Query 033937
Match_columns 108
No_of_seqs 106 out of 1079
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 07:59:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033937hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 100.0 4.5E-28 9.8E-33 159.7 10.8 87 20-107 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 1.7E-25 3.7E-30 145.5 9.8 82 21-105 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 3.7E-24 7.9E-29 137.9 10.3 74 20-106 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.9 2.6E-24 5.6E-29 136.9 9.3 71 19-105 2-72 (72)
5 cd01731 archaeal_Sm1 The archa 99.9 5.3E-24 1.1E-28 133.8 9.1 68 22-105 1-68 (68)
6 cd01718 Sm_E The eukaryotic Sm 99.9 1.3E-22 2.8E-27 131.7 9.8 76 17-105 2-79 (79)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.9E-22 4.1E-27 126.6 8.9 67 22-104 1-67 (67)
8 cd01729 LSm7 The eukaryotic Sm 99.9 6.4E-22 1.4E-26 128.7 10.0 76 22-106 4-79 (81)
9 cd01717 Sm_B The eukaryotic Sm 99.9 8.2E-22 1.8E-26 127.2 9.6 75 25-105 4-78 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.9 8.3E-22 1.8E-26 124.1 8.5 68 21-104 1-68 (68)
11 cd01719 Sm_G The eukaryotic Sm 99.9 1.2E-21 2.7E-26 124.8 8.9 68 23-106 2-69 (72)
12 cd01728 LSm1 The eukaryotic Sm 99.9 2.5E-21 5.4E-26 124.1 10.2 71 22-105 3-73 (74)
13 PTZ00138 small nuclear ribonuc 99.9 2.2E-21 4.7E-26 128.4 10.0 78 16-106 9-88 (89)
14 COG1958 LSM1 Small nuclear rib 99.9 7.2E-21 1.6E-25 122.7 9.7 76 18-105 4-79 (79)
15 cd01727 LSm8 The eukaryotic Sm 99.9 7.2E-21 1.6E-25 121.6 9.4 72 24-107 2-73 (74)
16 KOG3460 Small nuclear ribonucl 99.8 3.2E-22 6.9E-27 130.0 1.7 85 19-106 3-87 (91)
17 PF01423 LSM: LSM domain ; In 99.8 2.5E-20 5.4E-25 115.8 9.3 67 24-105 1-67 (67)
18 cd06168 LSm9 The eukaryotic Sm 99.8 5.4E-20 1.2E-24 118.2 9.9 72 24-105 3-74 (75)
19 smart00651 Sm snRNP Sm protein 99.8 6.6E-20 1.4E-24 113.8 9.0 66 25-105 2-67 (67)
20 cd01721 Sm_D3 The eukaryotic S 99.8 1.2E-19 2.6E-24 114.9 9.1 68 22-105 1-68 (70)
21 cd01723 LSm4 The eukaryotic Sm 99.8 1.2E-19 2.7E-24 116.4 9.0 71 21-106 1-71 (76)
22 KOG3459 Small nuclear ribonucl 99.8 3.6E-20 7.7E-25 125.7 1.6 103 4-107 5-109 (114)
23 cd00600 Sm_like The eukaryotic 99.8 1.3E-18 2.7E-23 106.6 8.2 63 26-104 1-63 (63)
24 cd01724 Sm_D1 The eukaryotic S 99.7 1.2E-17 2.6E-22 110.6 9.3 68 22-105 2-69 (90)
25 KOG1774 Small nuclear ribonucl 99.7 2.7E-18 5.8E-23 111.2 5.7 78 17-107 8-87 (88)
26 cd01733 LSm10 The eukaryotic S 99.7 3.3E-17 7.2E-22 105.9 9.0 69 21-105 9-77 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.7 5.5E-17 1.2E-21 105.4 9.4 72 21-106 1-72 (81)
28 KOG1775 U6 snRNA-associated Sm 99.7 1.8E-17 3.8E-22 106.3 4.6 77 17-106 3-79 (84)
29 KOG1780 Small Nuclear ribonucl 99.7 1.2E-16 2.7E-21 101.7 6.7 70 19-106 4-73 (77)
30 KOG1781 Small Nuclear ribonucl 99.6 2.1E-17 4.6E-22 110.4 0.7 78 23-106 17-94 (108)
31 KOG3482 Small nuclear ribonucl 99.6 7.4E-16 1.6E-20 98.0 6.4 73 19-107 6-78 (79)
32 KOG3168 U1 snRNP component [Tr 99.6 6.5E-16 1.4E-20 111.8 1.1 75 26-106 9-83 (177)
33 KOG1784 Small Nuclear ribonucl 99.4 1.9E-13 4.2E-18 90.2 4.8 71 24-106 3-73 (96)
34 KOG1783 Small nuclear ribonucl 99.4 5.2E-14 1.1E-18 89.5 1.5 71 20-106 5-75 (77)
35 KOG1782 Small Nuclear ribonucl 99.4 6.9E-14 1.5E-18 96.7 0.4 69 26-107 14-82 (129)
36 cd01739 LSm11_C The eukaryotic 99.4 2.3E-13 5E-18 85.0 2.6 45 26-70 1-49 (66)
37 KOG3293 Small nuclear ribonucl 99.3 1E-11 2.2E-16 86.1 6.3 70 21-105 2-71 (134)
38 KOG3448 Predicted snRNP core p 99.2 3.1E-10 6.8E-15 74.7 8.3 69 23-105 4-72 (96)
39 KOG3172 Small nuclear ribonucl 99.1 4.9E-10 1.1E-14 76.2 6.7 72 18-105 2-73 (119)
40 KOG3428 Small nuclear ribonucl 98.5 8.5E-07 1.8E-11 60.4 8.2 66 23-105 4-69 (109)
41 cd01716 Hfq Hfq, an abundant, 97.4 0.00048 1E-08 42.7 5.2 39 25-63 3-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.4 0.00064 1.4E-08 42.1 5.3 39 25-63 7-45 (61)
43 PF14438 SM-ATX: Ataxin 2 SM d 97.4 0.00068 1.5E-08 42.9 5.6 68 25-101 6-76 (77)
44 PRK00395 hfq RNA-binding prote 97.2 0.0012 2.6E-08 42.9 5.3 40 25-64 11-50 (79)
45 COG1923 Hfq Uncharacterized ho 96.4 0.0097 2.1E-07 38.4 4.8 36 25-60 11-46 (77)
46 PRK14091 RNA-binding protein H 95.9 0.023 5E-07 41.5 5.2 41 25-65 96-136 (165)
47 PRK14091 RNA-binding protein H 95.8 0.024 5.2E-07 41.4 5.2 40 25-64 16-55 (165)
48 cd01735 LSm12_N LSm12 belongs 95.1 0.056 1.2E-06 33.4 4.4 35 32-66 5-39 (61)
49 PF12701 LSM14: Scd6-like Sm d 94.8 0.25 5.4E-06 33.0 7.3 70 28-104 5-75 (96)
50 PF02237 BPL_C: Biotin protein 94.7 0.17 3.8E-06 29.2 5.6 33 33-66 3-35 (48)
51 PF11095 Gemin7: Gem-associate 93.4 0.98 2.1E-05 29.4 7.6 63 23-106 16-79 (80)
52 PF03614 Flag1_repress: Repres 92.1 0.29 6.3E-06 35.5 4.2 38 18-55 105-142 (165)
53 PRK14638 hypothetical protein; 91.7 0.35 7.6E-06 34.5 4.3 36 19-56 85-123 (150)
54 cd01736 LSm14_N LSm14 (also kn 91.1 2.6 5.7E-05 27.0 7.5 65 33-101 6-71 (74)
55 PRK02001 hypothetical protein; 90.3 0.56 1.2E-05 33.7 4.3 33 26-61 85-117 (152)
56 PRK14639 hypothetical protein; 89.9 0.64 1.4E-05 32.8 4.3 33 26-61 83-115 (140)
57 PF06372 Gemin6: Gemin6 protei 86.1 1.5 3.2E-05 32.1 4.3 43 20-66 7-50 (166)
58 PRK14644 hypothetical protein; 85.9 1.7 3.8E-05 30.5 4.4 40 20-62 72-117 (136)
59 cd01734 YlxS_C YxlS is a Bacil 84.6 2.5 5.4E-05 26.9 4.4 33 26-61 20-56 (83)
60 PF03614 Flag1_repress: Repres 83.9 2.4 5.1E-05 30.9 4.4 37 29-65 25-61 (165)
61 PRK14640 hypothetical protein; 83.6 2.5 5.4E-05 30.2 4.4 33 26-61 92-128 (152)
62 PRK14642 hypothetical protein; 82.8 2.6 5.6E-05 31.6 4.4 36 19-56 85-136 (197)
63 PRK14636 hypothetical protein; 82.5 2.6 5.7E-05 30.9 4.3 33 26-61 93-129 (176)
64 PF02576 DUF150: Uncharacteris 82.3 2.5 5.5E-05 29.3 4.0 35 19-55 72-113 (141)
65 PRK14633 hypothetical protein; 82.2 3 6.6E-05 29.7 4.4 41 19-62 79-126 (150)
66 PF11607 DUF3247: Protein of u 82.0 3.5 7.6E-05 27.7 4.3 26 25-50 20-45 (101)
67 PRK14643 hypothetical protein; 81.9 3 6.5E-05 30.3 4.4 34 26-61 99-137 (164)
68 COG0779 Uncharacterized protei 81.3 3.4 7.4E-05 29.8 4.4 39 20-61 85-130 (153)
69 PRK14645 hypothetical protein; 80.8 3.3 7.1E-05 29.7 4.2 32 26-61 97-128 (154)
70 PRK14646 hypothetical protein; 80.1 3.9 8.4E-05 29.3 4.4 33 26-61 95-131 (155)
71 PRK14632 hypothetical protein; 79.7 3.9 8.5E-05 29.8 4.4 33 26-61 93-132 (172)
72 PRK14634 hypothetical protein; 79.0 4.5 9.7E-05 29.0 4.4 33 26-61 95-131 (155)
73 PRK00092 ribosome maturation p 78.4 4.8 0.0001 28.5 4.4 28 26-55 93-124 (154)
74 PF14563 DUF4444: Domain of un 76.5 2.9 6.2E-05 24.0 2.3 22 46-67 10-31 (42)
75 PRK14647 hypothetical protein; 75.9 6.1 0.00013 28.3 4.4 34 20-55 85-130 (159)
76 PRK14637 hypothetical protein; 73.4 6.6 0.00014 28.1 4.0 41 19-62 83-127 (151)
77 PRK14631 hypothetical protein; 73.2 7 0.00015 28.6 4.2 27 26-54 112-142 (174)
78 PRK14641 hypothetical protein; 71.7 7.5 0.00016 28.5 4.1 34 19-54 89-129 (173)
79 PRK10898 serine endoprotease; 68.4 11 0.00024 30.0 4.8 34 32-65 100-133 (353)
80 TIGR02038 protease_degS peripl 67.4 12 0.00026 29.8 4.7 34 32-65 100-133 (351)
81 PF10842 DUF2642: Protein of u 67.2 16 0.00034 22.8 4.3 58 18-105 6-66 (66)
82 PRK06955 biotin--protein ligas 65.1 21 0.00046 27.8 5.6 35 29-63 245-279 (300)
83 PF08863 YolD: YolD-like prote 64.4 29 0.00063 21.6 5.3 38 25-62 34-74 (92)
84 PRK10139 serine endoprotease; 64.2 17 0.00036 30.2 5.1 36 30-65 111-146 (455)
85 PRK10942 serine endoprotease; 63.7 15 0.00031 30.7 4.7 34 31-64 133-166 (473)
86 TIGR02037 degP_htrA_DO peripla 56.9 26 0.00056 28.4 5.0 35 31-65 79-113 (428)
87 PRK11886 bifunctional biotin-- 52.3 44 0.00095 26.0 5.4 32 30-62 269-300 (319)
88 PRK14630 hypothetical protein; 50.6 30 0.00066 24.4 3.9 28 26-56 92-119 (143)
89 PTZ00275 biotin-acetyl-CoA-car 50.5 53 0.0011 25.5 5.6 34 29-63 233-266 (285)
90 TIGR00121 birA_ligase birA, bi 49.6 59 0.0013 24.2 5.6 33 29-62 189-221 (237)
91 PRK14635 hypothetical protein; 49.4 35 0.00077 24.4 4.2 33 26-61 94-131 (162)
92 PF07073 ROF: Modulator of Rho 44.3 28 0.00061 22.4 2.7 25 32-58 16-40 (80)
93 PRK13325 bifunctional biotin-- 40.4 80 0.0017 27.3 5.6 33 31-63 276-308 (592)
94 PF05071 NDUFA12: NADH ubiquin 39.9 12 0.00027 24.9 0.6 17 48-64 1-17 (105)
95 KOG3382 NADH:ubiquinone oxidor 39.0 17 0.00036 26.1 1.1 25 41-65 40-64 (151)
96 PF02604 PhdYeFM_antitox: Anti 37.9 67 0.0014 19.2 3.6 41 18-60 9-49 (75)
97 PRK08330 biotin--protein ligas 36.6 1.4E+02 0.003 22.2 5.9 33 30-63 185-218 (236)
98 PRK11625 Rho-binding antitermi 36.2 96 0.0021 20.1 4.3 32 25-58 15-46 (84)
99 TIGR02603 CxxCH_TIGR02603 puta 35.6 54 0.0012 22.4 3.2 37 21-60 48-85 (133)
100 PF06257 DUF1021: Protein of u 35.2 83 0.0018 20.1 3.8 27 25-53 11-41 (76)
101 PF11931 DUF3449: Domain of un 32.7 15 0.00032 27.6 0.0 40 16-58 70-123 (196)
102 COG0340 BirA Biotin-(acetyl-Co 32.1 1.5E+02 0.0032 22.6 5.4 33 32-64 189-221 (238)
103 PF09465 LBR_tudor: Lamin-B re 30.4 1E+02 0.0022 18.6 3.4 25 31-55 7-32 (55)
104 smart00166 UBX Domain present 29.2 59 0.0013 20.0 2.4 24 32-55 3-26 (80)
105 TIGR03170 flgA_cterm flagella 28.9 71 0.0015 21.1 2.9 20 33-52 96-116 (122)
106 cd01772 SAKS1_UBX SAKS1-like U 28.4 56 0.0012 20.3 2.2 23 32-54 3-25 (79)
107 PF14153 Spore_coat_CotO: Spor 27.3 86 0.0019 23.2 3.3 23 34-56 134-157 (185)
108 PF10246 MRP-S35: Mitochondria 26.7 40 0.00087 22.9 1.3 35 32-67 63-97 (104)
109 PF07317 YcgR: Flagellar regul 26.3 2E+02 0.0042 18.9 4.9 41 23-63 11-51 (108)
110 PRK08477 biotin--protein ligas 26.1 2.6E+02 0.0056 20.8 5.8 40 23-63 165-204 (211)
111 PRK07018 flgA flagellar basal 23.9 88 0.0019 23.5 2.9 20 33-52 207-227 (235)
112 KOG4401 Uncharacterized conser 23.2 1.3E+02 0.0027 22.5 3.5 33 33-65 11-43 (184)
113 PF11743 DUF3301: Protein of u 22.3 98 0.0021 20.3 2.6 22 86-107 75-96 (97)
114 PRK10708 hypothetical protein; 22.1 1E+02 0.0022 18.9 2.3 26 32-57 3-28 (62)
115 PF05989 Chordopox_A35R: Chord 22.0 58 0.0013 24.1 1.5 20 46-65 93-112 (176)
116 PF08067 ROKNT: ROKNT (NUC014) 21.7 36 0.00079 19.4 0.3 13 6-18 1-13 (43)
No 1
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.95 E-value=4.5e-28 Score=159.72 Aligned_cols=87 Identities=90% Similarity=1.381 Sum_probs=72.6
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 033937 20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 99 (108)
Q Consensus 20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~ 99 (108)
.||+++|.+++..+++|+|.|++|+.+.|+|+|||+||||+|+||+|++...++++.+. +.+....++++|.+|||||+
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~ 79 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDS 79 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCE
Confidence 48999999999889999999999999999999999999999999999987644332210 11112356789999999999
Q ss_pred EEEEEeCC
Q 033937 100 VIIVLRNP 107 (108)
Q Consensus 100 Iv~I~~~~ 107 (108)
|++|+++|
T Consensus 80 Vv~Is~~~ 87 (87)
T cd01720 80 VILVLRNP 87 (87)
T ss_pred EEEEecCC
Confidence 99999987
No 2
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.93 E-value=1.7e-25 Score=145.52 Aligned_cols=82 Identities=33% Similarity=0.579 Sum_probs=66.4
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
.|+++|+.++ +++|.|.|+|||.+.|+|+|||+||||+|+||+|++....+..+. +........|.+|.++||||+|
T Consensus 1 ~pl~~l~~~~--~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~-~~~~~~~~~r~lg~~~iRGd~V 77 (82)
T cd01730 1 EPLDLIRLSL--DERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEET-YEEIVKTTKRNIPMLFVRGDSV 77 (82)
T ss_pred CchHHHHHhC--CCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccc-cccccceeEEEcCeEEEeCCEE
Confidence 5999999999 999999999999999999999999999999999998754322110 0000012457899999999999
Q ss_pred EEEEe
Q 033937 101 IIVLR 105 (108)
Q Consensus 101 v~I~~ 105 (108)
++|+|
T Consensus 78 v~i~~ 82 (82)
T cd01730 78 ILVSP 82 (82)
T ss_pred EEECC
Confidence 99985
No 3
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=3.7e-24 Score=137.88 Aligned_cols=74 Identities=24% Similarity=0.463 Sum_probs=64.8
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 033937 20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 99 (108)
Q Consensus 20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~ 99 (108)
..|+++|.+++ +++|.|.+++|+.+.|+|+|||+||||+|+||+|++..+ +++ ..+++|.++|||+|
T Consensus 2 ~~P~~~L~~~~--~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~--~~~---------~~~~lg~v~iRG~n 68 (76)
T cd01732 2 LLPLELIDKCI--GSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITP--EGR---------KITKLDQILLNGNN 68 (76)
T ss_pred cChHHHHHHhC--CCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcC--CCc---------eeeEcCeEEEeCCe
Confidence 47999999999 999999999999999999999999999999999997431 111 23679999999999
Q ss_pred EEEEEeC
Q 033937 100 VIIVLRN 106 (108)
Q Consensus 100 Iv~I~~~ 106 (108)
|++|+|-
T Consensus 69 V~~i~p~ 75 (76)
T cd01732 69 ICMLVPG 75 (76)
T ss_pred EEEEECC
Confidence 9999973
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=2.6e-24 Score=136.94 Aligned_cols=71 Identities=31% Similarity=0.551 Sum_probs=63.3
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 033937 19 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 98 (108)
Q Consensus 19 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd 98 (108)
+..|+++|++++ +++|.|+|+||+.|+|+|+|||+|||++|+||+|.+.. + ..+.+|.++|||+
T Consensus 2 ~~~P~~~L~~~~--~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-----~---------~~~~lg~v~iRG~ 65 (72)
T PRK00737 2 AQRPLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-----E---------VVRKLGKVVIRGD 65 (72)
T ss_pred CcchHHHHHHhC--CCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-----C---------eEeEcCcEEEeCC
Confidence 368999999999 99999999999999999999999999999999997522 1 2357999999999
Q ss_pred cEEEEEe
Q 033937 99 SVIIVLR 105 (108)
Q Consensus 99 ~Iv~I~~ 105 (108)
+|++|+|
T Consensus 66 ~V~~i~~ 72 (72)
T PRK00737 66 NVVYVSP 72 (72)
T ss_pred EEEEEcC
Confidence 9999975
No 5
>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=99.91 E-value=5.3e-24 Score=133.84 Aligned_cols=68 Identities=34% Similarity=0.599 Sum_probs=61.8
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|+++|+.++ +++|+|.|++|+.|.|+|.|||+||||+|+||+|++.. + .++.+|.++|||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~------~--------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 1 PLDVLKDSL--NKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG------E--------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred ChHHHHHhc--CCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC------C--------eEeEcCcEEEeCCEEE
Confidence 899999999 99999999999999999999999999999999998642 1 2367999999999999
Q ss_pred EEEe
Q 033937 102 IVLR 105 (108)
Q Consensus 102 ~I~~ 105 (108)
+|+|
T Consensus 65 ~i~~ 68 (68)
T cd01731 65 FISP 68 (68)
T ss_pred EEcC
Confidence 9986
No 6
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=1.3e-22 Score=131.66 Aligned_cols=76 Identities=18% Similarity=0.420 Sum_probs=65.5
Q ss_pred ccCCCcHHHHHhhhhCCcEEEEEec--CCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEE
Q 033937 17 EFNTGPLSVLMMSVKNNTQVLINCR--NNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 94 (108)
Q Consensus 17 ~~~~~Pl~~L~~~~~~~krV~V~l~--~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~ 94 (108)
+....|++.|.+++....+|.||++ +|+.+.|+|.|||+||||+|+||+|+... ++ ..+.+|.++
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~----~~---------~~~~lG~il 68 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK----TK---------TRKPLGRIL 68 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC----Cc---------eEeEcCcEE
Confidence 3457899999999977779999998 89999999999999999999999998642 11 235699999
Q ss_pred EeCCcEEEEEe
Q 033937 95 LRGDSVIIVLR 105 (108)
Q Consensus 95 IRGd~Iv~I~~ 105 (108)
||||||++|+|
T Consensus 69 iRGnnV~~I~p 79 (79)
T cd01718 69 LKGDNITLIQN 79 (79)
T ss_pred EeCCEEEEEcC
Confidence 99999999985
No 7
>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=99.88 E-value=1.9e-22 Score=126.57 Aligned_cols=67 Identities=19% Similarity=0.330 Sum_probs=59.7
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|+++|++++ +++|.|.|++|++|+|+|.|||.||||+|+||+|.... . ..+.+|.++|||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~-----~---------~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 1 PSEFLKAII--GRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNG-----Q---------LKNKYGDAFIRGNNVL 64 (67)
T ss_pred CHHHHHhhC--CCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCC-----c---------eeeEeCCEEEECCEEE
Confidence 899999999 99999999999999999999999999999999986321 1 2256999999999999
Q ss_pred EEE
Q 033937 102 IVL 104 (108)
Q Consensus 102 ~I~ 104 (108)
+|+
T Consensus 65 ~I~ 67 (67)
T cd01726 65 YIS 67 (67)
T ss_pred EEC
Confidence 985
No 8
>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=99.88 E-value=6.4e-22 Score=128.67 Aligned_cols=76 Identities=21% Similarity=0.362 Sum_probs=61.5
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
+++ |.+++ +++|+|.|+|||.+.|+|+|||+||||+|+||+|+........+ .....+.+|.++|||+||+
T Consensus 4 ~~~-L~~~i--~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~------~~~~~~~lG~v~iRG~nV~ 74 (81)
T cd01729 4 ILD-LSKYV--DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYK------LTDKTRQLGLVVCRGTSVV 74 (81)
T ss_pred hhh-HHHhc--CCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccc------cccceeEccEEEEcCCEEE
Confidence 444 78889 99999999999999999999999999999999998654211100 0013467999999999999
Q ss_pred EEEeC
Q 033937 102 IVLRN 106 (108)
Q Consensus 102 ~I~~~ 106 (108)
+|++.
T Consensus 75 ~i~~~ 79 (81)
T cd01729 75 LISPV 79 (81)
T ss_pred EEecC
Confidence 99875
No 9
>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=8.2e-22 Score=127.24 Aligned_cols=75 Identities=21% Similarity=0.441 Sum_probs=60.9
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 104 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~ 104 (108)
-|..++ +++|+|.|+|||.+.|+|+|||+||||+|+||+|++...+..... ......|++|.++|||++|++|+
T Consensus 4 ~l~~~l--~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~----~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 4 KMLQLI--NYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKN----SEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred hhHHHc--CCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEecccccccc----ccCcceeEeeeEEEcCCEEEEEE
Confidence 467788 999999999999999999999999999999999998653321100 01124588999999999999997
Q ss_pred e
Q 033937 105 R 105 (108)
Q Consensus 105 ~ 105 (108)
.
T Consensus 78 v 78 (79)
T cd01717 78 V 78 (79)
T ss_pred E
Confidence 4
No 10
>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=99.87 E-value=8.3e-22 Score=124.06 Aligned_cols=68 Identities=18% Similarity=0.268 Sum_probs=59.8
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
.|+.+|++++ +++|+|.|++|+.++|+|.|||+|||++|+||+|.... . ....+|.++|||++|
T Consensus 1 ~p~~~L~~~~--g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~-----~---------~~~~lg~~~IRG~~I 64 (68)
T cd01722 1 NPKPFLNDLT--GKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDG-----K---------STGNLGEVLIRCNNV 64 (68)
T ss_pred CHHHHHHHcC--CCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCC-----c---------cccCcCcEEEECCEE
Confidence 4899999999 99999999999999999999999999999999987321 1 124589999999999
Q ss_pred EEEE
Q 033937 101 IIVL 104 (108)
Q Consensus 101 v~I~ 104 (108)
++|+
T Consensus 65 ~~i~ 68 (68)
T cd01722 65 LYIR 68 (68)
T ss_pred EEEC
Confidence 9984
No 11
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=1.2e-21 Score=124.79 Aligned_cols=68 Identities=22% Similarity=0.385 Sum_probs=59.7
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 102 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~ 102 (108)
-..|.+++ +++|+|.|++|+.+.|+|.|||+||||+|+||+|+... . ..+.+|.++|||++|++
T Consensus 2 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-----~---------~~~~lg~v~IRG~~I~~ 65 (72)
T cd01719 2 PPELKKYM--DKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-----G---------EKNNIGMVVIRGNSIVM 65 (72)
T ss_pred chhhHHhC--CCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-----C---------ceeEeceEEECCCEEEE
Confidence 35788999 99999999999999999999999999999999998521 1 23669999999999999
Q ss_pred EEeC
Q 033937 103 VLRN 106 (108)
Q Consensus 103 I~~~ 106 (108)
|++.
T Consensus 66 i~~~ 69 (72)
T cd01719 66 LEAL 69 (72)
T ss_pred EEcc
Confidence 9875
No 12
>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=99.86 E-value=2.5e-21 Score=124.15 Aligned_cols=71 Identities=25% Similarity=0.399 Sum_probs=61.1
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
++..|..++ +++|.|.+++||.+.|+|.|||+||||+|+||.|+..... + ..++.+|.++|||+||+
T Consensus 3 ~~~~L~~~l--~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~---~--------~~~~~lG~~viRG~~V~ 69 (74)
T cd01728 3 GTASLVDDL--DKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD---K--------YGDIPRGIFIIRGENVV 69 (74)
T ss_pred chHHHHHhc--CCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC---c--------cceeEeeEEEEECCEEE
Confidence 466789999 9999999999999999999999999999999999865421 1 12367999999999999
Q ss_pred EEEe
Q 033937 102 IVLR 105 (108)
Q Consensus 102 ~I~~ 105 (108)
+|+.
T Consensus 70 ~ig~ 73 (74)
T cd01728 70 LLGE 73 (74)
T ss_pred EEEc
Confidence 9985
No 13
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=2.2e-21 Score=128.41 Aligned_cols=78 Identities=22% Similarity=0.482 Sum_probs=67.8
Q ss_pred cccCCCcHHHHHhhhhCCcEEEEEecCC--eEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceE
Q 033937 16 EEFNTGPLSVLMMSVKNNTQVLINCRNN--KKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKM 93 (108)
Q Consensus 16 ~~~~~~Pl~~L~~~~~~~krV~V~l~~g--r~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i 93 (108)
......|+.+|.++++...+|.||+.++ +.+.|+|.|||+||||+|+||+|++.. ++ ..+.+|.+
T Consensus 9 ~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~~---------~~~~lG~i 75 (89)
T PTZ00138 9 QKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----KN---------TRKDLGRI 75 (89)
T ss_pred ceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----Cc---------eeeEcCeE
Confidence 3567799999999999999999999885 789999999999999999999998642 11 23679999
Q ss_pred EEeCCcEEEEEeC
Q 033937 94 FLRGDSVIIVLRN 106 (108)
Q Consensus 94 ~IRGd~Iv~I~~~ 106 (108)
+||||||++|++.
T Consensus 76 lIRGnnV~~I~~~ 88 (89)
T PTZ00138 76 LLKGDNITLIMAA 88 (89)
T ss_pred EEcCCEEEEEEcC
Confidence 9999999999875
No 14
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=7.2e-21 Score=122.65 Aligned_cols=76 Identities=30% Similarity=0.577 Sum_probs=62.9
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeC
Q 033937 18 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 97 (108)
Q Consensus 18 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRG 97 (108)
....|+++|++++ +++|.|+|++|+++.|+|+|||+||||+|+||+|.+.. ++. . ...+..+.++|||
T Consensus 4 ~~~~~~~~l~~~~--~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~--~-----~~~~~~~~~~IRG 71 (79)
T COG1958 4 LGPLPLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGE--K-----NVRRLGGEVLIRG 71 (79)
T ss_pred ccCCcHHHHHHhh--CCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCc--c-----ccceeccEEEEEC
Confidence 3457899999999 89999999999999999999999999999999998741 111 1 0124455999999
Q ss_pred CcEEEEEe
Q 033937 98 DSVIIVLR 105 (108)
Q Consensus 98 d~Iv~I~~ 105 (108)
++|++|++
T Consensus 72 ~~I~~I~~ 79 (79)
T COG1958 72 DNIVLISP 79 (79)
T ss_pred CcEEEEeC
Confidence 99999974
No 15
>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=99.85 E-value=7.2e-21 Score=121.55 Aligned_cols=72 Identities=21% Similarity=0.353 Sum_probs=60.9
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033937 24 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 103 (108)
Q Consensus 24 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I 103 (108)
+.|.+++ +++|+|.+++||.+.|+|+|||+||||+|+||+|+..... .+ ..++.+|.++|||+||++|
T Consensus 2 ~~L~~~l--~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~-~~---------~~~~~lG~~~iRG~~I~~i 69 (74)
T cd01727 2 STLEDYL--NKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSD-EG---------VEQVVLGLYIIRGDNIAVV 69 (74)
T ss_pred hhHHHhc--CCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCC-CC---------ceeeEeceEEECCCEEEEE
Confidence 4578888 9999999999999999999999999999999999864311 11 1346799999999999999
Q ss_pred EeCC
Q 033937 104 LRNP 107 (108)
Q Consensus 104 ~~~~ 107 (108)
++..
T Consensus 70 ~~~d 73 (74)
T cd01727 70 GEID 73 (74)
T ss_pred EccC
Confidence 9864
No 16
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.84 E-value=3.2e-22 Score=129.97 Aligned_cols=85 Identities=32% Similarity=0.518 Sum_probs=69.5
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 033937 19 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 98 (108)
Q Consensus 19 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd 98 (108)
+..|+++|+.++ +.||.|++|++|+++|+|.|||+|+||+|.||+|+......+....++. ....+|++..+|+|||
T Consensus 3 v~ePldllrlsL--dErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~-~k~~~r~~emlFvRGd 79 (91)
T KOG3460|consen 3 VEEPLDLLRLSL--DERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEI-VKTTKRTVEMLFVRGD 79 (91)
T ss_pred ccccHHHHhhcc--cceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHH-HhhhhcceeEEEEeCC
Confidence 467999999999 9999999999999999999999999999999999987643221111111 1135588999999999
Q ss_pred cEEEEEeC
Q 033937 99 SVIIVLRN 106 (108)
Q Consensus 99 ~Iv~I~~~ 106 (108)
+|++|+|-
T Consensus 80 ~Vilvspp 87 (91)
T KOG3460|consen 80 GVILVSPP 87 (91)
T ss_pred eEEEEcCc
Confidence 99999974
No 17
>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=99.84 E-value=2.5e-20 Score=115.82 Aligned_cols=67 Identities=24% Similarity=0.443 Sum_probs=59.5
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033937 24 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 103 (108)
Q Consensus 24 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I 103 (108)
.+|++++ +++|+|.|++|+.++|+|.+||+||||+|+||.|.+...+ ..+++|.++|||++|++|
T Consensus 1 ~~L~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I 65 (67)
T PF01423_consen 1 NFLQKLI--GKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYI 65 (67)
T ss_dssp HHHHHTT--TSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEE
T ss_pred ChhHHhC--CcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEE
Confidence 3688999 9999999999999999999999999999999999864310 347799999999999999
Q ss_pred Ee
Q 033937 104 LR 105 (108)
Q Consensus 104 ~~ 105 (108)
++
T Consensus 66 ~~ 67 (67)
T PF01423_consen 66 SL 67 (67)
T ss_dssp EE
T ss_pred EC
Confidence 86
No 18
>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=99.83 E-value=5.4e-20 Score=118.22 Aligned_cols=72 Identities=17% Similarity=0.320 Sum_probs=61.1
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033937 24 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 103 (108)
Q Consensus 24 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I 103 (108)
+-|.+++ +++|+|.|+|||.|.|+|.|||+||||+|+||+|++..+.+... ...|++|+++|||++|++|
T Consensus 3 ~~L~~~l--~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~--------~~~r~lGlv~IrG~~Iv~i 72 (75)
T cd06168 3 QKLRSLL--GRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSP--------TEPRVLGLVMIPGHHIVSI 72 (75)
T ss_pred hHHHHhc--CCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCC--------ccEEEeeeEEEeCCeEEEE
Confidence 3578888 99999999999999999999999999999999999865332111 2458899999999999998
Q ss_pred Ee
Q 033937 104 LR 105 (108)
Q Consensus 104 ~~ 105 (108)
..
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 74
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.82 E-value=6.6e-20 Score=113.78 Aligned_cols=66 Identities=27% Similarity=0.561 Sum_probs=58.3
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 104 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~ 104 (108)
+|..++ +++|+|.|+||+.+.|+|.+||+||||+|+||+|++... ...+++|.++|||++|++|+
T Consensus 2 ~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLI--GKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hhHHhC--CcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEe
Confidence 578888 999999999999999999999999999999999986431 13378999999999999997
Q ss_pred e
Q 033937 105 R 105 (108)
Q Consensus 105 ~ 105 (108)
+
T Consensus 67 ~ 67 (67)
T smart00651 67 L 67 (67)
T ss_pred C
Confidence 4
No 20
>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=99.82 E-value=1.2e-19 Score=114.92 Aligned_cols=68 Identities=15% Similarity=0.321 Sum_probs=59.4
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|+++|+.+. +++|.|.|++|..|+|+|.+||.|||++|+||++.... |+ ...++.+||||+||.
T Consensus 1 P~~~L~~~~--g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~----g~----------~~~~~~v~IRG~nI~ 64 (70)
T cd01721 1 PIKLLHEAE--GHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARD----GR----------VSQLEQVYIRGSKIR 64 (70)
T ss_pred ChHHHhhCC--CCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCC----Cc----------EeEcCcEEEeCCEEE
Confidence 899999999 99999999999999999999999999999999875321 21 145899999999999
Q ss_pred EEEe
Q 033937 102 IVLR 105 (108)
Q Consensus 102 ~I~~ 105 (108)
+|..
T Consensus 65 ~v~l 68 (70)
T cd01721 65 FFIL 68 (70)
T ss_pred EEEe
Confidence 9864
No 21
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=1.2e-19 Score=116.42 Aligned_cols=71 Identities=23% Similarity=0.313 Sum_probs=60.6
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
-|+.+|+.+. +++|.|.|++|+.++|+|.+||.|||++|+||+|... +|+ ....++.+||||++|
T Consensus 1 ~Pl~~L~~~~--g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g~---------~~~~~~~v~IRG~~I 65 (76)
T cd01723 1 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----DGD---------KFWKMPECYIRGNTI 65 (76)
T ss_pred CchHHHHhcC--CCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CCc---------EeeeCCcEEEeCCEE
Confidence 3999999998 9999999999999999999999999999999998621 121 113478999999999
Q ss_pred EEEEeC
Q 033937 101 IIVLRN 106 (108)
Q Consensus 101 v~I~~~ 106 (108)
.+|+..
T Consensus 66 ~~i~~p 71 (76)
T cd01723 66 KYLRVP 71 (76)
T ss_pred EEEEcC
Confidence 999753
No 22
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=99.78 E-value=3.6e-20 Score=125.66 Aligned_cols=103 Identities=83% Similarity=1.257 Sum_probs=91.1
Q ss_pred CCChhhh--hcccccccCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCcccc
Q 033937 4 RPMEEDN--VKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKA 81 (108)
Q Consensus 4 ~~~~~~~--~~~~~~~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~ 81 (108)
.|.+++- +..++.++..||++++..++.....|.|.+||++.+-|++.|||.|+|++|+++.|.|+..+++|++.+ .
T Consensus 5 ~pk~e~t~~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~ 83 (114)
T KOG3459|consen 5 KPKEECTPLEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-A 83 (114)
T ss_pred chhhhcCccccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-C
Confidence 4666555 666888999999999999999999999999999999999999999999999999999999888777744 4
Q ss_pred ccCcceeeeceEEEeCCcEEEEEeCC
Q 033937 82 LPVNKDRFISKMFLRGDSVIIVLRNP 107 (108)
Q Consensus 82 ~~~~~~r~lg~i~IRGd~Iv~I~~~~ 107 (108)
+++...|++|.+|||||+|+++..+|
T Consensus 84 ~~~~~~r~isK~flRGdsvI~v~r~p 109 (114)
T KOG3459|consen 84 KPVNKDRFISKMFLRGDSVILVLRNP 109 (114)
T ss_pred CccchhhhhheeeecCCeEEEEEecc
Confidence 55566799999999999999998766
No 23
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=1.3e-18 Score=106.59 Aligned_cols=63 Identities=35% Similarity=0.549 Sum_probs=55.1
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 104 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~ 104 (108)
|..++ +++|+|.|+||+.+.|+|.|||+|||++|+||.|.+.. + ..++++.++|||++|.+|.
T Consensus 1 l~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~----------~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLV--GKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----G----------KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHC--CCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----C----------cEEECCeEEEECCEEEEEC
Confidence 35667 99999999999999999999999999999999998643 1 2367999999999999874
No 24
>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=99.75 E-value=1.2e-17 Score=110.62 Aligned_cols=68 Identities=21% Similarity=0.280 Sum_probs=59.5
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 22 PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 22 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|+.+|+++. |++|+|.|++|..|+|+|.++|.|||++|+||+++... + ....++.++|||++|.
T Consensus 2 ~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~----~----------~~~~~~~v~IRG~nI~ 65 (90)
T cd01724 2 LVRFLMKLT--NETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG----R----------NPVPLDTLSIRGNNIR 65 (90)
T ss_pred HhHHHHhCC--CCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC----C----------ceeEcceEEEeCCEEE
Confidence 678999998 99999999999999999999999999999999987322 1 1246899999999999
Q ss_pred EEEe
Q 033937 102 IVLR 105 (108)
Q Consensus 102 ~I~~ 105 (108)
+|..
T Consensus 66 yi~l 69 (90)
T cd01724 66 YFIL 69 (90)
T ss_pred EEEc
Confidence 9874
No 25
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.74 E-value=2.7e-18 Score=111.20 Aligned_cols=78 Identities=21% Similarity=0.440 Sum_probs=66.4
Q ss_pred ccCCCcHHHHHhhhhCCcEEEEEecC--CeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEE
Q 033937 17 EFNTGPLSVLMMSVKNNTQVLINCRN--NKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 94 (108)
Q Consensus 17 ~~~~~Pl~~L~~~~~~~krV~V~l~~--gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~ 94 (108)
.....|+.++++++++..+|.|||.+ +-.+.|.++|||+|||+||+||+|.... + ...+.+|.++
T Consensus 8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k------~-------~~rk~lGRil 74 (88)
T KOG1774|consen 8 KVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSK------T-------KSRKELGRIL 74 (88)
T ss_pred ceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccc------c-------cCCCccccEE
Confidence 44589999999999999999999998 4689999999999999999999998543 1 0123699999
Q ss_pred EeCCcEEEEEeCC
Q 033937 95 LRGDSVIIVLRNP 107 (108)
Q Consensus 95 IRGd~Iv~I~~~~ 107 (108)
++||||.+|...-
T Consensus 75 LKGDnItli~~~~ 87 (88)
T KOG1774|consen 75 LKGDNITLIQSAG 87 (88)
T ss_pred EcCCcEEEEeecC
Confidence 9999999998653
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.73 E-value=3.3e-17 Score=105.89 Aligned_cols=69 Identities=20% Similarity=0.278 Sum_probs=58.5
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
.+..+|+.+. |+.|.|.||+|..|+|+|.++|.|||++|+||++.... + ....+|.++|||++|
T Consensus 9 tl~~~L~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~----~----------~~~~~~~v~IRG~nI 72 (78)
T cd01733 9 TLIILLQGLQ--GKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN----G----------KQVQVEEIMVTGRNI 72 (78)
T ss_pred hHHHHHHHCC--CCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC----C----------ceeECCcEEEECCEE
Confidence 4667888888 99999999999999999999999999999999876211 1 113589999999999
Q ss_pred EEEEe
Q 033937 101 IIVLR 105 (108)
Q Consensus 101 v~I~~ 105 (108)
.+|..
T Consensus 73 ~yI~l 77 (78)
T cd01733 73 RYVHI 77 (78)
T ss_pred EEEEc
Confidence 99863
No 27
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.72 E-value=5.5e-17 Score=105.39 Aligned_cols=72 Identities=21% Similarity=0.213 Sum_probs=59.6
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
.|+++|+++. |++|.|.|++|..|+|+|.++|.|||++|+||++.... +.. ....++.++|||++|
T Consensus 1 l~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~~~--------~~~~~~~v~IRG~~I 66 (81)
T cd01725 1 LFFSFFKTLV--GKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----KYP--------HMLSVKNCFIRGSVV 66 (81)
T ss_pred ChhHHHHhCC--CCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----Ccc--------cccccCeEEEECCEE
Confidence 3789999998 99999999999999999999999999999999876211 110 113478999999999
Q ss_pred EEEEeC
Q 033937 101 IIVLRN 106 (108)
Q Consensus 101 v~I~~~ 106 (108)
.+|...
T Consensus 67 ~~I~lp 72 (81)
T cd01725 67 RYVQLP 72 (81)
T ss_pred EEEEeC
Confidence 999853
No 28
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.70 E-value=1.8e-17 Score=106.28 Aligned_cols=77 Identities=22% Similarity=0.442 Sum_probs=66.2
Q ss_pred ccCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEe
Q 033937 17 EFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLR 96 (108)
Q Consensus 17 ~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IR 96 (108)
.+...|+.++++|+ +++|+|.+++++++.|+|+|||.|.|++|+||+|+-..+. ++ .-.+++++++.
T Consensus 3 ~~~llPlEliDkcI--gski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~e--gr---------~~tk~~~iLLn 69 (84)
T KOG1775|consen 3 PSTLLPLELIDKCI--GSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPE--GR---------RMTKLDQILLN 69 (84)
T ss_pred hhhcccHHHHHHhc--CceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCC--cc---------eeeeeeeeeec
Confidence 35678999999999 9999999999999999999999999999999999865421 11 22468999999
Q ss_pred CCcEEEEEeC
Q 033937 97 GDSVIIVLRN 106 (108)
Q Consensus 97 Gd~Iv~I~~~ 106 (108)
|+||.+..|-
T Consensus 70 GNni~mLvPG 79 (84)
T KOG1775|consen 70 GNNITMLVPG 79 (84)
T ss_pred CCcEEEEecC
Confidence 9999998873
No 29
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.68 E-value=1.2e-16 Score=101.74 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=59.7
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 033937 19 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 98 (108)
Q Consensus 19 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd 98 (108)
+..| -|++++ +|++.+.|.+||.+.|.|.|||.|||+||+||+|.-.. + .+..+|..+|||+
T Consensus 4 sg~P--eLkkym--dKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~----------~~~~ig~~vIrgn 65 (77)
T KOG1780|consen 4 SGHP--ELKKYM--DKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----G----------DKNNIGMVVIRGN 65 (77)
T ss_pred ccCc--hHHHhh--hheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----C----------CcceeeeEEEecc
Confidence 3457 789999 99999999999999999999999999999999997322 1 1245899999999
Q ss_pred cEEEEEeC
Q 033937 99 SVIIVLRN 106 (108)
Q Consensus 99 ~Iv~I~~~ 106 (108)
+|+++.+.
T Consensus 66 siv~~eaL 73 (77)
T KOG1780|consen 66 SIVMVEAL 73 (77)
T ss_pred EEEEEeec
Confidence 99998764
No 30
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.65 E-value=2.1e-17 Score=110.35 Aligned_cols=78 Identities=17% Similarity=0.293 Sum_probs=63.8
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 102 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~ 102 (108)
-++|+.+.+.+++|+|.+.+||.+.|+|+|||+.|||||+|++|+...++..-+. ....|.+|++++||..+++
T Consensus 17 EsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~------~~~tR~LGLvV~RGTalvl 90 (108)
T KOG1781|consen 17 ESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKL------TDETRKLGLVVCRGTALVL 90 (108)
T ss_pred hHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccch------hhhhheeeeEEEcccEEEE
Confidence 3455555555999999999999999999999999999999999997665432221 1234889999999999999
Q ss_pred EEeC
Q 033937 103 VLRN 106 (108)
Q Consensus 103 I~~~ 106 (108)
|+|+
T Consensus 91 isp~ 94 (108)
T KOG1781|consen 91 ISPA 94 (108)
T ss_pred EcCC
Confidence 9986
No 31
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.63 E-value=7.4e-16 Score=97.98 Aligned_cols=73 Identities=18% Similarity=0.266 Sum_probs=64.3
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCC
Q 033937 19 NTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGD 98 (108)
Q Consensus 19 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd 98 (108)
..+|-.+|.... +++|.|.|++|.+|.|+|++.|.||||.|.+|+|++.. . ..-.+|.++||.+
T Consensus 6 PvNPKpFL~~l~--gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-----~---------~~g~lGEilIRCN 69 (79)
T KOG3482|consen 6 PVNPKPFLNGLT--GKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-----V---------STGNLGEILIRCN 69 (79)
T ss_pred cCCchHHHhhcc--CCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-----c---------ccccceeEEEEec
Confidence 458889999999 99999999999999999999999999999999998643 1 1245999999999
Q ss_pred cEEEEEeCC
Q 033937 99 SVIIVLRNP 107 (108)
Q Consensus 99 ~Iv~I~~~~ 107 (108)
||.+|...|
T Consensus 70 Nvlyi~gv~ 78 (79)
T KOG3482|consen 70 NVLYIRGVP 78 (79)
T ss_pred cEEEEecCC
Confidence 999997655
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.56 E-value=6.5e-16 Score=111.75 Aligned_cols=75 Identities=23% Similarity=0.510 Sum_probs=61.3
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 105 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~~ 105 (108)
|-.++ |.+++|.++|||.+.|.+.+||+||||+|.||+|....+.+.++.. ...++|-+|++++||+||++.+.
T Consensus 9 ml~~i--Nyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~----~~eEkr~lgLvllRgenIvs~tV 82 (177)
T KOG3168|consen 9 MLQHI--NYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMT----DGEEKRVLGLVLLRGENIVSMTV 82 (177)
T ss_pred HHHhh--cceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccccc----ccceeeEEEEEEecCCcEEEEec
Confidence 34556 8999999999999999999999999999999999976655443210 12356889999999999999875
Q ss_pred C
Q 033937 106 N 106 (108)
Q Consensus 106 ~ 106 (108)
.
T Consensus 83 e 83 (177)
T KOG3168|consen 83 E 83 (177)
T ss_pred c
Confidence 4
No 33
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.43 E-value=1.9e-13 Score=90.24 Aligned_cols=71 Identities=18% Similarity=0.368 Sum_probs=60.0
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEE
Q 033937 24 SVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIV 103 (108)
Q Consensus 24 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I 103 (108)
+-|..++ +++|.|.+.|||.+.|.|+|||+-.||+|+||.|+...... +. ..-.+|..+|||+||.+|
T Consensus 3 s~L~~y~--n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~-gv---------~q~~lGlyiirgeNva~i 70 (96)
T KOG1784|consen 3 STLEDYM--NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE-GV---------EQIVLGLYIIRGENVAVI 70 (96)
T ss_pred hhHHHHh--hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc-ch---------hheeeEEEEEecCcccee
Confidence 3578889 99999999999999999999999999999999998754211 11 235689999999999999
Q ss_pred EeC
Q 033937 104 LRN 106 (108)
Q Consensus 104 ~~~ 106 (108)
.+.
T Consensus 71 g~i 73 (96)
T KOG1784|consen 71 GEI 73 (96)
T ss_pred eec
Confidence 875
No 34
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.42 E-value=5.2e-14 Score=89.54 Aligned_cols=71 Identities=20% Similarity=0.334 Sum_probs=63.2
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 033937 20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS 99 (108)
Q Consensus 20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~ 99 (108)
..|-++|...+ |++|.|+|.+|-.|+|+|.+.|.|||+-|+.++|... |+ ..+..|..||||++
T Consensus 5 ~~~~~fl~~ii--Gr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-----gq---------l~n~ygdaFirGnn 68 (77)
T KOG1783|consen 5 SMPGEFLKAII--GRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-----GQ---------LKNKYGDAFIRGNN 68 (77)
T ss_pred cCcHHHHHHHh--CCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-----Cc---------ccccccceeecccc
Confidence 56889999999 9999999999999999999999999999999999753 33 23568999999999
Q ss_pred EEEEEeC
Q 033937 100 VIIVLRN 106 (108)
Q Consensus 100 Iv~I~~~ 106 (108)
|.+|+..
T Consensus 69 VlyIs~~ 75 (77)
T KOG1783|consen 69 VLYISTQ 75 (77)
T ss_pred EEEEEec
Confidence 9999875
No 35
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.38 E-value=6.9e-14 Score=96.70 Aligned_cols=69 Identities=28% Similarity=0.400 Sum_probs=59.4
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEEe
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 105 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~~ 105 (108)
|..++ ++++.|.|||||.+-|.|++||+|-|++|.+|.|++..... .+++..|..+|||+||+++..
T Consensus 14 l~~~~--dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~-----------Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYL--DKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNK-----------YCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHh--cceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecce-----------ecccCceEEEEecCcEEEEec
Confidence 56677 99999999999999999999999999999999999765211 245678999999999999986
Q ss_pred CC
Q 033937 106 NP 107 (108)
Q Consensus 106 ~~ 107 (108)
.+
T Consensus 81 id 82 (129)
T KOG1782|consen 81 ID 82 (129)
T ss_pred CC
Confidence 54
No 36
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.38 E-value=2.3e-13 Score=85.02 Aligned_cols=45 Identities=31% Similarity=0.409 Sum_probs=39.6
Q ss_pred HHhhhhCCcEEEEEecCCe----EEEEEEEEecCccceEeeceEEEeec
Q 033937 26 LMMSVKNNTQVLINCRNNK----KLLGRVRAFDRHCNMVLENVREMWTE 70 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr----~i~G~L~~fD~hmNlvL~d~~E~~~~ 70 (108)
|.+|+.++.||+|+++.-+ .++|.|+|||+||||+|.||+|.|..
T Consensus 1 ~~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 1 LHRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CchhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3578888999999999843 67899999999999999999999865
No 37
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.28 E-value=1e-11 Score=86.08 Aligned_cols=70 Identities=23% Similarity=0.316 Sum_probs=60.3
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSV 100 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~I 100 (108)
.||++|+.+- +.++.|.|++|..|.|.|+..|.+|||.|.+|+++..+ |. + --.++.++|||++|
T Consensus 2 lPLsLL~~aq--~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----gd--k-------f~r~pEcYirGttI 66 (134)
T KOG3293|consen 2 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED----GD--K-------FFRMPECYIRGTTI 66 (134)
T ss_pred cchhHHHhcC--CCeEEEEecCCCEecceeecchhhhhcchheeEEeccC----CC--c-------eeecceeEEeccee
Confidence 6999999998 99999999999999999999999999999999987432 22 1 12378999999999
Q ss_pred EEEEe
Q 033937 101 IIVLR 105 (108)
Q Consensus 101 v~I~~ 105 (108)
-++..
T Consensus 67 kylri 71 (134)
T KOG3293|consen 67 KYLRI 71 (134)
T ss_pred EEEec
Confidence 98753
No 38
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.15 E-value=3.1e-10 Score=74.74 Aligned_cols=69 Identities=22% Similarity=0.311 Sum_probs=56.2
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 102 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~ 102 (108)
+++++.++ |++|.|.|+++-.|.|+|.+.|+|+||-|.|..-.-. .+ .|+. -.+..+||||..|.+
T Consensus 4 ysfFkslv--g~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~--~k--------yPhm--~Sv~ncfIRGSvvrY 69 (96)
T KOG3448|consen 4 YSFFKSLV--GKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDP--DK--------YPHM--LSVKNCFIRGSVVRY 69 (96)
T ss_pred HHHHHHhc--CCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCc--cc--------CCCe--eeeeeEEEeccEEEE
Confidence 46778888 9999999999999999999999999999999775421 11 2222 347889999999999
Q ss_pred EEe
Q 033937 103 VLR 105 (108)
Q Consensus 103 I~~ 105 (108)
|..
T Consensus 70 v~l 72 (96)
T KOG3448|consen 70 VQL 72 (96)
T ss_pred EEe
Confidence 865
No 39
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.07 E-value=4.9e-10 Score=76.22 Aligned_cols=72 Identities=14% Similarity=0.274 Sum_probs=61.7
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeC
Q 033937 18 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG 97 (108)
Q Consensus 18 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRG 97 (108)
+..-|+.+|+.+- +.-|.+.+..|..|+|+|+.-|++||+.|+|++-+..+ |. -.++.++||||
T Consensus 2 s~gvpiKlLhEaq--GhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~d----g~----------vs~le~V~IRG 65 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQ--GHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARD----GR----------VSQLEQVFIRG 65 (119)
T ss_pred ccccceeeeeccc--CcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccC----Cc----------ceeeeeEEEec
Confidence 4567999999998 99999999999999999999999999999998866432 22 24689999999
Q ss_pred CcEEEEEe
Q 033937 98 DSVIIVLR 105 (108)
Q Consensus 98 d~Iv~I~~ 105 (108)
+.|.++..
T Consensus 66 S~IRFlvl 73 (119)
T KOG3172|consen 66 SKIRFLVL 73 (119)
T ss_pred CeEEEEEC
Confidence 99988763
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.52 E-value=8.5e-07 Score=60.41 Aligned_cols=66 Identities=21% Similarity=0.349 Sum_probs=54.6
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEE
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVII 102 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~ 102 (108)
+.+|+++. +.+|+|.|++|..+.|++.+.|.+||..|.++.=. .+ |+ + ..+..+.|||+||.+
T Consensus 4 vr~L~kl~--~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t--~~---~~------p----v~l~~lsirgnniRy 66 (109)
T KOG3428|consen 4 VRFLKKLL--NERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMT--VK---GE------P----VRLDTLSIRGNNIRY 66 (109)
T ss_pred HHHHHHhh--CCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEe--cC---CC------c----eeEEEEEeecceEEE
Confidence 45788888 99999999999999999999999999999998743 21 11 1 237789999999998
Q ss_pred EEe
Q 033937 103 VLR 105 (108)
Q Consensus 103 I~~ 105 (108)
+..
T Consensus 67 ~~l 69 (109)
T KOG3428|consen 67 YIL 69 (109)
T ss_pred EEc
Confidence 864
No 41
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=97.43 E-value=0.00048 Score=42.70 Aligned_cols=39 Identities=23% Similarity=0.323 Sum_probs=34.5
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
+|..+.+++.+|.|.|.+|-.++|.+.|||+|+=|+-.+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 677778889999999999999999999999999777544
No 42
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=97.37 E-value=0.00064 Score=42.15 Aligned_cols=39 Identities=21% Similarity=0.227 Sum_probs=34.4
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
+|..+.+++.+|.|.|.+|-.++|.+.|||+|+=|+-.+
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 677777889999999999999999999999999777544
No 43
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.36 E-value=0.00068 Score=42.91 Aligned_cols=68 Identities=13% Similarity=0.183 Sum_probs=40.1
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecC---ccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDR---HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~---hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
++..++ |++|.|.++||..|+|.|.+++. =+-++|.-|.........+ . ..........++|.++.|+
T Consensus 6 l~~~lv--G~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~-~------~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLV--GQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSN-S------DPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTT--TSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE-----
T ss_pred HHHhCc--CCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccccc-C------CccCCCCCceEEEeccccC
Confidence 455566 99999999999999999999999 8999999888653211000 0 0112345667888888775
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.18 E-value=0.0012 Score=42.87 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=35.0
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 64 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~ 64 (108)
+|..+..++.+|.|.|.+|-.++|.+.|||+|+=|+-.+.
T Consensus 11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 6677777889999999999999999999999997776554
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.36 E-value=0.0097 Score=38.38 Aligned_cols=36 Identities=31% Similarity=0.321 Sum_probs=31.9
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMV 60 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlv 60 (108)
+|.....++.+|.|.|.||-.++|.+.+||+|.=|+
T Consensus 11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 567777789999999999999999999999997554
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.85 E-value=0.023 Score=41.53 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=36.1
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
+|..+.+++.+|.|.|.+|-.++|.+.|||+|+=|+..+..
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~gk 136 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGY 136 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCCc
Confidence 67788888999999999999999999999999977766643
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.82 E-value=0.024 Score=41.43 Aligned_cols=40 Identities=23% Similarity=0.174 Sum_probs=35.3
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 64 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~ 64 (108)
+|..+.+++.+|.|.|.+|-.++|.+.+||+|.=|+-.+.
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 6778888899999999999999999999999987776554
No 48
>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=95.12 E-value=0.056 Score=33.41 Aligned_cols=35 Identities=26% Similarity=0.300 Sum_probs=30.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeeceEE
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 66 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E 66 (108)
.|..|.+.+..|.+|+|.+.|||.-.++++-.|.+
T Consensus 5 iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 5 VGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred cccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 38999999999999999999999999998655443
No 49
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=94.81 E-value=0.25 Score=33.03 Aligned_cols=70 Identities=19% Similarity=0.307 Sum_probs=50.2
Q ss_pred hhhhCCcEEEEEecCCeEEEEEEEEecC-ccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEEEEE
Q 033937 28 MSVKNNTQVLINCRNNKKLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 104 (108)
Q Consensus 28 ~~~~~~krV~V~l~~gr~i~G~L~~fD~-hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv~I~ 104 (108)
.++ |++|.+..+.+-.|+|+|...|. --.|.|.+|..+-++-+.... ...+ .......+..||..|--+.
T Consensus 5 ~~I--Gs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~---~ipp--~~~v~~~I~Fr~sDIkdL~ 75 (96)
T PF12701_consen 5 PYI--GSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR---EIPP--SDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCT--TCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS------C---CSSSSEEEEETTTEEEEE
T ss_pred ccc--CCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc---ccCC--CCceeeEEEEEccccceEE
Confidence 356 99999999999999999999998 788999999876443211110 0011 2234788999999987554
No 50
>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=94.71 E-value=0.17 Score=29.18 Aligned_cols=33 Identities=9% Similarity=0.229 Sum_probs=29.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceEeeceEE
Q 033937 33 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVRE 66 (108)
Q Consensus 33 ~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E 66 (108)
|++|+|.+ ++..++|+..+.|..-.|+++....
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 89999999 6788899999999999999977544
No 51
>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=93.37 E-value=0.98 Score=29.36 Aligned_cols=63 Identities=22% Similarity=0.254 Sum_probs=43.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCcc-ceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHC-NMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hm-NlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|.+|.... |++|.+.|.++..+.|++.|+|... |+..++ -+ .+ . -..+..++|...|+
T Consensus 16 Lr~l~~~~--gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~-L~---TP------------l---Gv~~eAlLR~~DVi 74 (80)
T PF11095_consen 16 LRSLLAMV--GKPVEFTLHENTTVSARFGACDIDVSNFQVSN-LQ---TP------------L---GVQPEALLRCSDVI 74 (80)
T ss_dssp HHHHHHCT--TSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEE-EE---TT------------T---TEEEEEEEEGGGEE
T ss_pred HHHHHHhc--CCceEEEEeCCeEEEEEEEEecCchheEEhhh-cC---CC------------c---ccChhheeecCCEE
Confidence 34445555 9999999999999999999999754 444333 11 10 0 12578999999999
Q ss_pred EEEeC
Q 033937 102 IVLRN 106 (108)
Q Consensus 102 ~I~~~ 106 (108)
+++..
T Consensus 75 ~~~f~ 79 (80)
T PF11095_consen 75 SISFD 79 (80)
T ss_dssp EEEE-
T ss_pred EEEec
Confidence 99864
No 52
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=92.06 E-value=0.29 Score=35.54 Aligned_cols=38 Identities=5% Similarity=0.144 Sum_probs=32.6
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecC
Q 033937 18 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR 55 (108)
Q Consensus 18 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~ 55 (108)
+-..=+++..+|.++++-|+|.+.|||+++|.=.|.|.
T Consensus 105 srrDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 105 SRRDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred ccchHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccce
Confidence 33445888999999999999999999999999888764
No 53
>PRK14638 hypothetical protein; Provisional
Probab=91.69 E-value=0.35 Score=34.55 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=28.7
Q ss_pred CCCcHHH---HHhhhhCCcEEEEEecCCeEEEEEEEEecCc
Q 033937 19 NTGPLSV---LMMSVKNNTQVLINCRNNKKLLGRVRAFDRH 56 (108)
Q Consensus 19 ~~~Pl~~---L~~~~~~~krV~V~l~~gr~i~G~L~~fD~h 56 (108)
..-||.- +.++. |+.|+|.+++++.++|+|.++|.-
T Consensus 85 ldRpL~~~~~f~r~~--G~~v~V~~~~~k~~~G~L~~~~~~ 123 (150)
T PRK14638 85 LDRPLRGPKDYVRFT--GKLAKIVTKDGKTFIGRIESFVDG 123 (150)
T ss_pred CCCCCCCHHHHHHhC--CCEEEEEECCCcEEEEEEEEEeCC
Confidence 3445443 45667 999999999999999999999973
No 54
>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=91.12 E-value=2.6 Score=26.99 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=45.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccce-EeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCcEE
Q 033937 33 NTQVLINCRNNKKLLGRVRAFDRHCNM-VLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVI 101 (108)
Q Consensus 33 ~krV~V~l~~gr~i~G~L~~fD~hmNl-vL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~Iv 101 (108)
|++|.+..+.+-.|+|.|...|..=.- .|.||..+-++-++.+ . ....+ ...-...++.||+.|-
T Consensus 6 G~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~-~-~~ipp--~~~vyd~IvFrgsDIk 71 (74)
T cd01736 6 GSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTD-G-PEIPP--SDEVYDYIVFRGSDIK 71 (74)
T ss_pred CceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCC-C-CccCC--CCcceeEEEEcCCccc
Confidence 999999999999999999999987664 4888887654422111 0 00111 2234788999999874
No 55
>PRK02001 hypothetical protein; Validated
Probab=90.33 E-value=0.56 Score=33.72 Aligned_cols=33 Identities=18% Similarity=0.408 Sum_probs=27.7
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL 61 (108)
+.+++ |..|+|.+.+++.+.|+|.++|.- ++.|
T Consensus 85 f~r~~--G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 85 YKKNI--GRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHhC--CCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 45667 999999999999999999999985 4444
No 56
>PRK14639 hypothetical protein; Provisional
Probab=89.93 E-value=0.64 Score=32.82 Aligned_cols=33 Identities=24% Similarity=0.420 Sum_probs=27.7
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL 61 (108)
+.++. |+.|+|.+++++.+.|+|.++|.- ++.|
T Consensus 83 f~r~~--G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 83 FAKSI--GELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 45667 999999999999999999999983 4444
No 57
>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=86.15 E-value=1.5 Score=32.11 Aligned_cols=43 Identities=28% Similarity=0.368 Sum_probs=29.2
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecC-ccceEeeceEE
Q 033937 20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR-HCNMVLENVRE 66 (108)
Q Consensus 20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~-hmNlvL~d~~E 66 (108)
.+|+.+ ..++ +|.|+|.+.| +++.|.|..+|. .-|+||-+-.|
T Consensus 7 ~~p~~~-~~yv--~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEW-QDYV--GKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHH-HCTT--T-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHH-HHhh--CcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 456655 5666 9999999999 999999999997 35677765443
No 58
>PRK14644 hypothetical protein; Provisional
Probab=85.86 E-value=1.7 Score=30.54 Aligned_cols=40 Identities=8% Similarity=0.109 Sum_probs=30.2
Q ss_pred CCcHHH--HHhhhhCCcEEEEEecCC----eEEEEEEEEecCccceEee
Q 033937 20 TGPLSV--LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVLE 62 (108)
Q Consensus 20 ~~Pl~~--L~~~~~~~krV~V~l~~g----r~i~G~L~~fD~hmNlvL~ 62 (108)
.-||.. +.+++ |+.|.|.+++. +.+.|+|.++|.. ++.|.
T Consensus 72 dRpL~~~~f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 72 DMDYETDELENHI--GEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred CCCCCHHHHHHhC--CCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 344443 56777 99999999886 7899999999984 44443
No 59
>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=84.65 E-value=2.5 Score=26.89 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=25.6
Q ss_pred HHhhhhCCcEEEEEec---CC-eEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~---~g-r~i~G~L~~fD~hmNlvL 61 (108)
+.+++ |..|.|.++ +| +.+.|+|.++|.- ++.|
T Consensus 20 ~~r~~--G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 20 FERAV--GKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHhC--CCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 35666 999999998 55 5899999999984 3444
No 60
>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=83.94 E-value=2.4 Score=30.88 Aligned_cols=37 Identities=19% Similarity=0.077 Sum_probs=32.5
Q ss_pred hhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 29 SVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 29 ~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
+..++-+|+|.+.||..|.|++-+|+.-=|.+|+-+.
T Consensus 25 ~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 25 WRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred HHhcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 3345799999999999999999999999999987644
No 61
>PRK14640 hypothetical protein; Provisional
Probab=83.59 E-value=2.5 Score=30.16 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=26.2
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~hmNlvL 61 (108)
+.+++ |+.|.|.++ +.+.++|+|.++|.. ++.|
T Consensus 92 f~r~~--G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 92 FEKYV--GQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 45677 999999994 568999999999984 3444
No 62
>PRK14642 hypothetical protein; Provisional
Probab=82.83 E-value=2.6 Score=31.63 Aligned_cols=36 Identities=19% Similarity=0.205 Sum_probs=28.1
Q ss_pred CCCcHHH---HHhhhhCCcEEEEEec-------------CCeEEEEEEEEecCc
Q 033937 19 NTGPLSV---LMMSVKNNTQVLINCR-------------NNKKLLGRVRAFDRH 56 (108)
Q Consensus 19 ~~~Pl~~---L~~~~~~~krV~V~l~-------------~gr~i~G~L~~fD~h 56 (108)
..-||.- +.++. |+.|.|.|+ +.+.|+|+|.++|..
T Consensus 85 ldRPLk~~~df~rfi--G~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 85 IDRPLRHEQDFERFA--GEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred CCCCCCCHHHHHHhC--CCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 3455543 45666 999999998 678999999999984
No 63
>PRK14636 hypothetical protein; Provisional
Probab=82.53 E-value=2.6 Score=30.87 Aligned_cols=33 Identities=12% Similarity=0.263 Sum_probs=26.1
Q ss_pred HHhhhhCCcEEEEEec---CC-eEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCR---NN-KKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~---~g-r~i~G~L~~fD~hmNlvL 61 (108)
+.++. |+.|.|.++ +| +.++|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 93 FADWA--GHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHhC--CCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 45667 999999998 45 6999999999883 4444
No 64
>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=82.26 E-value=2.5 Score=29.34 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=24.4
Q ss_pred CCCcHH---HHHhhhhCCcEEEEEec----CCeEEEEEEEEecC
Q 033937 19 NTGPLS---VLMMSVKNNTQVLINCR----NNKKLLGRVRAFDR 55 (108)
Q Consensus 19 ~~~Pl~---~L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~ 55 (108)
..-||. -+.+++ |+.|.|+++ +.+.+.|+|.++|.
T Consensus 72 ~~r~L~~~~~~~~~i--G~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 72 IDRPLKSPRDFERFI--GRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp SSS--SSHHHHHHH---SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCCcCCCHHHHHHhc--CCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 345653 467788 999999995 44689999999999
No 65
>PRK14633 hypothetical protein; Provisional
Probab=82.21 E-value=3 Score=29.68 Aligned_cols=41 Identities=15% Similarity=0.126 Sum_probs=29.3
Q ss_pred CCCcHHH---HHhhhhCCcEEEEEec----CCeEEEEEEEEecCccceEee
Q 033937 19 NTGPLSV---LMMSVKNNTQVLINCR----NNKKLLGRVRAFDRHCNMVLE 62 (108)
Q Consensus 19 ~~~Pl~~---L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~hmNlvL~ 62 (108)
..-||.- +.+++ |+.|.|.++ +.+.++|+|.++|+. ++.|.
T Consensus 79 ldRpL~~~~~f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 79 MNRQIFNIIQAQALV--GFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCCCCCCHHHHHHhC--CCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 3445443 45667 999999995 457899999999985 44443
No 66
>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=82.00 E-value=3.5 Score=27.73 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=19.7
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEE
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRV 50 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L 50 (108)
-|-..+..+.+|.+.|+||+.+.|++
T Consensus 20 ~lv~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 20 HLVSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHHHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HHHhhcCCcceEEEEEcCCCeeeeee
Confidence 34455667899999999999999985
No 67
>PRK14643 hypothetical protein; Provisional
Probab=81.92 E-value=3 Score=30.26 Aligned_cols=34 Identities=21% Similarity=0.333 Sum_probs=26.6
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEecCc-cceEe
Q 033937 26 LMMSVKNNTQVLINCRN----NKKLLGRVRAFDRH-CNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~----gr~i~G~L~~fD~h-mNlvL 61 (108)
+.++. |+.|.|.++. .+.+.|+|.++|.- ..+.|
T Consensus 99 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 99 LVKAL--NQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHhc--CCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 45777 9999999976 57899999999864 34433
No 68
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.27 E-value=3.4 Score=29.79 Aligned_cols=39 Identities=23% Similarity=0.385 Sum_probs=30.6
Q ss_pred CCcHHH---HHhhhhCCcEEEEEe----cCCeEEEEEEEEecCccceEe
Q 033937 20 TGPLSV---LMMSVKNNTQVLINC----RNNKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 20 ~~Pl~~---L~~~~~~~krV~V~l----~~gr~i~G~L~~fD~hmNlvL 61 (108)
.-||.- +.++. |+.|.|+| .+.+.++|+|.++|.-. +++
T Consensus 85 dRpL~~~~~f~r~~--G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 85 DRPLKTAEHFARFI--GEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCcCCHHHHHHhc--CcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 446543 45667 99999999 67889999999999987 444
No 69
>PRK14645 hypothetical protein; Provisional
Probab=80.79 E-value=3.3 Score=29.74 Aligned_cols=32 Identities=9% Similarity=0.227 Sum_probs=25.3
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL 61 (108)
+.+++ |+.|.|.+ +++.+.|+|.++|.- .+.|
T Consensus 97 f~r~~--G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 97 FERFA--GLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHhC--CCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 45666 99999986 789999999999984 3444
No 70
>PRK14646 hypothetical protein; Provisional
Probab=80.12 E-value=3.9 Score=29.32 Aligned_cols=33 Identities=12% Similarity=0.084 Sum_probs=26.0
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~g----r~i~G~L~~fD~hmNlvL 61 (108)
+.++. |+.|.|.|++. +.+.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 95 FKTFK--GFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHhC--CCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 46677 99999999763 5789999999985 4444
No 71
>PRK14632 hypothetical protein; Provisional
Probab=79.65 E-value=3.9 Score=29.80 Aligned_cols=33 Identities=21% Similarity=0.325 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEecC-------CeEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRN-------NKKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~-------gr~i~G~L~~fD~hmNlvL 61 (108)
+.+++ |+.|.|.+++ .+.+.|+|.++|.- ++.|
T Consensus 93 f~r~i--G~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 93 MSPYV--GRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHhC--CCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 45667 9999999986 46899999999863 4444
No 72
>PRK14634 hypothetical protein; Provisional
Probab=78.98 E-value=4.5 Score=28.99 Aligned_cols=33 Identities=12% Similarity=0.209 Sum_probs=25.6
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCRNN----KKLLGRVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~g----r~i~G~L~~fD~hmNlvL 61 (108)
+.++. |+.|+|.+++. +.+.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 95 FQTFR--GFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHhC--CCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 45667 99999999742 6899999999984 3444
No 73
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=78.39 E-value=4.8 Score=28.53 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=24.0
Q ss_pred HHhhhhCCcEEEEEe----cCCeEEEEEEEEecC
Q 033937 26 LMMSVKNNTQVLINC----RNNKKLLGRVRAFDR 55 (108)
Q Consensus 26 L~~~~~~~krV~V~l----~~gr~i~G~L~~fD~ 55 (108)
+.+++ |+.|+|.+ .+++.+.|+|.++|.
T Consensus 93 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 93 FRRFI--GREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHhC--CCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 56777 99999997 456799999999998
No 74
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=76.51 E-value=2.9 Score=24.01 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=15.1
Q ss_pred EEEEEEEecCccceEeeceEEE
Q 033937 46 LLGRVRAFDRHCNMVLENVREM 67 (108)
Q Consensus 46 i~G~L~~fD~hmNlvL~d~~E~ 67 (108)
.+|++.|.|+.+.|+|++....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999987654
No 75
>PRK14647 hypothetical protein; Provisional
Probab=75.88 E-value=6.1 Score=28.33 Aligned_cols=34 Identities=18% Similarity=0.244 Sum_probs=26.1
Q ss_pred CCcHHH---HHhhhhCCcEEEEEecC---------CeEEEEEEEEecC
Q 033937 20 TGPLSV---LMMSVKNNTQVLINCRN---------NKKLLGRVRAFDR 55 (108)
Q Consensus 20 ~~Pl~~---L~~~~~~~krV~V~l~~---------gr~i~G~L~~fD~ 55 (108)
.-||.- +.+++ |+.|.|.++. .+.+.|+|.++|.
T Consensus 85 ~RpL~~~~~f~r~~--G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 85 DRPLKKEADYERYA--GRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CCcCCCHHHHHHhC--CcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 445443 45667 9999999963 4789999999997
No 76
>PRK14637 hypothetical protein; Provisional
Probab=73.38 E-value=6.6 Score=28.05 Aligned_cols=41 Identities=15% Similarity=0.159 Sum_probs=28.3
Q ss_pred CCCcHHH---HHhhhhCCcEEEEEecCCeEE-EEEEEEecCccceEee
Q 033937 19 NTGPLSV---LMMSVKNNTQVLINCRNNKKL-LGRVRAFDRHCNMVLE 62 (108)
Q Consensus 19 ~~~Pl~~---L~~~~~~~krV~V~l~~gr~i-~G~L~~fD~hmNlvL~ 62 (108)
..-||.- +.++. |+.|.|.+.+.+.+ +|+|.++|.- ++.|.
T Consensus 83 ldRpL~~~~~f~r~~--G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 83 IERVIKNAAEFSIFV--GETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CCCCCCCHHHHHHhC--CCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 3445443 45666 99999999555566 7999999985 44443
No 77
>PRK14631 hypothetical protein; Provisional
Probab=73.18 E-value=7 Score=28.61 Aligned_cols=27 Identities=22% Similarity=0.267 Sum_probs=23.0
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEec
Q 033937 26 LMMSVKNNTQVLINCRN----NKKLLGRVRAFD 54 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~----gr~i~G~L~~fD 54 (108)
+.++. |+.|.|.+++ .+.++|+|.++|
T Consensus 112 f~r~~--G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 112 LQGYI--GQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEee
Confidence 45667 9999999964 489999999998
No 78
>PRK14641 hypothetical protein; Provisional
Probab=71.72 E-value=7.5 Score=28.48 Aligned_cols=34 Identities=12% Similarity=0.257 Sum_probs=25.4
Q ss_pred CCCcHHH---HHhhhhCCcEEEEEecC----CeEEEEEEEEec
Q 033937 19 NTGPLSV---LMMSVKNNTQVLINCRN----NKKLLGRVRAFD 54 (108)
Q Consensus 19 ~~~Pl~~---L~~~~~~~krV~V~l~~----gr~i~G~L~~fD 54 (108)
..-||.- +.++. |+.|.|.+++ .+.++|+|.++|
T Consensus 89 ldRpL~~~~~f~r~~--G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 89 LGEPIILPRQYGRHV--GRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCCcCCCHHHHHHhC--CCEEEEEEecccCCeEEEEEEEEeee
Confidence 3445443 45666 9999999976 458999999995
No 79
>PRK10898 serine endoprotease; Provisional
Probab=68.39 E-value=11 Score=30.04 Aligned_cols=34 Identities=6% Similarity=0.220 Sum_probs=29.7
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
....+.|.+.||+.+.++++++|....|-|=.+.
T Consensus 100 ~a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 100 DADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 4568999999999999999999999999876654
No 80
>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=67.36 E-value=12 Score=29.80 Aligned_cols=34 Identities=9% Similarity=0.264 Sum_probs=29.4
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
....+.|.+.||+.+.++++++|...+|-|=.+.
T Consensus 100 ~~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 100 KADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 3457899999999999999999999999886554
No 81
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=67.16 E-value=16 Score=22.83 Aligned_cols=58 Identities=19% Similarity=0.289 Sum_probs=39.3
Q ss_pred cCCCc--HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecC-ccceEeeceEEEeecCCCCCCCccccccCcceeeeceEE
Q 033937 18 FNTGP--LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDR-HCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMF 94 (108)
Q Consensus 18 ~~~~P--l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~-hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~ 94 (108)
+...| ...|++.+ |++|.|.+-.| .++|+|.+.-. |. +|+. .-...+
T Consensus 6 s~vdpyvyq~lq~li--G~~vvV~T~~g-~v~G~L~~V~pDhI--vl~~-------------------------~~~~~~ 55 (66)
T PF10842_consen 6 SLVDPYVYQTLQSLI--GQRVVVQTTRG-SVRGILVDVKPDHI--VLEE-------------------------NGTPFF 55 (66)
T ss_pred eccCHHHHHHHHHhc--CCEEEEEEcCC-cEEEEEEeecCCEE--EEEe-------------------------CCcEEE
Confidence 44566 45688888 99999999655 45999987532 21 2111 123578
Q ss_pred EeCCcEEEEEe
Q 033937 95 LRGDSVIIVLR 105 (108)
Q Consensus 95 IRGd~Iv~I~~ 105 (108)
||=..|++|.|
T Consensus 56 IR~~~IV~v~p 66 (66)
T PF10842_consen 56 IRIAQIVWVMP 66 (66)
T ss_pred EEeeeEEEEcC
Confidence 88888988865
No 82
>PRK06955 biotin--protein ligase; Provisional
Probab=65.07 E-value=21 Score=27.83 Aligned_cols=35 Identities=11% Similarity=0.183 Sum_probs=29.3
Q ss_pred hhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 29 SVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 29 ~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
++..+++|+|...+++.++|+++|.|..-.|++++
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 34569999997666778999999999999999864
No 83
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=64.43 E-value=29 Score=21.65 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=31.1
Q ss_pred HHHhhhhCCcEEEEEecCCe---EEEEEEEEecCccceEee
Q 033937 25 VLMMSVKNNTQVLINCRNNK---KLLGRVRAFDRHCNMVLE 62 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr---~i~G~L~~fD~hmNlvL~ 62 (108)
.|..++..+..|+|..-++. .+.|++..+|..-+.+.-
T Consensus 34 ~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~ 74 (92)
T PF08863_consen 34 KLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKL 74 (92)
T ss_pred HHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEE
Confidence 47778888999999887764 688999999999887743
No 84
>PRK10139 serine endoprotease; Provisional
Probab=64.15 E-value=17 Score=30.19 Aligned_cols=36 Identities=8% Similarity=0.299 Sum_probs=31.0
Q ss_pred hhCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 30 VKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 30 ~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
+.....|.|.+.||+.+.++++++|....|-+=.+.
T Consensus 111 v~~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 111 INQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred hCCCCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 345679999999999999999999999999876554
No 85
>PRK10942 serine endoprotease; Provisional
Probab=63.74 E-value=15 Score=30.71 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=29.6
Q ss_pred hCCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033937 31 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 64 (108)
Q Consensus 31 ~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~ 64 (108)
.....|.|.+.||+++.++++++|...+|-|=.+
T Consensus 133 ~~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 133 DNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCCCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 3457899999999999999999999999987654
No 86
>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=56.87 E-value=26 Score=28.45 Aligned_cols=35 Identities=3% Similarity=0.229 Sum_probs=30.1
Q ss_pred hCCcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 31 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 31 ~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
..-..+.|.+.+++.+.++++++|.+.+|.|=.+.
T Consensus 79 ~~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 79 DGADEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CCCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 34568999999999999999999999999886654
No 87
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=52.27 E-value=44 Score=25.98 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=27.3
Q ss_pred hhCCcEEEEEecCCeEEEEEEEEecCccceEee
Q 033937 30 VKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 62 (108)
Q Consensus 30 ~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~ 62 (108)
...|++|.+.. ++..++|++.|.|..-.|++.
T Consensus 269 ~~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 269 LFLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred cccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 44599999987 456799999999999999986
No 88
>PRK14630 hypothetical protein; Provisional
Probab=50.57 E-value=30 Score=24.37 Aligned_cols=28 Identities=7% Similarity=-0.022 Sum_probs=22.3
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecCc
Q 033937 26 LMMSVKNNTQVLINCRNNKKLLGRVRAFDRH 56 (108)
Q Consensus 26 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~h 56 (108)
+.++. |+.|+|.+.+ ...+|+|.++|.-
T Consensus 92 f~r~~--G~~v~V~l~~-~~~~G~L~~~~d~ 119 (143)
T PRK14630 92 FKIFE--GKKIKLMLDN-DFEEGFILEAKAD 119 (143)
T ss_pred HHHhC--CCEEEEEEcC-cceEEEEEEEeCC
Confidence 45667 9999999965 4459999999984
No 89
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=50.52 E-value=53 Score=25.52 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=28.3
Q ss_pred hhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 29 SVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 29 ~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
+...+++|.|.. ++..+.|++.|.|..-.|+|..
T Consensus 233 ~~~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 233 LLYKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred hccCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 334599999875 6788999999999999999864
No 90
>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=49.56 E-value=59 Score=24.20 Aligned_cols=33 Identities=24% Similarity=0.377 Sum_probs=27.6
Q ss_pred hhhCCcEEEEEecCCeEEEEEEEEecCccceEee
Q 033937 29 SVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 62 (108)
Q Consensus 29 ~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~ 62 (108)
+...+++|.|... +..+.|++.|.|..-.|+|+
T Consensus 189 ~~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 189 SAHIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hhccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 3445999999874 46799999999999999996
No 91
>PRK14635 hypothetical protein; Provisional
Probab=49.42 E-value=35 Score=24.45 Aligned_cols=33 Identities=21% Similarity=0.127 Sum_probs=24.2
Q ss_pred HHhhhhCCcEEEEEec--CCeEEEE---EEEEecCccceEe
Q 033937 26 LMMSVKNNTQVLINCR--NNKKLLG---RVRAFDRHCNMVL 61 (108)
Q Consensus 26 L~~~~~~~krV~V~l~--~gr~i~G---~L~~fD~hmNlvL 61 (108)
+.++. |..|.|.+. ++..+.| +|.++|.- ++.|
T Consensus 94 ~~r~~--G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 94 LDRFR--GIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHhC--CCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 45667 999999876 4567777 99999874 3444
No 92
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=44.26 E-value=28 Score=22.37 Aligned_cols=25 Identities=20% Similarity=0.401 Sum_probs=14.4
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccc
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCN 58 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmN 58 (108)
-+.+|++.|+||..+.|+ |.|--.|
T Consensus 16 ~~~~v~L~l~dG~~~~g~--A~dt~~~ 40 (80)
T PF07073_consen 16 YRYPVKLTLKDGEQIEGK--ALDTRTN 40 (80)
T ss_dssp TTT-EEEE-TTT--EEES--S-EEE--
T ss_pred cCCeEEEEEeCCCEEEEE--EEEEEEe
Confidence 488999999999999997 4444333
No 93
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=40.40 E-value=80 Score=27.27 Aligned_cols=33 Identities=21% Similarity=0.287 Sum_probs=28.2
Q ss_pred hCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 31 KNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 31 ~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
..+++|.+...++..+.|+..|.|..-.|+|..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 358999987666778999999999999999964
No 94
>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=39.89 E-value=12 Score=24.94 Aligned_cols=17 Identities=29% Similarity=0.284 Sum_probs=14.9
Q ss_pred EEEEEecCccceEeece
Q 033937 48 GRVRAFDRHCNMVLENV 64 (108)
Q Consensus 48 G~L~~fD~hmNlvL~d~ 64 (108)
|+|+|.|.|-|.--.+-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999987664
No 95
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=39.02 E-value=17 Score=26.06 Aligned_cols=25 Identities=24% Similarity=0.368 Sum_probs=18.8
Q ss_pred cCCeEEEEEEEEecCccceEeeceE
Q 033937 41 RNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 41 ~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
+.+..=.|+|+|.|+|-|=.-+|-.
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~~ 64 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENND 64 (151)
T ss_pred hcccccceeeeeecccccchhcccc
Confidence 3344456899999999998877653
No 96
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=37.94 E-value=67 Score=19.15 Aligned_cols=41 Identities=15% Similarity=0.131 Sum_probs=28.5
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceE
Q 033937 18 FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMV 60 (108)
Q Consensus 18 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlv 60 (108)
+...+-.+++.....+.+| +.+++|+. .+.|+.+++|=++.
T Consensus 9 ~r~~~~~~l~~v~~~~~pv-~It~~g~~-~~vli~~~~ye~l~ 49 (75)
T PF02604_consen 9 FRNNFSELLDEVEEGEEPV-IITKNGKP-VAVLISVEDYERLQ 49 (75)
T ss_dssp HHHTHHHHHHHHHHCT-EE-EEEETTEE-EEEEEEHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeE-EEEECCCC-CeecccHHHHHHHH
Confidence 3446777888888666667 55777777 88888888775553
No 97
>PRK08330 biotin--protein ligase; Provisional
Probab=36.56 E-value=1.4e+02 Score=22.20 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=26.7
Q ss_pred hhCCcEEEEEecCCeEE-EEEEEEecCccceEeec
Q 033937 30 VKNNTQVLINCRNNKKL-LGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 30 ~~~~krV~V~l~~gr~i-~G~L~~fD~hmNlvL~d 63 (108)
...+++|.+.. ++..+ .|++.|.|..-.|++..
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 34589999875 56665 69999999999999874
No 98
>PRK11625 Rho-binding antiterminator; Provisional
Probab=36.17 E-value=96 Score=20.13 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=23.4
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecCccc
Q 033937 25 VLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCN 58 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmN 58 (108)
.|.-+...+.+|.+.+++|..+.|+ +.|=+.+
T Consensus 15 yLElAC~~~~~l~l~l~dGe~~~g~--A~D~~~~ 46 (84)
T PRK11625 15 NLELACQHHLMLTLELKDGEVLQAK--ASDLVSR 46 (84)
T ss_pred HHHHHHhcCCeEEEEECCCCEEEEE--EEeeecC
Confidence 3554444689999999999999997 4555533
No 99
>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=35.62 E-value=54 Score=22.36 Aligned_cols=37 Identities=11% Similarity=0.109 Sum_probs=24.4
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEec-CccceE
Q 033937 21 GPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFD-RHCNMV 60 (108)
Q Consensus 21 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD-~hmNlv 60 (108)
.|-..+..-. ....|.++||+.+.|.+++=| ....|.
T Consensus 48 ~P~~~i~~~y---~~~~v~~~dG~~~~G~~~~e~~~~~~l~ 85 (133)
T TIGR02603 48 DPSREVAPGF---EAYRVTLKDGRILSGIVASETADGVTVK 85 (133)
T ss_pred CchhhhCccc---ccEEEEECCCCEEEEEEEecCCCeEEEE
Confidence 4444444433 347899999999999988833 344443
No 100
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=35.19 E-value=83 Score=20.09 Aligned_cols=27 Identities=15% Similarity=0.179 Sum_probs=19.2
Q ss_pred HHHhhhhCCcEEEEEecCCe----EEEEEEEEe
Q 033937 25 VLMMSVKNNTQVLINCRNNK----KLLGRVRAF 53 (108)
Q Consensus 25 ~L~~~~~~~krV~V~l~~gr----~i~G~L~~f 53 (108)
-|..++ |++|.+..+.|| +-.|.|..-
T Consensus 11 ~l~~~v--G~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 11 ELESHV--GKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHTT--TSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHcC--CCEEEEEEcCCceEEEEEEEEEEee
Confidence 366777 999999999998 467988653
No 101
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=32.65 E-value=15 Score=27.59 Aligned_cols=40 Identities=25% Similarity=0.306 Sum_probs=0.0
Q ss_pred cccCCCcHHHHHhhhhCCcEEEEEec--------------CCeEEEEEEEEecCccc
Q 033937 16 EEFNTGPLSVLMMSVKNNTQVLINCR--------------NNKKLLGRVRAFDRHCN 58 (108)
Q Consensus 16 ~~~~~~Pl~~L~~~~~~~krV~V~l~--------------~gr~i~G~L~~fD~hmN 58 (108)
....-+|+.+.-.+= |++|=-||. +|..|.|. ++||+|++
T Consensus 70 ~~~~~np~~lPLG~D--GkPIPyWLYKLhGL~~ey~CEICGN~~Y~Gr-kaFekHF~ 123 (196)
T PF11931_consen 70 EEKIYNPLNLPLGWD--GKPIPYWLYKLHGLGVEYKCEICGNQSYKGR-KAFEKHFQ 123 (196)
T ss_dssp ---------------------------------------------------------
T ss_pred ccccCCcccCCCCCC--CCcccHHHHHHhCCCCeeeeEeCCCcceecH-HHHHHhcC
Confidence 344556666555544 666655554 45567787 99999987
No 102
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=32.09 E-value=1.5e+02 Score=22.57 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=30.1
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeece
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENV 64 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~ 64 (108)
.+++|++...++..+.|+..+.|..-.|+|+..
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 699999999888888889999999999999875
No 103
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=30.36 E-value=1e+02 Score=18.57 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=17.8
Q ss_pred hCCcEEEEEecCCeE-EEEEEEEecC
Q 033937 31 KNNTQVLINCRNNKK-LLGRVRAFDR 55 (108)
Q Consensus 31 ~~~krV~V~l~~gr~-i~G~L~~fD~ 55 (108)
..|..|.++=-++.. |.|.+.+||.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~ 32 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDS 32 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEET
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecc
Confidence 358899998877664 5999999996
No 104
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=29.23 E-value=59 Score=20.02 Aligned_cols=24 Identities=17% Similarity=0.320 Sum_probs=19.7
Q ss_pred CCcEEEEEecCCeEEEEEEEEecC
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDR 55 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~ 55 (108)
..++|.|.+-||..+.+++.+-|.
T Consensus 3 ~~~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 3 DQCRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred CeEEEEEEcCCCCEEEEEeCCCCc
Confidence 357999999999999998766544
No 105
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=28.88 E-value=71 Score=21.05 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=13.3
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033937 33 NTQVLIN-CRNNKKLLGRVRA 52 (108)
Q Consensus 33 ~krV~V~-l~~gr~i~G~L~~ 52 (108)
|..|+|. +.+++.+.|++.+
T Consensus 96 G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 96 GDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCEEEEEECCCCCEEEEEEeC
Confidence 6666766 5667777776654
No 106
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=28.41 E-value=56 Score=20.34 Aligned_cols=23 Identities=17% Similarity=0.229 Sum_probs=18.8
Q ss_pred CCcEEEEEecCCeEEEEEEEEec
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFD 54 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD 54 (108)
...+|.|.+-||..+++++-+-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 46899999999999999875543
No 107
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=27.29 E-value=86 Score=23.22 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=16.4
Q ss_pred cEEEEEec-CCeEEEEEEEEecCc
Q 033937 34 TQVLINCR-NNKKLLGRVRAFDRH 56 (108)
Q Consensus 34 krV~V~l~-~gr~i~G~L~~fD~h 56 (108)
-+|.|.+. ++..|+|+|++||.=
T Consensus 134 p~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 134 PPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred CCCceEEEeCCceEEEEEEeccCC
Confidence 34444433 478999999999975
No 108
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=26.73 E-value=40 Score=22.94 Aligned_cols=35 Identities=6% Similarity=0.165 Sum_probs=29.8
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCccceEeeceEEE
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREM 67 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~ 67 (108)
.|.+|++.|+ +-+.+..+.|-|+++-|.-.||+-.
T Consensus 63 ~G~rV~lrLk-dlELs~~FLG~~~d~TllEAd~~Ll 97 (104)
T PF10246_consen 63 RGSRVRLRLK-DLELSAHFLGASKDTTLLEADATLL 97 (104)
T ss_pred cCCEEEEEEC-CHhhhhhhccCCCCcEEEEeeeEEE
Confidence 4899999997 5788899999999999998887754
No 109
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=26.33 E-value=2e+02 Score=18.93 Aligned_cols=41 Identities=15% Similarity=0.221 Sum_probs=30.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
..+|+...+.+..|+|...+|..+.=+|.+.|.-=|.++=|
T Consensus 11 ~~~Lr~L~~~~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD 51 (108)
T PF07317_consen 11 LAVLRDLAKQRSPLTVRHPRGQSFITSILAVDPDRGTLVLD 51 (108)
T ss_dssp HHHHHHHHHTT--EEEETT-SSEEEE-EEEEETTTTEEEEE
T ss_pred HHHHHHHHhCCCeEEEEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence 34688888889999999888888999999999888766544
No 110
>PRK08477 biotin--protein ligase; Provisional
Probab=26.10 E-value=2.6e+02 Score=20.83 Aligned_cols=40 Identities=5% Similarity=0.092 Sum_probs=30.4
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeec
Q 033937 23 LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLEN 63 (108)
Q Consensus 23 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d 63 (108)
++..+.+...++.|+|.. +++.++|+..+.|+.--|++..
T Consensus 165 ~~~~~~~~~~~~~v~v~~-~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 165 FSKYKLEFEKSKSFSFHI-DGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred HHHHHHHHHcCCEEEEEE-CCEEEEEEEeeECCCCeEEECC
Confidence 333444445699999874 7899999999999988887765
No 111
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.92 E-value=88 Score=23.49 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=15.3
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q 033937 33 NTQVLIN-CRNNKKLLGRVRA 52 (108)
Q Consensus 33 ~krV~V~-l~~gr~i~G~L~~ 52 (108)
|..|+|. +.+|+.+.|++.+
T Consensus 207 Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 207 GQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCeEEEEECCCCCEEEEEEeC
Confidence 7778887 7778888887654
No 112
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.22 E-value=1.3e+02 Score=22.52 Aligned_cols=33 Identities=24% Similarity=0.264 Sum_probs=30.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecCccceEeeceE
Q 033937 33 NTQVLINCRNNKKLLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 33 ~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~ 65 (108)
+.+|.|..-++...+|.+.+||---++..-++.
T Consensus 11 g~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 11 GSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 789999999999999999999999998887776
No 113
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=22.28 E-value=98 Score=20.26 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=19.2
Q ss_pred ceeeeceEEEeCCcEEEEEeCC
Q 033937 86 KDRFISKMFLRGDSVIIVLRNP 107 (108)
Q Consensus 86 ~~r~lg~i~IRGd~Iv~I~~~~ 107 (108)
..|+-|.+.++|..+..|...|
T Consensus 75 ~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 75 EDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hhcceEEEEEECCeeeEEEcCC
Confidence 3478999999999999998776
No 114
>PRK10708 hypothetical protein; Provisional
Probab=22.13 E-value=1e+02 Score=18.94 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=21.1
Q ss_pred CCcEEEEEecCCeEEEEEEEEecCcc
Q 033937 32 NNTQVLINCRNNKKLLGRVRAFDRHC 57 (108)
Q Consensus 32 ~~krV~V~l~~gr~i~G~L~~fD~hm 57 (108)
-+.+|.|++.++-.=.|++.+...|-
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 37899999988888889888877663
No 115
>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=21.95 E-value=58 Score=24.12 Aligned_cols=20 Identities=10% Similarity=0.072 Sum_probs=16.9
Q ss_pred EEEEEEEecCccceEeeceE
Q 033937 46 LLGRVRAFDRHCNMVLENVR 65 (108)
Q Consensus 46 i~G~L~~fD~hmNlvL~d~~ 65 (108)
-+|.+.+||++.+|.+++-.
T Consensus 93 ~n~~iiccD~~~~l~i~~k~ 112 (176)
T PF05989_consen 93 KNSFIICCDKDPKLSIDNKF 112 (176)
T ss_pred CCcEEEEecCcceEEECCCc
Confidence 45889999999999998843
No 116
>PF08067 ROKNT: ROKNT (NUC014) domain; InterPro: IPR012987 This presumed domain is found at the N terminus of RNP K-like proteins that also contain KH domains IPR004088 from INTERPRO [].
Probab=21.73 E-value=36 Score=19.43 Aligned_cols=13 Identities=46% Similarity=0.659 Sum_probs=8.4
Q ss_pred Chhhhhccccccc
Q 033937 6 MEEDNVKNEEEEF 18 (108)
Q Consensus 6 ~~~~~~~~~~~~~ 18 (108)
||++.+||++..+
T Consensus 1 Mete~~~Q~e~tF 13 (43)
T PF08067_consen 1 METEIEQQEEETF 13 (43)
T ss_pred CCcccccCccccc
Confidence 6777777766544
Done!