Query 045948
Match_columns 184
No_of_seqs 104 out of 1126
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:11:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045948hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01718 Sm_E The eukaryotic Sm 99.9 4.1E-23 8.9E-28 151.9 10.4 79 7-85 1-79 (79)
2 PTZ00138 small nuclear ribonuc 99.9 4.4E-22 9.6E-27 149.4 11.4 86 1-86 3-88 (89)
3 PRK00737 small nuclear ribonuc 99.8 1.4E-20 3.1E-25 134.6 8.6 70 11-85 3-72 (72)
4 cd01732 LSm5 The eukaryotic Sm 99.8 3.6E-20 7.7E-25 134.7 9.4 72 11-86 2-75 (76)
5 KOG1774 Small nuclear ribonucl 99.8 1.5E-20 3.1E-25 140.0 6.4 86 1-86 1-86 (88)
6 cd01731 archaeal_Sm1 The archa 99.8 4.9E-20 1.1E-24 129.8 8.6 68 13-85 1-68 (68)
7 cd01720 Sm_D2 The eukaryotic S 99.8 9.6E-20 2.1E-24 135.9 9.7 74 11-86 1-86 (87)
8 cd01726 LSm6 The eukaryotic Sm 99.8 9.1E-20 2E-24 128.5 8.3 67 13-84 1-67 (67)
9 cd01730 LSm3 The eukaryotic Sm 99.8 1.3E-19 2.8E-24 132.5 8.4 70 12-85 1-82 (82)
10 cd01719 Sm_G The eukaryotic Sm 99.8 3.7E-19 8.1E-24 127.9 9.0 71 13-88 1-71 (72)
11 cd01722 Sm_F The eukaryotic Sm 99.8 4E-19 8.6E-24 125.7 7.8 68 12-84 1-68 (68)
12 cd01729 LSm7 The eukaryotic Sm 99.8 1E-18 2.2E-23 128.1 9.1 72 12-88 3-81 (81)
13 cd01723 LSm4 The eukaryotic Sm 99.8 1.2E-18 2.5E-23 125.8 8.3 72 12-87 1-72 (76)
14 cd01721 Sm_D3 The eukaryotic S 99.8 2.6E-18 5.6E-23 122.5 8.9 70 13-87 1-70 (70)
15 COG1958 LSM1 Small nuclear rib 99.8 5.4E-18 1.2E-22 122.5 8.8 73 9-85 4-79 (79)
16 cd01727 LSm8 The eukaryotic Sm 99.7 2.5E-17 5.5E-22 118.2 9.2 69 16-88 3-74 (74)
17 cd01728 LSm1 The eukaryotic Sm 99.7 2.9E-17 6.4E-22 119.0 9.5 69 13-85 3-73 (74)
18 smart00651 Sm snRNP Sm protein 99.7 3.1E-17 6.8E-22 113.3 8.3 66 16-85 2-67 (67)
19 PF01423 LSM: LSM domain ; In 99.7 4.6E-17 1E-21 112.7 7.9 67 15-85 1-67 (67)
20 cd01724 Sm_D1 The eukaryotic S 99.7 1E-16 2.3E-21 119.8 9.4 73 12-89 1-73 (90)
21 cd01717 Sm_B The eukaryotic Sm 99.7 9.9E-17 2.1E-21 116.2 8.9 66 16-85 4-78 (79)
22 KOG1780 Small Nuclear ribonucl 99.7 4.3E-17 9.4E-22 119.4 6.4 70 12-88 6-75 (77)
23 cd01725 LSm2 The eukaryotic Sm 99.7 4.2E-16 9.1E-21 114.1 8.2 74 12-89 1-75 (81)
24 KOG1781 Small Nuclear ribonucl 99.7 1.3E-17 2.7E-22 128.1 -0.1 96 1-103 1-108 (108)
25 cd01733 LSm10 The eukaryotic S 99.6 7.1E-16 1.5E-20 112.6 8.4 70 12-86 9-78 (78)
26 cd00600 Sm_like The eukaryotic 99.6 1.4E-15 3E-20 103.6 8.1 63 17-84 1-63 (63)
27 KOG3482 Small nuclear ribonucl 99.6 1.7E-15 3.6E-20 111.0 6.3 72 11-87 7-78 (79)
28 cd06168 LSm9 The eukaryotic Sm 99.6 8.3E-15 1.8E-19 106.5 9.4 67 15-85 3-74 (75)
29 KOG3460 Small nuclear ribonucl 99.5 1.5E-15 3.1E-20 113.8 1.1 74 10-87 3-88 (91)
30 KOG1783 Small nuclear ribonucl 99.5 1.1E-14 2.4E-19 106.6 1.1 72 11-87 5-76 (77)
31 KOG1775 U6 snRNA-associated Sm 99.4 2.9E-13 6.2E-18 100.1 3.2 74 10-87 5-80 (84)
32 KOG3293 Small nuclear ribonucl 99.3 9E-12 2E-16 99.2 5.9 73 11-87 1-73 (134)
33 KOG1784 Small Nuclear ribonucl 99.2 1.3E-11 2.8E-16 93.8 4.5 68 17-88 5-75 (96)
34 KOG3459 Small nuclear ribonucl 99.0 4.6E-11 9.9E-16 93.3 -0.1 73 11-85 23-107 (114)
35 KOG3168 U1 snRNP component [Tr 98.9 1.8E-10 3.8E-15 95.8 0.6 71 12-87 5-84 (177)
36 KOG1782 Small Nuclear ribonucl 98.9 2.4E-10 5.1E-15 90.9 -0.2 70 17-90 14-85 (129)
37 KOG3448 Predicted snRNP core p 98.7 3.7E-08 8E-13 74.9 7.4 72 14-89 4-76 (96)
38 KOG3172 Small nuclear ribonucl 98.7 2.4E-08 5.2E-13 78.2 6.1 73 10-87 3-75 (119)
39 KOG3428 Small nuclear ribonucl 98.6 1.5E-07 3.3E-12 73.5 8.4 72 14-91 4-75 (109)
40 cd01739 LSm11_C The eukaryotic 98.4 1.7E-07 3.7E-12 67.5 2.7 46 18-63 2-49 (66)
41 cd01716 Hfq Hfq, an abundant, 96.5 0.0069 1.5E-07 43.1 5.1 38 15-54 2-39 (61)
42 TIGR02383 Hfq RNA chaperone Hf 96.5 0.0076 1.6E-07 42.9 5.2 38 15-54 6-43 (61)
43 PRK00395 hfq RNA-binding prote 96.0 0.016 3.4E-07 43.3 5.1 40 15-56 10-49 (79)
44 COG1923 Hfq Uncharacterized ho 95.2 0.045 9.7E-07 40.8 4.9 35 16-52 11-45 (77)
45 PF14438 SM-ATX: Ataxin 2 SM d 94.8 0.049 1.1E-06 38.8 4.1 62 16-81 6-76 (77)
46 PF12701 LSM14: Scd6-like Sm d 93.7 0.42 9E-06 36.6 7.5 67 19-89 5-80 (96)
47 PRK14091 RNA-binding protein H 93.5 0.16 3.4E-06 42.6 5.2 38 15-54 15-52 (165)
48 PRK14091 RNA-binding protein H 93.4 0.17 3.6E-06 42.5 5.2 41 14-56 94-134 (165)
49 cd01736 LSm14_N LSm14 (also kn 87.1 2.8 6E-05 31.0 6.2 59 19-81 3-71 (74)
50 cd01734 YlxS_C YxlS is a Bacil 86.3 1.7 3.6E-05 31.5 4.7 45 2-49 6-52 (83)
51 PRK14633 hypothetical protein; 86.1 1.6 3.4E-05 35.4 4.9 49 2-54 75-125 (150)
52 PF02237 BPL_C: Biotin protein 84.6 4.9 0.00011 26.3 5.9 47 21-76 2-48 (48)
53 PRK14634 hypothetical protein; 84.0 2.2 4.8E-05 34.8 4.9 49 2-54 81-131 (155)
54 PRK14638 hypothetical protein; 80.8 2.8 6.1E-05 34.0 4.3 42 2-48 81-122 (150)
55 PRK14639 hypothetical protein; 79.5 3.4 7.3E-05 33.2 4.3 47 2-54 69-115 (140)
56 COG0779 Uncharacterized protei 77.4 4.1 8.8E-05 33.6 4.3 51 2-54 80-130 (153)
57 PRK02001 hypothetical protein; 76.9 4.4 9.5E-05 33.2 4.4 47 2-54 71-117 (152)
58 PRK14640 hypothetical protein; 76.1 4.7 0.0001 32.7 4.3 49 2-54 78-128 (152)
59 PRK14636 hypothetical protein; 76.0 4.5 9.9E-05 33.8 4.3 44 2-48 79-124 (176)
60 PRK14632 hypothetical protein; 76.0 5.5 0.00012 33.1 4.8 49 2-54 79-132 (172)
61 PRK14647 hypothetical protein; 73.7 7.2 0.00016 31.8 4.8 44 2-48 80-130 (159)
62 PRK14643 hypothetical protein; 73.5 5.9 0.00013 32.7 4.4 45 2-49 85-131 (164)
63 PRK14646 hypothetical protein; 72.5 6.4 0.00014 32.1 4.3 49 2-54 81-131 (155)
64 PRK14645 hypothetical protein; 71.5 6.9 0.00015 32.0 4.3 42 2-49 83-124 (154)
65 PRK00092 ribosome maturation p 68.6 8.7 0.00019 30.9 4.2 44 2-48 79-124 (154)
66 PRK14631 hypothetical protein; 67.7 9.2 0.0002 31.9 4.3 43 2-47 98-142 (174)
67 PF10842 DUF2642: Protein of u 67.3 27 0.00059 25.1 6.1 56 11-84 8-65 (66)
68 PRK14642 hypothetical protein; 67.0 10 0.00022 32.5 4.5 49 2-54 81-140 (197)
69 cd01735 LSm12_N LSm12 belongs 66.6 14 0.00031 26.1 4.5 31 27-59 9-39 (61)
70 PRK14635 hypothetical protein; 65.4 12 0.00027 30.5 4.6 49 2-54 80-131 (162)
71 PRK14641 hypothetical protein; 65.3 12 0.00026 31.3 4.5 43 2-47 85-129 (173)
72 PF11095 Gemin7: Gem-associate 64.7 31 0.00066 25.8 6.1 62 14-85 16-78 (80)
73 PRK14637 hypothetical protein; 63.4 14 0.00029 30.2 4.4 48 2-54 79-126 (151)
74 PF02576 DUF150: Uncharacteris 59.0 9.8 0.00021 29.9 2.8 39 7-48 73-113 (141)
75 PRK14644 hypothetical protein; 52.4 20 0.00043 28.8 3.6 49 2-55 67-117 (136)
76 PF14563 DUF4444: Domain of un 49.6 17 0.00037 24.4 2.3 22 39-60 10-31 (42)
77 PRK06955 biotin--protein ligas 42.7 76 0.0016 28.0 6.1 30 25-56 250-279 (300)
78 PRK14630 hypothetical protein; 41.6 38 0.00083 27.3 3.7 41 2-48 78-118 (143)
79 PF06372 Gemin6: Gemin6 protei 36.8 42 0.0009 28.2 3.3 66 11-89 7-73 (166)
80 PRK13325 bifunctional biotin-- 34.9 93 0.002 30.5 5.8 30 25-56 279-308 (592)
81 PF07317 YcgR: Flagellar regul 34.8 34 0.00074 25.8 2.3 79 14-101 11-89 (108)
82 PF08863 YolD: YolD-like prote 34.8 1.6E+02 0.0035 20.6 6.6 40 15-55 33-74 (92)
83 cd07684 F-BAR_srGAP3 The F-BAR 30.8 18 0.00038 32.4 0.2 12 156-167 240-251 (253)
84 cd07683 F-BAR_srGAP1 The F-BAR 30.8 18 0.00039 32.3 0.3 12 156-167 240-251 (253)
85 cd07682 F-BAR_srGAP2 The F-BAR 30.4 19 0.00041 32.4 0.3 11 157-167 251-261 (263)
86 PRK11886 bifunctional biotin-- 30.1 1.5E+02 0.0033 26.0 5.9 45 25-77 273-317 (319)
87 KOG1073 Uncharacterized mRNA-a 26.7 1.4E+02 0.003 28.1 5.2 66 18-87 5-80 (361)
88 TIGR00121 birA_ligase birA, bi 23.3 3.8E+02 0.0081 22.5 6.9 28 25-55 194-221 (237)
89 PF14153 Spore_coat_CotO: Spor 21.4 1.3E+02 0.0027 25.6 3.6 35 14-49 123-157 (185)
No 1
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=4.1e-23 Score=151.88 Aligned_cols=79 Identities=81% Similarity=1.278 Sum_probs=73.0
Q ss_pred cceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 7 QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 7 ~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
+|.|+.|++.+.++++++.+|.|++++++|++++|+|+|||+|||++|+||+|+..+++.++.+|.++||||||++|++
T Consensus 1 ~~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 1 QKVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 4789999999999999999999999988999999999999999999999999995445677889999999999999874
No 2
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.88 E-value=4.4e-22 Score=149.41 Aligned_cols=86 Identities=67% Similarity=1.132 Sum_probs=77.1
Q ss_pred CCcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcE
Q 045948 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNI 80 (184)
Q Consensus 1 ms~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNV 80 (184)
|+-.+-||.|..|+.++.++++++.+|.|+++++++++++|+|+|||+|||++|+||+|+..+++..+.+|.++||||||
T Consensus 3 ~~~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV 82 (89)
T PTZ00138 3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNI 82 (89)
T ss_pred CcccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEE
Confidence 34334488999999999999999999999999999999999999999999999999999854456778999999999999
Q ss_pred EEEEec
Q 045948 81 TLMMNT 86 (184)
Q Consensus 81 v~I~~~ 86 (184)
++|++.
T Consensus 83 ~~I~~~ 88 (89)
T PTZ00138 83 TLIMAA 88 (89)
T ss_pred EEEEcC
Confidence 999864
No 3
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.83 E-value=1.4e-20 Score=134.59 Aligned_cols=70 Identities=30% Similarity=0.566 Sum_probs=62.7
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
..|+++|+++++++ |.|+++ +|++++|+|+|||+|||++|+||+|+ .+++..+++|.++|||+||++|++
T Consensus 3 ~~P~~~L~~~~~k~--V~V~lk--~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSP--VLVRLK--GGREFRGELQGYDIHMNLVLDNAEEI-QDGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCE--EEEEEC--CCCEEEEEEEEEcccceeEEeeEEEE-cCCCeEeEcCcEEEeCCEEEEEcC
Confidence 36999999999976 888886 46999999999999999999999998 466677899999999999999864
No 4
>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=99.83 E-value=3.6e-20 Score=134.75 Aligned_cols=72 Identities=32% Similarity=0.612 Sum_probs=62.8
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEe--cCcceeecCeEEEeCCcEEEEEec
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSV--KKKSRKPLGRILLKGDNITLMMNT 86 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~--dg~~~r~LG~v~IRGdNVv~I~~~ 86 (184)
..|+++|+++++++ |.|+++ +||+++|+|+|||+|||++|+||+|++. ++++.+.+|.++||||||.+|++.
T Consensus 2 ~~P~~~L~~~~~~~--V~V~l~--~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSR--IWIVMK--SDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCE--EEEEEC--CCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 47999999999965 888776 5699999999999999999999999963 344678899999999999999864
No 5
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.82 E-value=1.5e-20 Score=139.98 Aligned_cols=86 Identities=74% Similarity=1.173 Sum_probs=80.5
Q ss_pred CCcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcE
Q 045948 1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNI 80 (184)
Q Consensus 1 ms~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNV 80 (184)
||..++||+|..|+.++.+|++.+.||.||+..+-|-.++|.++|||+|||+||+||+|...+....+.+|.++++||||
T Consensus 1 ms~~kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnI 80 (88)
T KOG1774|consen 1 MSREKVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNI 80 (88)
T ss_pred CCcccccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcE
Confidence 89999999999999999999999999999999999999999999999999999999999976666666999999999999
Q ss_pred EEEEec
Q 045948 81 TLMMNT 86 (184)
Q Consensus 81 v~I~~~ 86 (184)
.+|...
T Consensus 81 tli~~~ 86 (88)
T KOG1774|consen 81 TLIQSA 86 (88)
T ss_pred EEEeec
Confidence 998764
No 6
>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=99.82 E-value=4.9e-20 Score=129.83 Aligned_cols=68 Identities=28% Similarity=0.585 Sum_probs=61.1
Q ss_pred ccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 13 PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
|+++|+++++++ |.|+++ +|++++|+|+|||+|||++|+||+|+. ++..++.+|.++|||+||++|++
T Consensus 1 p~~~L~~~~~~~--V~V~l~--~g~~~~G~L~~~D~~mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKP--VLVKLK--GGKEVRGRLKSYDQHMNLVLEDAEEID-DGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCE--EEEEEC--CCCEEEEEEEEECCcceEEEeeEEEEe-cCCeEeEcCcEEEeCCEEEEEcC
Confidence 899999999975 888887 469999999999999999999999984 55577899999999999999974
No 7
>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=99.81 E-value=9.6e-20 Score=135.90 Aligned_cols=74 Identities=22% Similarity=0.484 Sum_probs=63.5
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecC------------cceeecCeEEEeCC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKK------------KSRKPLGRILLKGD 78 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg------------~~~r~LG~v~IRGd 78 (184)
++|+++|++++.++++|.|++++ |+++.|+|+|||+||||+|+||+|.+... ..++.+|.+|||||
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~--~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd 78 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGD 78 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcC--CCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCC
Confidence 48999999999655689998874 59999999999999999999999986431 13567999999999
Q ss_pred cEEEEEec
Q 045948 79 NITLMMNT 86 (184)
Q Consensus 79 NVv~I~~~ 86 (184)
||++|++.
T Consensus 79 ~Vv~Is~~ 86 (87)
T cd01720 79 SVILVLRN 86 (87)
T ss_pred EEEEEecC
Confidence 99999864
No 8
>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=99.81 E-value=9.1e-20 Score=128.49 Aligned_cols=67 Identities=21% Similarity=0.454 Sum_probs=60.8
Q ss_pred ccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEE
Q 045948 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMM 84 (184)
Q Consensus 13 PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~ 84 (184)
|+++|+++++++ |+|++| +|++++|+|+|||+|||++|+||+|. .++++++.+|.++|||++|.+|+
T Consensus 1 p~~~L~~~~~~~--V~V~Lk--~g~~~~G~L~~~D~~mNlvL~~~~~~-~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRP--VVVKLN--SGVDYRGILACLDGYMNIALEQTEEY-VNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCe--EEEEEC--CCCEEEEEEEEEccceeeEEeeEEEE-eCCceeeEeCCEEEECCEEEEEC
Confidence 899999999975 999887 45999999999999999999999997 56777889999999999999984
No 9
>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=99.80 E-value=1.3e-19 Score=132.51 Aligned_cols=70 Identities=23% Similarity=0.508 Sum_probs=60.5
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecC------------cceeecCeEEEeCCc
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKK------------KSRKPLGRILLKGDN 79 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg------------~~~r~LG~v~IRGdN 79 (184)
.|+++|+++++|+ |.|+++ +||++.|+|+|||+||||+|+||+|++... ...|.+|.++|||||
T Consensus 1 ~pl~~l~~~~~k~--V~V~l~--~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~ 76 (82)
T cd01730 1 EPLDLIRLSLDER--VYVKLR--GDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDS 76 (82)
T ss_pred CchHHHHHhCCCE--EEEEEC--CCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCE
Confidence 4999999999975 888776 569999999999999999999999996421 246789999999999
Q ss_pred EEEEEe
Q 045948 80 ITLMMN 85 (184)
Q Consensus 80 Vv~I~~ 85 (184)
|++|++
T Consensus 77 Vv~i~~ 82 (82)
T cd01730 77 VILVSP 82 (82)
T ss_pred EEEECC
Confidence 999864
No 10
>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=99.79 E-value=3.7e-19 Score=127.85 Aligned_cols=71 Identities=25% Similarity=0.492 Sum_probs=62.6
Q ss_pred ccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCC
Q 045948 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYV 88 (184)
Q Consensus 13 PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~ 88 (184)
|-..|+++++|+ |.|+++ +|++++|+|+|||+|||++|+||+|+ .++...+.+|.++|||+||++|++.|+
T Consensus 1 ~~~~L~~~i~k~--V~V~L~--~g~~~~G~L~~~D~~mNlvL~~~~E~-~~~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 1 HPPELKKYMDKK--LSLKLN--GNRKVSGILRGFDPFMNLVLDDAVEV-NSGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCe--EEEEEC--CCeEEEEEEEEEcccccEEeccEEEE-ccCCceeEeceEEECCCEEEEEEcccc
Confidence 456789999976 888776 56999999999999999999999998 466678899999999999999998874
No 11
>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=99.79 E-value=4e-19 Score=125.71 Aligned_cols=68 Identities=25% Similarity=0.447 Sum_probs=60.9
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEE
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMM 84 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~ 84 (184)
.|+++|+++++++ |.|++| +|++++|+|.|||+|||++|+||+|. .++.+...+|.++|||+||.+|+
T Consensus 1 ~p~~~L~~~~g~~--V~V~Lk--~g~~~~G~L~~~D~~mNi~L~~~~e~-~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKP--VIVKLK--WGMEYKGTLVSVDSYMNLQLANTEEY-IDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCE--EEEEEC--CCcEEEEEEEEECCCEEEEEeeEEEE-eCCccccCcCcEEEECCEEEEEC
Confidence 4899999999975 888887 45999999999999999999999998 56667788999999999999984
No 12
>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=99.78 E-value=1e-18 Score=128.07 Aligned_cols=72 Identities=21% Similarity=0.430 Sum_probs=60.3
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecC-------cceeecCeEEEeCCcEEEEE
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKK-------KSRKPLGRILLKGDNITLMM 84 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg-------~~~r~LG~v~IRGdNVv~I~ 84 (184)
.|++ |.++++++ |.|+++ +||++.|+|+|||+||||+|+||+|+.... +.++.+|.++|||+||++|+
T Consensus 3 ~~~~-L~~~i~k~--V~V~l~--~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 3 SILD-LSKYVDKK--IRVKFQ--GGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred chhh-HHHhcCCe--EEEEEC--CCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEe
Confidence 3455 68999976 777775 569999999999999999999999995432 25688999999999999999
Q ss_pred ecCC
Q 045948 85 NTYV 88 (184)
Q Consensus 85 ~~d~ 88 (184)
+.++
T Consensus 78 ~~~~ 81 (81)
T cd01729 78 PVDG 81 (81)
T ss_pred cCCC
Confidence 8763
No 13
>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=99.77 E-value=1.2e-18 Score=125.84 Aligned_cols=72 Identities=17% Similarity=0.230 Sum_probs=64.0
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
.|+++|+++.+++ |+|++|+ |++++|+|.+||+|||++|+||+|...+|+....++.++|||++|.+|..+|
T Consensus 1 ~Pl~~L~~~~g~~--V~VeLkn--g~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 1 LPLSLLKTAQNHP--MLVELKN--GETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred CchHHHHhcCCCE--EEEEECC--CCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCH
Confidence 4999999999965 9999985 5999999999999999999999998556666677899999999999998776
No 14
>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=99.76 E-value=2.6e-18 Score=122.45 Aligned_cols=70 Identities=17% Similarity=0.274 Sum_probs=61.9
Q ss_pred ccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 13 PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
|+++|+++.++ +|+|++|+ |.+++|+|.++|+|||++|+||+|...+| +..+++.++|||+||.+|..||
T Consensus 1 P~~~L~~~~g~--~V~VeLk~--g~~~~G~L~~~D~~MNl~L~~~~~~~~~g-~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGH--IVTVELKT--GEVYRGKLIEAEDNMNCQLKDVTVTARDG-RVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCC--EEEEEECC--CcEEEEEEEEEcCCceeEEEEEEEECCCC-cEeEcCcEEEeCCEEEEEEeCC
Confidence 88999999995 59999985 59999999999999999999999874444 4567899999999999999876
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.75 E-value=5.4e-18 Score=122.50 Aligned_cols=73 Identities=34% Similarity=0.674 Sum_probs=61.8
Q ss_pred eecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEe-cCcc-eeecC-eEEEeCCcEEEEEe
Q 045948 9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSV-KKKS-RKPLG-RILLKGDNITLMMN 85 (184)
Q Consensus 9 ~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~-dg~~-~r~LG-~v~IRGdNVv~I~~ 85 (184)
.+..|+++|++++++ +|.|++|+ |+++.|+|+|||+|||++|+|++|+.. +++. .+.++ .++|||+||++|.+
T Consensus 4 ~~~~~~~~l~~~~~~--~V~V~lk~--g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 4 LGPLPLSFLKKLLNK--RVLVKLKN--GREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred ccCCcHHHHHHhhCC--EEEEEECC--CCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 456799999999995 59999975 599999999999999999999999953 5554 45555 99999999999863
No 16
>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=99.73 E-value=2.5e-17 Score=118.19 Aligned_cols=69 Identities=25% Similarity=0.397 Sum_probs=58.9
Q ss_pred HHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec---CcceeecCeEEEeCCcEEEEEecCC
Q 045948 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK---KKSRKPLGRILLKGDNITLMMNTYV 88 (184)
Q Consensus 16 lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d---g~~~r~LG~v~IRGdNVv~I~~~d~ 88 (184)
-|.++++++ |.|++ .+||.+.|+|+|||+|||++|+||+|+..+ +.+++.+|.+++||+||++|++.|+
T Consensus 3 ~L~~~l~~~--V~V~l--~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 3 TLEDYLNKT--VSVIT--VDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hHHHhcCCE--EEEEE--CCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 478999977 77766 467999999999999999999999998542 3457789999999999999998774
No 17
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.73 E-value=2.9e-17 Score=119.02 Aligned_cols=69 Identities=23% Similarity=0.396 Sum_probs=58.8
Q ss_pred ccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCc--ceeecCeEEEeCCcEEEEEe
Q 045948 13 PINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKK--SRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 13 PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~--~~r~LG~v~IRGdNVv~I~~ 85 (184)
++..|.++++|+ |.|.++ +||++.|+|+|||+|||++|+||+|+...+. .++.+|.++||||||++|+.
T Consensus 3 ~~~~L~~~l~k~--v~V~l~--~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKK--VVVLLR--DGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCE--EEEEEc--CCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 456789999976 777775 5699999999999999999999999865432 46789999999999999975
No 18
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.72 E-value=3.1e-17 Score=113.34 Aligned_cols=66 Identities=26% Similarity=0.583 Sum_probs=58.1
Q ss_pred HHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 16 lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
+|+++++++ |.|+++ +|+.+.|+|.+||+|||++|+||+|+..++.+.+.+|.++|||++|.+|.+
T Consensus 2 ~L~~~~~~~--V~V~l~--~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKR--VLVELK--NGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcE--EEEEEC--CCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 678899965 888887 459999999999999999999999995444678899999999999999864
No 19
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.71 E-value=4.6e-17 Score=112.71 Aligned_cols=67 Identities=24% Similarity=0.541 Sum_probs=58.4
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
.+|+++++++ |.|+++ +|+.++|+|.+||+|||++|+||.|...++.+.+.+|.++|||++|.+|.+
T Consensus 1 ~~L~~~~g~~--V~V~l~--~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKR--VRVELK--NGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSE--EEEEET--TSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcE--EEEEEe--CCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 3689999965 888776 569999999999999999999999995433388999999999999999975
No 20
>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=99.70 E-value=1e-16 Score=119.84 Aligned_cols=73 Identities=21% Similarity=0.359 Sum_probs=64.7
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCCC
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYVN 89 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~~ 89 (184)
.|+.+|+++.++ +|+|++|+ |..|+|+|.++|+|||++|+||+|. .+++....+|.++|||+||.+|..||.-
T Consensus 1 ~~~~fL~~l~g~--~V~VeLKn--g~~~~G~L~~vD~~MNl~L~~a~~~-~~~~~~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 1 KLVRFLMKLTNE--TVTIELKN--GTIVHGTITGVDPSMNTHLKNVKLT-LKGRNPVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred CHhHHHHhCCCC--EEEEEECC--CCEEEEEEEEEcCceeEEEEEEEEE-cCCCceeEcceEEEeCCEEEEEEcCCcC
Confidence 367899999885 59999985 5999999999999999999999998 4566778899999999999999999854
No 21
>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=99.69 E-value=9.9e-17 Score=116.24 Aligned_cols=66 Identities=29% Similarity=0.570 Sum_probs=56.5
Q ss_pred HHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec---------CcceeecCeEEEeCCcEEEEEe
Q 045948 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK---------KKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 16 lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d---------g~~~r~LG~v~IRGdNVv~I~~ 85 (184)
-|.++++++ |.|.++ +||++.|+|+|||+||||+|+||+|++.. +.+++.+|.++|||++|++|+.
T Consensus 4 ~l~~~l~~~--V~V~l~--dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYR--LRVTLQ--DGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCE--EEEEEC--CCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 578899976 777775 66999999999999999999999998642 2356889999999999999974
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.69 E-value=4.3e-17 Score=119.36 Aligned_cols=70 Identities=24% Similarity=0.489 Sum_probs=60.4
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCC
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYV 88 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~ 88 (184)
-| -|++|++|| +.+|.|+||...|+|+|||.|||+||+|++|. ...+.+..+|.++|||++|+++.+.+.
T Consensus 6 ~P--eLkkymdKk----i~lklnG~r~v~GiLrGyD~FmNiVlde~vE~-~~~~~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 6 HP--ELKKYMDKK----IVLKLNGGRKVTGILRGYDPFMNIVLDETVEP-NGDGDKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred Cc--hHHHhhhhe----EEEEeCCCcEEEEEEeccchHHhhhhhhceee-cCcCCcceeeeEEEeccEEEEEeeccc
Confidence 47 569999998 45555889999999999999999999999998 344567889999999999999998774
No 23
>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=99.66 E-value=4.2e-16 Score=114.15 Aligned_cols=74 Identities=15% Similarity=0.243 Sum_probs=61.8
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCc-ceeecCeEEEeCCcEEEEEecCCC
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKK-SRKPLGRILLKGDNITLMMNTYVN 89 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~-~~r~LG~v~IRGdNVv~I~~~d~~ 89 (184)
.|+++|+++.++ +|+|++|+ |..++|+|.++|+|||++|+||++...++. ....++.++|||++|.+|..+|+.
T Consensus 1 l~~~fL~~l~g~--~V~VeLKn--g~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 1 LFFSFFKTLVGK--EVTVELKN--DLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred ChhHHHHhCCCC--EEEEEECC--CcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence 478999999886 59999985 599999999999999999999988733322 234678999999999999988743
No 24
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.65 E-value=1.3e-17 Score=128.08 Aligned_cols=96 Identities=24% Similarity=0.413 Sum_probs=77.1
Q ss_pred CCcccccc-eecCc----cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec-------Cccee
Q 045948 1 MASTKVQR-IMTQP----INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK-------KKSRK 68 (184)
Q Consensus 1 ms~~~~~~-~m~~P----L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d-------g~~~r 68 (184)
||.-|.|+ ..+.| .--|.+|++|+ |++|..+||+..|+|+|||+.|||||+|++|+..+ +.+.|
T Consensus 1 M~~~~~~~~~~e~~kkEsilDLsky~Dk~----Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR 76 (108)
T KOG1781|consen 1 MSDKHSQRKKFEKPKKESILDLSKYLDKK----IRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETR 76 (108)
T ss_pred CcchhhccccccccchhHHhhHHHhhccc----eEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhh
Confidence 66654333 33333 22358999998 55566789999999999999999999999999664 23569
Q ss_pred ecCeEEEeCCcEEEEEecCCCccccccCCCcccCC
Q 045948 69 PLGRILLKGDNITLMMNTYVNSFSFSLSPPLITQT 103 (184)
Q Consensus 69 ~LG~v~IRGdNVv~I~~~d~~~~~~s~~~P~i~~~ 103 (184)
++|.+++||..+++|++.|+++ +++|||++++
T Consensus 77 ~LGLvV~RGTalvlisp~dG~e---~I~npf~~~e 108 (108)
T KOG1781|consen 77 KLGLVVCRGTALVLISPADGSE---EIANPFVQQE 108 (108)
T ss_pred eeeeEEEcccEEEEEcCCcchh---hhccchhcCC
Confidence 9999999999999999999886 7899999863
No 25
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.64 E-value=7.1e-16 Score=112.59 Aligned_cols=70 Identities=20% Similarity=0.317 Sum_probs=60.7
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEec
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNT 86 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~ 86 (184)
.+..+|+.+.++ +|+|+||++ ..++|+|.++|+|||++|+||++. .++.....+|.++|||+||.+|..|
T Consensus 9 tl~~~L~~l~g~--~V~VeLKng--~~~~G~L~~vD~~MNl~L~~~~~~-~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGK--VVTVELRNE--TTVTGRIASVDAFMNIRLAKVTII-DRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCC--EEEEEECCC--CEEEEEEEEEcCCceeEEEEEEEE-cCCCceeECCcEEEECCEEEEEEcC
Confidence 567889999885 599999854 899999999999999999999987 3455666899999999999999864
No 26
>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=99.63 E-value=1.4e-15 Score=103.57 Aligned_cols=63 Identities=35% Similarity=0.657 Sum_probs=54.7
Q ss_pred HHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEE
Q 045948 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMM 84 (184)
Q Consensus 17 L~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~ 84 (184)
|+++++++ |.|+++ +|+.+.|+|.+||+|||++|+|++|.. .+.+.+.+|.++|||++|.+|.
T Consensus 1 l~~~~g~~--V~V~l~--~g~~~~G~L~~~D~~~Ni~L~~~~~~~-~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKT--VRVELK--DGRVLEGVLVAFDKYMNLVLDDVEETI-KEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCE--EEEEEC--CCcEEEEEEEEECCCCCEEECCEEEEe-cCCcEEECCeEEEECCEEEEEC
Confidence 46788864 888887 459999999999999999999999995 3467889999999999999873
No 27
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.60 E-value=1.7e-15 Score=110.99 Aligned_cols=72 Identities=25% Similarity=0.371 Sum_probs=66.7
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
.+|-.||+.+.+| +|.|+||++ .+|+|+|++.|.||||.|.+++|+ ++|.....+|.++||.|||.+|...+
T Consensus 7 vNPKpFL~~l~gk--~V~vkLKwg--~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 7 VNPKPFLNGLTGK--PVLVKLKWG--QEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CCchHHHhhccCC--eEEEEEecC--cEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEecCC
Confidence 4899999999995 599999997 999999999999999999999998 79999999999999999999997654
No 28
>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=99.59 E-value=8.3e-15 Score=106.46 Aligned_cols=67 Identities=18% Similarity=0.290 Sum_probs=57.5
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec-----CcceeecCeEEEeCCcEEEEEe
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK-----KKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d-----g~~~r~LG~v~IRGdNVv~I~~ 85 (184)
+-|+++++++ |.|.++ |||.+.|+|.+||+|||++|+||.|+... +.+.|.+|.++|||++|+.|..
T Consensus 3 ~~L~~~l~~~--v~V~l~--dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRT--MRIHMT--DGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCe--EEEEEc--CCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 3578999976 777665 67999999999999999999999999643 2568899999999999999874
No 29
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.54 E-value=1.5e-15 Score=113.80 Aligned_cols=74 Identities=23% Similarity=0.484 Sum_probs=63.5
Q ss_pred ecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec--C----------cceeecCeEEEeC
Q 045948 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK--K----------KSRKPLGRILLKG 77 (184)
Q Consensus 10 m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d--g----------~~~r~LG~v~IRG 77 (184)
|..|+++|+-++++| |.|+++ ++|+++|+|.|||+|.||+|.|++|+... + ..+|.+..+|+||
T Consensus 3 v~ePldllrlsLdEr--VyVKlr--~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRG 78 (91)
T KOG3460|consen 3 VEEPLDLLRLSLDER--VYVKLR--SDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRG 78 (91)
T ss_pred ccccHHHHhhcccce--EEEEec--CChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeC
Confidence 789999999999976 777665 56999999999999999999999998542 1 2367899999999
Q ss_pred CcEEEEEecC
Q 045948 78 DNITLMMNTY 87 (184)
Q Consensus 78 dNVv~I~~~d 87 (184)
|+|++|+++-
T Consensus 79 d~Vilvspp~ 88 (91)
T KOG3460|consen 79 DGVILVSPPL 88 (91)
T ss_pred CeEEEEcCcc
Confidence 9999998863
No 30
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.47 E-value=1.1e-14 Score=106.60 Aligned_cols=72 Identities=19% Similarity=0.445 Sum_probs=65.1
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
..|.++|++++++ +|.|++ ++|-.|+|+|...|.|||+.|+.++|. .+|+.++++|..||||+||.+|+...
T Consensus 5 ~~~~~fl~~iiGr--~V~VKl--~sgvdyrG~l~~lDgymNiaLe~tee~-~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGR--TVVVKL--NSGVDYRGTLVCLDGYMNIALESTEEY-VNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCC--eEEEEe--cCCccccceehhhhhHHHHHHHHHHHH-hcCcccccccceeeccccEEEEEecc
Confidence 4699999999996 577766 678999999999999999999999999 68999999999999999999998753
No 31
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.37 E-value=2.9e-13 Score=100.14 Aligned_cols=74 Identities=32% Similarity=0.664 Sum_probs=63.6
Q ss_pred ecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec--CcceeecCeEEEeCCcEEEEEecC
Q 045948 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK--KKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 10 m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d--g~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
...|++++.+.++.| |++.++++|++.|+|+|||.|.|++|+|++|+-.. |+...+++++++.||||.+..+..
T Consensus 5 ~llPlEliDkcIgsk----i~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 5 TLLPLELIDKCIGSK----IWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred hcccHHHHHHhcCce----EEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 368999999999987 45555567999999999999999999999999654 556678999999999999988754
No 32
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.26 E-value=9e-12 Score=99.15 Aligned_cols=73 Identities=18% Similarity=0.207 Sum_probs=67.3
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
+.||.+|+.+-+ +|+.|+||++ ..|.|.|+.+|.+|||.|.+++++..||.+.-.++.+.|||++|.++..+|
T Consensus 1 mlPLsLL~~aq~--~pmlvELKNg--et~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 1 MLPLSLLKTAQN--HPMLVELKNG--ETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred CcchhHHHhcCC--CeEEEEecCC--CEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccH
Confidence 479999988866 6899999965 899999999999999999999999888888889999999999999999987
No 33
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.21 E-value=1.3e-11 Score=93.84 Aligned_cols=68 Identities=21% Similarity=0.423 Sum_probs=59.7
Q ss_pred HHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec---CcceeecCeEEEeCCcEEEEEecCC
Q 045948 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK---KKSRKPLGRILLKGDNITLMMNTYV 88 (184)
Q Consensus 17 L~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d---g~~~r~LG~v~IRGdNVv~I~~~d~ 88 (184)
|..|++++ |.|. .+|||.+.|.|+|||+-.|++|+|+-|+..+ +.+.-.+|..+|||+||.+|.+.|+
T Consensus 5 L~~y~n~~--V~vI--t~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 5 LEDYMNQR--VSVI--TNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE 75 (96)
T ss_pred HHHHhhce--EEEE--ecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch
Confidence 68999976 6664 4689999999999999999999999998654 5677889999999999999999983
No 34
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.01 E-value=4.6e-11 Score=93.34 Aligned_cols=73 Identities=22% Similarity=0.484 Sum_probs=65.5
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec------Cc------ceeecCeEEEeCC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK------KK------SRKPLGRILLKGD 78 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d------g~------~~r~LG~v~IRGd 78 (184)
.+|++++...+.+..+|.|.++++ +.+.|++.|||.|.|++|+|+.|.|.. |+ ..|.+|.+|||||
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn--~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGd 100 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNN--VKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGD 100 (114)
T ss_pred cCchhhhHHHhhcCceeEEEeccc--HHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCC
Confidence 399999999999999999999866 999999999999999999999999863 22 2688999999999
Q ss_pred cEEEEEe
Q 045948 79 NITLMMN 85 (184)
Q Consensus 79 NVv~I~~ 85 (184)
+|+.+..
T Consensus 101 svI~v~r 107 (114)
T KOG3459|consen 101 SVILVLR 107 (114)
T ss_pred eEEEEEe
Confidence 9998874
No 35
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.94 E-value=1.8e-10 Score=95.77 Aligned_cols=71 Identities=28% Similarity=0.491 Sum_probs=57.8
Q ss_pred CccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec---------CcceeecCeEEEeCCcEEE
Q 045948 12 QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK---------KKSRKPLGRILLKGDNITL 82 (184)
Q Consensus 12 ~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d---------g~~~r~LG~v~IRGdNVv~ 82 (184)
.|..+| ..++.+ ..|.+ +|||.+.|.+.+||+|||++|.||+|+... ++++|.+|.+++||.||++
T Consensus 5 ~sskml-~~iNyr--~rv~~--qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs 79 (177)
T KOG3168|consen 5 KSSKML-QHINYR--MRVRL--QDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVS 79 (177)
T ss_pred chhHHH-Hhhcce--EEEEe--ccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEE
Confidence 344454 577877 44433 688999999999999999999999998542 4678999999999999999
Q ss_pred EEecC
Q 045948 83 MMNTY 87 (184)
Q Consensus 83 I~~~d 87 (184)
.+..+
T Consensus 80 ~tVeg 84 (177)
T KOG3168|consen 80 MTVEG 84 (177)
T ss_pred EeccC
Confidence 98876
No 36
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.89 E-value=2.4e-10 Score=90.89 Aligned_cols=70 Identities=23% Similarity=0.448 Sum_probs=60.1
Q ss_pred HHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCc--ceeecCeEEEeCCcEEEEEecCCCc
Q 045948 17 IFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKK--SRKPLGRILLKGDNITLMMNTYVNS 90 (184)
Q Consensus 17 L~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~--~~r~LG~v~IRGdNVv~I~~~d~~~ 90 (184)
+.+++++| +.|-|+ |||.+.|.|++||+|-|++|+++.|+..-++ -....|..+|||.||++++..|...
T Consensus 14 l~~~~dkK--llVlLR--DGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dk 85 (129)
T KOG1782|consen 14 LVEYLDKK--LLVLLR--DGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDK 85 (129)
T ss_pred HHHHhcce--EEEEEe--cCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcch
Confidence 56899987 888776 5699999999999999999999999976544 3566889999999999999999654
No 37
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.75 E-value=3.7e-08 Score=74.89 Aligned_cols=72 Identities=15% Similarity=0.236 Sum_probs=58.1
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEec-CcceeecCeEEEeCCcEEEEEecCCC
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVK-KKSRKPLGRILLKGDNITLMMNTYVN 89 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~d-g~~~r~LG~v~IRGdNVv~I~~~d~~ 89 (184)
.++.+..++++ |+|+||+ +-.+.|+|.|+|+|+|+-|+|......+ -..-.+...++|||..|.+|..+.+.
T Consensus 4 ysfFkslvg~~--V~VeLKn--d~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~ 76 (96)
T KOG3448|consen 4 YSFFKSLVGKE--VVVELKN--DLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDA 76 (96)
T ss_pred HHHHHHhcCCe--EEEEEcC--CcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhH
Confidence 46788899965 9999995 4999999999999999999998876321 11234567899999999999987643
No 38
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.73 E-value=2.4e-08 Score=78.23 Aligned_cols=73 Identities=15% Similarity=0.243 Sum_probs=63.7
Q ss_pred ecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecC
Q 045948 10 MTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 10 m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d 87 (184)
+..|+.+|++.-+. -|+++++. |..|+|+|+..|.+||.+|+|.+.+..+ .....+.+++|||+.|.++..+|
T Consensus 3 ~gvpiKlLhEaqGh--IVt~Et~t--Ge~YRGkliEaeDnmNcql~di~vT~~d-g~vs~le~V~IRGS~IRFlvlPd 75 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGH--IVTVETKT--GEVYRGKLIEAEDNMNCQLRDITVTARD-GRVSQLEQVFIRGSKIRFLVLPD 75 (119)
T ss_pred cccceeeeecccCc--EEEEEecC--CceeeeeeEEeccccccEEEEEEEEccC-CcceeeeeEEEecCeEEEEECch
Confidence 45799999999885 59998874 5999999999999999999999998544 45667899999999999999988
No 39
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.65 E-value=1.5e-07 Score=73.46 Aligned_cols=72 Identities=22% Similarity=0.302 Sum_probs=61.4
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCCCcc
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYVNSF 91 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~~~~ 91 (184)
..+|++..++ +|+|+||+ |....|++.++|.+||..|.++.-. .+| +..++....|||+||.++..+|+..+
T Consensus 4 vr~L~kl~~e--~vtIeLkn--gt~v~G~I~~Vd~~Mn~~l~~v~~t-~~~-~pv~l~~lsirgnniRy~~lpD~l~l 75 (109)
T KOG3428|consen 4 VRFLKKLLNE--RVTIELKN--GTIVHGTIDSVDVQMNTHLKHVKMT-VKG-EPVRLDTLSIRGNNIRYYILPDSLNL 75 (109)
T ss_pred HHHHHHhhCC--eEEEEecC--CcEEeeeEEEEEhhheeEEEEEEEe-cCC-CceeEEEEEeecceEEEEEccCCcCc
Confidence 4577888775 59999985 4999999999999999999999887 345 66788999999999999999997643
No 40
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=98.41 E-value=1.7e-07 Score=67.50 Aligned_cols=46 Identities=24% Similarity=0.421 Sum_probs=36.5
Q ss_pred HHHhcCCceEEEEEEeCCC--eEEEEEEEEEcCccceEEceeEEEEec
Q 045948 18 FRFLQSKARIQIWLFEQKD--LRIEGRIIGFDEYMNLVLDEAEEVSVK 63 (184)
Q Consensus 18 ~k~L~Kr~~V~V~LK~~~G--r~i~G~LvgfD~~MNLVLeDa~E~~~d 63 (184)
++++..+.+|.|.++..+| -.++|.|++||+||||+|.|++|.+..
T Consensus 2 ~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 2 HRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred chhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 4566666777777765443 369999999999999999999999754
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=96.49 E-value=0.0069 Score=43.11 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=32.8
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
.+|+.+..++.+|+|.|++ |-.++|.+.|||+|+=+.-
T Consensus 2 ~fln~~r~~~~~Vtv~L~N--G~~l~G~I~~fD~ftVll~ 39 (61)
T cd01716 2 QFLNAARKEKIPVTIYLVN--GVQLKGQIESFDNFTVLLE 39 (61)
T ss_pred HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEcceEEEEE
Confidence 3678888999999999985 5999999999999986653
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=96.46 E-value=0.0076 Score=42.95 Aligned_cols=38 Identities=16% Similarity=0.449 Sum_probs=32.9
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
.+|+.+..++.+|+|.|.+ |-.++|.++|||+|+=+.-
T Consensus 6 ~fln~~r~~~~~Vti~L~n--G~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVN--GVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred HHHHHHHHcCCcEEEEEeC--CcEEEEEEEEEeeeEEEEE
Confidence 4788888899999999985 5999999999999986653
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=96.02 E-value=0.016 Score=43.29 Aligned_cols=40 Identities=18% Similarity=0.522 Sum_probs=33.6
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEce
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDE 56 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeD 56 (184)
.+|+.+..++.+|+|.|.+ |-.++|.++|||+|+=+.-.+
T Consensus 10 ~fLn~lr~~~~~VtifL~N--G~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVN--GIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHcCCCEEEEEeC--CcEEEEEEEEEccEEEEEEEC
Confidence 4778888899999999985 599999999999998666433
No 44
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.20 E-value=0.045 Score=40.79 Aligned_cols=35 Identities=20% Similarity=0.563 Sum_probs=30.2
Q ss_pred HHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccce
Q 045948 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNL 52 (184)
Q Consensus 16 lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNL 52 (184)
+|+....++.+|+|.|.+ |-.+.|.+.|||+|.=|
T Consensus 11 fLn~~Rk~~i~VtIfLvN--G~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 11 FLNALRKEKIPVTIFLVN--GFKLQGQVESFDNFVVL 45 (77)
T ss_pred HHHHHHhcCCeEEEEEEc--CEEEEEEEEeeeeEEEE
Confidence 677788888999999985 49999999999999643
No 45
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=94.77 E-value=0.049 Score=38.78 Aligned_cols=62 Identities=13% Similarity=0.214 Sum_probs=36.1
Q ss_pred HHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcC---ccceEEceeEEEEecC---c---ceeecCeEEEeCCcEE
Q 045948 16 LIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE---YMNLVLDEAEEVSVKK---K---SRKPLGRILLKGDNIT 81 (184)
Q Consensus 16 lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~---~MNLVLeDa~E~~~dg---~---~~r~LG~v~IRGdNVv 81 (184)
++..++|. +|.|.++ +|..|+|++.+++. -+-++|+-+....... . .......++|+++.|+
T Consensus 6 l~~~lvG~--~V~V~~~--~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLVGQ--TVEVTTK--NGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTTTS--EEEEEET--TS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHhCcCC--EEEEEEC--CCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 45667885 5888887 56999999999999 8999999988762211 1 1233446667766654
No 46
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=93.75 E-value=0.42 Score=36.55 Aligned_cols=67 Identities=19% Similarity=0.349 Sum_probs=51.4
Q ss_pred HHhcCCceEEEEEEeCCCeEEEEEEEEEcC-ccceEEceeEEEEecCc--------ceeecCeEEEeCCcEEEEEecCCC
Q 045948 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDEAEEVSVKKK--------SRKPLGRILLKGDNITLMMNTYVN 89 (184)
Q Consensus 19 k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~-~MNLVLeDa~E~~~dg~--------~~r~LG~v~IRGdNVv~I~~~d~~ 89 (184)
+|+|++ |.+ ..+.+..|+|+|..+|. --.+.|+|+.-+..++. ....++.+..||..|.-+...+..
T Consensus 5 ~~IGs~--ISl--isk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~ 80 (96)
T PF12701_consen 5 PYIGSK--ISL--ISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPP 80 (96)
T ss_dssp CCTTCE--EEE--EETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred cccCCE--EEE--EECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCC
Confidence 578876 555 44567999999999998 78899999877755432 234678999999999998887755
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.52 E-value=0.16 Score=42.63 Aligned_cols=38 Identities=18% Similarity=0.428 Sum_probs=32.7
Q ss_pred HHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 15 NLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
.+|+.+..+|.+|+|.|.+ |-.++|+++|||+|.=+.-
T Consensus 15 ~fLn~~Rk~k~~VtvfL~n--G~rl~G~I~~fD~ftVlL~ 52 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVK--GVKLQGIITWFDNFSILLR 52 (165)
T ss_pred HHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEE
Confidence 4788888899999999985 4999999999999985553
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.41 E-value=0.17 Score=42.48 Aligned_cols=41 Identities=17% Similarity=0.329 Sum_probs=34.0
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEce
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDE 56 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeD 56 (184)
-.+|+.+..+|.+|+|.|.+ |-.++|.++|||+|.=+.-.|
T Consensus 94 d~fLn~~rk~k~~VtvfL~N--G~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 94 DVFLSAVRDSGEPVTMFLVN--GVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHHhcCCcEEEEEec--CcEEEEEEEEEcceEEEEEeC
Confidence 35788888899999999985 599999999999998665433
No 49
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=87.13 E-value=2.8 Score=31.03 Aligned_cols=59 Identities=20% Similarity=0.405 Sum_probs=41.3
Q ss_pred HHhcCCceEEEEEEeCCCeEEEEEEEEEcCccce-EEceeEEEEecCc---------ceeecCeEEEeCCcEE
Q 045948 19 RFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNL-VLDEAEEVSVKKK---------SRKPLGRILLKGDNIT 81 (184)
Q Consensus 19 k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNL-VLeDa~E~~~dg~---------~~r~LG~v~IRGdNVv 81 (184)
++++++ +.+ ..+.+.+|+|+|-.+|..=.. .|+|+..+..+|. ....++.++.||+.|.
T Consensus 3 ~~IG~~--isL--ISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 3 PYIGSK--ISL--ISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred cccCce--EEE--EecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 578876 444 445669999999999987654 4888877755432 2234667888888775
No 50
>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=86.34 E-value=1.7 Score=31.54 Aligned_cols=45 Identities=18% Similarity=0.389 Sum_probs=32.9
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcCc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEY 49 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~~ 49 (184)
||--.++....|-++ .+++++. |.|+++. ++.++++|+|.++|+-
T Consensus 6 SSPGl~RpL~~~~~~-~r~~G~~--v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 6 SSPGAERPLKKEADF-ERAVGKY--VHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred cCCCCCCcCCCHHHH-HHhCCCE--EEEEEEcccCCeEEEEEEEEeEeCC
Confidence 554556677777766 6788865 7777763 3457899999999983
No 51
>PRK14633 hypothetical protein; Provisional
Probab=86.06 E-value=1.6 Score=35.40 Aligned_cols=49 Identities=12% Similarity=0.202 Sum_probs=35.5
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|++ |.|+++. +++++++|+|.++|+- ++.|
T Consensus 75 SSPGldRpL~~~~~f-~r~~G~~--v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 75 SSPGMNRQIFNIIQA-QALVGFN--VKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 454556677777776 6788976 7776654 5779999999999984 4444
No 52
>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=84.55 E-value=4.9 Score=26.33 Aligned_cols=47 Identities=21% Similarity=0.270 Sum_probs=31.8
Q ss_pred hcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEe
Q 045948 21 LQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLK 76 (184)
Q Consensus 21 L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IR 76 (184)
+++ +|.+.. ++..++|+.+|+|+.=.|+++..... ...-.-|.+.+|
T Consensus 2 lG~--~V~v~~---~~~~~~G~~~gId~~G~L~v~~~~g~----~~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQ--EVRVET---GDGEIEGIAEGIDDDGALLVRTEDGS----IRTISSGDVSLR 48 (48)
T ss_dssp TTS--EEEEEE---TSCEEEEEEEEEETTSEEEEEETTEE----EEEESSSEEEEE
T ss_pred CCC--EEEEEE---CCeEEEEEEEEECCCCEEEEEECCCC----EEEEEEEEEEeC
Confidence 454 466765 35788999999999999999875442 122344566554
No 53
>PRK14634 hypothetical protein; Provisional
Probab=84.01 E-value=2.2 Score=34.78 Aligned_cols=49 Identities=14% Similarity=0.236 Sum_probs=35.9
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|++ |.|+++. ++.+.++|+|.++|+- ++.|
T Consensus 81 SSPGldRpL~~~~~f-~r~~G~~--V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 81 SSPGIGDQLSSDRDF-QTFRGFP--VEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCe--EEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 555567788888877 6788976 7787764 3448999999999983 4444
No 54
>PRK14638 hypothetical protein; Provisional
Probab=80.80 E-value=2.8 Score=34.00 Aligned_cols=42 Identities=24% Similarity=0.302 Sum_probs=31.6
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcC
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE 48 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~ 48 (184)
||--.+|+...|-++ .+++|++ |.|+++ +++.++|+|.++|+
T Consensus 81 SSPGldRpL~~~~~f-~r~~G~~--v~V~~~--~~k~~~G~L~~~~~ 122 (150)
T PRK14638 81 SSPGLDRPLRGPKDY-VRFTGKL--AKIVTK--DGKTFIGRIESFVD 122 (150)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCE--EEEEEC--CCcEEEEEEEEEeC
Confidence 444456677777776 5788865 777665 56999999999996
No 55
>PRK14639 hypothetical protein; Provisional
Probab=79.47 E-value=3.4 Score=33.20 Aligned_cols=47 Identities=19% Similarity=0.352 Sum_probs=34.2
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--..|+...|-++ ++++|++ |.|+++ +++.++|+|.++|+ -++.|
T Consensus 69 SSPGl~RpL~~~~~f-~r~~G~~--v~v~l~--~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 69 SSPGLERKLSKIEHF-AKSIGEL--VKITTN--EKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEC--CCcEEEEEEEEEeC-CEEEE
Confidence 444456677777766 6788976 777664 56999999999998 35555
No 56
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.40 E-value=4.1 Score=33.62 Aligned_cols=51 Identities=22% Similarity=0.396 Sum_probs=35.3
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...+-++ .+++|+...|..+...++++.++|+|.++|+-. +++
T Consensus 80 SSPGldRpL~~~~~f-~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 80 SSPGLDRPLKTAEHF-ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred eCCCCCCCcCCHHHH-HHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 454446777777776 678997733333334467789999999999987 443
No 57
>PRK02001 hypothetical protein; Validated
Probab=76.90 E-value=4.4 Score=33.20 Aligned_cols=47 Identities=17% Similarity=0.290 Sum_probs=34.5
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|++ |.|++. +++.++|+|.++|+- ++.|
T Consensus 71 SSPGldRpL~~~~~f-~r~~G~~--v~V~l~--~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 71 GSAGLTSPLKVPRQY-KKNIGRE--LEVLTK--NGKKIEGELKSADEN-DITL 117 (152)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEC--CCCEEEEEEEEEeCC-EEEE
Confidence 454556677777777 6788965 777664 569999999999984 4444
No 58
>PRK14640 hypothetical protein; Provisional
Probab=76.09 E-value=4.7 Score=32.67 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=35.2
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|++ |.|+++. +++++++|+|.++|+- ++.|
T Consensus 78 SSPGl~RpL~~~~~f-~r~~G~~--v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 78 SSPGLDRPLFKVAQF-EKYVGQE--AAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCe--EEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 454556677777777 6788976 7776643 4668999999999984 4444
No 59
>PRK14636 hypothetical protein; Provisional
Probab=76.01 E-value=4.5 Score=33.76 Aligned_cols=44 Identities=23% Similarity=0.381 Sum_probs=32.7
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcC
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDE 48 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~ 48 (184)
||--..|+...|-++ .+++|++ |.|+++. ++.++++|+|.++|+
T Consensus 79 SSPGldRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~v~~ 124 (176)
T PRK14636 79 SSPGIDRPLTRPKDF-ADWAGHE--ARIALSEPLDGRKQFRGELKGIDG 124 (176)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEecccCCeEEEEEEEEEEeC
Confidence 555556777788777 6788966 7777652 345799999999988
No 60
>PRK14632 hypothetical protein; Provisional
Probab=75.96 E-value=5.5 Score=33.07 Aligned_cols=49 Identities=14% Similarity=0.331 Sum_probs=34.6
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe-----CCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE-----QKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~-----~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|+. |.|+++. ++.+.++|+|.++|+- ++.|
T Consensus 79 SSPGldRpL~~~~~f-~r~iG~~--V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 79 SSPGLERPFFRAEQM-SPYVGRQ--IELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 444455666677666 6788865 8888876 2468999999999863 4444
No 61
>PRK14647 hypothetical protein; Provisional
Probab=73.68 E-value=7.2 Score=31.80 Aligned_cols=44 Identities=18% Similarity=0.356 Sum_probs=32.1
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe-------CCCeEEEEEEEEEcC
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE-------QKDLRIEGRIIGFDE 48 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~-------~~Gr~i~G~LvgfD~ 48 (184)
||--..|+...|-++ .+++|++ |.|+++. ++.+.++|+|.++|+
T Consensus 80 SSPG~~RpL~~~~~f-~r~~G~~--v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 80 SSPGLDRPLKKEADY-ERYAGRL--VKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred cCCCCCCcCCCHHHH-HHhCCcE--EEEEEeccccccccCCceEEEEEEEeecC
Confidence 454456677777766 6788865 7777763 145899999999996
No 62
>PRK14643 hypothetical protein; Provisional
Probab=73.52 E-value=5.9 Score=32.72 Aligned_cols=45 Identities=16% Similarity=0.255 Sum_probs=33.5
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEcCc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFDEY 49 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD~~ 49 (184)
||--..|+...|-++ .+++|++ |.|+++. ++.+.++|+|.++|.-
T Consensus 85 SSPGleRpL~~~~df-~r~~G~~--V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 85 SSSGIEKQIRSQEEL-VKALNQW--VYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred cCCCCCCCCCCHHHH-HHhcCCe--EEEEEecccCCceEEEEEEEEEeCC
Confidence 555556677777777 6789976 7777654 3568999999999864
No 63
>PRK14646 hypothetical protein; Provisional
Probab=72.46 E-value=6.4 Score=32.12 Aligned_cols=49 Identities=16% Similarity=0.124 Sum_probs=35.1
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeC--CCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~--~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--..|+...|-++ .+++|++ |.|+++.. +.+.++|+|.++|+- ++.|
T Consensus 81 SSPGldRpL~~~~df-~r~~G~~--v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 81 SSQGVSDELTSERDF-KTFKGFP--VNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred cCCCCCCcCCCHHHH-HHhCCCE--EEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 555556777777777 6789976 77777543 346899999999984 4554
No 64
>PRK14645 hypothetical protein; Provisional
Probab=71.51 E-value=6.9 Score=32.01 Aligned_cols=42 Identities=19% Similarity=0.172 Sum_probs=30.5
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~ 49 (184)
||--.+|+...|-++ .+++|++ |.|+ . ++++++|+|.++|+-
T Consensus 83 SSPGldRpL~~~~df-~r~~G~~--v~v~--~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 83 ESPGPKRPLFTARHF-ERFAGLK--AKVR--G-PGENFTGRIKAVSGD 124 (154)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCE--EEEE--c-CCeEEEEEEEEEeCC
Confidence 454556677777766 5788865 6664 3 579999999999984
No 65
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=68.57 E-value=8.7 Score=30.87 Aligned_cols=44 Identities=16% Similarity=0.400 Sum_probs=31.6
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEE--eCCCeEEEEEEEEEcC
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLF--EQKDLRIEGRIIGFDE 48 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK--~~~Gr~i~G~LvgfD~ 48 (184)
||--..|+...|-++ .+++|+. |.|+++ .++++.++|+|.++|+
T Consensus 79 SSPGi~RpL~~~~~f-~r~~G~~--v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 79 SSPGLDRPLKKARDF-RRFIGRE--VKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCe--EEEEEEcccCCceEEEEEEEEeeC
Confidence 444445666666666 6788866 666654 3567899999999998
No 66
>PRK14631 hypothetical protein; Provisional
Probab=67.73 E-value=9.2 Score=31.94 Aligned_cols=43 Identities=14% Similarity=0.297 Sum_probs=31.6
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFD 47 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD 47 (184)
||--..|+...|-++ .+++|++ |.|+++. ++.+.++|+|.++|
T Consensus 98 SSPGldRpL~~~~df-~r~~G~~--V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 98 SSPGWDRPFFQLEQL-QGYIGQQ--VALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCe--EEEEEecccCCceEEEEEEEEee
Confidence 454556677777766 6788966 7777653 35689999999998
No 67
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=67.32 E-value=27 Score=25.14 Aligned_cols=56 Identities=13% Similarity=0.262 Sum_probs=38.0
Q ss_pred cCc--cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEE
Q 045948 11 TQP--INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMM 84 (184)
Q Consensus 11 ~~P--L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~ 84 (184)
.+| .+.|++++|++ |.|.... ..++|+|++...= .++|+.. -...+||=..|+.|.
T Consensus 8 vdpyvyq~lq~liG~~--vvV~T~~---g~v~G~L~~V~pD-hIvl~~~------------~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 8 VDPYVYQTLQSLIGQR--VVVQTTR---GSVRGILVDVKPD-HIVLEEN------------GTPFFIRIAQIVWVM 65 (66)
T ss_pred cCHHHHHHHHHhcCCE--EEEEEcC---CcEEEEEEeecCC-EEEEEeC------------CcEEEEEeeeEEEEc
Confidence 456 67889999976 8887743 4779999987542 1233322 124788888888774
No 68
>PRK14642 hypothetical protein; Provisional
Probab=67.04 E-value=10 Score=32.54 Aligned_cols=49 Identities=16% Similarity=0.203 Sum_probs=33.9
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeC-----------CCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ-----------KDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~-----------~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--..|....|-++ .++++++ |.|+++.. +.+.++|+|.++|+- ++.|
T Consensus 81 SSPGldRPLk~~~df-~rfiG~~--V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 81 SSPGIDRPLRHEQDF-ERFAGEV--IDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCe--EEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 444455666667666 5788865 77777621 458999999999984 4444
No 69
>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=66.62 E-value=14 Score=26.15 Aligned_cols=31 Identities=13% Similarity=0.295 Sum_probs=23.7
Q ss_pred EEEEEEeCCCeEEEEEEEEEcCccceEEceeEE
Q 045948 27 IQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEE 59 (184)
Q Consensus 27 V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E 59 (184)
|.+ |.-.|.+++|.+.+||.-.+|++=.+.+
T Consensus 9 V~~--kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 9 VSC--RTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred EEE--EecCCceEEEEEEEecCCCcEEEEECcc
Confidence 555 4456799999999999999988655433
No 70
>PRK14635 hypothetical protein; Provisional
Probab=65.42 E-value=12 Score=30.55 Aligned_cols=49 Identities=18% Similarity=0.278 Sum_probs=35.4
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEE---EEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEG---RIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G---~LvgfD~~MNLVL 54 (184)
||--..|+...|-++ .++.|++ |.|+++.++++.+.| +|.++|+- ++.|
T Consensus 80 SSPGldRpL~~~~~~-~r~~G~~--v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 80 SSAGAERKLRLPEDL-DRFRGIP--VRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred cCCCCCCcCCCHHHH-HHhCCCE--EEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 555567777788777 5788865 777776556678888 99999874 4444
No 71
>PRK14641 hypothetical protein; Provisional
Probab=65.26 E-value=12 Score=31.29 Aligned_cols=43 Identities=9% Similarity=0.154 Sum_probs=29.8
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEe--CCCeEEEEEEEEEc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFE--QKDLRIEGRIIGFD 47 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~--~~Gr~i~G~LvgfD 47 (184)
||--..|....|-++ .+++|+. |.|+++. ++.+.++|+|.++|
T Consensus 85 SSPGldRpL~~~~~f-~r~~G~~--V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 85 SSPGLGEPIILPRQY-GRHVGRL--LRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEecccCCeEEEEEEEEeee
Confidence 444445566666666 6788865 7777764 34568999999995
No 72
>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=64.74 E-value=31 Score=25.83 Aligned_cols=62 Identities=11% Similarity=0.168 Sum_probs=40.0
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCcc-ceEEceeEEEEecCcceeecCeEEEeCCcEEEEEe
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYM-NLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMN 85 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~M-NLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~ 85 (184)
|..+..+.++ +|.+.+..+ .+..|+..|+|..- |+..+|- ++ .-...+..++|.+-|+.+..
T Consensus 16 Lr~l~~~~gk--~v~f~l~e~--t~V~a~F~a~d~~~~~f~Vs~L-~T-----PlGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 16 LRSLLAMVGK--PVEFTLHEN--TTVSARFGACDIDVSNFQVSNL-QT-----PLGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHCTTS--EEEEEEGGG---EEEEEEEEE-TTS-EEEEEEE-ET-----TTTEEEEEEEEGGGEEEEEE
T ss_pred HHHHHHhcCC--ceEEEEeCC--eEEEEEEEEecCchheEEhhhc-CC-----CcccChhheeecCCEEEEEe
Confidence 4455555554 688888754 89999999999764 4433331 21 11234578999999998875
No 73
>PRK14637 hypothetical protein; Provisional
Probab=63.44 E-value=14 Score=30.17 Aligned_cols=48 Identities=23% Similarity=0.396 Sum_probs=31.5
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEE
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVL 54 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVL 54 (184)
||--.+|+...|-++ .+++|++ |.|++. +.++.++|+|.++|+- ++.|
T Consensus 79 SSPGldRpL~~~~~f-~r~~G~~--V~V~l~-~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 79 SSPGIERVIKNAAEF-SIFVGET--VKVWFE-CTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred eCCCCCCCCCCHHHH-HHhCCCE--EEEEEC-CCCcEEEEEEEEEeCC-EEEE
Confidence 444556677777766 6788866 777662 2334448999999984 4444
No 74
>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=59.05 E-value=9.8 Score=29.89 Aligned_cols=39 Identities=26% Similarity=0.478 Sum_probs=24.5
Q ss_pred cceecCccHHHHHHhcCCceEEEEEE--eCCCeEEEEEEEEEcC
Q 045948 7 QRIMTQPINLIFRFLQSKARIQIWLF--EQKDLRIEGRIIGFDE 48 (184)
Q Consensus 7 ~~~m~~PL~lL~k~L~Kr~~V~V~LK--~~~Gr~i~G~LvgfD~ 48 (184)
+|+...|-++ .+++|++ |.|+++ .++.++++|+|.++|+
T Consensus 73 ~r~L~~~~~~-~~~iG~~--v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 73 DRPLKSPRDF-ERFIGRK--VKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp SS--SSHHHH-HHH-SEE--EEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCcCCCHHHH-HHhcCCe--EEEEEeccCCCcEEEEEEEEEEeC
Confidence 4455555544 7899965 777763 2345789999999999
No 75
>PRK14644 hypothetical protein; Provisional
Probab=52.43 E-value=20 Score=28.75 Aligned_cols=49 Identities=14% Similarity=0.142 Sum_probs=31.4
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeC--CCeEEEEEEEEEcCccceEEc
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQ--KDLRIEGRIIGFDEYMNLVLD 55 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~--~Gr~i~G~LvgfD~~MNLVLe 55 (184)
||--..|+...+ + ..+++|++ |.|+++.. +.+.++|+|.++|+- ++.|+
T Consensus 67 SSPGldRpL~~~-~-f~r~~G~~--v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 67 SSPGFDMDYETD-E-LENHIGEI--IDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred ECCCCCCCCCHH-H-HHHhCCCe--EEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 444444554443 3 57888866 77776543 337899999999983 34443
No 76
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=49.64 E-value=17 Score=24.37 Aligned_cols=22 Identities=23% Similarity=0.613 Sum_probs=15.0
Q ss_pred EEEEEEEEcCccceEEceeEEE
Q 045948 39 IEGRIIGFDEYMNLVLDEAEEV 60 (184)
Q Consensus 39 i~G~LvgfD~~MNLVLeDa~E~ 60 (184)
.+|+..|+|+.+.|.|++....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 4999999999999999987654
No 77
>PRK06955 biotin--protein ligase; Provisional
Probab=42.72 E-value=76 Score=28.04 Aligned_cols=30 Identities=23% Similarity=0.246 Sum_probs=23.2
Q ss_pred ceEEEEEEeCCCeEEEEEEEEEcCccceEEce
Q 045948 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDE 56 (184)
Q Consensus 25 ~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeD 56 (184)
++|.+.. ++++.++|+.+|+|+.=.|++++
T Consensus 250 ~~V~v~~--~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 250 REVVLLE--DGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred CeEEEEE--CCCcEEEEEEeeECCCceEEEEe
Confidence 4566642 34577999999999999999864
No 78
>PRK14630 hypothetical protein; Provisional
Probab=41.64 E-value=38 Score=27.27 Aligned_cols=41 Identities=20% Similarity=0.168 Sum_probs=29.3
Q ss_pred CcccccceecCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcC
Q 045948 2 ASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDE 48 (184)
Q Consensus 2 s~~~~~~~m~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~ 48 (184)
||--..|+...|-++ .+++|++ |.|+++. ...+|+|.++|+
T Consensus 78 SSPGldRpL~~~~df-~r~~G~~--v~V~l~~---~~~~G~L~~~~d 118 (143)
T PRK14630 78 STPGINRKIKSDREF-KIFEGKK--IKLMLDN---DFEEGFILEAKA 118 (143)
T ss_pred eCCCCCCcCCCHHHH-HHhCCCE--EEEEEcC---cceEEEEEEEeC
Confidence 454456677777777 6788976 7776643 456999999988
No 79
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=36.83 E-value=42 Score=28.16 Aligned_cols=66 Identities=12% Similarity=0.237 Sum_probs=42.4
Q ss_pred cCccHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCc-cceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCCC
Q 045948 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY-MNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYVN 89 (184)
Q Consensus 11 ~~PL~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~-MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~~ 89 (184)
..|+.+ ..|++|. |.|.+. + +++.|.|-.+|.= -|+||-+-.| ++ .. ..-+|=|..|..|...++.
T Consensus 7 ~~p~~~-~~yv~K~--VkV~~~--d-~~~~G~v~TiDPVS~siVL~~~~e---~~--~~--sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 7 KSPLEW-QDYVGKE--VKVTLS--D-KEYKGWVYTIDPVSASIVLVNFQE---DG--KR--SVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp S-HHHH-HCTTT-E--EEEEET--T-EEEEEEEEEE-TTT--EEEEEE-T---TS---E--EEEEE-GGGEEEEEEEE--
T ss_pred CCHHHH-HHhhCcE--EEEEEe--c-cEEEEEEEEeCCCCCeEEEEEccc---CC--ce--eEEEEEccceEEEEEccCC
Confidence 468876 6899976 777664 5 9999999999985 4777775433 12 22 3478889999999988754
No 80
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=34.88 E-value=93 Score=30.51 Aligned_cols=30 Identities=20% Similarity=0.290 Sum_probs=23.1
Q ss_pred ceEEEEEEeCCCeEEEEEEEEEcCccceEEce
Q 045948 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDE 56 (184)
Q Consensus 25 ~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeD 56 (184)
++|.+. ..+++.++|+.+|+|+.=.|+|++
T Consensus 279 k~V~v~--~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 279 KAVLLL--RDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CeEEEE--eCCCcEEEEEEEEECCCCEEEEEE
Confidence 356653 234567999999999999999974
No 81
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=34.76 E-value=34 Score=25.83 Aligned_cols=79 Identities=9% Similarity=0.179 Sum_probs=49.8
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeCCcEEEEEecCCCcccc
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKGDNITLMMNTYVNSFSF 93 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRGdNVv~I~~~d~~~~~~ 93 (184)
..+|+...+++.+|+|. .++|..+.=.|.++|.-=|.+.=|.-- + ......+..++.+.++...++.++.|
T Consensus 11 ~~~Lr~L~~~~~~l~v~--~~~g~~f~T~iL~VD~~~~~l~lD~~~---~----~~~n~~~l~a~~~~~~a~~~gVkI~F 81 (108)
T PF07317_consen 11 LAVLRDLAKQRSPLTVR--HPRGQSFITSILAVDPDRGTLVLDEGS---D----EEENQRLLNAEELTFVAELDGVKIQF 81 (108)
T ss_dssp HHHHHHHHHTT--EEEE--TT-SSEEEE-EEEEETTTTEEEEE--B---S----GGGHHHHHTT--EEEEEEETTEEEEE
T ss_pred HHHHHHHHhCCCeEEEE--eCCCCEEEEEEEEEeCCCCEEEEEcCC---C----hHHHHHHhcCCcEEEEEEeCCeEEEE
Confidence 35788888888777776 466777999999999988776655311 1 11233566788888888888888888
Q ss_pred ccCCCccc
Q 045948 94 SLSPPLIT 101 (184)
Q Consensus 94 s~~~P~i~ 101 (184)
....+-..
T Consensus 82 ~~~~~~~~ 89 (108)
T PF07317_consen 82 TLGQLRLV 89 (108)
T ss_dssp EE-S-EEE
T ss_pred EcCCcEEE
Confidence 77665443
No 82
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=34.75 E-value=1.6e+02 Score=20.64 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=31.2
Q ss_pred HHHHHHhcCCceEEEEEEeCCC--eEEEEEEEEEcCccceEEc
Q 045948 15 NLIFRFLQSKARIQIWLFEQKD--LRIEGRIIGFDEYMNLVLD 55 (184)
Q Consensus 15 ~lL~k~L~Kr~~V~V~LK~~~G--r~i~G~LvgfD~~MNLVLe 55 (184)
..|..++..+.+|+|..-. +| ..++|++..+|..-+.+.-
T Consensus 33 ~~l~~a~~~~~~v~ity~~-~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 33 EKLSEAYQENQPVTITYYE-DGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HHHHHHhcCCCEEEEEEEE-CCeeEEEEEEEEEEcCCCCEEEE
Confidence 3566777777899998876 45 4799999999999887653
No 83
>cd07684 F-BAR_srGAP3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP3, also called MEGAP (MEntal disorder associated GTPase-Activating Protein), is a Rho GAP with activity towards Rac1 and Cdc42. It impacts cell migration by regulating actin and microtubule cytoskeletal dynamics. The association between srGAP3 haploinsufficiency and mental retardation is under debate. srGAP3 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers wit
Probab=30.82 E-value=18 Score=32.40 Aligned_cols=12 Identities=50% Similarity=1.179 Sum_probs=9.6
Q ss_pred HHHHhcccccce
Q 045948 156 VLLACDLGYHAA 167 (184)
Q Consensus 156 ~~~~~~~~~~~~ 167 (184)
.+=+||+|||++
T Consensus 240 l~~c~DlG~h~~ 251 (253)
T cd07684 240 LIDCCDLGFHAS 251 (253)
T ss_pred HHHHHhccchhh
Confidence 445799999986
No 84
>cd07683 F-BAR_srGAP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP1, also called Rho GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and RhoA-specific GAP and is expressed later in the development of CNS (central nervous system) tissues. It is an important downstream signaling molecule of Robo1. srGAP1 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-cha
Probab=30.76 E-value=18 Score=32.32 Aligned_cols=12 Identities=58% Similarity=1.254 Sum_probs=9.5
Q ss_pred HHHHhcccccce
Q 045948 156 VLLACDLGYHAA 167 (184)
Q Consensus 156 ~~~~~~~~~~~~ 167 (184)
.+=+||+|||++
T Consensus 240 Lidc~DlG~h~~ 251 (253)
T cd07683 240 LIDCCDLGYHAS 251 (253)
T ss_pred HHHHHhccchhc
Confidence 345799999986
No 85
>cd07682 F-BAR_srGAP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP2 is expressed in zones of neuronal differentiation. It plays a role in the regeneration of neurons and axons. srGAP2 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=30.43 E-value=19 Score=32.40 Aligned_cols=11 Identities=64% Similarity=1.313 Sum_probs=8.9
Q ss_pred HHHhcccccce
Q 045948 157 LLACDLGYHAA 167 (184)
Q Consensus 157 ~~~~~~~~~~~ 167 (184)
+=.||+|||++
T Consensus 251 iDC~DlGfh~s 261 (263)
T cd07682 251 IDCCDLGYHAS 261 (263)
T ss_pred HHHHhccchhc
Confidence 34799999986
No 86
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=30.07 E-value=1.5e+02 Score=25.97 Aligned_cols=45 Identities=24% Similarity=0.341 Sum_probs=29.8
Q ss_pred ceEEEEEEeCCCeEEEEEEEEEcCccceEEceeEEEEecCcceeecCeEEEeC
Q 045948 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDEAEEVSVKKKSRKPLGRILLKG 77 (184)
Q Consensus 25 ~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLeDa~E~~~dg~~~r~LG~v~IRG 77 (184)
++|.+.. ++..++|++.|+|+.=.|++++.- +.+.-..|.+.+|+
T Consensus 273 ~~v~~~~---~~~~~~G~~~gi~~~G~L~i~~~g-----~~~~~~~gev~~~~ 317 (319)
T PRK11886 273 REVKLII---GDKEISGIARGIDEQGALLLEDDG-----VEKPFNGGEISLRS 317 (319)
T ss_pred CeEEEEe---CCcEEEEEEEEECCCceEEEEeCC-----cEEEEEEeEEEEec
Confidence 4577753 346799999999999999996211 11233456666664
No 87
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.73 E-value=1.4e+02 Score=28.12 Aligned_cols=66 Identities=20% Similarity=0.298 Sum_probs=45.0
Q ss_pred HHHhcCCceEEEEEEeCCCeEEEEEEEEEcC-ccceEEceeEEEEecCc---------ceeecCeEEEeCCcEEEEEecC
Q 045948 18 FRFLQSKARIQIWLFEQKDLRIEGRIIGFDE-YMNLVLDEAEEVSVKKK---------SRKPLGRILLKGDNITLMMNTY 87 (184)
Q Consensus 18 ~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~-~MNLVLeDa~E~~~dg~---------~~r~LG~v~IRGdNVv~I~~~d 87 (184)
..||+++ |.+.- +.+.+|+|+|--+|- =--|-|++|--+..+++ ....+..++.||+.|.-+...+
T Consensus 5 t~yIGS~--ISLIS--k~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSF--ISLIS--KNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccce--eEEee--cccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 4688987 55554 456999999987763 34566777644433321 1227889999999999776655
No 88
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=23.32 E-value=3.8e+02 Score=22.54 Aligned_cols=28 Identities=25% Similarity=0.313 Sum_probs=22.4
Q ss_pred ceEEEEEEeCCCeEEEEEEEEEcCccceEEc
Q 045948 25 ARIQIWLFEQKDLRIEGRIIGFDEYMNLVLD 55 (184)
Q Consensus 25 ~~V~V~LK~~~Gr~i~G~LvgfD~~MNLVLe 55 (184)
++|++.. ++..++|+..|+|+.=.|+++
T Consensus 194 ~~V~v~~---~~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 194 REVSLTT---GNGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred CeEEEEe---CCcEEEEEEEeECCCceEEEE
Confidence 4577753 346799999999999999997
No 89
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=21.38 E-value=1.3e+02 Score=25.62 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=24.4
Q ss_pred cHHHHHHhcCCceEEEEEEeCCCeEEEEEEEEEcCc
Q 045948 14 INLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEY 49 (184)
Q Consensus 14 L~lL~k~L~Kr~~V~V~LK~~~Gr~i~G~LvgfD~~ 49 (184)
+++|-.+-+.--++.-.+.. ++..|+|+++++|+=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t-~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIET-KDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEe-CCceEEEEEEeccCC
Confidence 45665555544556666665 468999999999874
Done!