130 5 KNNTQLLGRVRAFDR 19 (72)
Q Consensus 5 ~~gr~~~G~L~~fD~ 19 (72)
.++++++|+|.++|.
T Consensus 110 ~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 110 DGRKKFQGILLAVDG 124 (154)
T ss_pred CCceEEEEEEEEeeC
Confidence 478899999999977
No 96
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=20.73 E-value=70 Score=21.16 Aligned_cols=15 Identities=27% Similarity=0.264 Sum_probs=4.4
Q ss_pred EEEEEEEEecCeece
Q 035130 9 QLLGRVRAFDRHCNM 23 (72)
Q Consensus 9 ~~~G~L~~fD~~mNl 23 (72)
...=..++||+|+|+
T Consensus 15 ~~~Iv~R~~~KFFN~ 29 (221)
T PF09511_consen 15 TGRIVARPFDKFFNI 29 (221)
T ss_dssp EEEEEE-------BT
T ss_pred CCeEEECCCCCcccC
Confidence 344446799999996
No 97
>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=20.30 E-value=56 Score=19.29 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=11.6
Q ss_pred eeeCeEEEeCCcEEE
Q 035130 52 RFISKMFLRGDSVII 66 (72)
Q Consensus 52 r~lg~i~iRG~nV~~ 66 (72)
-.+|.+++|||...+
T Consensus 76 l~~Gr~~LRGNHF~v 90 (92)
T PF05413_consen 76 LPLGRMLLRGNHFSV 90 (92)
T ss_pred Cchhheeecccceee
Confidence 358999999997544
Done!