Query psy1222
Match_columns 60
No_of_seqs 135 out of 1002
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 21:51:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01717 Sm_B The eukaryotic Sm 99.9 6.2E-23 1.4E-27 112.9 3.4 59 1-60 17-75 (79)
2 cd06168 LSm9 The eukaryotic Sm 99.9 1.5E-22 3.3E-27 110.9 3.7 55 1-60 17-71 (75)
3 cd01730 LSm3 The eukaryotic Sm 99.9 1.6E-22 3.4E-27 112.0 3.0 60 1-60 18-79 (82)
4 cd01729 LSm7 The eukaryotic Sm 99.8 7.2E-22 1.6E-26 109.4 3.4 57 1-60 19-75 (81)
5 cd01720 Sm_D2 The eukaryotic S 99.8 1.1E-21 2.4E-26 110.1 3.2 60 1-60 21-82 (87)
6 cd01732 LSm5 The eukaryotic Sm 99.8 7.8E-21 1.7E-25 104.3 2.7 52 1-60 20-71 (76)
7 cd01728 LSm1 The eukaryotic Sm 99.8 1E-20 2.3E-25 103.3 3.2 52 1-60 19-70 (74)
8 cd01727 LSm8 The eukaryotic Sm 99.8 2.8E-20 6.1E-25 101.3 3.0 53 1-60 16-68 (74)
9 cd01719 Sm_G The eukaryotic Sm 99.8 7E-20 1.5E-24 99.5 3.4 49 1-60 17-65 (72)
10 PRK00737 small nuclear ribonuc 99.8 7.9E-20 1.7E-24 99.1 2.8 48 1-59 21-68 (72)
11 cd01731 archaeal_Sm1 The archa 99.8 8.9E-20 1.9E-24 97.8 2.9 48 1-59 17-64 (68)
12 cd01718 Sm_E The eukaryotic Sm 99.8 1.1E-19 2.4E-24 100.4 3.3 48 2-59 28-75 (79)
13 PTZ00138 small nuclear ribonuc 99.7 7.8E-19 1.7E-23 98.9 3.2 48 3-60 37-84 (89)
14 cd01726 LSm6 The eukaryotic Sm 99.7 2.9E-18 6.2E-23 91.8 3.2 48 1-59 17-64 (67)
15 cd01722 Sm_F The eukaryotic Sm 99.7 2.4E-18 5.3E-23 92.3 2.9 48 1-59 18-65 (68)
16 smart00651 Sm snRNP Sm protein 99.7 2.5E-18 5.4E-23 91.1 2.7 49 1-59 15-63 (67)
17 KOG3168|consensus 99.7 3.1E-19 6.6E-24 109.4 -1.9 59 1-60 21-79 (177)
18 PF01423 LSM: LSM domain ; In 99.7 8.9E-18 1.9E-22 89.1 2.3 49 1-59 15-63 (67)
19 cd00600 Sm_like The eukaryotic 99.7 3.8E-17 8.3E-22 85.5 3.2 48 1-59 13-60 (63)
20 KOG1780|consensus 99.7 1.9E-17 4E-22 90.1 1.6 48 1-59 21-68 (77)
21 COG1958 LSM1 Small nuclear rib 99.7 5.5E-17 1.2E-21 89.1 3.5 52 1-59 24-75 (79)
22 KOG1781|consensus 99.6 1.3E-17 2.8E-22 94.9 -2.2 57 1-60 34-90 (108)
23 cd01721 Sm_D3 The eukaryotic S 99.6 4.1E-15 8.9E-20 80.2 3.5 48 1-59 17-64 (70)
24 cd01723 LSm4 The eukaryotic Sm 99.5 3.9E-15 8.6E-20 81.3 3.3 49 1-59 18-66 (76)
25 KOG3460|consensus 99.5 3.1E-16 6.8E-21 87.0 -1.7 59 1-59 22-82 (91)
26 cd01724 Sm_D1 The eukaryotic S 99.5 2.3E-14 4.9E-19 80.7 3.7 48 1-59 18-65 (90)
27 cd01733 LSm10 The eukaryotic S 99.5 4.9E-14 1.1E-18 77.5 3.6 48 1-59 26-73 (78)
28 KOG1782|consensus 99.5 1.5E-15 3.2E-20 89.3 -3.5 51 1-59 26-76 (129)
29 KOG1784|consensus 99.4 2E-13 4.3E-18 76.9 3.1 51 2-59 18-68 (96)
30 cd01725 LSm2 The eukaryotic Sm 99.4 2.5E-13 5.5E-18 75.1 3.5 50 1-59 18-67 (81)
31 KOG1774|consensus 99.3 5.2E-13 1.1E-17 73.9 1.0 46 4-59 36-81 (88)
32 KOG3482|consensus 99.2 4.7E-12 1E-16 68.9 2.4 48 1-59 25-72 (79)
33 KOG1775|consensus 99.2 2.8E-12 6E-17 70.3 -0.1 51 1-59 24-74 (84)
34 KOG3459|consensus 99.2 2.1E-12 4.6E-17 74.8 -1.6 59 1-59 43-103 (114)
35 KOG1783|consensus 99.1 6.7E-12 1.4E-16 68.2 -1.6 48 1-59 23-70 (77)
36 cd01739 LSm11_C The eukaryotic 98.7 1E-08 2.2E-13 54.8 1.8 26 6-31 24-49 (66)
37 KOG3448|consensus 97.7 3.8E-05 8.1E-10 43.3 3.0 49 1-58 19-67 (96)
38 KOG3293|consensus 97.7 1.7E-05 3.7E-10 47.1 1.6 48 1-58 19-66 (134)
39 KOG3172|consensus 97.4 0.00026 5.7E-09 41.2 3.6 46 2-58 23-68 (119)
40 KOG3428|consensus 97.4 0.00031 6.7E-09 40.8 3.5 46 1-58 19-64 (109)
41 PF14438 SM-ATX: Ataxin 2 SM d 96.7 0.0021 4.5E-08 34.6 2.7 56 1-60 19-77 (77)
42 cd01716 Hfq Hfq, an abundant, 92.2 0.16 3.5E-06 26.8 2.3 21 1-21 18-38 (61)
43 TIGR02383 Hfq RNA chaperone Hf 91.6 0.2 4.4E-06 26.4 2.2 21 1-21 22-42 (61)
44 PRK00395 hfq RNA-binding prote 91.0 0.25 5.5E-06 27.3 2.3 24 1-24 26-49 (79)
45 PF02237 BPL_C: Biotin protein 89.9 0.75 1.6E-05 22.5 3.3 25 3-27 11-35 (48)
46 PF14563 DUF4444: Domain of un 89.1 0.67 1.4E-05 22.7 2.7 23 7-29 10-32 (42)
47 COG1923 Hfq Uncharacterized ho 87.5 0.52 1.1E-05 25.9 1.9 22 1-23 26-47 (77)
48 cd01736 LSm14_N LSm14 (also kn 80.7 6.6 0.00014 21.4 4.4 53 5-58 17-70 (74)
49 KOG3382|consensus 80.1 0.99 2.2E-05 27.4 1.1 19 7-25 45-63 (151)
50 KOG3168|consensus 79.2 5.9 0.00013 24.9 4.3 57 1-59 58-114 (177)
51 cd01735 LSm12_N LSm12 belongs 78.8 4.2 9E-05 21.3 3.1 25 3-27 15-39 (61)
52 PRK14091 RNA-binding protein H 78.2 2.2 4.8E-05 26.6 2.3 25 1-25 111-135 (165)
53 PF03614 Flag1_repress: Repres 77.5 3 6.5E-05 25.8 2.7 26 1-26 36-61 (165)
54 PF05071 NDUFA12: NADH ubiquin 77.4 1.1 2.3E-05 25.6 0.7 17 9-25 1-17 (105)
55 PRK14091 RNA-binding protein H 74.7 3.1 6.7E-05 25.9 2.2 24 1-24 31-54 (165)
56 PF03122 Herpes_MCP: Herpes vi 68.5 1.6 3.5E-05 34.6 0.0 50 2-60 255-304 (1354)
57 PF12701 LSM14: Scd6-like Sm d 66.4 16 0.00034 20.7 3.8 54 3-58 17-71 (96)
58 PRK06630 hypothetical protein; 58.4 5.9 0.00013 22.8 1.1 19 7-25 11-29 (99)
59 TIGR02038 protease_degS peripl 53.4 19 0.0004 24.3 3.0 26 1-26 108-133 (351)
60 PLN03095 NADH:ubiquinone oxido 53.4 8.4 0.00018 22.7 1.2 20 8-27 9-28 (115)
61 PLN02732 Probable NADH dehydro 51.1 15 0.00032 22.8 2.1 19 9-27 49-67 (159)
62 PF11095 Gemin7: Gem-associate 50.8 20 0.00044 19.7 2.4 23 2-24 32-55 (80)
63 PF01887 SAM_adeno_trans: S-ad 49.3 24 0.00052 23.1 2.9 23 6-28 169-191 (258)
64 PRK10898 serine endoprotease; 49.0 26 0.00056 23.7 3.2 26 1-26 108-133 (353)
65 PRK10942 serine endoprotease; 45.7 29 0.00063 24.5 3.1 25 1-25 142-166 (473)
66 PRK08183 NADH dehydrogenase; V 45.5 12 0.00027 22.4 1.1 19 8-26 25-43 (133)
67 PF06372 Gemin6: Gemin6 protei 43.2 32 0.00069 21.4 2.7 25 2-27 25-50 (166)
68 PF07202 Tcp10_C: T-complex pr 42.2 16 0.00034 22.9 1.2 19 5-23 159-177 (179)
69 TIGR02603 CxxCH_TIGR02603 puta 42.2 39 0.00085 19.6 2.9 24 1-25 64-87 (133)
70 PRK06955 biotin--protein ligas 40.8 40 0.00087 22.3 3.0 23 3-25 258-280 (300)
71 PTZ00275 biotin-acetyl-CoA-car 40.4 44 0.00096 22.0 3.2 23 3-25 245-267 (285)
72 PRK10139 serine endoprotease; 38.8 43 0.00092 23.6 3.0 26 1-26 121-146 (455)
73 TIGR00121 birA_ligase birA, bi 38.7 48 0.001 20.9 3.1 21 3-23 201-221 (237)
74 PF10894 DUF2689: Protein of u 38.3 2.8 6.1E-05 21.9 -2.1 18 15-32 21-38 (61)
75 COG0779 Uncharacterized protei 38.3 52 0.0011 20.1 3.0 21 2-23 111-131 (153)
76 PTZ00276 biotin/lipoate protei 36.7 58 0.0013 20.9 3.2 23 3-25 210-232 (245)
77 PRK11886 bifunctional biotin-- 35.6 56 0.0012 21.5 3.1 21 3-23 280-300 (319)
78 PF02707 MOSP_N: Major Outer S 35.6 29 0.00062 22.4 1.6 16 6-21 31-46 (204)
79 PRK14638 hypothetical protein; 35.4 39 0.00085 20.4 2.2 21 2-23 108-128 (150)
80 TIGR02037 degP_htrA_DO peripla 35.3 55 0.0012 22.5 3.1 26 1-26 88-113 (428)
81 PF05413 Peptidase_C34: Putati 34.5 17 0.00037 20.3 0.5 15 44-58 74-88 (92)
82 PF11607 DUF3247: Protein of u 34.2 29 0.00063 19.9 1.4 11 1-11 35-45 (101)
83 PF12869 tRNA_anti-like: tRNA_ 33.1 47 0.001 19.0 2.2 22 5-26 123-144 (144)
84 PF10622 Ehbp: Energy-converti 32.6 38 0.00083 18.6 1.6 39 17-55 20-58 (78)
85 PRK14639 hypothetical protein; 31.6 50 0.0011 19.7 2.2 21 2-23 96-116 (140)
86 PF05989 Chordopox_A35R: Chord 31.5 36 0.00079 21.4 1.6 21 7-27 93-113 (176)
87 PRK14633 hypothetical protein; 30.7 58 0.0012 19.6 2.4 21 2-23 106-126 (150)
88 PRK02001 hypothetical protein; 30.1 54 0.0012 19.9 2.2 21 2-23 98-118 (152)
89 PRK14640 hypothetical protein; 29.9 91 0.002 18.7 3.1 21 2-23 109-129 (152)
90 PRK14645 hypothetical protein; 29.7 57 0.0012 19.8 2.2 20 3-23 110-129 (154)
91 PRK08330 biotin--protein ligas 29.4 88 0.0019 19.7 3.2 23 3-25 196-219 (236)
92 PRK14643 hypothetical protein; 26.9 97 0.0021 19.0 2.9 17 2-18 116-132 (164)
93 PRK13325 bifunctional biotin-- 26.8 94 0.002 22.8 3.2 22 3-24 287-308 (592)
94 cd01734 YlxS_C YxlS is a Bacil 26.6 1E+02 0.0022 16.4 2.7 19 4-23 39-57 (83)
95 COG1912 Uncharacterized conser 26.2 90 0.002 21.0 2.8 21 3-23 170-190 (268)
96 PF01398 JAB: JAB1/Mov34/MPN/P 25.0 87 0.0019 17.1 2.3 26 6-31 27-53 (114)
97 PF02576 DUF150: Uncharacteris 23.8 1.5E+02 0.0032 17.3 3.3 19 3-22 100-118 (141)
98 cd01403 Cyt_c_Oxidase_VIIb Cyt 23.6 40 0.00086 17.1 0.6 14 15-28 7-20 (51)
99 PRK08477 biotin--protein ligas 23.3 1.2E+02 0.0025 19.3 2.9 24 2-25 182-205 (211)
100 cd08057 MPN_euk_non_mb Mpr1p, 20.8 1.6E+02 0.0034 17.3 3.0 27 5-31 23-49 (157)
101 PRK14631 hypothetical protein; 20.7 1.1E+02 0.0023 19.0 2.3 21 2-23 129-151 (174)
102 smart00232 JAB_MPN JAB/MPN dom 20.4 1.5E+02 0.0032 16.3 2.7 25 5-29 22-46 (135)
No 1
>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=99.87 E-value=6.2e-23 Score=112.89 Aligned_cols=59 Identities=37% Similarity=0.683 Sum_probs=47.6
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||++.|+|+|||+||||||++|+|++...+..+. .....+.|.+|+++|||++|+|
T Consensus 17 l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~-~~~~~~~r~lG~v~iRG~~Vv~ 75 (79)
T cd01717 17 LQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK-NSEREEKRTLGLVLLRGENIVS 75 (79)
T ss_pred ECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc-cccCcceeEeeeEEEcCCEEEE
Confidence 5899999999999999999999999999875432210 0113467899999999999985
No 2
>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=99.86 E-value=1.5e-22 Score=110.86 Aligned_cols=55 Identities=62% Similarity=1.017 Sum_probs=47.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||.|+|+|.|||+||||||++|.|++....+. ...+.|.+|+++|||++|++
T Consensus 17 l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~-----~~~~~r~lGlv~IrG~~Iv~ 71 (75)
T cd06168 17 MTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSF-----SPTEPRVLGLVMIPGHHIVS 71 (75)
T ss_pred EcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCcc-----CCccEEEeeeEEEeCCeEEE
Confidence 58999999999999999999999999998764321 13468999999999999974
No 3
>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=99.86 E-value=1.6e-22 Score=112.04 Aligned_cols=60 Identities=23% Similarity=0.336 Sum_probs=48.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCcccccc--ccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFES--KEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~--~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||++.|+|+|||+||||||+||+|++....++. +++......|.+|+++|||++|++
T Consensus 18 l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~ 79 (82)
T cd01730 18 LRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVIL 79 (82)
T ss_pred ECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEE
Confidence 589999999999999999999999999987643321 111123467899999999999974
No 4
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=7.2e-22 Score=109.39 Aligned_cols=57 Identities=26% Similarity=0.338 Sum_probs=46.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||+++|+|+|||+||||||++|+|+........ ......+.+|+++|||+||++
T Consensus 19 l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~---~~~~~~~~lG~v~iRG~nV~~ 75 (81)
T cd01729 19 FQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPY---KLTDKTRQLGLVVCRGTSVVL 75 (81)
T ss_pred ECCCcEEEEEEEEEcCcccEEecCEEEEEccCCccc---ccccceeEccEEEEcCCEEEE
Confidence 589999999999999999999999999986432110 112467889999999999974
No 5
>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=99.84 E-value=1.1e-21 Score=110.05 Aligned_cols=60 Identities=17% Similarity=0.299 Sum_probs=47.8
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccc--cccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESK--EENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~--~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|++||.+.|+|+|||+||||||+||+|++...++++. +.......|.+|+++||||+|++
T Consensus 21 lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 21 CRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred EcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 5899999999999999999999999999876543221 11113467889999999999974
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=99.81 E-value=7.8e-21 Score=104.28 Aligned_cols=52 Identities=25% Similarity=0.370 Sum_probs=44.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
+++||++.|+|+|||+||||||+||+|++..+. ....+.+|+++|||++|++
T Consensus 20 l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~--------~~~~~~lg~v~iRG~nV~~ 71 (76)
T cd01732 20 MKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPE--------GRKITKLDQILLNGNNICM 71 (76)
T ss_pred ECCCeEEEEEEEEeccceEEEEccEEEEEEcCC--------CceeeEcCeEEEeCCeEEE
Confidence 579999999999999999999999999984321 1246789999999999863
No 7
>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=99.81 E-value=1e-20 Score=103.35 Aligned_cols=52 Identities=23% Similarity=0.329 Sum_probs=44.5
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||++.|+|+|||+||||+|+||.|+..... ...++.+|+++|||++|++
T Consensus 19 l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~--------~~~~~~lG~~viRG~~V~~ 70 (74)
T cd01728 19 LRDGRKLIGILRSFDQFANLVLQDTVERIYVGD--------KYGDIPRGIFIIRGENVVL 70 (74)
T ss_pred EcCCeEEEEEEEEECCcccEEecceEEEEecCC--------ccceeEeeEEEEECCEEEE
Confidence 589999999999999999999999999876431 1246789999999999873
No 8
>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=99.80 E-value=2.8e-20 Score=101.28 Aligned_cols=53 Identities=34% Similarity=0.493 Sum_probs=44.5
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
++|||.++|+|+|||+||||||++|.|+...+.. ....+.+|++++||+||++
T Consensus 16 l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~-------~~~~~~lG~~~iRG~~I~~ 68 (74)
T cd01727 16 TVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE-------GVEQVVLGLYIIRGDNIAV 68 (74)
T ss_pred ECCCcEEEEEEEEEccccCEEccceEEEEecCCC-------CceeeEeceEEECCCEEEE
Confidence 5799999999999999999999999998754311 2356789999999999873
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=7e-20 Score=99.51 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=43.5
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
|+|||++.|+|+|||+||||+|++|+|+... ...+.+|+++|||++|++
T Consensus 17 L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-----------~~~~~lg~v~IRG~~I~~ 65 (72)
T cd01719 17 LNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-----------GEKNNIGMVVIRGNSIVM 65 (72)
T ss_pred ECCCeEEEEEEEEEcccccEEeccEEEEccC-----------CceeEeceEEECCCEEEE
Confidence 5899999999999999999999999999742 246889999999999863
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.78 E-value=7.9e-20 Score=99.12 Aligned_cols=48 Identities=25% Similarity=0.412 Sum_probs=42.6
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+|||+|.|+|++||+|||++|+||.|++.. +..+.+|.++|||++|+
T Consensus 21 lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-----------~~~~~lg~v~iRG~~V~ 68 (72)
T PRK00737 21 LKGGREFRGELQGYDIHMNLVLDNAEEIQDG-----------EVVRKLGKVVIRGDNVV 68 (72)
T ss_pred ECCCCEEEEEEEEEcccceeEEeeEEEEcCC-----------CeEeEcCcEEEeCCEEE
Confidence 5899999999999999999999999997532 24678999999999986
No 11
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.78 E-value=8.9e-20 Score=97.77 Aligned_cols=48 Identities=23% Similarity=0.400 Sum_probs=43.0
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+|||++.|+|.|||+||||+|++|+|++... ..+.+|+++|||++|+
T Consensus 17 l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~-----------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 17 LKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE-----------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred ECCCCEEEEEEEEECCcceEEEeeEEEEecCC-----------eEeEcCcEEEeCCEEE
Confidence 57999999999999999999999999987542 4678999999999986
No 12
>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=99.78 E-value=1.1e-19 Score=100.43 Aligned_cols=48 Identities=19% Similarity=0.313 Sum_probs=42.2
Q ss_pred CCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 2 TDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
++||+++|+|+|||+||||||+||+|+.... .+.+.+|+++|||+||+
T Consensus 28 ~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~----------~~~~~lG~iliRGnnV~ 75 (79)
T cd01718 28 QTDLRIEGVIIGFDEYMNLVLDDAEEVHLKT----------KTRKPLGRILLKGDNIT 75 (79)
T ss_pred CCCcEEEEEEEEEccceeEEEcCEEEEecCC----------ceEeEcCcEEEeCCEEE
Confidence 4899999999999999999999999997521 35678999999999986
No 13
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.75 E-value=7.8e-19 Score=98.87 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=41.6
Q ss_pred CCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
++|++.|+|+|||+||||||+||+|++... +..+.+|+++|||+||++
T Consensus 37 ~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~----------~~~~~lG~ilIRGnnV~~ 84 (89)
T PTZ00138 37 PNLRIEGKILGFDEYMNMVLDDAEEVYTKK----------NTRKDLGRILLKGDNITL 84 (89)
T ss_pred CCcEEEEEEEEEcccceEEEccEEEEecCC----------ceeeEcCeEEEcCCEEEE
Confidence 469999999999999999999999987531 357789999999999863
No 14
>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=99.73 E-value=2.9e-18 Score=91.79 Aligned_cols=48 Identities=23% Similarity=0.382 Sum_probs=42.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++||+|.|+|.|||+||||+|++|+|.... ...+.+|+++|||++|+
T Consensus 17 Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-----------~~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 17 LNSGVDYRGILACLDGYMNIALEQTEEYVNG-----------QLKNKYGDAFIRGNNVL 64 (67)
T ss_pred ECCCCEEEEEEEEEccceeeEEeeEEEEeCC-----------ceeeEeCCEEEECCEEE
Confidence 6899999999999999999999999886532 24678999999999985
No 15
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.72 E-value=2.4e-18 Score=92.33 Aligned_cols=48 Identities=23% Similarity=0.342 Sum_probs=42.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+|||++.|+|.|||+|||++|++|+|+... ...+.+|.++|||++|+
T Consensus 18 Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-----------~~~~~lg~~~IRG~~I~ 65 (68)
T cd01722 18 LKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-----------KSTGNLGEVLIRCNNVL 65 (68)
T ss_pred ECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-----------ccccCcCcEEEECCEEE
Confidence 5899999999999999999999999988542 24567999999999985
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.72 E-value=2.5e-18 Score=91.12 Aligned_cols=49 Identities=31% Similarity=0.474 Sum_probs=43.9
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+|||.+.|+|.|||+||||+|++|.|+.... ...+.+|.++|||++|+
T Consensus 15 l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~----------~~~~~~~~~~IrG~~I~ 63 (67)
T smart00651 15 LKNGREYRGTLKGFDQFMNLVLEDVEETVKDG----------EKKRKLGLVFIRGNNIV 63 (67)
T ss_pred ECCCcEEEEEEEEECccccEEEccEEEEecCC----------cEEeEeCCEEEcCCEEE
Confidence 57999999999999999999999999998642 35788999999999986
No 17
>KOG3168|consensus
Probab=99.71 E-value=3.1e-19 Score=109.45 Aligned_cols=59 Identities=32% Similarity=0.634 Sum_probs=51.7
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
++|||.|+|+|.+||+|||+||.||+|++..+.++.+.. ..+++|.+|++++||+||||
T Consensus 21 ~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~-~~eEkr~lgLvllRgenIvs 79 (177)
T KOG3168|consen 21 LQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMT-DGEEKRVLGLVLLRGENIVS 79 (177)
T ss_pred eccCceeechhhhhHHHHHHHHHHHHHHhcccccccccc-ccceeeEEEEEEecCCcEEE
Confidence 579999999999999999999999999998877654322 35789999999999999987
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.69 E-value=8.9e-18 Score=89.07 Aligned_cols=49 Identities=33% Similarity=0.546 Sum_probs=44.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+||+.+.|+|.+||+|||++|++|.|+.... .+.+++|.++|||++|.
T Consensus 15 l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~----------~~~~~~~~~~irG~~I~ 63 (67)
T PF01423_consen 15 LKNGRTYRGTLVSFDQFMNLVLSDVTETIKNG----------PEKRSLGLVFIRGSNIR 63 (67)
T ss_dssp ETTSEEEEEEEEEEETTEEEEEEEEEEEETTE----------SEEEEEEEEEEEGGGEE
T ss_pred EeCCEEEEEEEEEeechheEEeeeEEEEECCC----------CcEeECcEEEEECCEEE
Confidence 57999999999999999999999999998753 16788999999999986
No 19
>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=99.67 E-value=3.8e-17 Score=85.45 Aligned_cols=48 Identities=33% Similarity=0.652 Sum_probs=43.4
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+||+.+.|+|.|||+|||++|++|.|++.. ...+.+|.++|||++|.
T Consensus 13 l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~-----------~~~~~~~~~~irG~~I~ 60 (63)
T cd00600 13 LKDGRVLEGVLVAFDKYMNLVLDDVEETIKE-----------GKKRVLGLVLIRGDNVR 60 (63)
T ss_pred ECCCcEEEEEEEEECCCCCEEECCEEEEecC-----------CcEEECCeEEEECCEEE
Confidence 5799999999999999999999999999874 25688999999999985
No 20
>KOG1780|consensus
Probab=99.67 E-value=1.9e-17 Score=90.09 Aligned_cols=48 Identities=23% Similarity=0.351 Sum_probs=42.9
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++||.+.|+|+|||.|||+||++|+|.... ..+..+|+++|||++|+
T Consensus 21 lnG~r~v~GiLrGyD~FmNiVlde~vE~~~~-----------~~~~~ig~~vIrgnsiv 68 (77)
T KOG1780|consen 21 LNGGRKVTGILRGYDPFMNIVLDETVEPNGD-----------GDKNNIGMVVIRGNSIV 68 (77)
T ss_pred eCCCcEEEEEEeccchHHhhhhhhceeecCc-----------CCcceeeeEEEeccEEE
Confidence 5789999999999999999999999998764 34677999999999986
No 21
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.67 E-value=5.5e-17 Score=89.05 Aligned_cols=52 Identities=29% Similarity=0.411 Sum_probs=41.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++||+|.|+|.|||+|||++|+||.|+...... ....+..|.++|||++|+
T Consensus 24 lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~-------~~~~~~~~~~~IRG~~I~ 75 (79)
T COG1958 24 LKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGE-------KNVRRLGGEVLIRGDNIV 75 (79)
T ss_pred ECCCCEEEEEEEEEccceeEEEeceEEEeccCCc-------cccceeccEEEEECCcEE
Confidence 5899999999999999999999999999851100 012344459999999986
No 22
>KOG1781|consensus
Probab=99.62 E-value=1.3e-17 Score=94.91 Aligned_cols=57 Identities=32% Similarity=0.349 Sum_probs=47.7
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
+.+||+..|+|+|||+.|||||++|+||..++..+.+ ...++|.||++++||..+++
T Consensus 34 f~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~---~~~~tR~LGLvV~RGTalvl 90 (108)
T KOG1781|consen 34 FTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYK---LTDETRKLGLVVCRGTALVL 90 (108)
T ss_pred eecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccc---hhhhhheeeeEEEcccEEEE
Confidence 4689999999999999999999999999887654322 34567999999999998763
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=99.55 E-value=4.1e-15 Score=80.23 Aligned_cols=48 Identities=19% Similarity=0.266 Sum_probs=40.6
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++|.++.|+|.++|.|||++|++|.|..... ....+|.++|||+||.
T Consensus 17 Lk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g-----------~~~~~~~v~IRG~nI~ 64 (70)
T cd01721 17 LKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG-----------RVSQLEQVYIRGSKIR 64 (70)
T ss_pred ECCCcEEEEEEEEEcCCceeEEEEEEEECCCC-----------cEeEcCcEEEeCCEEE
Confidence 68999999999999999999999998754321 2356899999999984
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=99.55 E-value=3.9e-15 Score=81.35 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=40.9
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++|+++.|+|.+||+|||++|++|+|..... +....++.++|||++|.
T Consensus 18 Lkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g----------~~~~~~~~v~IRG~~I~ 66 (76)
T cd01723 18 LKNGETYNGHLVNCDNWMNIHLREVICTSKDG----------DKFWKMPECYIRGNTIK 66 (76)
T ss_pred ECCCCEEEEEEEEEcCCCceEEEeEEEECCCC----------cEeeeCCcEEEeCCEEE
Confidence 58999999999999999999999999874431 23345789999999985
No 25
>KOG3460|consensus
Probab=99.54 E-value=3.1e-16 Score=87.04 Aligned_cols=59 Identities=24% Similarity=0.362 Sum_probs=47.3
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccc--cccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFE--SKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~--~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+++|++.|+|.|||+|+||||+|++|.+...... ..++.....+|.+-++|+||++|+
T Consensus 22 lr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vi 82 (91)
T KOG3460|consen 22 LRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVI 82 (91)
T ss_pred ecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEE
Confidence 57899999999999999999999999998754321 112223467889999999999986
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=99.50 E-value=2.3e-14 Score=80.73 Aligned_cols=48 Identities=21% Similarity=0.295 Sum_probs=41.9
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++|..|.|+|.++|.|||++|+||+|+... .....+|.++|||++|.
T Consensus 18 LKng~~~~G~L~~vD~~MNl~L~~a~~~~~~-----------~~~~~~~~v~IRG~nI~ 65 (90)
T cd01724 18 LKNGTIVHGTITGVDPSMNTHLKNVKLTLKG-----------RNPVPLDTLSIRGNNIR 65 (90)
T ss_pred ECCCCEEEEEEEEEcCceeEEEEEEEEEcCC-----------CceeEcceEEEeCCEEE
Confidence 6899999999999999999999999888643 24567899999999984
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=99.47 E-value=4.9e-14 Score=77.55 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=40.8
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++|..|.|+|.++|.+||++|+||++.... .....+|.++|||++|.
T Consensus 26 LKng~~~~G~L~~vD~~MNl~L~~~~~~~~~-----------~~~~~~~~v~IRG~nI~ 73 (78)
T cd01733 26 LRNETTVTGRIASVDAFMNIRLAKVTIIDRN-----------GKQVQVEEIMVTGRNIR 73 (78)
T ss_pred ECCCCEEEEEEEEEcCCceeEEEEEEEEcCC-----------CceeECCcEEEECCEEE
Confidence 6899999999999999999999999876532 13346899999999984
No 28
>KOG1782|consensus
Probab=99.45 E-value=1.5e-15 Score=89.27 Aligned_cols=51 Identities=25% Similarity=0.334 Sum_probs=45.4
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+|||.+.|+|++||||.|+||++|+|++.-.. ....+..|..+|||+||+
T Consensus 26 LRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~--------~Y~di~~glfiIRGENVv 76 (129)
T KOG1782|consen 26 LRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN--------KYCDIPRGLFIIRGENVV 76 (129)
T ss_pred EecCcchhhhhhhHHHHHHHHHHhhhhheeecc--------eecccCceEEEEecCcEE
Confidence 689999999999999999999999999987642 346677899999999997
No 29
>KOG1784|consensus
Probab=99.40 E-value=2e-13 Score=76.90 Aligned_cols=51 Identities=31% Similarity=0.563 Sum_probs=44.7
Q ss_pred CCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 2 TDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
.|||.++|.|+||||-.||+|+++-|+..... ...++-.+|+.+|||+|+-
T Consensus 18 ~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~-------~gv~q~~lGlyiirgeNva 68 (96)
T KOG1784|consen 18 NDGRVIVGSLKGFDQTTNLIIDESHERIFSET-------EGVEQIVLGLYIIRGENVA 68 (96)
T ss_pred cCCeEEEEEeccccccceeeehhhHhhhhhhh-------cchhheeeEEEEEecCccc
Confidence 59999999999999999999999999987542 2356788999999999984
No 30
>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=99.40 E-value=2.5e-13 Score=75.07 Aligned_cols=50 Identities=12% Similarity=0.116 Sum_probs=40.2
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|++|..+.|+|.++|.|||++|+||++..... ......++.++|||++|.
T Consensus 18 LKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~---------~~~~~~~~~v~IRG~~I~ 67 (81)
T cd01725 18 LKNDLSIRGTLHSVDQYLNIKLTNISVTDPEK---------YPHMLSVKNCFIRGSVVR 67 (81)
T ss_pred ECCCcEEEEEEEEECCCcccEEEEEEEEcCCC---------cccccccCeEEEECCEEE
Confidence 68999999999999999999999997764321 112345689999999974
No 31
>KOG1774|consensus
Probab=99.31 E-value=5.2e-13 Score=73.91 Aligned_cols=46 Identities=24% Similarity=0.395 Sum_probs=39.0
Q ss_pred CceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 4 GRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 4 gR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|-.+.|.+.|||.|||+||++|+|..... ...+++|.+++.||||.
T Consensus 36 ~~rieG~IvGFDEyMNvVlD~aeev~~k~----------~~rk~lGRilLKGDnIt 81 (88)
T KOG1774|consen 36 GLRIEGRIVGFDEYMNLVLDDAEEVHSKT----------KSRKELGRILLKGDNIT 81 (88)
T ss_pred CcEEeEEEechHHhhhhhhcchhhccccc----------cCCCccccEEEcCCcEE
Confidence 45689999999999999999999987642 23448999999999986
No 32
>KOG3482|consensus
Probab=99.24 E-value=4.7e-12 Score=68.86 Aligned_cols=48 Identities=21% Similarity=0.352 Sum_probs=42.9
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+.|.+|.|+|.+.|.+|||.|.+|+|++.. .....+|.++||++||.
T Consensus 25 LKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-----------~~~g~lGEilIRCNNvl 72 (79)
T KOG3482|consen 25 LKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-----------VSTGNLGEILIRCNNVL 72 (79)
T ss_pred EecCcEEEEEEEEecchhheehhhhhhhhcc-----------cccccceeEEEEeccEE
Confidence 4678999999999999999999999999874 35677999999999984
No 33
>KOG1775|consensus
Probab=99.19 E-value=2.8e-12 Score=70.33 Aligned_cols=51 Identities=24% Similarity=0.373 Sum_probs=42.8
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|+..|+|+|+|.|||.|.|+||+|++||-..++ .....+++++++.|+||.
T Consensus 24 mksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e--------gr~~tk~~~iLLnGNni~ 74 (84)
T KOG1775|consen 24 MKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE--------GRRMTKLDQILLNGNNIT 74 (84)
T ss_pred EccCceeeeEEechHHHHHHHHHhhhheeeCCC--------cceeeeeeeeeecCCcEE
Confidence 578899999999999999999999999976542 124557899999999974
No 34
>KOG3459|consensus
Probab=99.15 E-value=2.1e-12 Score=74.75 Aligned_cols=59 Identities=17% Similarity=0.276 Sum_probs=49.0
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCcccccccc--ccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKE--ENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~--~~~~~~~r~lG~v~irG~~Iv 59 (60)
.+|++.+.|...|||.|+|++|+++.|.|.+.+++++. ...-...|.+|.++||||+|+
T Consensus 43 cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI 103 (114)
T KOG3459|consen 43 CRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI 103 (114)
T ss_pred ecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence 36889999999999999999999999999987765432 112356899999999999986
No 35
>KOG1783|consensus
Probab=99.08 E-value=6.7e-12 Score=68.25 Aligned_cols=48 Identities=27% Similarity=0.439 Sum_probs=42.8
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
|.+|-.|.|+|.|.|.+|||-|+.|+|+... +.++..|.+||||++|.
T Consensus 23 l~sgvdyrG~l~~lDgymNiaLe~tee~~ng-----------ql~n~ygdaFirGnnVl 70 (77)
T KOG1783|consen 23 LNSGVDYRGTLVCLDGYMNIALESTEEYVNG-----------QLKNKYGDAFIRGNNVL 70 (77)
T ss_pred ecCCccccceehhhhhHHHHHHHHHHHHhcC-----------cccccccceeeccccEE
Confidence 5688999999999999999999999999864 35778999999999984
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=98.67 E-value=1e-08 Score=54.79 Aligned_cols=26 Identities=23% Similarity=0.175 Sum_probs=24.5
Q ss_pred eEEEEEEeecCCCceEecccccccCc
Q psy1222 6 VLVGTFLCTDRDANVILGSCGEYLSP 31 (60)
Q Consensus 6 ~~~G~l~~~D~~~NlvL~~~~E~~~~ 31 (60)
.++|.|.|||+|+||+|.|+.|.+..
T Consensus 24 ~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 24 VCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred EEEEEEEeeeeehhheehhhhhhhcc
Confidence 68999999999999999999999875
No 37
>KOG3448|consensus
Probab=97.73 E-value=3.8e-05 Score=43.35 Aligned_cols=49 Identities=12% Similarity=0.094 Sum_probs=35.7
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
|+++-.+.|+|.+.|++.|+=|.|..-...+ + ...--.+-..+|||..|
T Consensus 19 LKnd~~i~GtL~svDqyLNlkL~di~v~d~~--k-------yPhm~Sv~ncfIRGSvv 67 (96)
T KOG3448|consen 19 LKNDLSICGTLHSVDQYLNLKLTDISVTDPD--K-------YPHMLSVKNCFIRGSVV 67 (96)
T ss_pred EcCCcEEEEEecccchhheeEEeeeEeeCcc--c-------CCCeeeeeeEEEeccEE
Confidence 5788899999999999999999987544332 1 11234456788998754
No 38
>KOG3293|consensus
Probab=97.72 E-value=1.7e-05 Score=47.08 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=38.3
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
|++|-.|.|.|...|..|||-|.+++++..+.. .--.+..+.|||.+|
T Consensus 19 LKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd----------kf~r~pEcYirGttI 66 (134)
T KOG3293|consen 19 LKNGETYNGHLVNCDNWMNLHLREVICTSEDGD----------KFFRMPECYIRGTTI 66 (134)
T ss_pred ecCCCEecceeecchhhhhcchheeEEeccCCC----------ceeecceeEEeccee
Confidence 689999999999999999999999999876532 223345677888765
No 39
>KOG3172|consensus
Probab=97.40 E-value=0.00026 Score=41.23 Aligned_cols=46 Identities=20% Similarity=0.269 Sum_probs=37.6
Q ss_pred CCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 2 TDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
+.|-.|.|.|+-.+..||+.|+|.+-...+. ....+-+|+|||..|
T Consensus 23 ~tGe~YRGkliEaeDnmNcql~di~vT~~dg-----------~vs~le~V~IRGS~I 68 (119)
T KOG3172|consen 23 KTGEVYRGKLIEAEDNMNCQLRDITVTARDG-----------RVSQLEQVFIRGSKI 68 (119)
T ss_pred cCCceeeeeeEEeccccccEEEEEEEEccCC-----------cceeeeeEEEecCeE
Confidence 5688999999999999999999987665432 345577899999876
No 40
>KOG3428|consensus
Probab=97.36 E-value=0.00031 Score=40.84 Aligned_cols=46 Identities=22% Similarity=0.297 Sum_probs=36.0
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
|++|....|++.+.|.+||..|.+..=.... +...+-.+.|||++|
T Consensus 19 Lkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~------------~pv~l~~lsirgnni 64 (109)
T KOG3428|consen 19 LKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG------------EPVRLDTLSIRGNNI 64 (109)
T ss_pred ecCCcEEeeeEEEEEhhheeEEEEEEEecCC------------CceeEEEEEeecceE
Confidence 6799999999999999999999887654431 234466778888876
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.67 E-value=0.0021 Score=34.62 Aligned_cols=56 Identities=14% Similarity=0.313 Sum_probs=29.3
Q ss_pred CCCCceEEEEEEeecC---CCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDR---DANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~---~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
++||..|.|+|.+++. .+-++|.-|.........+. ..........++|+++.|++
T Consensus 19 ~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~----~~~~~~~~~tlii~~~dvv~ 77 (77)
T PF14438_consen 19 TKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNS----DPLSSEIVETLIIPAKDVVQ 77 (77)
T ss_dssp ETTS-EEEEEEEEE-T---T--EEEEEEEETTS----------EEEEEEE-GGGEEE------
T ss_pred ECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccC----CccCCCCCceEEEeccccCC
Confidence 4799999999999999 88999988877765432110 01223345578888887763
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=92.23 E-value=0.16 Score=26.76 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=18.0
Q ss_pred CCCCceEEEEEEeecCCCceE
Q psy1222 1 MTDGRVLVGTFLCTDRDANVI 21 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~Nlv 21 (60)
|.+|-.+.|.+.+||+|+=++
T Consensus 18 L~NG~~l~G~I~~fD~ftVll 38 (61)
T cd01716 18 LVNGVQLKGQIESFDNFTVLL 38 (61)
T ss_pred EeCCcEEEEEEEEEcceEEEE
Confidence 568999999999999999444
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=91.60 E-value=0.2 Score=26.38 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=17.9
Q ss_pred CCCCceEEEEEEeecCCCceE
Q psy1222 1 MTDGRVLVGTFLCTDRDANVI 21 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~Nlv 21 (60)
|.+|-.+.|.+.+||+|+=++
T Consensus 22 L~nG~~l~G~I~~fD~ftVll 42 (61)
T TIGR02383 22 LVNGVQLKGVIESFDNFTVLL 42 (61)
T ss_pred EeCCcEEEEEEEEEeeeEEEE
Confidence 468999999999999999444
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=90.97 E-value=0.25 Score=27.31 Aligned_cols=24 Identities=17% Similarity=0.216 Sum_probs=19.4
Q ss_pred CCCCceEEEEEEeecCCCceEecc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGS 24 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~ 24 (60)
|.+|-.+.|.+.+||+|+=++-.+
T Consensus 26 L~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 26 LVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred EeCCcEEEEEEEEEccEEEEEEEC
Confidence 568999999999999998555434
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=89.86 E-value=0.75 Score=22.53 Aligned_cols=25 Identities=12% Similarity=0.122 Sum_probs=21.6
Q ss_pred CCceEEEEEEeecCCCceEeccccc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSCGE 27 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~~E 27 (60)
++..+.|++.++|.+..|++.....
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 5678899999999999999976654
No 46
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=89.13 E-value=0.67 Score=22.74 Aligned_cols=23 Identities=35% Similarity=0.449 Sum_probs=15.6
Q ss_pred EEEEEEeecCCCceEeccccccc
Q psy1222 7 LVGTFLCTDRDANVILGSCGEYL 29 (60)
Q Consensus 7 ~~G~l~~~D~~~NlvL~~~~E~~ 29 (60)
..|+|.|+|....|+|.+..+..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T~ 32 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTTH 32 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-EE
T ss_pred cceeEEeeccccceEEEeCCccE
Confidence 57999999999999999887654
No 47
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=87.47 E-value=0.52 Score=25.93 Aligned_cols=22 Identities=27% Similarity=0.315 Sum_probs=17.9
Q ss_pred CCCCceEEEEEEeecCCCceEec
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
|.+|=.+.|.+.+||+|. ++|.
T Consensus 26 LvNG~~L~G~V~sfD~f~-VlL~ 47 (77)
T COG1923 26 LVNGFKLQGQVESFDNFV-VLLK 47 (77)
T ss_pred EEcCEEEEEEEEeeeeEE-EEEE
Confidence 457889999999999998 4444
No 48
>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=80.74 E-value=6.6 Score=21.41 Aligned_cols=53 Identities=8% Similarity=0.119 Sum_probs=32.7
Q ss_pred ceEEEEEEeecCCC-ceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 5 RVLVGTFLCTDRDA-NVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 5 R~~~G~l~~~D~~~-NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
-.|+|+|..+|..- -+-|.++..+=.+...... ++..........++.||..|
T Consensus 17 iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~-~~ipp~~~vyd~IvFrgsDI 70 (74)
T cd01736 17 IRYEGILYTINTEDSTIALKNVRSFGTEGRPTDG-PEIPPSDEVYDYIVFRGSDI 70 (74)
T ss_pred cEEEEEEEeeccccCEEEeeeeEeecccCCCCCC-CccCCCCcceeEEEEcCCcc
Confidence 45899999999884 4668887655433211100 01122344567899999876
No 49
>KOG3382|consensus
Probab=80.09 E-value=0.99 Score=27.43 Aligned_cols=19 Identities=21% Similarity=0.265 Sum_probs=16.0
Q ss_pred EEEEEEeecCCCceEeccc
Q psy1222 7 LVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 7 ~~G~l~~~D~~~NlvL~~~ 25 (60)
=+|+|.|.|+|.|=--++-
T Consensus 45 kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 45 KIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred cceeeeeecccccchhccc
Confidence 3699999999999877665
No 50
>KOG3168|consensus
Probab=79.18 E-value=5.9 Score=24.89 Aligned_cols=57 Identities=28% Similarity=0.209 Sum_probs=38.8
Q ss_pred CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCC
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIP 59 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv 59 (60)
++|+++..+...++|.-.|||+--+++.....++...-. ....+..|+..+.|-.|.
T Consensus 58 ~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~v~--ag~~~g~G~ar~~Grgip 114 (177)
T KOG3168|consen 58 MTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRRVP--AGAARGPGIARVAGRGIP 114 (177)
T ss_pred ccccceeeEEEEEEecCCcEEEEeccCCCCCcccccccc--ccccCCcccccccCCCcc
Confidence 468999999999999999999988888766543221000 123455666666666554
No 51
>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=78.85 E-value=4.2 Score=21.33 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=19.9
Q ss_pred CCceEEEEEEeecCCCceEeccccc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSCGE 27 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~~E 27 (60)
.|-+|.|.+.|||.-.+|++=.|.+
T Consensus 15 ~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 15 FEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred CCceEEEEEEEecCCCcEEEEECcc
Confidence 4789999999999998877555433
No 52
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=78.20 E-value=2.2 Score=26.56 Aligned_cols=25 Identities=16% Similarity=0.187 Sum_probs=19.5
Q ss_pred CCCCceEEEEEEeecCCCceEeccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
|.+|-.+.|.+.+||+|+=|+-.+.
T Consensus 111 L~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 111 LVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred EecCcEEEEEEEEEcceEEEEEeCC
Confidence 4678899999999999984444443
No 53
>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=77.48 E-value=3 Score=25.84 Aligned_cols=26 Identities=19% Similarity=0.080 Sum_probs=23.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~ 26 (60)
+.||..|.|.+.+|+.--|.||..+.
T Consensus 36 ~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 36 SENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred ecCCcEEEEEEeccCcccCEEeccCC
Confidence 35899999999999999999997664
No 54
>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=77.38 E-value=1.1 Score=25.60 Aligned_cols=17 Identities=29% Similarity=0.255 Sum_probs=15.2
Q ss_pred EEEEeecCCCceEeccc
Q psy1222 9 GTFLCTDRDANVILGSC 25 (60)
Q Consensus 9 G~l~~~D~~~NlvL~~~ 25 (60)
|+|+|.|.|.|---+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999988766
No 55
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=74.72 E-value=3.1 Score=25.92 Aligned_cols=24 Identities=17% Similarity=0.167 Sum_probs=18.5
Q ss_pred CCCCceEEEEEEeecCCCceEecc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGS 24 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~ 24 (60)
|.+|-.+.|.+.+||+|.=|+-.+
T Consensus 31 L~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 31 LVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred EecCcEEEEEEEEEcceEEEEEeC
Confidence 457889999999999998444333
No 56
>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=68.48 E-value=1.6 Score=34.64 Aligned_cols=50 Identities=16% Similarity=0.302 Sum_probs=0.0
Q ss_pred CCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222 2 TDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA 60 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~ 60 (60)
.+|+.+-|.|...|.-++.+|+--.+..... ......+|.++|+|+|.|+
T Consensus 255 ~~G~~v~GVlvTT~~V~q~Ll~~l~~i~~~~---------v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 255 SSGRPVDGVLVTTANVMQKLLNLLGQISDTS---------VSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -----------------------------------------------------------
T ss_pred CCCCEeceEEeccHHHHHHHHHHHhhhccce---------eecchhheeeeecCccHHH
Confidence 4799999999999999988876544422211 1345678999999999875
No 57
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=66.37 E-value=16 Score=20.70 Aligned_cols=54 Identities=11% Similarity=0.174 Sum_probs=31.0
Q ss_pred CCceEEEEEEeecC-CCceEecccccccCccccccccccchhhheeeeeeeecCCCC
Q psy1222 3 DGRVLVGTFLCTDR-DANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58 (60)
Q Consensus 3 dgR~~~G~l~~~D~-~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~I 58 (60)
.+-.|+|+|...|. ...|.|.++.-+=.+..... ............++.||..|
T Consensus 17 ~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~--~~ipp~~~v~~~I~Fr~sDI 71 (96)
T PF12701_consen 17 SDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTD--REIPPSDEVYDYIVFRGSDI 71 (96)
T ss_dssp TTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-S--S---C-CSSSSEEEEETTTE
T ss_pred CCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcC--cccCCCCceeeEEEEEcccc
Confidence 44578999999998 47899998865543211000 00111223355677777654
No 58
>PRK06630 hypothetical protein; Provisional
Probab=58.39 E-value=5.9 Score=22.77 Aligned_cols=19 Identities=16% Similarity=-0.043 Sum_probs=16.4
Q ss_pred EEEEEEeecCCCceEeccc
Q psy1222 7 LVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 7 ~~G~l~~~D~~~NlvL~~~ 25 (60)
..|+|.|-|++.|---++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3699999999999988774
No 59
>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=53.36 E-value=19 Score=24.30 Aligned_cols=26 Identities=15% Similarity=0.259 Sum_probs=22.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~ 26 (60)
+.||+.+.+++.++|...+|-|=...
T Consensus 108 ~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 108 LQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred ECCCCEEEEEEEEecCCCCEEEEEec
Confidence 36899999999999999999885544
No 60
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=53.35 E-value=8.4 Score=22.66 Aligned_cols=20 Identities=15% Similarity=0.092 Sum_probs=16.9
Q ss_pred EEEEEeecCCCceEeccccc
Q psy1222 8 VGTFLCTDRDANVILGSCGE 27 (60)
Q Consensus 8 ~G~l~~~D~~~NlvL~~~~E 27 (60)
.|.|+|.|++.|---++..+
T Consensus 9 ~g~lVG~D~~GNkYYE~~~~ 28 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPSY 28 (115)
T ss_pred cceEeEEcCCCCeeeEcCCC
Confidence 58999999999998886544
No 61
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=51.06 E-value=15 Score=22.77 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=16.6
Q ss_pred EEEEeecCCCceEeccccc
Q psy1222 9 GTFLCTDRDANVILGSCGE 27 (60)
Q Consensus 9 G~l~~~D~~~NlvL~~~~E 27 (60)
|+|+|-|++.|---++..+
T Consensus 49 G~lVG~D~~GNkYYE~~~~ 67 (159)
T PLN02732 49 ATLVGVDKFGNKYYQKLGD 67 (159)
T ss_pred cEEEEecCCCCeeeecCCC
Confidence 9999999999999887643
No 62
>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=50.76 E-value=20 Score=19.75 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=15.7
Q ss_pred CCCceEEEEEEeecCC-CceEecc
Q psy1222 2 TDGRVLVGTFLCTDRD-ANVILGS 24 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~-~NlvL~~ 24 (60)
-++..+.|+|.|+|.. .|+..++
T Consensus 32 ~e~t~V~a~F~a~d~~~~~f~Vs~ 55 (80)
T PF11095_consen 32 HENTTVSARFGACDIDVSNFQVSN 55 (80)
T ss_dssp GGG-EEEEEEEEE-TTS-EEEEEE
T ss_pred eCCeEEEEEEEEecCchheEEhhh
Confidence 4677899999999988 4666554
No 63
>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=49.26 E-value=24 Score=23.11 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=19.4
Q ss_pred eEEEEEEeecCCCceEecccccc
Q psy1222 6 VLVGTFLCTDRDANVILGSCGEY 28 (60)
Q Consensus 6 ~~~G~l~~~D~~~NlvL~~~~E~ 28 (60)
.+.|.+.-+|+|.|+++.=..+.
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~~~ 191 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISREL 191 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEHHH
T ss_pred eEEEEEEEECccCCeeeCCCHHH
Confidence 78999999999999998755444
No 64
>PRK10898 serine endoprotease; Provisional
Probab=48.97 E-value=26 Score=23.70 Aligned_cols=26 Identities=19% Similarity=0.334 Sum_probs=21.7
Q ss_pred CCCCceEEEEEEeecCCCceEecccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~ 26 (60)
+.||+.+.+.+.++|...+|-|=...
T Consensus 108 ~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 108 LQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred eCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 36899999999999999998765543
No 65
>PRK10942 serine endoprotease; Provisional
Probab=45.67 E-value=29 Score=24.52 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=21.4
Q ss_pred CCCCceEEEEEEeecCCCceEeccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
+.|||++.+++.++|...+|-|=..
T Consensus 142 ~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 142 LSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred ECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999877643
No 66
>PRK08183 NADH dehydrogenase; Validated
Probab=45.51 E-value=12 Score=22.45 Aligned_cols=19 Identities=26% Similarity=0.233 Sum_probs=16.1
Q ss_pred EEEEEeecCCCceEecccc
Q psy1222 8 VGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 8 ~G~l~~~D~~~NlvL~~~~ 26 (60)
.|.|+|.|++.|---++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 5899999999999886654
No 67
>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=43.24 E-value=32 Score=21.40 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=18.4
Q ss_pred CCCceEEEEEEeecCC-CceEeccccc
Q psy1222 2 TDGRVLVGTFLCTDRD-ANVILGSCGE 27 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~-~NlvL~~~~E 27 (60)
.| +++.|.+.++|.- .||||-+..|
T Consensus 25 ~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 25 SD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp TT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred ec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 57 9999999999998 5999986666
No 68
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=42.18 E-value=16 Score=22.87 Aligned_cols=19 Identities=37% Similarity=0.552 Sum_probs=16.4
Q ss_pred ceEEEEEEeecCCCceEec
Q psy1222 5 RVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 5 R~~~G~l~~~D~~~NlvL~ 23 (60)
|.-.|.++.-|+..||||+
T Consensus 159 ~y~~gr~r~kd~~g~~~~d 177 (179)
T PF07202_consen 159 RYASGRVRIKDKDGNVIMD 177 (179)
T ss_pred EeCCCcEEEecCCCCEEec
Confidence 4456999999999999996
No 69
>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=42.17 E-value=39 Score=19.57 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=17.3
Q ss_pred CCCCceEEEEEEeecCCCceEeccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
++||+.+.|.+..=|.. .+.|.++
T Consensus 64 ~~dG~~~~G~~~~e~~~-~~~l~~~ 87 (133)
T TIGR02603 64 LKDGRILSGIVASETAD-GVTVKMP 87 (133)
T ss_pred ECCCCEEEEEEEecCCC-eEEEEcC
Confidence 47999999999886544 3555554
No 70
>PRK06955 biotin--protein ligase; Provisional
Probab=40.76 E-value=40 Score=22.27 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=19.4
Q ss_pred CCceEEEEEEeecCCCceEeccc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
+++.+.|++.++|....|++...
T Consensus 258 ~~~~~~G~~~gId~~G~L~v~~~ 280 (300)
T PRK06955 258 GAELARGVAHGIDETGQLLLDTP 280 (300)
T ss_pred CCcEEEEEEeeECCCceEEEEeC
Confidence 45678999999999999999643
No 71
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=40.42 E-value=44 Score=21.99 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=20.0
Q ss_pred CCceEEEEEEeecCCCceEeccc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
++..+.|++.++|....|+|...
T Consensus 245 ~~~~~~G~~~gId~~G~L~i~~~ 267 (285)
T PTZ00275 245 DNELIVGYLQGLLHDGSLLLLRE 267 (285)
T ss_pred CCCEEEEEEEEECCCCeEEEEeC
Confidence 57789999999999999999643
No 72
>PRK10139 serine endoprotease; Provisional
Probab=38.83 E-value=43 Score=23.57 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=22.1
Q ss_pred CCCCceEEEEEEeecCCCceEecccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~ 26 (60)
+.||+.+.+++.++|....|-+=...
T Consensus 121 ~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 121 LNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred ECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 46899999999999999998775543
No 73
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=38.73 E-value=48 Score=20.94 Aligned_cols=21 Identities=19% Similarity=0.279 Sum_probs=18.7
Q ss_pred CCceEEEEEEeecCCCceEec
Q psy1222 3 DGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~ 23 (60)
++..+.|++.++|....|+|.
T Consensus 201 ~~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 201 GNGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred CCcEEEEEEEeECCCceEEEE
Confidence 456799999999999999996
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=38.35 E-value=2.8 Score=21.86 Aligned_cols=18 Identities=17% Similarity=0.305 Sum_probs=14.9
Q ss_pred cCCCceEecccccccCcc
Q psy1222 15 DRDANVILGSCGEYLSPE 32 (60)
Q Consensus 15 D~~~NlvL~~~~E~~~~~ 32 (60)
|.||+-||++|.-++..+
T Consensus 21 DDFmhaVlSNCtTrIvLp 38 (61)
T PF10894_consen 21 DDFMHAVLSNCTTRIVLP 38 (61)
T ss_pred HHHHHHHHhcCceeEEec
Confidence 889999999999876543
No 75
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.28 E-value=52 Score=20.12 Aligned_cols=21 Identities=19% Similarity=0.368 Sum_probs=17.5
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+.+.|.|+|.++|..+ +++.
T Consensus 111 ~~~k~~~G~i~~~d~~~-v~~~ 131 (153)
T COG0779 111 EGRKKFEGKIVAVDGET-VTLE 131 (153)
T ss_pred CCceEEEEEEEEEcCCe-EEEE
Confidence 57899999999999988 5553
No 76
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=36.72 E-value=58 Score=20.90 Aligned_cols=23 Identities=13% Similarity=-0.094 Sum_probs=19.8
Q ss_pred CCceEEEEEEeecCCCceEeccc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
++..+.|++.++|....|++...
T Consensus 210 ~~~~~~G~~~gId~~G~Lvv~~~ 232 (245)
T PTZ00276 210 GRDPEELTALSLNEWGHLIVRRP 232 (245)
T ss_pred CCcEEEEEEEEECCCCeEEEEEC
Confidence 56778999999999999999743
No 77
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=35.62 E-value=56 Score=21.50 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=18.6
Q ss_pred CCceEEEEEEeecCCCceEec
Q psy1222 3 DGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~ 23 (60)
++..+.|++.++|....|++.
T Consensus 280 ~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 280 GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred CCcEEEEEEEEECCCceEEEE
Confidence 456799999999999999995
No 78
>PF02707 MOSP_N: Major Outer Sheath Protein N-terminal region; InterPro: IPR003857 This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [].
Probab=35.55 E-value=29 Score=22.39 Aligned_cols=16 Identities=13% Similarity=0.152 Sum_probs=14.0
Q ss_pred eEEEEEEeecCCCceE
Q psy1222 6 VLVGTFLCTDRDANVI 21 (60)
Q Consensus 6 ~~~G~l~~~D~~~Nlv 21 (60)
.++.+|+||+.+|+|-
T Consensus 31 s~eAtLh~ygaYltig 46 (204)
T PF02707_consen 31 SIEATLHCYGAYLTIG 46 (204)
T ss_pred eEEEEEEEEeeEEEec
Confidence 5889999999999874
No 79
>PRK14638 hypothetical protein; Provisional
Probab=35.38 E-value=39 Score=20.35 Aligned_cols=21 Identities=14% Similarity=0.395 Sum_probs=16.7
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+++.|+|+|.++|.. ++.|.
T Consensus 108 ~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 108 KDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CCCcEEEEEEEEEeCC-EEEEE
Confidence 4789999999999864 46664
No 80
>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=35.28 E-value=55 Score=22.49 Aligned_cols=26 Identities=15% Similarity=0.339 Sum_probs=22.0
Q ss_pred CCCCceEEEEEEeecCCCceEecccc
Q psy1222 1 MTDGRVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 1 l~dgR~~~G~l~~~D~~~NlvL~~~~ 26 (60)
+.||+.+.+.+.++|...+|.|=...
T Consensus 88 ~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 88 LSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred eCCCCEEEEEEEEecCCCCEEEEEec
Confidence 35899999999999999998876554
No 81
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=34.50 E-value=17 Score=20.34 Aligned_cols=15 Identities=27% Similarity=0.474 Sum_probs=12.2
Q ss_pred hheeeeeeeecCCCC
Q psy1222 44 EARLLGLVMVPGQHI 58 (60)
Q Consensus 44 ~~r~lG~v~irG~~I 58 (60)
.--++|.+++||+|-
T Consensus 74 ~Gl~~Gr~~LRGNHF 88 (92)
T PF05413_consen 74 IGLPLGRMLLRGNHF 88 (92)
T ss_pred ccCchhheeecccce
Confidence 456789999999984
No 82
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=34.22 E-value=29 Score=19.92 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=8.6
Q ss_pred CCCCceEEEEE
Q psy1222 1 MTDGRVLVGTF 11 (60)
Q Consensus 1 l~dgR~~~G~l 11 (60)
|+||+.+.|++
T Consensus 35 L~DGs~l~Gtv 45 (101)
T PF11607_consen 35 LDDGSMLRGTV 45 (101)
T ss_dssp ETTS-EEEEEE
T ss_pred EcCCCeeeeee
Confidence 57999999986
No 83
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=33.05 E-value=47 Score=18.99 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=9.4
Q ss_pred ceEEEEEEeecCCCceEecccc
Q psy1222 5 RVLVGTFLCTDRDANVILGSCG 26 (60)
Q Consensus 5 R~~~G~l~~~D~~~NlvL~~~~ 26 (60)
-.+.|++.++|-..++.|++|.
T Consensus 123 Vti~G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 123 VTIKGICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp EEEEEE-----SSS-EEEE---
T ss_pred EEEEEEEEeeecCCcEEeeccC
Confidence 3578999999845678888773
No 84
>PF10622 Ehbp: Energy-converting hydrogenase B subunit P (EhbP); InterPro: IPR019597 Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This entry contains subunit P of Ehb.
Probab=32.64 E-value=38 Score=18.56 Aligned_cols=39 Identities=31% Similarity=0.306 Sum_probs=20.2
Q ss_pred CCceEecccccccCccccccccccchhhheeeeeeeecC
Q psy1222 17 DANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPG 55 (60)
Q Consensus 17 ~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG 55 (60)
|-|+|.-|-.+-...-+-..-+++=-++.|.||+.++|=
T Consensus 20 yRNvIV~Npt~EpIKidvPv~d~~WIE~Hr~LGL~vvPv 58 (78)
T PF10622_consen 20 YRNVIVGNPTDEPIKIDVPVYDEEWIEEHRKLGLIVVPV 58 (78)
T ss_pred cccEEEeCCCCCCEEeeccccCHHHHHHHHhCCeEEEec
Confidence 468887765543211100001111135788999999873
No 85
>PRK14639 hypothetical protein; Provisional
Probab=31.61 E-value=50 Score=19.67 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=16.6
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+++.|.|+|.++|.. ++.|.
T Consensus 96 ~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 96 NEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred CCCcEEEEEEEEEeCC-EEEEE
Confidence 4689999999999885 46553
No 86
>PF05989 Chordopox_A35R: Chordopoxvirus A35R protein; InterPro: IPR009247 This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown.
Probab=31.54 E-value=36 Score=21.44 Aligned_cols=21 Identities=14% Similarity=0.309 Sum_probs=16.8
Q ss_pred EEEEEEeecCCCceEeccccc
Q psy1222 7 LVGTFLCTDRDANVILGSCGE 27 (60)
Q Consensus 7 ~~G~l~~~D~~~NlvL~~~~E 27 (60)
-.+.+.|||++.++.+++-..
T Consensus 93 ~n~~iiccD~~~~l~i~~k~q 113 (176)
T PF05989_consen 93 KNSFIICCDKDPKLSIDNKFQ 113 (176)
T ss_pred CCcEEEEecCcceEEECCCcc
Confidence 356789999999999986543
No 87
>PRK14633 hypothetical protein; Provisional
Probab=30.72 E-value=58 Score=19.59 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=16.5
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+.+.|.|+|.+++.. ++.|.
T Consensus 106 ~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 106 GSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCcEEEEEEEEEEeCC-EEEEE
Confidence 4679999999999875 46554
No 88
>PRK02001 hypothetical protein; Validated
Probab=30.06 E-value=54 Score=19.90 Aligned_cols=21 Identities=19% Similarity=0.526 Sum_probs=16.7
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+++.|.|+|.++|.. ++.|.
T Consensus 98 ~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 98 KNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred CCCCEEEEEEEEEeCC-EEEEE
Confidence 4789999999999975 45553
No 89
>PRK14640 hypothetical protein; Provisional
Probab=29.87 E-value=91 Score=18.74 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=16.5
Q ss_pred CCCceEEEEEEeecCCCceEec
Q psy1222 2 TDGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~ 23 (60)
.+.+.|.|+|.++|.. ++.|.
T Consensus 109 ~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 109 NNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CCceEEEEEEEEEeCC-EEEEE
Confidence 4679999999999875 46664
No 90
>PRK14645 hypothetical protein; Provisional
Probab=29.71 E-value=57 Score=19.82 Aligned_cols=20 Identities=20% Similarity=0.363 Sum_probs=15.9
Q ss_pred CCceEEEEEEeecCCCceEec
Q psy1222 3 DGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~ 23 (60)
+++.|.|+|.++|.. .+.|.
T Consensus 110 ~~k~~~G~L~~~~d~-~i~l~ 129 (154)
T PRK14645 110 PGENFTGRIKAVSGD-QVTFD 129 (154)
T ss_pred CCeEEEEEEEEEeCC-EEEEE
Confidence 579999999999875 46554
No 91
>PRK08330 biotin--protein ligase; Provisional
Probab=29.42 E-value=88 Score=19.74 Aligned_cols=23 Identities=30% Similarity=0.267 Sum_probs=18.8
Q ss_pred CCceE-EEEEEeecCCCceEeccc
Q psy1222 3 DGRVL-VGTFLCTDRDANVILGSC 25 (60)
Q Consensus 3 dgR~~-~G~l~~~D~~~NlvL~~~ 25 (60)
++..+ .|++.++|....|++...
T Consensus 196 ~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 196 DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred CCcEEEEEEEEEECCCCEEEEEEC
Confidence 45665 699999999999999744
No 92
>PRK14643 hypothetical protein; Provisional
Probab=26.88 E-value=97 Score=18.99 Aligned_cols=17 Identities=6% Similarity=0.003 Sum_probs=13.9
Q ss_pred CCCceEEEEEEeecCCC
Q psy1222 2 TDGRVLVGTFLCTDRDA 18 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~ 18 (60)
.+.+.|.|+|.++|...
T Consensus 116 ~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 116 KKVKEFEGYVTKYNVNT 132 (164)
T ss_pred CCceEEEEEEEEEeCCc
Confidence 35689999999998764
No 93
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=26.75 E-value=94 Score=22.79 Aligned_cols=22 Identities=23% Similarity=0.228 Sum_probs=19.0
Q ss_pred CCceEEEEEEeecCCCceEecc
Q psy1222 3 DGRVLVGTFLCTDRDANVILGS 24 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~~ 24 (60)
+++.+.|+..++|....|+|..
T Consensus 287 ~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 287 GETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCcEEEEEEEEECCCCEEEEEE
Confidence 4457999999999999999964
No 94
>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=26.57 E-value=1e+02 Score=16.41 Aligned_cols=19 Identities=37% Similarity=0.503 Sum_probs=14.5
Q ss_pred CceEEEEEEeecCCCceEec
Q psy1222 4 GRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 4 gR~~~G~l~~~D~~~NlvL~ 23 (60)
.+.+.|.|.++|.. +++|.
T Consensus 39 ~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 39 QKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred eEEEEEEEEeEeCC-EEEEE
Confidence 36899999999885 45553
No 95
>COG1912 Uncharacterized conserved protein [Function unknown]
Probab=26.23 E-value=90 Score=20.97 Aligned_cols=21 Identities=33% Similarity=0.411 Sum_probs=18.0
Q ss_pred CCceEEEEEEeecCCCceEec
Q psy1222 3 DGRVLVGTFLCTDRDANVILG 23 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL~ 23 (60)
++-.+.|+..-+|+|.|++..
T Consensus 170 ~~~~v~g~V~~iD~FGNv~TN 190 (268)
T COG1912 170 EDGGVKGTVIYVDRFGNVITN 190 (268)
T ss_pred cCCeEEEEEEEECCcCceeec
Confidence 456789999999999999975
No 96
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=25.03 E-value=87 Score=17.15 Aligned_cols=26 Identities=15% Similarity=0.133 Sum_probs=21.9
Q ss_pred eEEEEEEeecCCC-ceEecccccccCc
Q psy1222 6 VLVGTFLCTDRDA-NVILGSCGEYLSP 31 (60)
Q Consensus 6 ~~~G~l~~~D~~~-NlvL~~~~E~~~~ 31 (60)
++.|.|.|+.... .+.+.+|.+....
T Consensus 27 ~v~G~LlG~~~~~~~v~I~~~f~~p~~ 53 (114)
T PF01398_consen 27 EVIGLLLGTQDGDNTVEITNSFPVPHS 53 (114)
T ss_dssp EEEEEEEEEEETT-EEEEEEEEEESEE
T ss_pred EEEEEEEEEecCceEEEEEEEEEeeEe
Confidence 7899999998888 8889999886554
No 97
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=23.77 E-value=1.5e+02 Score=17.26 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=14.5
Q ss_pred CCceEEEEEEeecCCCceEe
Q psy1222 3 DGRVLVGTFLCTDRDANVIL 22 (60)
Q Consensus 3 dgR~~~G~l~~~D~~~NlvL 22 (60)
+.+.|.|+|.++|. -.++|
T Consensus 100 ~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 100 GRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp S-SEEEEEEEEEET-TEEEE
T ss_pred CcEEEEEEEEEEeC-CEEEE
Confidence 45789999999998 44666
No 98
>cd01403 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family.
Probab=23.61 E-value=40 Score=17.06 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=10.1
Q ss_pred cCCCceEecccccc
Q psy1222 15 DRDANVILGSCGEY 28 (60)
Q Consensus 15 D~~~NlvL~~~~E~ 28 (60)
||+.|++|-.-.-+
T Consensus 7 dKYGn~~l~~Ga~F 20 (51)
T cd01403 7 DKYGNAVLISGATF 20 (51)
T ss_pred hhcCceEEecccch
Confidence 88999998754433
No 99
>PRK08477 biotin--protein ligase; Provisional
Probab=23.30 E-value=1.2e+02 Score=19.29 Aligned_cols=24 Identities=13% Similarity=0.153 Sum_probs=19.9
Q ss_pred CCCceEEEEEEeecCCCceEeccc
Q psy1222 2 TDGRVLVGTFLCTDRDANVILGSC 25 (60)
Q Consensus 2 ~dgR~~~G~l~~~D~~~NlvL~~~ 25 (60)
.+++.+.|+..+.|...-|++.--
T Consensus 182 ~~~~~~~g~a~~I~~~G~L~v~~~ 205 (211)
T PRK08477 182 IDGKLVSLKDAELLEDGSILINGK 205 (211)
T ss_pred ECCEEEEEEEeeECCCCeEEECCE
Confidence 367889999999999999988643
No 100
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=20.81 E-value=1.6e+02 Score=17.33 Aligned_cols=27 Identities=11% Similarity=0.081 Sum_probs=23.6
Q ss_pred ceEEEEEEeecCCCceEecccccccCc
Q psy1222 5 RVLVGTFLCTDRDANVILGSCGEYLSP 31 (60)
Q Consensus 5 R~~~G~l~~~D~~~NlvL~~~~E~~~~ 31 (60)
..+.|.|.|+..-..+.+.||-+....
T Consensus 23 ~~v~G~LlG~~~~~~veV~nsF~lp~~ 49 (157)
T cd08057 23 KRVIGVLLGYVDGDKIEVTNSFELPFD 49 (157)
T ss_pred CeEEEEEEeEEeCCEEEEEEeEEcccc
Confidence 468899999998889999999998764
No 101
>PRK14631 hypothetical protein; Provisional
Probab=20.72 E-value=1.1e+02 Score=19.04 Aligned_cols=21 Identities=14% Similarity=0.359 Sum_probs=15.6
Q ss_pred CCCceEEEEEEeec--CCCceEec
Q psy1222 2 TDGRVLVGTFLCTD--RDANVILG 23 (60)
Q Consensus 2 ~dgR~~~G~l~~~D--~~~NlvL~ 23 (60)
.+.+.|.|+|.++| .. ++.|.
T Consensus 129 ~~~k~~~G~L~~v~~~~~-~v~l~ 151 (174)
T PRK14631 129 ENRRKFQAKLLAVDLENE-EIQVE 151 (174)
T ss_pred CCceEEEEEEEEeecCCC-EEEEE
Confidence 35699999999998 53 45553
No 102
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=20.40 E-value=1.5e+02 Score=16.33 Aligned_cols=25 Identities=8% Similarity=0.004 Sum_probs=19.9
Q ss_pred ceEEEEEEeecCCCceEeccccccc
Q psy1222 5 RVLVGTFLCTDRDANVILGSCGEYL 29 (60)
Q Consensus 5 R~~~G~l~~~D~~~NlvL~~~~E~~ 29 (60)
.+..|.|.|.+...++.+.++....
T Consensus 22 ~e~~G~L~G~~~~~~~~i~~~~~~p 46 (135)
T smart00232 22 EEVCGVLLGKSNKDRPEVKEVFAVP 46 (135)
T ss_pred cEEEEEEEEEEcCCEEEEEEEEecC
Confidence 5789999999877788887776643
Done!