Query psy1140
Match_columns 142
No_of_seqs 132 out of 1016
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 17:29:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01727 LSm8 The eukaryotic Sm 99.8 8.2E-20 1.8E-24 126.0 8.9 62 3-64 13-74 (74)
2 cd01729 LSm7 The eukaryotic Sm 99.8 2.2E-19 4.9E-24 126.5 8.8 61 3-63 16-80 (81)
3 KOG1782|consensus 99.8 1.2E-20 2.7E-25 143.9 -0.7 87 3-91 23-109 (129)
4 cd01728 LSm1 The eukaryotic Sm 99.8 1.4E-18 3.1E-23 121.2 9.0 59 3-62 16-74 (74)
5 cd01730 LSm3 The eukaryotic Sm 99.8 2.1E-18 4.5E-23 121.2 8.3 59 3-61 15-82 (82)
6 cd01732 LSm5 The eukaryotic Sm 99.8 3.1E-18 6.7E-23 119.9 8.9 59 3-62 17-75 (76)
7 cd01719 Sm_G The eukaryotic Sm 99.8 3.8E-18 8.2E-23 118.0 8.3 58 3-64 14-71 (72)
8 cd01717 Sm_B The eukaryotic Sm 99.7 2.2E-17 4.8E-22 115.0 8.5 58 3-60 14-77 (79)
9 cd01731 archaeal_Sm1 The archa 99.7 2.4E-17 5.3E-22 111.6 7.9 55 3-61 14-68 (68)
10 cd01718 Sm_E The eukaryotic Sm 99.7 2.9E-17 6.3E-22 116.4 8.1 52 7-61 28-79 (79)
11 PRK00737 small nuclear ribonuc 99.7 3.4E-17 7.3E-22 112.6 7.7 55 3-61 18-72 (72)
12 KOG1784|consensus 99.7 8.4E-18 1.8E-22 123.0 3.4 76 3-78 14-89 (96)
13 cd01720 Sm_D2 The eukaryotic S 99.7 1.6E-16 3.5E-21 114.1 8.6 59 3-61 18-85 (87)
14 cd06168 LSm9 The eukaryotic Sm 99.7 2.3E-16 4.9E-21 110.3 8.6 58 3-60 14-73 (75)
15 cd01726 LSm6 The eukaryotic Sm 99.7 5.4E-16 1.2E-20 105.0 8.1 55 2-60 13-67 (67)
16 PTZ00138 small nuclear ribonuc 99.7 4E-16 8.6E-21 112.9 7.7 52 8-62 37-88 (89)
17 cd01722 Sm_F The eukaryotic Sm 99.6 6.8E-16 1.5E-20 104.9 7.3 55 2-60 14-68 (68)
18 smart00651 Sm snRNP Sm protein 99.6 3.1E-15 6.7E-20 99.2 8.3 57 2-61 11-67 (67)
19 PF01423 LSM: LSM domain ; In 99.6 7.1E-15 1.5E-19 97.7 9.0 57 2-61 11-67 (67)
20 COG1958 LSM1 Small nuclear rib 99.6 5.5E-15 1.2E-19 102.6 8.2 58 3-61 21-79 (79)
21 KOG1780|consensus 99.6 4.3E-15 9.2E-20 105.2 4.9 58 3-64 18-75 (77)
22 KOG1781|consensus 99.5 3.7E-16 8.1E-21 116.0 -1.0 72 3-74 31-106 (108)
23 cd00600 Sm_like The eukaryotic 99.5 6.5E-14 1.4E-18 91.5 8.3 54 2-59 9-62 (63)
24 cd01721 Sm_D3 The eukaryotic S 99.4 6.6E-13 1.4E-17 91.0 8.2 58 2-63 13-70 (70)
25 cd01723 LSm4 The eukaryotic Sm 99.4 6.7E-13 1.5E-17 92.1 7.2 59 2-63 14-72 (76)
26 cd01724 Sm_D1 The eukaryotic S 99.4 1.9E-12 4.2E-17 93.1 8.6 59 2-64 14-72 (90)
27 cd01733 LSm10 The eukaryotic S 99.3 6.6E-12 1.4E-16 88.2 7.6 55 2-60 22-76 (78)
28 cd01725 LSm2 The eukaryotic Sm 99.3 9.5E-12 2.1E-16 87.6 7.7 64 2-67 14-77 (81)
29 KOG3482|consensus 99.2 1.3E-11 2.8E-16 87.6 4.6 58 3-64 22-79 (79)
30 KOG3168|consensus 99.2 1.3E-12 2.7E-17 104.6 -0.8 60 3-62 18-83 (177)
31 KOG3460|consensus 99.2 2.7E-12 5.8E-17 93.1 0.7 60 3-62 19-87 (91)
32 KOG1775|consensus 99.1 3.7E-11 8E-16 86.0 3.1 60 3-63 21-80 (84)
33 KOG1774|consensus 99.0 9.3E-11 2E-15 84.8 2.6 53 8-63 35-87 (88)
34 KOG1783|consensus 98.8 8.1E-10 1.7E-14 78.4 -0.9 56 3-62 20-75 (77)
35 KOG3448|consensus 97.6 0.00025 5.5E-09 52.3 6.5 58 2-61 15-72 (96)
36 cd01739 LSm11_C The eukaryotic 97.4 8.9E-05 1.9E-09 51.7 1.6 25 10-34 23-47 (66)
37 KOG3293|consensus 97.1 0.00071 1.5E-08 52.5 4.3 58 3-63 16-73 (134)
38 KOG3428|consensus 97.0 0.0034 7.4E-08 47.5 7.4 67 2-78 15-81 (109)
39 KOG3172|consensus 96.9 0.0037 7.9E-08 47.7 6.7 61 2-66 18-78 (119)
40 KOG3459|consensus 96.7 0.00016 3.4E-09 54.9 -2.0 58 4-61 41-107 (114)
41 PF14438 SM-ATX: Ataxin 2 SM d 94.2 0.071 1.5E-06 36.4 3.6 55 2-57 15-76 (77)
42 cd01716 Hfq Hfq, an abundant, 88.5 0.99 2.1E-05 30.9 4.2 28 2-29 14-41 (61)
43 TIGR02383 Hfq RNA chaperone Hf 87.6 1.2 2.6E-05 30.5 4.2 28 2-29 18-45 (61)
44 PRK00395 hfq RNA-binding prote 86.0 1.6 3.4E-05 31.5 4.2 29 2-30 22-50 (79)
45 PF02237 BPL_C: Biotin protein 82.5 4.6 0.0001 25.4 4.9 25 8-32 11-35 (48)
46 PRK14091 RNA-binding protein H 68.2 9.1 0.0002 31.0 4.2 29 2-30 27-55 (165)
47 PRK14091 RNA-binding protein H 67.6 9.5 0.00021 30.9 4.2 29 2-30 107-135 (165)
48 COG1923 Hfq Uncharacterized ho 61.7 16 0.00034 26.3 4.0 27 3-29 23-49 (77)
49 PF01581 FARP: FMRFamide relat 52.8 5.5 0.00012 18.7 0.3 8 92-99 3-10 (11)
50 KOG3382|consensus 46.5 10 0.00022 30.2 1.0 20 11-30 44-63 (151)
51 PF12701 LSM14: Scd6-like Sm d 42.4 1.3E+02 0.0029 21.9 6.6 63 4-66 13-81 (96)
52 PF03614 Flag1_repress: Repres 40.5 38 0.00082 27.5 3.5 29 3-31 33-61 (165)
53 PF05071 NDUFA12: NADH ubiquin 36.4 14 0.00031 27.0 0.5 17 14-30 1-17 (105)
54 PF03122 Herpes_MCP: Herpes vi 33.2 14 0.00031 38.2 0.0 56 2-59 250-305 (1354)
55 PF09734 Tau95: RNA polymerase 31.1 21 0.00045 30.1 0.6 12 95-106 288-299 (310)
56 PF11095 Gemin7: Gem-associate 29.7 2.1E+02 0.0046 20.5 6.6 51 2-60 27-77 (80)
57 PF07998 Peptidase_M54: Peptid 27.2 23 0.00051 28.9 0.3 27 115-141 85-111 (194)
58 PRK14639 hypothetical protein; 27.0 1.1E+02 0.0024 23.4 4.0 24 3-27 92-115 (140)
59 PRK14638 hypothetical protein; 26.6 86 0.0019 24.3 3.4 24 3-27 104-127 (150)
60 PF06570 DUF1129: Protein of u 25.3 20 0.00043 28.6 -0.4 31 77-112 35-65 (206)
61 PRK10942 serine endoprotease; 25.2 99 0.0022 28.0 3.9 27 3-29 139-165 (473)
62 PRK10898 serine endoprotease; 24.8 1.1E+02 0.0024 26.5 4.0 28 3-30 105-132 (353)
63 TIGR02038 protease_degS peripl 24.6 1.2E+02 0.0025 26.2 4.1 28 3-30 105-132 (351)
64 TIGR02603 CxxCH_TIGR02603 puta 24.6 1.9E+02 0.0041 21.4 4.8 19 2-20 60-78 (133)
65 KOG2473|consensus 24.1 32 0.00068 32.2 0.6 14 94-107 283-296 (484)
66 PRK02001 hypothetical protein; 24.0 1E+02 0.0022 24.2 3.3 24 3-27 94-117 (152)
67 cd01735 LSm12_N LSm12 belongs 23.2 1E+02 0.0022 20.9 2.8 25 8-32 15-39 (61)
68 PRK06955 biotin--protein ligas 22.5 2.4E+02 0.0053 23.8 5.6 22 7-28 257-278 (300)
69 PRK10139 serine endoprotease; 21.7 1.3E+02 0.0029 27.1 4.0 28 3-30 118-145 (455)
70 PF15007 CEP44: Centrosomal sp 21.0 65 0.0014 25.0 1.7 26 97-122 80-105 (131)
71 PHA00672 hypothetical protein 20.8 4.4E+02 0.0096 21.0 6.5 28 2-31 50-77 (152)
72 PF14563 DUF4444: Domain of un 20.4 1.1E+02 0.0025 19.7 2.4 21 12-32 10-30 (42)
No 1
>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=99.82 E-value=8.2e-20 Score=126.01 Aligned_cols=62 Identities=60% Similarity=0.860 Sum_probs=55.7
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS 64 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe 64 (142)
.|++++||.++|+|+|||+|||+||++|+|++..++++..++.+|.+++||+||++|+++|+
T Consensus 13 ~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 13 SVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred EEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 57899999999999999999999999999997655445568899999999999999999885
No 2
>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=99.80 E-value=2.2e-19 Score=126.49 Aligned_cols=61 Identities=28% Similarity=0.445 Sum_probs=53.5
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCC----eeeEEeceEEEecCcEEEeeeCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAG----VEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~----~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
.|.+++||+++|+|+|||+||||||++|+|++..+++. ..++.+|+++|||+||++|++.+
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 57899999999999999999999999999998654321 35788999999999999999876
No 3
>KOG1782|consensus
Probab=99.78 E-value=1.2e-20 Score=143.87 Aligned_cols=87 Identities=24% Similarity=0.280 Sum_probs=77.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCCCCCCCCCCcccchhhhcc
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILL 82 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDee~e~~v~~~~v~~~~il~ 82 (142)
-|.|.+||.+.|+|++||||.|+||++|+||++.. +.+..++.|.++|||+||+++|++|.++| ..++++++.+|+++
T Consensus 23 lVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~-~~Y~di~~glfiIRGENVvllGeid~dkE-~~~l~~i~~~e~~~ 100 (129)
T KOG1782|consen 23 LVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVG-NKYCDIPRGLFIIRGENVVLLGEIDLDKE-EEPLEQISFEEALN 100 (129)
T ss_pred EEEEecCcchhhhhhhHHHHHHHHHHhhhhheeec-ceecccCceEEEEecCcEEEEecCCcchh-hccceeCCHHHHHH
Confidence 37899999999999999999999999999999876 45789999999999999999999999999 69999999999996
Q ss_pred ccccccccc
Q psy1140 83 PQIWGIERR 91 (142)
Q Consensus 83 ~q~~~~~~~ 91 (142)
.+...+++|
T Consensus 101 ~~~~~q~~k 109 (129)
T KOG1782|consen 101 EIKREQEAK 109 (129)
T ss_pred HHHHHHHHh
Confidence 665554444
No 4
>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=99.78 E-value=1.4e-18 Score=121.15 Aligned_cols=59 Identities=31% Similarity=0.496 Sum_probs=52.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~v 62 (142)
.|.+++||+++|+|+|||+|||+||+||+|++..+ +...++.+|.+++|||||++||++
T Consensus 16 ~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~-~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 16 VVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG-DKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred EEEEcCCeEEEEEEEEECCcccEEecceEEEEecC-CccceeEeeEEEEECCEEEEEEcC
Confidence 57899999999999999999999999999997654 334578999999999999999974
No 5
>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=99.76 E-value=2.1e-18 Score=121.23 Aligned_cols=59 Identities=20% Similarity=0.357 Sum_probs=50.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCC---------CeeeEEeceEEEecCcEEEeee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTA---------GVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~---------~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
.|.+++||+++|+|+|||+||||||+||+|++....+ ....+.+|.++||||||++|++
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 5789999999999999999999999999999754321 1247899999999999999974
No 6
>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=99.76 E-value=3.1e-18 Score=119.85 Aligned_cols=59 Identities=31% Similarity=0.409 Sum_probs=52.2
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~v 62 (142)
.+.+++||++.|+|+|||+|||+||+||+|+...+ ++.+.+.+|.++||||||++|++.
T Consensus 17 ~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~-~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 17 WIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP-EGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC-CCceeeEcCeEEEeCCeEEEEECC
Confidence 57899999999999999999999999999997554 334578899999999999999874
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=99.76 E-value=3.8e-18 Score=117.95 Aligned_cols=58 Identities=29% Similarity=0.499 Sum_probs=52.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS 64 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe 64 (142)
.|.+++||++.|+|+|||+||||||++|+|+.. +.+.+.+|.++|||+||++|+++|+
T Consensus 14 ~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~----~~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 14 SLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS----GGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred EEEECCCeEEEEEEEEEcccccEEeccEEEEcc----CCceeEeceEEECCCEEEEEEcccc
Confidence 578999999999999999999999999999872 2457899999999999999999874
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=99.72 E-value=2.2e-17 Score=114.98 Aligned_cols=58 Identities=31% Similarity=0.424 Sum_probs=50.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCC------CCeeeEEeceEEEecCcEEEee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPT------AGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~------~~~~~r~LGlvlIRGdNIVlIg 60 (142)
.|++++||++.|+|+|||+||||||++|+|+...+. ...+++.+|+++|||+||++|+
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 578999999999999999999999999999875432 1245789999999999999997
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=99.72 E-value=2.4e-17 Score=111.57 Aligned_cols=55 Identities=27% Similarity=0.367 Sum_probs=49.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
+|.+++||+|.|+|+|||+|||++|++|+|+... .+++.+|.++|||+||++|++
T Consensus 14 ~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 14 LVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG----EPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEEECCCCEEEEEEEEECCcceEEEeeEEEEecC----CeEeEcCcEEEeCCEEEEEcC
Confidence 6789999999999999999999999999998632 357889999999999999975
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=2.9e-17 Score=116.41 Aligned_cols=52 Identities=29% Similarity=0.515 Sum_probs=46.4
Q ss_pred cCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 7 LSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 7 ~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
++||+++|+|+|||+|||+||+||+|++.. +.+++.+|.++||||||++|++
T Consensus 28 ~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~---~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 28 QTDLRIEGVIIGFDEYMNLVLDDAEEVHLK---TKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCCcEEEEEEEEEccceeEEEcCEEEEecC---CceEeEcCcEEEeCCEEEEEcC
Confidence 499999999999999999999999999742 2457789999999999999975
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.71 E-value=3.4e-17 Score=112.61 Aligned_cols=55 Identities=31% Similarity=0.477 Sum_probs=49.0
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
+|.+++||+|.|+|+|||+|||++|+||.|.. ++...+.+|.++|||+||++|++
T Consensus 18 ~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~----~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 18 LVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ----DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEEECCCCEEEEEEEEEcccceeEEeeEEEEc----CCCeEeEcCcEEEeCCEEEEEcC
Confidence 67899999999999999999999999999964 22457789999999999999964
No 12
>KOG1784|consensus
Probab=99.70 E-value=8.4e-18 Score=122.98 Aligned_cols=76 Identities=42% Similarity=0.656 Sum_probs=71.0
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCCCCCCCCCCcccchh
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDN 78 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDee~e~~v~~~~v~~~ 78 (142)
.|.-++||.++|.|.||||..||+|++|.||+++...+.++..+|+++|||+||.+||++||++++.++|.++.++
T Consensus 14 ~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld~tkir~e 89 (96)
T KOG1784|consen 14 SVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLDLTKIRAE 89 (96)
T ss_pred EEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhhhhhcccC
Confidence 3556899999999999999999999999999988777788999999999999999999999999999999998876
No 13
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.68 E-value=1.6e-16 Score=114.10 Aligned_cols=59 Identities=17% Similarity=0.264 Sum_probs=50.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecC-CC--------CeeeEEeceEEEecCcEEEeee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSP-TA--------GVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~-~~--------~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
.|.|++||.+.|+|+|||+||||||+||+|..... ++ ...++.+|.++||||||++|++
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 57899999999999999999999999999976442 11 1346789999999999999986
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=99.68 E-value=2.3e-16 Score=110.31 Aligned_cols=58 Identities=28% Similarity=0.306 Sum_probs=51.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCC--CCeeeEEeceEEEecCcEEEee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPT--AGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~--~~~~~r~LGlvlIRGdNIVlIg 60 (142)
.|++++||.|+|+|.+||+|||+||++|.|+...+. ...+.+.+|+++|||++|+.|.
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 689999999999999999999999999999986543 2356899999999999999986
No 15
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.65 E-value=5.4e-16 Score=105.02 Aligned_cols=55 Identities=27% Similarity=0.374 Sum_probs=48.7
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg 60 (142)
.+|.|++||+|.|+|+|||+|||++|++|+|.. ++...+.+|.++|||+||.+|+
T Consensus 13 V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~----~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 13 VVVKLNSGVDYRGILACLDGYMNIALEQTEEYV----NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred EEEEECCCCEEEEEEEEEccceeeEEeeEEEEe----CCceeeEeCCEEEECCEEEEEC
Confidence 478999999999999999999999999999864 2245778999999999999884
No 16
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.65 E-value=4e-16 Score=112.91 Aligned_cols=52 Identities=29% Similarity=0.490 Sum_probs=45.8
Q ss_pred CCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeC
Q psy1140 8 SLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 8 sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~v 62 (142)
++|+++|+|+|||+|||+||+||+|++.. +..++.+|.++||||||++|++.
T Consensus 37 ~~r~~~G~L~gfD~~mNlVL~d~~E~~~~---~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 37 PNLRIEGKILGFDEYMNMVLDDAEEVYTK---KNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred CCcEEEEEEEEEcccceEEEccEEEEecC---CceeeEcCeEEEcCCEEEEEEcC
Confidence 47999999999999999999999997632 23578999999999999999875
No 17
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.64 E-value=6.8e-16 Score=104.95 Aligned_cols=55 Identities=24% Similarity=0.309 Sum_probs=48.5
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg 60 (142)
.+|.|++||+|.|+|.|||+|||++|++|+|+. ++.....+|.++|||+||.+|+
T Consensus 14 V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~----~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 14 VIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI----DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe----CCccccCcCcEEEECCEEEEEC
Confidence 478999999999999999999999999999975 2234678999999999999873
No 18
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.61 E-value=3.1e-15 Score=99.22 Aligned_cols=57 Identities=37% Similarity=0.505 Sum_probs=50.6
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
.++.+++||.+.|+|.+||+|||++|++|.|+...+ ...+.+|.++|||++|++|++
T Consensus 11 V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~---~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 11 VLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG---EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEEECCCcEEEEEEEEECccccEEEccEEEEecCC---cEEeEeCCEEEcCCEEEEEeC
Confidence 368999999999999999999999999999986431 468899999999999999864
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=99.60 E-value=7.1e-15 Score=97.65 Aligned_cols=57 Identities=33% Similarity=0.487 Sum_probs=50.7
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
.++.+++|+++.|+|.+||+|||++|++|.|....+ .+.+.+|.++|||++|.+|.+
T Consensus 11 V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~---~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 11 VRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG---PEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTE---SEEEEEEEEEEEGGGEEEEEE
T ss_pred EEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCC---CcEeECcEEEEECCEEEEEEC
Confidence 368999999999999999999999999999987321 278899999999999999975
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.59 E-value=5.5e-15 Score=102.58 Aligned_cols=58 Identities=33% Similarity=0.454 Sum_probs=47.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCe-eeEEeceEEEecCcEEEeee
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGV-EQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~-~~r~LGlvlIRGdNIVlIg~ 61 (142)
.|.+++||+|.|+|+|||+|||++|+||+|+... +... ..+..|.++|||+||++|++
T Consensus 21 ~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 21 LVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-DGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEEECCCCEEEEEEEEEccceeEEEeceEEEecc-CCccccceeccEEEEECCcEEEEeC
Confidence 5789999999999999999999999999998741 1112 23444599999999999864
No 21
>KOG1780|consensus
Probab=99.56 E-value=4.3e-15 Score=105.24 Aligned_cols=58 Identities=24% Similarity=0.423 Sum_probs=50.7
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS 64 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe 64 (142)
.+.|++||...|+|+|||+|||+||++|+|.-. ...+..+|..+|||++|+++.+++.
T Consensus 18 ~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~----~~~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 18 VLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG----DGDKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred EEEeCCCcEEEEEEeccchHHhhhhhhceeecC----cCCcceeeeEEEeccEEEEEeeccc
Confidence 367999999999999999999999999999642 2357789999999999999988763
No 22
>KOG1781|consensus
Probab=99.55 E-value=3.7e-16 Score=115.96 Aligned_cols=72 Identities=29% Similarity=0.369 Sum_probs=65.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCC----eeeEEeceEEEecCcEEEeeeCCCCCCCCCCCcc
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAG----VEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQ 74 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~----~~~r~LGlvlIRGdNIVlIg~vDee~e~~v~~~~ 74 (142)
.|.+.+||+.+|+|+||||.||+||++|+|+...|+++ .+.|.+|++++||..+++|++.|..++..+||.+
T Consensus 31 rvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I~npf~~ 106 (108)
T KOG1781|consen 31 RVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEIANPFVQ 106 (108)
T ss_pred EEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhhccchhc
Confidence 57899999999999999999999999999998777644 3569999999999999999999999999998854
No 23
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.53 E-value=6.5e-14 Score=91.48 Aligned_cols=54 Identities=33% Similarity=0.588 Sum_probs=48.6
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEe
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIP 59 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlI 59 (142)
.++.+++|+.|.|+|.+||+|||++|++|.|.... ...+.+|.++|||++|.+|
T Consensus 9 V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 9 VRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----GKKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred EEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----CcEEECCeEEEECCEEEEE
Confidence 36889999999999999999999999999998632 3578999999999999987
No 24
>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=99.44 E-value=6.6e-13 Score=91.00 Aligned_cols=58 Identities=21% Similarity=0.224 Sum_probs=48.7
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCC
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
.+|-|++|++|.|+|.++|+|||++|++|.|... ++ +...+|.++|||+||.++-..|
T Consensus 13 V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~---~g-~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR---DG-RVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred EEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC---CC-cEeEcCcEEEeCCEEEEEEeCC
Confidence 4688999999999999999999999999987432 22 3467899999999999987543
No 25
>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=99.42 E-value=6.7e-13 Score=92.09 Aligned_cols=59 Identities=20% Similarity=0.135 Sum_probs=49.2
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCC
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
.+|.|++|+++.|+|.+||+|||++|++|+|... ++.....+|.++|||+||.+|...|
T Consensus 14 V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~---~g~~~~~~~~v~IRG~~I~~i~~p~ 72 (76)
T cd01723 14 MLVELKNGETYNGHLVNCDNWMNIHLREVICTSK---DGDKFWKMPECYIRGNTIKYLRVPD 72 (76)
T ss_pred EEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC---CCcEeeeCCcEEEeCCEEEEEEcCH
Confidence 3688999999999999999999999999998532 3333456799999999999997654
No 26
>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=99.39 E-value=1.9e-12 Score=93.14 Aligned_cols=59 Identities=27% Similarity=0.343 Sum_probs=51.5
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS 64 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe 64 (142)
.+|.|++|.+|.|+|.++|+|||++|+||+|... +.....+|.++|||+||.+|...|.
T Consensus 14 V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~----~~~~~~~~~v~IRG~nI~yi~lPd~ 72 (90)
T cd01724 14 VTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLK----GRNPVPLDTLSIRGNNIRYFILPDS 72 (90)
T ss_pred EEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcC----CCceeEcceEEEeCCEEEEEEcCCc
Confidence 4788999999999999999999999999988652 2346689999999999999988765
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=99.32 E-value=6.6e-12 Score=88.18 Aligned_cols=55 Identities=20% Similarity=0.181 Sum_probs=47.0
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg 60 (142)
.+|.|++|.+|.|+|.++|+|||++|+||.+.. + + .....+|.++|||+||.+|.
T Consensus 22 V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~--~-~-~~~~~~~~v~IRG~nI~yI~ 76 (78)
T cd01733 22 VTVELRNETTVTGRIASVDAFMNIRLAKVTIID--R-N-GKQVQVEEIMVTGRNIRYVH 76 (78)
T ss_pred EEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc--C-C-CceeECCcEEEECCEEEEEE
Confidence 468899999999999999999999999998653 2 2 23557899999999999885
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=99.31 E-value=9.5e-12 Score=87.60 Aligned_cols=64 Identities=20% Similarity=0.224 Sum_probs=51.2
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCCCCC
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTR 67 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDee~e 67 (142)
.+|.|++|.++.|+|.++|.|||++|++|.+.. ++.......+|.++|||+||.+|...|...+
T Consensus 14 V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 14 VTVELKNDLSIRGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred EEEEECCCcEEEEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeChhHcC
Confidence 478899999999999999999999999997653 2111224467999999999999987765443
No 29
>KOG3482|consensus
Probab=99.22 E-value=1.3e-11 Score=87.64 Aligned_cols=58 Identities=24% Similarity=0.307 Sum_probs=52.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS 64 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe 64 (142)
.|.|++|.+|.|+|.+.|.|||+.|.+|+|++ ++.....+|.++||++||..|..+++
T Consensus 22 ~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i----dG~~~g~lGEilIRCNNvlyi~gv~~ 79 (79)
T KOG3482|consen 22 LVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI----DGVSTGNLGEILIRCNNVLYIRGVPE 79 (79)
T ss_pred EEEEecCcEEEEEEEEecchhheehhhhhhhh----cccccccceeEEEEeccEEEEecCCC
Confidence 47899999999999999999999999999988 55678899999999999999987653
No 30
>KOG3168|consensus
Probab=99.22 E-value=1.3e-12 Score=104.60 Aligned_cols=60 Identities=35% Similarity=0.502 Sum_probs=52.2
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEec-CC-----CCeeeEEeceEEEecCcEEEeeeC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYS-PT-----AGVEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~-~~-----~~~~~r~LGlvlIRGdNIVlIg~v 62 (142)
.++++|||.|+|.+.+||+|||+||.||+|.... ++ +++++|.+|++++||+||++.+..
T Consensus 18 rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 18 RVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred EEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence 5899999999999999999999999999997532 21 457899999999999999998753
No 31
>KOG3460|consensus
Probab=99.21 E-value=2.7e-12 Score=93.09 Aligned_cols=60 Identities=22% Similarity=0.370 Sum_probs=51.1
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCC---C------eeeEEeceEEEecCcEEEeeeC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTA---G------VEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~---~------~~~r~LGlvlIRGdNIVlIg~v 62 (142)
-|.+.++|++.|+|+|||+|.|+||+|++|.+..-+. . ..++.+...++|||+|++|++.
T Consensus 19 yVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp 87 (91)
T KOG3460|consen 19 YVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP 87 (91)
T ss_pred EEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence 4678999999999999999999999999998754321 1 2477889999999999999985
No 32
>KOG1775|consensus
Probab=99.12 E-value=3.7e-11 Score=86.03 Aligned_cols=60 Identities=30% Similarity=0.418 Sum_probs=52.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
-+..++.|+++|+|.|||.|.|+||+|++|+-..+ ++.....++.+++.||||+++-+..
T Consensus 21 ~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~-egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 21 WIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITP-EGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred EEEEccCceeeeEEechHHHHHHHHHhhhheeeCC-CcceeeeeeeeeecCCcEEEEecCC
Confidence 36789999999999999999999999999997766 3345778999999999999998765
No 33
>KOG1774|consensus
Probab=99.05 E-value=9.3e-11 Score=84.77 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=43.1
Q ss_pred CCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCC
Q psy1140 8 SLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 8 sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
-|-.+.|.+.|||+|||+||+||+|..... ....++|.++++||||.+|-..+
T Consensus 35 ~~~rieG~IvGFDEyMNvVlD~aeev~~k~---~~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 35 VGLRIEGRIVGFDEYMNLVLDDAEEVHSKT---KSRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred cCcEEeEEEechHHhhhhhhcchhhccccc---cCCCccccEEEcCCcEEEEeecC
Confidence 356789999999999999999999964221 23448999999999999997643
No 34
>KOG1783|consensus
Probab=98.77 E-value=8.1e-10 Score=78.39 Aligned_cols=56 Identities=29% Similarity=0.365 Sum_probs=50.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKI 62 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~v 62 (142)
.|.|+||-.|.|+|...|.|||+-|+.++|.. ++..++..|..+|||+||..|+..
T Consensus 20 ~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~----ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 20 VVKLNSGVDYRGTLVCLDGYMNIALESTEEYV----NGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred EEEecCCccccceehhhhhHHHHHHHHHHHHh----cCcccccccceeeccccEEEEEec
Confidence 47899999999999999999999999999987 455688899999999999999874
No 35
>KOG3448|consensus
Probab=97.59 E-value=0.00025 Score=52.28 Aligned_cols=58 Identities=21% Similarity=0.234 Sum_probs=45.3
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~ 61 (142)
.+|.|+.+-.+.|+|.|.|||.|+-|.|..- .++++----.....++|||..|-++-.
T Consensus 15 V~VeLKnd~~i~GtL~svDqyLNlkL~di~v--~d~~kyPhm~Sv~ncfIRGSvvrYv~l 72 (96)
T KOG3448|consen 15 VVVELKNDLSICGTLHSVDQYLNLKLTDISV--TDPDKYPHMLSVKNCFIRGSVVRYVQL 72 (96)
T ss_pred EEEEEcCCcEEEEEecccchhheeEEeeeEe--eCcccCCCeeeeeeEEEeccEEEEEEe
Confidence 3688999999999999999999999998653 233222224456788999999998865
No 36
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.36 E-value=8.9e-05 Score=51.68 Aligned_cols=25 Identities=32% Similarity=0.327 Sum_probs=23.1
Q ss_pred eEEEEEEEEecceecEEecceEEEE
Q psy1140 10 IFFQGTLKGFDQTINIILDDSHERV 34 (142)
Q Consensus 10 R~ivG~L~gFDqfmNLVL~davEri 34 (142)
..++|.|.+||+|+|++|.|+.|..
T Consensus 23 G~~~G~lvAFDK~wNm~L~DV~E~y 47 (66)
T cd01739 23 GVCSGFLVAFDKFWNMALVDVDETY 47 (66)
T ss_pred cEEEEEEEeeeeehhheehhhhhhh
Confidence 3789999999999999999999965
No 37
>KOG3293|consensus
Probab=97.11 E-value=0.00071 Score=52.47 Aligned_cols=58 Identities=19% Similarity=0.130 Sum_probs=48.0
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCC
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKIS 63 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vD 63 (142)
-|.|+.|-+|.|.|...|.+|||.|.++++... ++..--.+-.+-|||++|-++-..|
T Consensus 16 lvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~---Dgdkf~r~pEcYirGttIkylri~d 73 (134)
T KOG3293|consen 16 LVELKNGETYNGHLVNCDNWMNLHLREVICTSE---DGDKFFRMPECYIRGTTIKYLRIPD 73 (134)
T ss_pred EEEecCCCEecceeecchhhhhcchheeEEecc---CCCceeecceeEEecceeEEEeccH
Confidence 478999999999999999999999999998653 3344456678999999999996544
No 38
>KOG3428|consensus
Probab=97.04 E-value=0.0034 Score=47.53 Aligned_cols=67 Identities=25% Similarity=0.279 Sum_probs=52.4
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCCCCCCCCCCcccchh
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDN 78 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDee~e~~v~~~~v~~~ 78 (142)
+|+-|..|+...|++.+.|.+||..|-++.=.. .+ +...+....+||+||=++-..| ++++..+-..
T Consensus 15 vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~----~~-~pv~l~~lsirgnniRy~~lpD-----~l~ld~Llvd 81 (109)
T KOG3428|consen 15 VTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV----KG-EPVRLDTLSIRGNNIRYYILPD-----SLNLDTLLVD 81 (109)
T ss_pred EEEEecCCcEEeeeEEEEEhhheeEEEEEEEec----CC-CceeEEEEEeecceEEEEEccC-----CcCcceeeee
Confidence 589999999999999999999999998765332 22 4567888999999999996544 5555555443
No 39
>KOG3172|consensus
Probab=96.93 E-value=0.0037 Score=47.67 Aligned_cols=61 Identities=18% Similarity=0.134 Sum_probs=49.7
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCCCC
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSST 66 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDee~ 66 (142)
.|+..++|-.|.|+|+-.+.+||+.|+|.+-... + .....+..++|||+.|-++-..|-=+
T Consensus 18 Vt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~---d-g~vs~le~V~IRGS~IRFlvlPdmLK 78 (119)
T KOG3172|consen 18 VTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR---D-GRVSQLEQVFIRGSKIRFLVLPDMLK 78 (119)
T ss_pred EEEEecCCceeeeeeEEeccccccEEEEEEEEcc---C-CcceeeeeEEEecCeEEEEECchHhh
Confidence 5788999999999999999999999999774321 2 24567889999999999988766433
No 40
>KOG3459|consensus
Probab=96.74 E-value=0.00016 Score=54.95 Aligned_cols=58 Identities=19% Similarity=0.361 Sum_probs=46.3
Q ss_pred EEEcCCeEEEEEEEEecceecEEecceEEEEec-CC-----C--C-eeeEEeceEEEecCcEEEeee
Q psy1140 4 FTILSLIFFQGTLKGFDQTINIILDDSHERVYS-PT-----A--G-VEQVVLGLHIIRGDNIKIPTK 61 (142)
Q Consensus 4 ~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~-~~-----~--~-~~~r~LGlvlIRGdNIVlIg~ 61 (142)
|-..+.+.+-|...|||-|.|++|+++.|.... ++ + . ...|.+|.++||||+|+++..
T Consensus 41 i~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r 107 (114)
T KOG3459|consen 41 INCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLR 107 (114)
T ss_pred EEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEe
Confidence 456788899999999999999999999986422 11 1 1 237899999999999998863
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=94.18 E-value=0.071 Score=36.39 Aligned_cols=55 Identities=9% Similarity=0.183 Sum_probs=31.0
Q ss_pred eEEEEcCCeEEEEEEEEecc---eecEEecceEEEEecCCC----CeeeEEeceEEEecCcEE
Q psy1140 2 TTFTILSLIFFQGTLKGFDQ---TINIILDDSHERVYSPTA----GVEQVVLGLHIIRGDNIK 57 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDq---fmNLVL~davEri~~~~~----~~~~r~LGlvlIRGdNIV 57 (142)
.++|+++|..|.|+|.+++. -+.++|.-+.... .+.. .........+++.++.|+
T Consensus 15 V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~-~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 15 VEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVP-KSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEEEETTS-EEEEEEEEE-T---T--EEEEEEEETT-S------EEEEEEE-GGGEEE-----
T ss_pred EEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecc-ccccccCCccCCCCCceEEEeccccC
Confidence 37899999999999999999 7889997666532 2211 123445567777777765
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=88.53 E-value=0.99 Score=30.90 Aligned_cols=28 Identities=18% Similarity=0.395 Sum_probs=24.6
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecc
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDD 29 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~d 29 (142)
.|+-|.+|-.+.|..+|||+|+=++-.+
T Consensus 14 Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 14 VTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred EEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 4788999999999999999999777544
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=87.63 E-value=1.2 Score=30.54 Aligned_cols=28 Identities=14% Similarity=0.336 Sum_probs=24.3
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecc
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDD 29 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~d 29 (142)
.|+-|.+|-.+.|..+|||+|+=++-.+
T Consensus 18 Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 18 VTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred EEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 4788999999999999999999777543
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=86.00 E-value=1.6 Score=31.47 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=25.1
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
.|+-|.+|-.+.|..+|||+|+=++-.+-
T Consensus 22 VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 22 VTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred EEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 47889999999999999999998775543
No 45
>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=82.50 E-value=4.6 Score=25.37 Aligned_cols=25 Identities=12% Similarity=0.162 Sum_probs=21.3
Q ss_pred CCeEEEEEEEEecceecEEecceEE
Q psy1140 8 SLIFFQGTLKGFDQTINIILDDSHE 32 (142)
Q Consensus 8 sGR~ivG~L~gFDqfmNLVL~davE 32 (142)
+++.+.|+..|+|....|++.....
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 5888899999999999999865443
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=68.19 E-value=9.1 Score=30.99 Aligned_cols=29 Identities=21% Similarity=0.293 Sum_probs=25.0
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
.|+-|.+|-.+.|+.+|||+|+=|+-.+.
T Consensus 27 VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 27 VTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred EEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 47889999999999999999997776554
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=67.58 E-value=9.5 Score=30.90 Aligned_cols=29 Identities=21% Similarity=0.392 Sum_probs=25.1
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
.|+-|.+|-.+.|..+|||+|+=|.-.+.
T Consensus 107 VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 107 VTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred EEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 47889999999999999999997776554
No 48
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=61.74 E-value=16 Score=26.32 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=22.9
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecc
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDD 29 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~d 29 (142)
|+-|..|-.+.|..+|||+|.=++=.+
T Consensus 23 tIfLvNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 23 TIFLVNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred EEEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence 677899999999999999998666444
No 49
>PF01581 FARP: FMRFamide related peptide family; InterPro: IPR002544 The neuropeptide Phe-Met-Arg-Phe-NH2 (FMRFamide) is a potent cardioactive neuropeptide in Lymnaea stagnalis []. FMRFamide (Phe-Met-Arg-Phe-NH2) was first demonstrated to be cardioactive in several molluscan species. FMRFamide is now known to be cardioexcitatory in mammals, to inhibit morphine-induced antinociception, and to block morphine-, defeat-, and deprivation-induced feeding []. Thirteen neuropeptides varying in length from 7 to 11 residues and ending C-terminally in -Phe-Met-Arg-Phe-NH2 (calliFMRFamides 1-13) and one dodecapeptide ending in -Met-Ile-Arg-Phe-NH2 (calliMIRFamide 1) have been isolated from thoracic ganglia of the blowfly Calliphora vomitoria. Results indicate that the N terminus (in addition to the C terminus as previously found for FMRFamides of other organisms) is crucial for at least some biological activities [].; GO: 0007218 neuropeptide signaling pathway
Probab=52.81 E-value=5.5 Score=18.70 Aligned_cols=8 Identities=63% Similarity=1.144 Sum_probs=5.9
Q ss_pred cccceecc
Q psy1140 92 TLSFMRFG 99 (142)
Q Consensus 92 ~~~~~~~~ 99 (142)
...|||||
T Consensus 3 ~~~~~RFG 10 (11)
T PF01581_consen 3 DNNFMRFG 10 (11)
T ss_pred cccccccC
Confidence 34589998
No 50
>KOG3382|consensus
Probab=46.51 E-value=10 Score=30.23 Aligned_cols=20 Identities=30% Similarity=0.320 Sum_probs=16.2
Q ss_pred EEEEEEEEecceecEEecce
Q psy1140 11 FFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 11 ~ivG~L~gFDqfmNLVL~da 30 (142)
.=+|+|.|.|+|.|=.-++-
T Consensus 44 ~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 44 HKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred ccceeeeeecccccchhccc
Confidence 34799999999999776554
No 51
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=42.45 E-value=1.3e+02 Score=21.92 Aligned_cols=63 Identities=21% Similarity=0.192 Sum_probs=42.0
Q ss_pred EEEcCCeEEEEEEEEecc-eecEEecceEEEEecCC--CC---eeeEEeceEEEecCcEEEeeeCCCCC
Q psy1140 4 FTILSLIFFQGTLKGFDQ-TINIILDDSHERVYSPT--AG---VEQVVLGLHIIRGDNIKIPTKISSST 66 (142)
Q Consensus 4 ~~l~sGR~ivG~L~gFDq-fmNLVL~davEri~~~~--~~---~~~r~LGlvlIRGdNIVlIg~vDee~ 66 (142)
+.=+++-.|.|+|..+|. -..|.|.++...=..+. +. -.+.....++.||..|--+.-.+...
T Consensus 13 lisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 13 LISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp EEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred EEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 445778899999999998 67788888765311110 00 12335688999999998887765544
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=40.46 E-value=38 Score=27.48 Aligned_cols=29 Identities=21% Similarity=0.087 Sum_probs=26.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecceE
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDSH 31 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~dav 31 (142)
.||..+|+.|.|+..||++--|.||+...
T Consensus 33 rvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 33 RVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred EEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 58999999999999999999999987644
No 53
>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=36.44 E-value=14 Score=26.99 Aligned_cols=17 Identities=35% Similarity=0.429 Sum_probs=14.3
Q ss_pred EEEEEecceecEEecce
Q psy1140 14 GTLKGFDQTINIILDDS 30 (142)
Q Consensus 14 G~L~gFDqfmNLVL~da 30 (142)
|+|.|.|.|.|.--+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999986544
No 54
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=33.19 E-value=14 Score=38.21 Aligned_cols=56 Identities=18% Similarity=0.198 Sum_probs=0.0
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEe
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIP 59 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlI 59 (142)
+|-|-.+||.+.|+|.+-|.-|+.+|.---+ +.+. .-......|.++|||+|.|.-
T Consensus 250 ~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~-~v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 250 STYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDT-SVSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp ----------------------------------------------------------
T ss_pred ceeecCCCCEeceEEeccHHHHHHHHHHHhh-hccc-eeecchhheeeeecCccHHHH
Confidence 3556689999999999999999988865444 3221 113466889999999998764
No 55
>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Probab=31.14 E-value=21 Score=30.08 Aligned_cols=12 Identities=50% Similarity=1.099 Sum_probs=10.2
Q ss_pred ceecccCCchhh
Q psy1140 95 FMRFGYRPSVDV 106 (142)
Q Consensus 95 ~~~~~~~~~~~~ 106 (142)
+.||||||..|.
T Consensus 288 ~vr~GyDPR~d~ 299 (310)
T PF09734_consen 288 WVRFGYDPRKDP 299 (310)
T ss_pred eEecccCCCcCc
Confidence 579999999885
No 56
>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=29.72 E-value=2.1e+02 Score=20.48 Aligned_cols=51 Identities=14% Similarity=0.186 Sum_probs=33.7
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEee
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPT 60 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg 60 (142)
..|++-++.+..|++.|.|...--++ ++-...| -+ .....++|+..|+++.
T Consensus 27 v~f~l~e~t~V~a~F~a~d~~~~~f~---Vs~L~TP-lG----v~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 27 VEFTLHENTTVSARFGACDIDVSNFQ---VSNLQTP-LG----VQPEALLRCSDVISIS 77 (80)
T ss_dssp EEEEEGGG-EEEEEEEEE-TTS-EEE---EEEEETT-TT----EEEEEEEEGGGEEEEE
T ss_pred eEEEEeCCeEEEEEEEEecCchheEE---hhhcCCC-cc----cChhheeecCCEEEEE
Confidence 36899999999999999998654442 2222232 12 2467899999999886
No 57
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=27.22 E-value=23 Score=28.93 Aligned_cols=27 Identities=26% Similarity=0.457 Sum_probs=15.2
Q ss_pred hhhhhhhhhccccccccccccccCCCC
Q psy1140 115 KVESMAFIMGLTLPCVLSHDLFLPPWN 141 (142)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (142)
+...++-|+|++...+-+-|+|.|-||
T Consensus 85 ~~d~~~k~~gi~~l~it~~DlY~~~~n 111 (194)
T PF07998_consen 85 PDDKVTKIFGITVLGITDRDLYSPGLN 111 (194)
T ss_dssp --SEE------SEEEEESS-EEETTES
T ss_pred hhhhhhhccccceEEEeccccCCCCCc
Confidence 345566688999999999999988887
No 58
>PRK14639 hypothetical protein; Provisional
Probab=27.03 E-value=1.1e+02 Score=23.44 Aligned_cols=24 Identities=29% Similarity=0.324 Sum_probs=19.4
Q ss_pred EEEEcCCeEEEEEEEEecceecEEe
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIIL 27 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL 27 (142)
.|++.+++.+.|+|.++|. .++.|
T Consensus 92 ~v~l~~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 92 KITTNEKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred EEEECCCcEEEEEEEEEeC-CEEEE
Confidence 4677889999999999998 45554
No 59
>PRK14638 hypothetical protein; Provisional
Probab=26.56 E-value=86 Score=24.31 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=19.0
Q ss_pred EEEEcCCeEEEEEEEEecceecEEe
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIIL 27 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL 27 (142)
.|++.+++.++|+|.++|.- ++.|
T Consensus 104 ~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 104 KIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred EEEECCCcEEEEEEEEEeCC-EEEE
Confidence 56778999999999999963 4444
No 60
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=25.31 E-value=20 Score=28.57 Aligned_cols=31 Identities=29% Similarity=0.259 Sum_probs=25.3
Q ss_pred hhhhccccccccccccccceecccCCchhhhhhhhh
Q psy1140 77 DNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSAS 112 (142)
Q Consensus 77 ~~~il~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (142)
-+++++.|.+|+-+|++ || +|+.=...++..
T Consensus 35 l~~LleaQk~G~tA~~l----fG-~P~~~a~eli~~ 65 (206)
T PF06570_consen 35 LPHLLEAQKKGKTARQL----FG-DPKEYADELIKP 65 (206)
T ss_pred HHHHHHHHhCCCcHHHH----cC-CHHHHHHHHhcc
Confidence 35689999999999999 99 999766666543
No 61
>PRK10942 serine endoprotease; Provisional
Probab=25.24 E-value=99 Score=27.99 Aligned_cols=27 Identities=19% Similarity=0.153 Sum_probs=24.3
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecc
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDD 29 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~d 29 (142)
+|++.+||++.+++.++|...+|-|=.
T Consensus 139 ~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 139 KVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred EEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 688999999999999999999997654
No 62
>PRK10898 serine endoprotease; Provisional
Probab=24.79 E-value=1.1e+02 Score=26.47 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=24.4
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
+|++.+|+.+.+++.++|....|-+=..
T Consensus 105 ~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 105 IVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred EEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5888999999999999999999976544
No 63
>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=24.63 E-value=1.2e+02 Score=26.21 Aligned_cols=28 Identities=14% Similarity=0.131 Sum_probs=24.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
.|++.+|+.+.+++.++|...+|-+=..
T Consensus 105 ~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 105 VVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred EEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5788999999999999999999987543
No 64
>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=24.60 E-value=1.9e+02 Score=21.36 Aligned_cols=19 Identities=11% Similarity=0.037 Sum_probs=15.7
Q ss_pred eEEEEcCCeEEEEEEEEec
Q psy1140 2 TTFTILSLIFFQGTLKGFD 20 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFD 20 (142)
++|++.+|+.+.|.+..=|
T Consensus 60 ~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 60 YRVTLKDGRILSGIVASET 78 (133)
T ss_pred EEEEECCCCEEEEEEEecC
Confidence 5789999999999987733
No 65
>KOG2473|consensus
Probab=24.10 E-value=32 Score=32.16 Aligned_cols=14 Identities=43% Similarity=0.842 Sum_probs=11.5
Q ss_pred cceecccCCchhhh
Q psy1140 94 SFMRFGYRPSVDVL 107 (142)
Q Consensus 94 ~~~~~~~~~~~~~~ 107 (142)
.+.||||||.=|+-
T Consensus 283 ~wirFGyDPRkD~~ 296 (484)
T KOG2473|consen 283 LWIRFGYDPRKDPN 296 (484)
T ss_pred eeeeecCCCCCCcC
Confidence 36799999998874
No 66
>PRK02001 hypothetical protein; Validated
Probab=23.99 E-value=1e+02 Score=24.19 Aligned_cols=24 Identities=25% Similarity=0.253 Sum_probs=19.5
Q ss_pred EEEEcCCeEEEEEEEEecceecEEe
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIIL 27 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL 27 (142)
.|++.+++.|.|+|.++|.- +++|
T Consensus 94 ~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 94 EVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred EEEECCCCEEEEEEEEEeCC-EEEE
Confidence 56778999999999999974 4444
No 67
>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=23.24 E-value=1e+02 Score=20.93 Aligned_cols=25 Identities=16% Similarity=0.189 Sum_probs=20.6
Q ss_pred CCeEEEEEEEEecceecEEecceEE
Q psy1140 8 SLIFFQGTLKGFDQTINIILDDSHE 32 (142)
Q Consensus 8 sGR~ivG~L~gFDqfmNLVL~davE 32 (142)
.|-+|.|.+.+||.-.++++=.|.+
T Consensus 15 ~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 15 FEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred CCceEEEEEEEecCCCcEEEEECcc
Confidence 4899999999999999988655444
No 68
>PRK06955 biotin--protein ligase; Provisional
Probab=22.45 E-value=2.4e+02 Score=23.77 Aligned_cols=22 Identities=27% Similarity=0.406 Sum_probs=19.3
Q ss_pred cCCeEEEEEEEEecceecEEec
Q psy1140 7 LSLIFFQGTLKGFDQTINIILD 28 (142)
Q Consensus 7 ~sGR~ivG~L~gFDqfmNLVL~ 28 (142)
.+++.+.|+.+|+|....|++.
T Consensus 257 ~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 257 DGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred CCCcEEEEEEeeECCCceEEEE
Confidence 4667799999999999999984
No 69
>PRK10139 serine endoprotease; Provisional
Probab=21.68 E-value=1.3e+02 Score=27.06 Aligned_cols=28 Identities=21% Similarity=0.176 Sum_probs=24.6
Q ss_pred EEEEcCCeEEEEEEEEecceecEEecce
Q psy1140 3 TFTILSLIFFQGTLKGFDQTINIILDDS 30 (142)
Q Consensus 3 ~~~l~sGR~ivG~L~gFDqfmNLVL~da 30 (142)
+|++.+|+++.+++.|+|....|-+=..
T Consensus 118 ~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 118 SIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred EEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 6889999999999999999999876443
No 70
>PF15007 CEP44: Centrosomal spindle body, CEP44
Probab=20.95 E-value=65 Score=25.05 Aligned_cols=26 Identities=15% Similarity=0.451 Sum_probs=22.0
Q ss_pred ecccCCchhhhhhhhhhhhhhhhhhh
Q psy1140 97 RFGYRPSVDVLHLSASALKVESMAFI 122 (142)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 (142)
-|||+|++-.....++-.-++-|.++
T Consensus 80 ef~YkP~lT~~QF~s~gFAErKi~i~ 105 (131)
T PF15007_consen 80 EFNYKPSLTKAQFFSKGFAERKIIIV 105 (131)
T ss_pred HhCCCCCCCHHHHHHhhHHHHHHHHH
Confidence 39999999999999988888876654
No 71
>PHA00672 hypothetical protein
Probab=20.76 E-value=4.4e+02 Score=21.04 Aligned_cols=28 Identities=18% Similarity=0.255 Sum_probs=23.1
Q ss_pred eEEEEcCCeEEEEEEEEecceecEEecceE
Q psy1140 2 TTFTILSLIFFQGTLKGFDQTINIILDDSH 31 (142)
Q Consensus 2 ~~~~l~sGR~ivG~L~gFDqfmNLVL~dav 31 (142)
.+++|..|-.++|.++-||.+ |+++--.
T Consensus 50 Rei~IPkGt~LtG~~hkf~~~--ii~sG~i 77 (152)
T PHA00672 50 RTIRIPAGVALTGALIKVSTV--LIFSGHA 77 (152)
T ss_pred EEEeccCceeeeeeeeEeeEE--EEecccE
Confidence 368899999999999999988 6665544
No 72
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=20.44 E-value=1.1e+02 Score=19.67 Aligned_cols=21 Identities=29% Similarity=0.635 Sum_probs=14.2
Q ss_pred EEEEEEEecceecEEecceEE
Q psy1140 12 FQGTLKGFDQTINIILDDSHE 32 (142)
Q Consensus 12 ivG~L~gFDqfmNLVL~davE 32 (142)
.+|++.|.|+...+.|.+..+
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 689999999999999987654
Done!