Query psy10177
Match_columns 116
No_of_seqs 176 out of 1145
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 19:45:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10177.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10177hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1782|consensus 100.0 2.4E-34 5.2E-39 206.4 3.3 106 1-108 23-128 (129)
2 cd01728 LSm1 The eukaryotic Sm 99.8 1.3E-20 2.9E-25 125.1 7.8 59 1-59 16-74 (74)
3 cd01729 LSm7 The eukaryotic Sm 99.8 3E-20 6.6E-25 125.0 7.6 60 1-60 16-80 (81)
4 cd01727 LSm8 The eukaryotic Sm 99.8 7.6E-20 1.6E-24 120.7 8.0 60 2-61 14-74 (74)
5 cd01732 LSm5 The eukaryotic Sm 99.8 5.9E-19 1.3E-23 117.7 7.7 59 1-59 17-75 (76)
6 cd01730 LSm3 The eukaryotic Sm 99.8 5.6E-19 1.2E-23 118.7 7.3 58 1-58 15-82 (82)
7 cd01719 Sm_G The eukaryotic Sm 99.8 1E-18 2.2E-23 115.2 7.2 58 1-61 14-71 (72)
8 cd01717 Sm_B The eukaryotic Sm 99.8 3.5E-18 7.6E-23 113.9 7.3 57 1-57 14-77 (79)
9 cd01731 archaeal_Sm1 The archa 99.7 6E-18 1.3E-22 109.7 7.1 55 1-58 14-68 (68)
10 cd01718 Sm_E The eukaryotic Sm 99.7 2E-17 4.4E-22 111.4 7.4 55 2-58 23-79 (79)
11 cd01720 Sm_D2 The eukaryotic S 99.7 3.3E-17 7.1E-22 112.0 7.5 58 1-58 18-85 (87)
12 PRK00737 small nuclear ribonuc 99.7 3.3E-17 7.1E-22 107.7 6.8 55 1-58 18-72 (72)
13 KOG1784|consensus 99.7 3.6E-18 7.7E-23 117.6 1.8 76 2-77 15-91 (96)
14 cd06168 LSm9 The eukaryotic Sm 99.7 3.2E-16 6.9E-21 104.3 7.7 57 1-57 14-73 (75)
15 COG1958 LSM1 Small nuclear rib 99.7 3E-16 6.5E-21 104.3 7.3 58 1-58 21-79 (79)
16 PTZ00138 small nuclear ribonuc 99.7 3.9E-16 8.4E-21 107.3 7.7 56 2-59 31-88 (89)
17 smart00651 Sm snRNP Sm protein 99.6 7.6E-16 1.6E-20 98.2 7.5 56 1-58 12-67 (67)
18 cd01722 Sm_F The eukaryotic Sm 99.6 8.9E-16 1.9E-20 99.8 6.7 53 1-56 15-67 (68)
19 cd01726 LSm6 The eukaryotic Sm 99.6 1E-15 2.2E-20 99.1 7.0 54 1-57 14-67 (67)
20 PF01423 LSM: LSM domain ; In 99.6 1.5E-15 3.2E-20 97.1 7.1 55 2-58 13-67 (67)
21 cd00600 Sm_like The eukaryotic 99.6 1.8E-14 3.9E-19 90.6 7.7 53 1-56 10-62 (63)
22 KOG1780|consensus 99.6 3.8E-15 8.2E-20 99.2 4.4 58 1-61 18-75 (77)
23 cd01721 Sm_D3 The eukaryotic S 99.5 1.7E-13 3.8E-18 89.6 7.3 57 1-60 14-70 (70)
24 cd01723 LSm4 The eukaryotic Sm 99.5 1.6E-13 3.4E-18 91.0 6.7 58 1-60 15-72 (76)
25 cd01724 Sm_D1 The eukaryotic S 99.4 9.1E-13 2E-17 90.3 7.5 59 1-62 15-73 (90)
26 KOG1781|consensus 99.4 6E-14 1.3E-18 98.0 -1.3 70 2-71 32-106 (108)
27 cd01733 LSm10 The eukaryotic S 99.3 3.2E-12 6.8E-17 85.5 6.7 54 1-57 23-76 (78)
28 cd01725 LSm2 The eukaryotic Sm 99.3 6.1E-12 1.3E-16 84.5 7.1 62 1-63 15-76 (81)
29 KOG3460|consensus 99.2 1.1E-12 2.5E-17 89.2 0.4 59 2-60 20-88 (91)
30 KOG3482|consensus 99.2 1E-11 2.2E-16 82.7 4.5 57 1-60 22-78 (79)
31 KOG1775|consensus 99.2 1.4E-11 3E-16 82.8 2.5 59 2-60 22-80 (84)
32 KOG3168|consensus 99.2 2.1E-12 4.5E-17 97.5 -1.8 60 2-61 19-85 (177)
33 KOG1774|consensus 99.0 3.6E-10 7.7E-15 76.8 2.8 52 7-60 36-87 (88)
34 KOG1783|consensus 98.7 2.1E-09 4.5E-14 71.6 -1.0 56 1-59 20-75 (77)
35 KOG3459|consensus 98.2 1.2E-07 2.5E-12 67.6 -2.0 60 1-60 40-109 (114)
36 KOG3448|consensus 97.9 3.9E-05 8.4E-10 53.1 5.8 55 2-58 17-72 (96)
37 KOG3293|consensus 97.7 4.4E-05 9.5E-10 55.6 3.7 58 1-60 16-73 (134)
38 cd01739 LSm11_C The eukaryotic 97.2 0.00018 3.9E-09 47.1 1.5 25 9-33 24-48 (66)
39 KOG3428|consensus 96.8 0.0057 1.2E-07 43.6 6.7 68 2-78 17-84 (109)
40 KOG3172|consensus 96.6 0.01 2.2E-07 42.5 6.3 59 2-63 20-78 (119)
41 PF14438 SM-ATX: Ataxin 2 SM d 95.5 0.022 4.8E-07 37.1 3.6 53 2-54 17-76 (77)
42 cd01716 Hfq Hfq, an abundant, 90.6 0.48 1E-05 30.5 3.8 27 2-28 16-42 (61)
43 TIGR02383 Hfq RNA chaperone Hf 89.8 0.61 1.3E-05 30.1 3.7 26 2-27 20-45 (61)
44 PRK00395 hfq RNA-binding prote 88.4 0.84 1.8E-05 30.9 3.8 27 2-28 24-50 (79)
45 COG1923 Hfq Uncharacterized ho 81.7 2 4.4E-05 28.9 3.2 26 2-27 24-49 (77)
46 PF02237 BPL_C: Biotin protein 80.7 7.6 0.00016 23.0 5.2 25 6-30 11-35 (48)
47 PF11095 Gemin7: Gem-associate 70.5 25 0.00054 23.7 6.1 48 2-57 29-77 (80)
48 PRK14091 RNA-binding protein H 70.4 6.9 0.00015 29.9 3.7 27 2-28 109-135 (165)
49 PRK14091 RNA-binding protein H 68.3 8 0.00017 29.5 3.7 27 2-28 29-55 (165)
50 PF12701 LSM14: Scd6-like Sm d 66.9 36 0.00079 23.5 6.5 63 2-64 13-82 (96)
51 KOG3382|consensus 61.1 4.4 9.6E-05 30.2 1.1 21 8-28 43-63 (151)
52 PF03614 Flag1_repress: Repres 56.9 15 0.00032 28.0 3.3 28 2-29 34-61 (165)
53 cd01736 LSm14_N LSm14 (also kn 56.6 54 0.0012 21.9 5.6 52 3-54 12-71 (74)
54 cd01735 LSm12_N LSm12 belongs 54.6 27 0.00059 22.3 3.8 27 2-28 11-37 (61)
55 PF03122 Herpes_MCP: Herpes vi 51.7 4.9 0.00011 39.2 0.0 51 4-55 254-304 (1354)
56 PF05071 NDUFA12: NADH ubiquin 51.7 6.4 0.00014 27.3 0.6 17 12-28 1-17 (105)
57 PRK10942 serine endoprotease; 50.2 50 0.0011 28.4 5.9 26 2-27 140-165 (473)
58 PRK10139 serine endoprotease; 49.5 59 0.0013 27.9 6.2 26 2-27 119-144 (455)
59 PRK14638 hypothetical protein; 44.1 40 0.00087 24.8 3.9 24 2-26 105-128 (150)
60 PF14563 DUF4444: Domain of un 41.4 37 0.00081 20.4 2.7 21 10-30 10-30 (42)
61 TIGR02603 CxxCH_TIGR02603 puta 37.6 34 0.00073 24.2 2.5 18 1-18 61-78 (133)
62 PRK14639 hypothetical protein; 35.6 66 0.0014 23.4 3.9 23 2-25 93-115 (140)
63 TIGR02037 degP_htrA_DO peripla 34.5 1.3E+02 0.0029 25.1 6.0 27 2-28 86-112 (428)
64 PRK06630 hypothetical protein; 32.2 24 0.00053 24.8 1.0 19 10-28 11-29 (99)
65 TIGR02038 protease_degS peripl 31.7 73 0.0016 26.1 3.9 27 2-28 106-132 (351)
66 PRK02001 hypothetical protein; 31.3 62 0.0013 24.0 3.2 23 2-25 95-117 (152)
67 KOG3819|consensus 31.1 1E+02 0.0022 27.4 4.8 38 66-103 33-71 (513)
68 PF06372 Gemin6: Gemin6 protei 30.8 1.2E+02 0.0026 23.0 4.7 50 2-61 22-72 (166)
69 PRK10898 serine endoprotease; 30.3 82 0.0018 26.0 4.0 27 2-28 106-132 (353)
70 PLN02732 Probable NADH dehydro 29.8 42 0.00092 25.4 2.1 17 12-28 49-65 (159)
71 PLN03095 NADH:ubiquinone oxido 26.2 37 0.0008 24.4 1.2 18 11-28 9-26 (115)
72 cd01734 YlxS_C YxlS is a Bacil 25.1 1.4E+02 0.0029 19.4 3.7 19 6-25 37-56 (83)
73 PF01887 SAM_adeno_trans: S-ad 24.7 1E+02 0.0022 24.6 3.5 21 9-29 169-189 (258)
74 PF10894 DUF2689: Protein of u 24.3 12 0.00026 24.0 -1.5 19 17-35 20-38 (61)
75 PF11831 Myb_Cef: pre-mRNA spl 23.2 3.1E+02 0.0067 21.5 5.9 42 70-111 100-141 (231)
76 COG0602 NrdG Organic radical a 22.0 2E+02 0.0044 22.1 4.6 61 21-83 2-67 (212)
77 PRK08183 NADH dehydrogenase; V 20.4 53 0.0011 24.1 1.0 18 11-28 25-42 (133)
No 1
>KOG1782|consensus
Probab=100.00 E-value=2.4e-34 Score=206.36 Aligned_cols=106 Identities=60% Similarity=0.913 Sum_probs=101.7
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCccccCCCCcccCHHHHHHH
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNA 80 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~v~~~~~~~~ 80 (116)
+|.|||||+++|+|+|||||+|+||++|+||++.++.|+++++|+|+|||+||+++|++|.++| +.|++++|+++++..
T Consensus 23 lVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE-~~~l~~i~~~e~~~~ 101 (129)
T KOG1782|consen 23 LVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE-EEPLEQISFEEALNE 101 (129)
T ss_pred EEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh-hccceeCCHHHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999999999 799999999999999
Q ss_pred HHHHHHHHHHHhHHHHHHHHHcCCCCCC
Q psy10177 81 QRKEQEVKQERSRMLAKRLKERGLSFVP 108 (116)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~l~~~g~~~~~ 108 (116)
++.+++++++.+..|. .|+++|++.+.
T Consensus 102 ~~~~q~~k~e~~~lkg-~m~~rg~~~D~ 128 (129)
T KOG1782|consen 102 IKREQEAKKEEERLKG-TMAERGEFLDF 128 (129)
T ss_pred HHHHHHHhhhHHHHHH-HHHHhcccccC
Confidence 9999999999999888 99999999854
No 2
>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=99.83 E-value=1.3e-20 Score=125.10 Aligned_cols=59 Identities=80% Similarity=1.289 Sum_probs=54.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeec
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~i 59 (116)
.|+|+|||+|.|+|+|||+||||+|++|.|+++.++.+.++++|.++|||+||++||++
T Consensus 16 ~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 16 VVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred EEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 47899999999999999999999999999998876666778999999999999999975
No 3
>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=99.82 E-value=3e-20 Score=124.97 Aligned_cols=60 Identities=35% Similarity=0.542 Sum_probs=52.6
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcc-----cceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQ-----YGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~-----~~~~~~G~~lIRG~nVv~ig~id 60 (116)
.|+|+|||+|.|+|+|||+||||||++|+|+++.++. ...+.+|.++|||+||++|++.+
T Consensus 16 ~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 16 RVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred EEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 3789999999999999999999999999999875321 24578999999999999999876
No 4
>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=99.81 E-value=7.6e-20 Score=120.69 Aligned_cols=60 Identities=37% Similarity=0.723 Sum_probs=53.5
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcC-cccceeecceEEEeeccEEEEeecCC
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVG-NQYGDIPRGIFIIRGENVVLMGEVDK 61 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~-~~~~~~~~G~~lIRG~nVv~ig~id~ 61 (116)
|+|+|||.+.|+|+|||+|||+||++|+|++... +....+.+|.+++||+||++|+++|.
T Consensus 14 V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 14 VITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred EEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 7899999999999999999999999999987643 23456789999999999999999884
No 5
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=5.9e-19 Score=117.68 Aligned_cols=59 Identities=15% Similarity=0.300 Sum_probs=51.3
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeec
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~i 59 (116)
+|.|++||++.|+|+|||+||||||++|+|+++..+.-..+.+|.++|||+||++|.+.
T Consensus 17 ~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 17 WIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 37899999999999999999999999999997544332357899999999999999863
No 6
>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=99.78 E-value=5.6e-19 Score=118.66 Aligned_cols=58 Identities=29% Similarity=0.405 Sum_probs=49.9
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcc----------cceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQ----------YGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~----------~~~~~~G~~lIRG~nVv~ig~ 58 (116)
+|.|+|||++.|+|+|||+||||||++|+|++..... ...+.+|.++|||+||++|++
T Consensus 15 ~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 15 YVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred EEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEECC
Confidence 4789999999999999999999999999999865321 135689999999999999864
No 7
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=1e-18 Score=115.21 Aligned_cols=58 Identities=31% Similarity=0.579 Sum_probs=51.5
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDK 61 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~ 61 (116)
+|.|++||++.|+|+|||+||||+|++|+|++. ++ ..+.+|.++|||+||++|+++|.
T Consensus 14 ~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-~~--~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 14 SLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-GG--EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred EEEECCCeEEEEEEEEEcccccEEeccEEEEcc-CC--ceeEeceEEECCCEEEEEEcccc
Confidence 378999999999999999999999999999863 22 35789999999999999999874
No 8
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.75 E-value=3.5e-18 Score=113.87 Aligned_cols=57 Identities=35% Similarity=0.514 Sum_probs=49.7
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCc-------ccceeecceEEEeeccEEEEe
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMG 57 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~-------~~~~~~~G~~lIRG~nVv~ig 57 (116)
.|.|+|||.+.|+|+|||+||||||++|.|+++... ....+.+|.++|||+||++|.
T Consensus 14 ~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 14 RVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred EEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 378999999999999999999999999999875432 134678999999999999986
No 9
>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=99.74 E-value=6e-18 Score=109.66 Aligned_cols=55 Identities=35% Similarity=0.461 Sum_probs=49.0
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~ 58 (116)
.|.|++||.|.|+|+|||+||||+|++|+|++..+ ..+.+|.++|||+||++|++
T Consensus 14 ~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 14 LVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE---PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC---eEeEcCcEEEeCCEEEEEcC
Confidence 37899999999999999999999999999986533 35789999999999999975
No 10
>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=99.72 E-value=2e-17 Score=111.36 Aligned_cols=55 Identities=24% Similarity=0.408 Sum_probs=47.2
Q ss_pred EEec--CCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEee
Q psy10177 2 VLLR--DGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 2 V~Lr--dGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~ 58 (116)
|.++ +||.+.|+|+|||+||||||+||+|++..+. ..+.+|.++|||+||++|++
T Consensus 23 V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 23 IWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred EEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 4454 9999999999999999999999999875332 35689999999999999874
No 11
>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=99.71 E-value=3.3e-17 Score=111.98 Aligned_cols=58 Identities=22% Similarity=0.369 Sum_probs=49.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcc----------cceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQ----------YGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~----------~~~~~~G~~lIRG~nVv~ig~ 58 (116)
+|.|++||.+.|+|+|||+||||||+||.|.+...++ ...+.+|.++|||+||++|++
T Consensus 18 ~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is~ 85 (87)
T cd01720 18 LINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVLR 85 (87)
T ss_pred EEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEec
Confidence 4889999999999999999999999999997654321 134578999999999999975
No 12
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.71 E-value=3.3e-17 Score=107.70 Aligned_cols=55 Identities=36% Similarity=0.487 Sum_probs=47.7
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~ 58 (116)
.|.|+||+.|.|+|+|||+|||++|++|.|... +. ..+.+|.++|||+||++|.+
T Consensus 18 ~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 18 LVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-GE--VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-CC--eEeEcCcEEEeCCEEEEEcC
Confidence 378999999999999999999999999999642 22 34689999999999999864
No 13
>KOG1784|consensus
Probab=99.70 E-value=3.6e-18 Score=117.58 Aligned_cols=76 Identities=37% Similarity=0.663 Sum_probs=67.9
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCc-ccceeecceEEEeeccEEEEeecCCccccCCCCcccCHHHH
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN-QYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDI 77 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~-~~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~v~~~~~ 77 (116)
|++.|||.++|.|+||||-.||+|+++.||++... ..+..++|+++|||+||.+||++|++++....|+++..+++
T Consensus 15 vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld~tkir~epl 91 (96)
T KOG1784|consen 15 VITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLDLTKIRAEPL 91 (96)
T ss_pred EEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhhhhhcccCCC
Confidence 67899999999999999999999999999998654 35678999999999999999999999988888888776654
No 14
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.66 E-value=3.2e-16 Score=104.34 Aligned_cols=57 Identities=25% Similarity=0.369 Sum_probs=50.2
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCc---ccceeecceEEEeeccEEEEe
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN---QYGDIPRGIFIIRGENVVLMG 57 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~---~~~~~~~G~~lIRG~nVv~ig 57 (116)
.|+|+|||.|.|+|.|||+||||||++|.|++.... ....+.+|+++|||++|++|.
T Consensus 14 ~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 14 RIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred EEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 378999999999999999999999999999876432 235689999999999999986
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.66 E-value=3e-16 Score=104.34 Aligned_cols=58 Identities=36% Similarity=0.515 Sum_probs=47.6
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCccc-ceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQY-GDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~-~~~~~G~~lIRG~nVv~ig~ 58 (116)
.|.|++|++|.|+|+|||+||||+|++|.|+...+... ..+..|.++|||+||++|++
T Consensus 21 ~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 21 LVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 37899999999999999999999999999987522222 23345599999999999874
No 16
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.66 E-value=3.9e-16 Score=107.26 Aligned_cols=56 Identities=23% Similarity=0.386 Sum_probs=47.3
Q ss_pred EEecC--CcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeec
Q psy10177 2 VLLRD--GRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59 (116)
Q Consensus 2 V~Lrd--GR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~i 59 (116)
|.+.| +|.+.|+|+|||+||||||+||+|.+..+. ..+.+|.++|||+||++|++.
T Consensus 31 i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 31 IWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred EEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEcC
Confidence 45556 599999999999999999999999764332 356899999999999999875
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.64 E-value=7.6e-16 Score=98.24 Aligned_cols=56 Identities=38% Similarity=0.564 Sum_probs=49.3
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEee
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~ 58 (116)
.|.|+||+.+.|+|.|||+|||++|++|.|....+ ...+.+|.++|||+||++|++
T Consensus 12 ~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~--~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 12 LVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEECCCcEEEEEEEEECccccEEEccEEEEecCC--cEEeEeCCEEEcCCEEEEEeC
Confidence 37899999999999999999999999999986542 246789999999999999874
No 18
>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=99.63 E-value=8.9e-16 Score=99.76 Aligned_cols=53 Identities=38% Similarity=0.454 Sum_probs=46.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEE
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~i 56 (116)
.|.|+||++|.|+|.|||+|||++|++|.|... ++ ....+|.++|||+||.+|
T Consensus 15 ~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~-~~--~~~~lg~~~IRG~~I~~i 67 (68)
T cd01722 15 IVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-GK--STGNLGEVLIRCNNVLYI 67 (68)
T ss_pred EEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-Cc--cccCcCcEEEECCEEEEE
Confidence 378999999999999999999999999998743 22 245789999999999987
No 19
>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=99.63 E-value=1e-15 Score=99.13 Aligned_cols=54 Identities=31% Similarity=0.467 Sum_probs=46.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEe
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 57 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig 57 (116)
.|.|++|++|.|+|+|||+||||+|++|.|... +. ....+|.++|||+||.+|+
T Consensus 14 ~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-~~--~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 14 VVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-GQ--LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred EEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-Cc--eeeEeCCEEEECCEEEEEC
Confidence 378999999999999999999999999988542 22 2457899999999999874
No 20
>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=99.62 E-value=1.5e-15 Score=97.07 Aligned_cols=55 Identities=42% Similarity=0.585 Sum_probs=48.9
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEee
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~ 58 (116)
|.|+||+.+.|+|.+||+|||++|.+|.|....+. ..+++|.++|||+||++|.+
T Consensus 13 V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 13 VELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred EEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence 78999999999999999999999999999764332 46789999999999999974
No 21
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.56 E-value=1.8e-14 Score=90.57 Aligned_cols=53 Identities=42% Similarity=0.578 Sum_probs=47.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEE
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~i 56 (116)
.|.|+||+.|.|+|.+||+|||++|++|.+.... .....+|.++|||++|.+|
T Consensus 10 ~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~---~~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 10 RVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE---GKKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred EEEECCCcEEEEEEEEECCCCCEEECCEEEEecC---CcEEECCeEEEECCEEEEE
Confidence 3789999999999999999999999999997654 2457899999999999987
No 22
>KOG1780|consensus
Probab=99.56 E-value=3.8e-15 Score=99.17 Aligned_cols=58 Identities=33% Similarity=0.631 Sum_probs=50.0
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDK 61 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~ 61 (116)
++.|..||.+.|+|+|||+|||+||++|+|.-..+. ...+|..+|||++|+++..++.
T Consensus 18 ~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 18 VLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred EEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEEeeccc
Confidence 368999999999999999999999999999743332 3578999999999999988764
No 23
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.48 E-value=1.7e-13 Score=89.58 Aligned_cols=57 Identities=21% Similarity=0.181 Sum_probs=47.7
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
.|.|++|.+|.|+|.++|+|||++|++|.+....++ ...+|.++|||+||.++-..|
T Consensus 14 ~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 14 TVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred EEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence 378999999999999999999999999987433332 356899999999999987554
No 24
>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=99.47 E-value=1.6e-13 Score=91.00 Aligned_cols=58 Identities=26% Similarity=0.338 Sum_probs=47.8
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
.|.|++|+.+.|+|.+||+|||++|++|.+.-..++. ....|.++|||+||.++...|
T Consensus 15 ~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 15 LVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred EEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCH
Confidence 3789999999999999999999999999985333332 235689999999999997554
No 25
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.41 E-value=9.1e-13 Score=90.34 Aligned_cols=59 Identities=24% Similarity=0.300 Sum_probs=50.7
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCc
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKE 62 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~ 62 (116)
.|.|++|..|.|+|.++|+|||++|++|.+....+. ...+|.++|||+||.++-..|.-
T Consensus 15 ~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~---~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 15 TIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN---PVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred EEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc---eeEcceEEEeCCEEEEEEcCCcC
Confidence 378999999999999999999999999988643322 45789999999999999988763
No 26
>KOG1781|consensus
Probab=99.35 E-value=6e-14 Score=98.01 Aligned_cols=70 Identities=30% Similarity=0.431 Sum_probs=59.1
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCc-c----cceeecceEEEeeccEEEEeecCCccccCCCCcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN-Q----YGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQ 71 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~-~----~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~ 71 (116)
|++.+||..+|+|+||||.+||||++|+|+...+. . ...+.+|++++||..+++|++-|.-.+...||-+
T Consensus 32 vkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I~npf~~ 106 (108)
T KOG1781|consen 32 VKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEIANPFVQ 106 (108)
T ss_pred EEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhhccchhc
Confidence 78999999999999999999999999999765432 2 1348999999999999999999987776666543
No 27
>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=99.34 E-value=3.2e-12 Score=85.55 Aligned_cols=54 Identities=26% Similarity=0.329 Sum_probs=45.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEe
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 57 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig 57 (116)
.|.|++|..|.|+|.++|+|||++|.+|.+.. .+. ....+|.++|||+||.+|.
T Consensus 23 ~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~--~~~~~~~v~IRG~nI~yI~ 76 (78)
T cd01733 23 TVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNG--KQVQVEEIMVTGRNIRYVH 76 (78)
T ss_pred EEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCC--ceeECCcEEEECCEEEEEE
Confidence 37799999999999999999999999998642 222 2347899999999999885
No 28
>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=99.32 E-value=6.1e-12 Score=84.50 Aligned_cols=62 Identities=24% Similarity=0.192 Sum_probs=49.3
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCcc
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEK 63 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~~ 63 (116)
+|.|++|..+.|+|.++|+|||++|++|.+.. .+.......++.++|||+||.+|...|...
T Consensus 15 ~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~-~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i 76 (81)
T cd01725 15 TVELKNDLSIRGTLHSVDQYLNIKLTNISVTD-PEKYPHMLSVKNCFIRGSVVRYVQLPADEV 76 (81)
T ss_pred EEEECCCcEEEEEEEEECCCcccEEEEEEEEc-CCCcccccccCeEEEECCEEEEEEeChhHc
Confidence 37899999999999999999999999997642 111112345689999999999999877543
No 29
>KOG3460|consensus
Probab=99.25 E-value=1.1e-12 Score=89.23 Aligned_cols=59 Identities=29% Similarity=0.400 Sum_probs=49.9
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCc----------ccceeecceEEEeeccEEEEeecC
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN----------QYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~----------~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
|+||++|++.|+|.+||+|.|+||.++.|.++.-+ +...+.+-.++|||++|+++++.-
T Consensus 20 VKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp~ 88 (91)
T KOG3460|consen 20 VKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPPL 88 (91)
T ss_pred EEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCcc
Confidence 79999999999999999999999999999776411 124556779999999999999753
No 30
>KOG3482|consensus
Probab=99.24 E-value=1e-11 Score=82.74 Aligned_cols=57 Identities=35% Similarity=0.427 Sum_probs=50.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
+|+|++|.+|.|+|.|.|.||||.|.+|.|.+. +. ....+|.++||.+||.+|..++
T Consensus 22 ~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id-G~--~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 22 LVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID-GV--STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred EEEEecCcEEEEEEEEecchhheehhhhhhhhc-cc--ccccceeEEEEeccEEEEecCC
Confidence 488999999999999999999999999999764 22 3468999999999999998765
No 31
>KOG1775|consensus
Probab=99.17 E-value=1.4e-11 Score=82.81 Aligned_cols=59 Identities=17% Similarity=0.329 Sum_probs=50.9
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
|++++.|++.|+|.|||.|.|+||+|++|+-.....-.-.+++.+++.|+||.++.+.-
T Consensus 22 iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 22 IIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred EEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 78999999999999999999999999999765444323458899999999999998765
No 32
>KOG3168|consensus
Probab=99.16 E-value=2.1e-12 Score=97.53 Aligned_cols=60 Identities=35% Similarity=0.487 Sum_probs=50.2
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCc-------ccceeecceEEEeeccEEEEeecCC
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMGEVDK 61 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~-------~~~~~~~G~~lIRG~nVv~ig~id~ 61 (116)
|+++|||.|+|.|..||.||||||++|.|...... ..+.+.+|++++||+||+++.--+.
T Consensus 19 v~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp 85 (177)
T KOG3168|consen 19 VRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP 85 (177)
T ss_pred EEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence 78999999999999999999999999999543321 2356789999999999999875443
No 33
>KOG1774|consensus
Probab=98.97 E-value=3.6e-10 Score=76.76 Aligned_cols=52 Identities=25% Similarity=0.473 Sum_probs=42.7
Q ss_pred CcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 7 GRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 7 GR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
|-.+.|..+|||.|||+||++|+|. +.++. ...++|.+++.|+||.+|-..+
T Consensus 36 ~~rieG~IvGFDEyMNvVlD~aeev-~~k~~-~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 36 GLRIEGRIVGFDEYMNLVLDDAEEV-HSKTK-SRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred CcEEeEEEechHHhhhhhhcchhhc-ccccc-CCCccccEEEcCCcEEEEeecC
Confidence 5678999999999999999999995 33332 2348999999999999997653
No 34
>KOG1783|consensus
Probab=98.68 E-value=2.1e-09 Score=71.65 Aligned_cols=56 Identities=30% Similarity=0.392 Sum_probs=48.0
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeec
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~i 59 (116)
.|+|.+|-.|.|+|.+.|.|||+-|+.|.|... .+ .....|-.+|||+||.+|+..
T Consensus 20 ~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n--gq-l~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 20 VVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN--GQ-LKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred EEEecCCccccceehhhhhHHHHHHHHHHHHhc--Cc-ccccccceeeccccEEEEEec
Confidence 378999999999999999999999999998642 22 245788999999999999864
No 35
>KOG3459|consensus
Probab=98.20 E-value=1.2e-07 Score=67.58 Aligned_cols=60 Identities=22% Similarity=0.312 Sum_probs=50.6
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCc------c----cceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN------Q----YGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~------~----~~~~~~G~~lIRG~nVv~ig~id 60 (116)
+|.+||++++.|..++||-|.|++|+++.|.+..-. . ..++.+|.++|||++|+++....
T Consensus 40 Li~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 40 LINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred EEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEecc
Confidence 578999999999999999999999999999765421 1 23789999999999999987543
No 36
>KOG3448|consensus
Probab=97.89 E-value=3.9e-05 Score=53.05 Aligned_cols=55 Identities=29% Similarity=0.364 Sum_probs=44.0
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccc-eeecceEEEeeccEEEEee
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYG-DIPRGIFIIRGENVVLMGE 58 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~-~~~~G~~lIRG~nVv~ig~ 58 (116)
|.|+++-.+.|+|.|.|||.|+-|.|.. +....+|. -..+..++|||..|-++-.
T Consensus 17 VeLKnd~~i~GtL~svDqyLNlkL~di~--v~d~~kyPhm~Sv~ncfIRGSvvrYv~l 72 (96)
T KOG3448|consen 17 VELKNDLSICGTLHSVDQYLNLKLTDIS--VTDPDKYPHMLSVKNCFIRGSVVRYVQL 72 (96)
T ss_pred EEEcCCcEEEEEecccchhheeEEeeeE--eeCcccCCCeeeeeeEEEeccEEEEEEe
Confidence 6799999999999999999999999985 33344442 2356689999999988753
No 37
>KOG3293|consensus
Probab=97.69 E-value=4.4e-05 Score=55.57 Aligned_cols=58 Identities=28% Similarity=0.402 Sum_probs=47.4
Q ss_pred CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecC
Q psy10177 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id 60 (116)
+|-|++|-+|.|.|...|.+|||.|.++++....+.++ -..-.+.|||.+|-++-..|
T Consensus 16 lvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf--~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 16 LVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKF--FRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred EEEecCCCEecceeecchhhhhcchheeEEeccCCCce--eecceeEEecceeEEEeccH
Confidence 47899999999999999999999999999875555543 24457899999999886443
No 38
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.19 E-value=0.00018 Score=47.10 Aligned_cols=25 Identities=28% Similarity=0.400 Sum_probs=22.7
Q ss_pred EEEEEEEEeccccceEEcceEEEEE
Q psy10177 9 TLIGYLRSVDQFANLVLHKTIERIH 33 (116)
Q Consensus 9 ~l~G~L~~fDqf~NLVL~d~~Eri~ 33 (116)
.+.|.|.+||.|+||+|.|+.|.+.
T Consensus 24 ~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 24 VCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred EEEEEEEeeeeehhheehhhhhhhc
Confidence 7899999999999999999999643
No 39
>KOG3428|consensus
Probab=96.84 E-value=0.0057 Score=43.58 Aligned_cols=68 Identities=25% Similarity=0.281 Sum_probs=50.3
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCccccCCCCcccCHHHHH
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDIL 78 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~v~~~~~~ 78 (116)
|-|++|+...|++.+.|-+||..|.++.=. ..+ +...+-...|||+||=++-..| +.++...-+.+..
T Consensus 17 IeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t--~~~--~pv~l~~lsirgnniRy~~lpD-----~l~ld~Llvd~~~ 84 (109)
T KOG3428|consen 17 IELKNGTIVHGTIDSVDVQMNTHLKHVKMT--VKG--EPVRLDTLSIRGNNIRYYILPD-----SLNLDTLLVDDAP 84 (109)
T ss_pred EEecCCcEEeeeEEEEEhhheeEEEEEEEe--cCC--CceeEEEEEeecceEEEEEccC-----CcCcceeeeehhh
Confidence 679999999999999999999999988733 222 2346678899999999987654 4444444444333
No 40
>KOG3172|consensus
Probab=96.56 E-value=0.01 Score=42.50 Aligned_cols=59 Identities=20% Similarity=0.163 Sum_probs=47.5
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEK 63 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~~ 63 (116)
+-+..|-.|.|.|.-.+.+||+.|.|.+=....+. ...+..++|||+.|-.+-..|.=+
T Consensus 20 ~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLK 78 (119)
T KOG3172|consen 20 VETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLK 78 (119)
T ss_pred EEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhh
Confidence 45789999999999999999999999974332222 235678999999999998887644
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=95.46 E-value=0.022 Score=37.09 Aligned_cols=53 Identities=19% Similarity=0.211 Sum_probs=29.9
Q ss_pred EEecCCcEEEEEEEEecc---ccceEEcceEEEEEcC---cc-cceeecceEEEeeccEE
Q psy10177 2 VLLRDGRTLIGYLRSVDQ---FANLVLHKTIERIHVG---NQ-YGDIPRGIFIIRGENVV 54 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDq---f~NLVL~d~~Eri~~~---~~-~~~~~~G~~lIRG~nVv 54 (116)
|.++||..|.|+|.+++. -..++|.-|...-... .. ........++|.++.|+
T Consensus 17 V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 17 VTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred EEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 789999999999999998 7889998887532111 11 12345567888887765
No 42
>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=90.64 E-value=0.48 Score=30.51 Aligned_cols=27 Identities=30% Similarity=0.460 Sum_probs=23.1
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|.|.+|-.+.|..+|||+|+=|+-.+.
T Consensus 16 v~L~NG~~l~G~I~~fD~ftVll~~~g 42 (61)
T cd01716 16 IYLVNGVQLKGQIESFDNFTVLLESDG 42 (61)
T ss_pred EEEeCCcEEEEEEEEEcceEEEEEECC
Confidence 679999999999999999987765543
No 43
>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=89.81 E-value=0.61 Score=30.08 Aligned_cols=26 Identities=35% Similarity=0.542 Sum_probs=22.5
Q ss_pred EEecCCcEEEEEEEEeccccceEEcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHK 27 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d 27 (116)
|.|.+|-.+.|..+|||+|+=|+-.+
T Consensus 20 i~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 20 VFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred EEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 67999999999999999998776544
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=88.39 E-value=0.84 Score=30.89 Aligned_cols=27 Identities=30% Similarity=0.472 Sum_probs=23.3
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|-|.+|-.+.|..+|||+|.=|+-.+.
T Consensus 24 ifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 24 IYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred EEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 679999999999999999987766554
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=81.69 E-value=2 Score=28.92 Aligned_cols=26 Identities=31% Similarity=0.508 Sum_probs=21.5
Q ss_pred EEecCCcEEEEEEEEeccccceEEcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHK 27 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d 27 (116)
|-|.+|-.+.|..+|||+|.=|+=.+
T Consensus 24 IfLvNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 24 IFLVNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred EEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence 56899999999999999997554443
No 46
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=80.72 E-value=7.6 Score=23.02 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=21.5
Q ss_pred CCcEEEEEEEEeccccceEEcceEE
Q psy10177 6 DGRTLIGYLRSVDQFANLVLHKTIE 30 (116)
Q Consensus 6 dGR~l~G~L~~fDqf~NLVL~d~~E 30 (116)
++..+.|+..++|....|++...-.
T Consensus 11 ~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCeEEEEEEEEECCCCEEEEEECCC
Confidence 6788899999999999999976543
No 47
>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=70.51 E-value=25 Score=23.74 Aligned_cols=48 Identities=13% Similarity=0.178 Sum_probs=31.0
Q ss_pred EEecCCcEEEEEEEEec-cccceEEcceEEEEEcCcccceeecceEEEeeccEEEEe
Q psy10177 2 VLLRDGRTLIGYLRSVD-QFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 57 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fD-qf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig 57 (116)
+.|-++.++.|.+.++| ...|+..++-. .+-+ .....++|...|+++.
T Consensus 29 f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TPlG----v~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 29 FTLHENTTVSARFGACDIDVSNFQVSNLQ----TPLG----VQPEALLRCSDVISIS 77 (80)
T ss_dssp EEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TTTT----EEEEEEEEGGGEEEEE
T ss_pred EEEeCCeEEEEEEEEecCchheEEhhhcC----CCcc----cChhheeecCCEEEEE
Confidence 56888999999999999 45666444432 1111 2236899999999886
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=70.37 E-value=6.9 Score=29.86 Aligned_cols=27 Identities=26% Similarity=0.404 Sum_probs=23.2
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|-|.+|-.+.|..+|||+|.=|+-.+.
T Consensus 109 vfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 109 MFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred EEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 678999999999999999987766554
No 49
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=68.33 E-value=8 Score=29.52 Aligned_cols=27 Identities=26% Similarity=0.402 Sum_probs=23.0
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|-|.+|-.+.|..+|||+|.=|+-.+.
T Consensus 29 vfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 29 MFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred EEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 678999999999999999987765554
No 50
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=66.92 E-value=36 Score=23.47 Aligned_cols=63 Identities=14% Similarity=0.178 Sum_probs=43.2
Q ss_pred EEecCCcEEEEEEEEecc-ccceEEcceEEEEEcCcc------cceeecceEEEeeccEEEEeecCCccc
Q psy10177 2 VLLRDGRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQ------YGDIPRGIFIIRGENVVLMGEVDKEKE 64 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDq-f~NLVL~d~~Eri~~~~~------~~~~~~G~~lIRG~nVv~ig~id~~~e 64 (116)
+..+++-.|.|+|..+|. -.++.|+++.-.-..+.. -.+.....++.||..|--+.-++....
T Consensus 13 lisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~~ 82 (96)
T PF12701_consen 13 LISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPPP 82 (96)
T ss_dssp EEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-S
T ss_pred EEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCCC
Confidence 456788899999999995 789999998642121110 112346789999999988877766543
No 51
>KOG3382|consensus
Probab=61.14 E-value=4.4 Score=30.20 Aligned_cols=21 Identities=33% Similarity=0.442 Sum_probs=16.6
Q ss_pred cEEEEEEEEeccccceEEcce
Q psy10177 8 RTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 8 R~l~G~L~~fDqf~NLVL~d~ 28 (116)
-.=+|+|+|.|.|.|=--++-
T Consensus 43 ~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 43 DHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred cccceeeeeecccccchhccc
Confidence 334899999999999766555
No 52
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=56.88 E-value=15 Score=27.99 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=25.7
Q ss_pred EEecCCcEEEEEEEEeccccceEEcceE
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKTI 29 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~ 29 (116)
|++.||..|.|...||++--|.||..+-
T Consensus 34 vv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 34 VVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred EEecCCcEEEEEEeccCcccCEEeccCC
Confidence 6889999999999999999999988764
No 53
>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=56.57 E-value=54 Score=21.86 Aligned_cols=52 Identities=13% Similarity=0.187 Sum_probs=33.0
Q ss_pred EecCCcEEEEEEEEecc-ccceEEcceEEEEEcCcc-------cceeecceEEEeeccEE
Q psy10177 3 LLRDGRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQ-------YGDIPRGIFIIRGENVV 54 (116)
Q Consensus 3 ~LrdGR~l~G~L~~fDq-f~NLVL~d~~Eri~~~~~-------~~~~~~G~~lIRG~nVv 54 (116)
+.+.+-.|.|+|.++|. -.-+.|+++.-.=..+.. ........++.||..|-
T Consensus 12 ISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 12 ISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred EecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 45667789999999994 456668887643222111 12234567888887764
No 54
>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=54.56 E-value=27 Score=22.31 Aligned_cols=27 Identities=15% Similarity=0.084 Sum_probs=21.8
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
+++..|.++.|.+.+||.-.++++=.|
T Consensus 11 ~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 11 CRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred EEecCCceEEEEEEEecCCCcEEEEEC
Confidence 567889999999999998877764443
No 55
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=51.71 E-value=4.9 Score=39.25 Aligned_cols=51 Identities=25% Similarity=0.283 Sum_probs=0.0
Q ss_pred ecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEE
Q psy10177 4 LRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVL 55 (116)
Q Consensus 4 LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ 55 (116)
..+|+.+-|+|.+-|.-++.+|+---+ +....-......|.|+|+|+|.|-
T Consensus 254 t~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 254 TSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTSVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp ----------------------------------------------------
T ss_pred cCCCCEeceEEeccHHHHHHHHHHHhh-hccceeecchhheeeeecCccHHH
Confidence 578999999999999988887766554 322222234578999999999873
No 56
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=51.68 E-value=6.4 Score=27.33 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=14.6
Q ss_pred EEEEEeccccceEEcce
Q psy10177 12 GYLRSVDQFANLVLHKT 28 (116)
Q Consensus 12 G~L~~fDqf~NLVL~d~ 28 (116)
|+|+|.|.|+|.--+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999866655
No 57
>PRK10942 serine endoprotease; Provisional
Probab=50.20 E-value=50 Score=28.44 Aligned_cols=26 Identities=27% Similarity=0.355 Sum_probs=22.8
Q ss_pred EEecCCcEEEEEEEEeccccceEEcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHK 27 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d 27 (116)
|.+.||+++.+.+.++|...+|-|=.
T Consensus 140 V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 140 VQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred EEECCCCEEEEEEEEecCCCCEEEEE
Confidence 77899999999999999999885543
No 58
>PRK10139 serine endoprotease; Provisional
Probab=49.51 E-value=59 Score=27.87 Aligned_cols=26 Identities=27% Similarity=0.413 Sum_probs=22.6
Q ss_pred EEecCCcEEEEEEEEeccccceEEcc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHK 27 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d 27 (116)
|.+.||+.+.+.+.++|....|-+=.
T Consensus 119 V~~~dg~~~~a~vvg~D~~~DlAvlk 144 (455)
T PRK10139 119 IQLNDGREFDAKLIGSDDQSDIALLQ 144 (455)
T ss_pred EEECCCCEEEEEEEEEcCCCCEEEEE
Confidence 78899999999999999998885533
No 59
>PRK14638 hypothetical protein; Provisional
Probab=44.14 E-value=40 Score=24.79 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=18.7
Q ss_pred EEecCCcEEEEEEEEeccccceEEc
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLH 26 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~ 26 (116)
|++.+++.+.|+|.++|. .++.|.
T Consensus 105 V~~~~~k~~~G~L~~~~~-~~i~l~ 128 (150)
T PRK14638 105 IVTKDGKTFIGRIESFVD-GTITIS 128 (150)
T ss_pred EEECCCcEEEEEEEEEeC-CEEEEE
Confidence 567899999999999996 345443
No 60
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=41.39 E-value=37 Score=20.37 Aligned_cols=21 Identities=24% Similarity=0.279 Sum_probs=13.7
Q ss_pred EEEEEEEeccccceEEcceEE
Q psy10177 10 LIGYLRSVDQFANLVLHKTIE 30 (116)
Q Consensus 10 l~G~L~~fDqf~NLVL~d~~E 30 (116)
..|++.|.|+...++|.+...
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 489999999999998887653
No 61
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=37.55 E-value=34 Score=24.18 Aligned_cols=18 Identities=44% Similarity=0.595 Sum_probs=15.5
Q ss_pred CEEecCCcEEEEEEEEec
Q psy10177 1 MVLLRDGRTLIGYLRSVD 18 (116)
Q Consensus 1 lV~LrdGR~l~G~L~~fD 18 (116)
.|.++||+.+.|.+.+=|
T Consensus 61 ~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 61 RVTLKDGRILSGIVASET 78 (133)
T ss_pred EEEECCCCEEEEEEEecC
Confidence 378999999999998855
No 62
>PRK14639 hypothetical protein; Provisional
Probab=35.63 E-value=66 Score=23.37 Aligned_cols=23 Identities=26% Similarity=0.426 Sum_probs=18.6
Q ss_pred EEecCCcEEEEEEEEeccccceEE
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVL 25 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL 25 (116)
|.+.+++.+.|+|.++|. .++.|
T Consensus 93 v~l~~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 93 ITTNEKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred EEECCCcEEEEEEEEEeC-CEEEE
Confidence 567789999999999998 45554
No 63
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=34.52 E-value=1.3e+02 Score=25.08 Aligned_cols=27 Identities=30% Similarity=0.375 Sum_probs=23.2
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|.+.||+.+.+.+.++|...+|.|=..
T Consensus 86 V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 86 VTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred EEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 678899999999999999999866544
No 64
>PRK06630 hypothetical protein; Provisional
Probab=32.25 E-value=24 Score=24.82 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=15.7
Q ss_pred EEEEEEEeccccceEEcce
Q psy10177 10 LIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 10 l~G~L~~fDqf~NLVL~d~ 28 (116)
..|.|+|-|+|+|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999866653
No 65
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=31.66 E-value=73 Score=26.13 Aligned_cols=27 Identities=33% Similarity=0.473 Sum_probs=23.0
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|.+.||+.+.+.+.++|...+|.|=..
T Consensus 106 V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 106 VALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred EEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 678999999999999999988866443
No 66
>PRK02001 hypothetical protein; Validated
Probab=31.26 E-value=62 Score=24.00 Aligned_cols=23 Identities=35% Similarity=0.663 Sum_probs=18.3
Q ss_pred EEecCCcEEEEEEEEeccccceEE
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVL 25 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL 25 (116)
|.+.+++.|.|+|.++|.- +++|
T Consensus 95 V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 95 VLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred EEECCCCEEEEEEEEEeCC-EEEE
Confidence 5678999999999999963 4444
No 67
>KOG3819|consensus
Probab=31.10 E-value=1e+02 Score=27.39 Aligned_cols=38 Identities=26% Similarity=0.313 Sum_probs=30.1
Q ss_pred CCCCcccCHHHHHHHHHHHHHHHHHH-hHHHHHHHHHcC
Q psy10177 66 CPQLQQVSVEDILNAQRKEQEVKQER-SRMLAKRLKERG 103 (116)
Q Consensus 66 ~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~g 103 (116)
...+.+++-++++.+++++...+.++ +..|...|.+.|
T Consensus 33 ~~g~Sq~sdee~~klqkEel~rr~rr~e~er~slm~~~g 71 (513)
T KOG3819|consen 33 IEGLSQVSDEELLKLQKEELQRRLRRAEAERVSLMLAHG 71 (513)
T ss_pred cccccccCHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34578999999999999998888554 777777777654
No 68
>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=30.84 E-value=1.2e+02 Score=22.99 Aligned_cols=50 Identities=26% Similarity=0.385 Sum_probs=33.9
Q ss_pred EEecCCcEEEEEEEEec-cccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCC
Q psy10177 2 VLLRDGRTLIGYLRSVD-QFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDK 61 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fD-qf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~ 61 (116)
|.+.| +++.|.+.++| -..|+||-+..| +. ....-+|-|..|-.+.-++.
T Consensus 22 V~~~d-~~~~G~v~TiDPVS~siVL~~~~e----~~-----~~sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 22 VTLSD-KEYKGWVYTIDPVSASIVLVNFQE----DG-----KRSVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp EEETT-EEEEEEEEEE-TTT--EEEEEE-T----TS------EEEEEE-GGGEEEEEEEE-
T ss_pred EEEec-cEEEEEEEEeCCCCCeEEEEEccc----CC-----ceeEEEEEccceEEEEEccC
Confidence 67888 99999999999 467998885543 11 23367899999999888875
No 69
>PRK10898 serine endoprotease; Provisional
Probab=30.25 E-value=82 Score=25.96 Aligned_cols=27 Identities=33% Similarity=0.509 Sum_probs=22.8
Q ss_pred EEecCCcEEEEEEEEeccccceEEcce
Q psy10177 2 VLLRDGRTLIGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 2 V~LrdGR~l~G~L~~fDqf~NLVL~d~ 28 (116)
|.+.||+.+.+.+.++|....|-|=..
T Consensus 106 V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 106 VALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred EEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 678999999999999999988855443
No 70
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=29.83 E-value=42 Score=25.40 Aligned_cols=17 Identities=35% Similarity=0.428 Sum_probs=14.7
Q ss_pred EEEEEeccccceEEcce
Q psy10177 12 GYLRSVDQFANLVLHKT 28 (116)
Q Consensus 12 G~L~~fDqf~NLVL~d~ 28 (116)
|.|+|-|+|.|---++.
T Consensus 49 G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 49 ATLVGVDKFGNKYYQKL 65 (159)
T ss_pred cEEEEecCCCCeeeecC
Confidence 99999999999866654
No 71
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=26.23 E-value=37 Score=24.39 Aligned_cols=18 Identities=28% Similarity=0.377 Sum_probs=15.4
Q ss_pred EEEEEEeccccceEEcce
Q psy10177 11 IGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 11 ~G~L~~fDqf~NLVL~d~ 28 (116)
.|.|+|-|+|.|---++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 799999999999876654
No 72
>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=25.06 E-value=1.4e+02 Score=19.42 Aligned_cols=19 Identities=37% Similarity=0.543 Sum_probs=14.1
Q ss_pred CC-cEEEEEEEEeccccceEE
Q psy10177 6 DG-RTLIGYLRSVDQFANLVL 25 (116)
Q Consensus 6 dG-R~l~G~L~~fDqf~NLVL 25 (116)
+| +.+.|.|.++|.- +++|
T Consensus 37 ~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 37 DGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CCeEEEEEEEEeEeCC-EEEE
Confidence 55 6899999999883 4444
No 73
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=24.73 E-value=1e+02 Score=24.62 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=18.3
Q ss_pred EEEEEEEEeccccceEEcceE
Q psy10177 9 TLIGYLRSVDQFANLVLHKTI 29 (116)
Q Consensus 9 ~l~G~L~~fDqf~NLVL~d~~ 29 (116)
.+.|...-+|.|.|+++.=..
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~ 189 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISR 189 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEH
T ss_pred eEEEEEEEECccCCeeeCCCH
Confidence 889999999999999886543
No 74
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=24.27 E-value=12 Score=24.00 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=15.9
Q ss_pred eccccceEEcceEEEEEcC
Q psy10177 17 VDQFANLVLHKTIERIHVG 35 (116)
Q Consensus 17 fDqf~NLVL~d~~Eri~~~ 35 (116)
-|.||+-||++|..||.-.
T Consensus 20 sDDFmhaVlSNCtTrIvLp 38 (61)
T PF10894_consen 20 SDDFMHAVLSNCTTRIVLP 38 (61)
T ss_pred cHHHHHHHHhcCceeEEec
Confidence 3889999999999988643
No 75
>PF11831 Myb_Cef: pre-mRNA splicing factor component; InterPro: IPR021786 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 73 to 279 amino acids in length.
Probab=23.18 E-value=3.1e+02 Score=21.46 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=30.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHhHHHHHHHHHcCCCCCCCCC
Q psy10177 70 QQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLI 111 (116)
Q Consensus 70 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~ 111 (116)
......++....+++++++.+++-.|...--+|||.-|..+.
T Consensus 100 ~eeDaad~d~r~~~~~~~~e~~e~~rRSqvvQR~LPRP~~v~ 141 (231)
T PF11831_consen 100 MEEDAADRDARERAEREEEEEKELKRRSQVVQRGLPRPSEVN 141 (231)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHhhHHHHccCCCCCccc
Confidence 456677787777777777777777776667789998887553
No 76
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=22.01 E-value=2e+02 Score=22.05 Aligned_cols=61 Identities=16% Similarity=0.130 Sum_probs=38.8
Q ss_pred cceEEcceEEEEEcCcccceeecceEEEe--eccEEEEeecCCcccc---CCCCcccCHHHHHHHHHH
Q psy10177 21 ANLVLHKTIERIHVGNQYGDIPRGIFIIR--GENVVLMGEVDKEKEH---CPQLQQVSVEDILNAQRK 83 (116)
Q Consensus 21 ~NLVL~d~~Eri~~~~~~~~~~~G~~lIR--G~nVv~ig~id~~~e~---~~~~~~v~~~~~~~~~~~ 83 (116)
|++-+......+.....+.-++ .++|| |.|+-+-+.-....-+ ..+++.++.++|++.-+.
T Consensus 2 ~~~~i~EiF~siQGEG~~~Gr~--~vFVR~~GC~l~C~~Cdt~~t~~~~~~~~~~~~~~~~I~~~i~~ 67 (212)
T COG0602 2 MKYRIVEIFDSIQGEGKNIGRP--SVFVRFAGCNLRCPGCDTKYTWDFNYGKPGTPMSADEILADIKS 67 (212)
T ss_pred CceeEEEEEEEEecCcccccce--eEEEEcCCCCCCCCCCCChhhhcccccCCCCccCHHHHHHHHHh
Confidence 4554555554333222222223 79999 9999988876654422 247899999999987776
No 77
>PRK08183 NADH dehydrogenase; Validated
Probab=20.43 E-value=53 Score=24.11 Aligned_cols=18 Identities=22% Similarity=0.285 Sum_probs=14.9
Q ss_pred EEEEEEeccccceEEcce
Q psy10177 11 IGYLRSVDQFANLVLHKT 28 (116)
Q Consensus 11 ~G~L~~fDqf~NLVL~d~ 28 (116)
.|.|+|-|+|.|---++.
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 699999999999866544
Done!