Query psy11157
Match_columns 111
No_of_seqs 120 out of 1034
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 19:25:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11157.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11157hhsearch_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 99.9 5.8E-27 1.3E-31 154.8 10.8 87 19-106 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 3.2E-25 7E-30 144.6 10.0 82 20-104 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 3.1E-24 6.8E-29 138.5 10.1 74 19-105 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.9 3.3E-24 7.2E-29 136.8 9.2 71 18-104 2-72 (72)
5 cd01731 archaeal_Sm1 The archa 99.9 1.3E-23 2.8E-28 132.5 9.0 68 21-104 1-68 (68)
6 cd01718 Sm_E The eukaryotic Sm 99.9 2.2E-22 4.9E-27 130.8 9.7 75 17-104 3-79 (79)
7 cd01726 LSm6 The eukaryotic Sm 99.9 2.1E-22 4.6E-27 126.7 8.8 67 21-103 1-67 (67)
8 cd01729 LSm7 The eukaryotic Sm 99.9 4.4E-22 9.6E-27 129.8 10.1 75 24-106 6-80 (81)
9 cd01719 Sm_G The eukaryotic Sm 99.9 8.2E-22 1.8E-26 125.9 9.2 71 21-107 1-71 (72)
10 cd01722 Sm_F The eukaryotic Sm 99.9 5.7E-22 1.2E-26 125.1 8.4 68 20-103 1-68 (68)
11 cd01717 Sm_B The eukaryotic Sm 99.9 1.3E-21 2.8E-26 126.6 9.6 75 24-104 4-78 (79)
12 cd01728 LSm1 The eukaryotic Sm 99.9 2E-21 4.4E-26 124.9 10.1 71 21-104 3-73 (74)
13 cd01727 LSm8 The eukaryotic Sm 99.9 2E-21 4.2E-26 124.5 9.5 72 23-106 2-73 (74)
14 PTZ00138 small nuclear ribonuc 99.9 3.7E-21 8E-26 127.6 10.1 77 16-105 10-88 (89)
15 COG1958 LSM1 Small nuclear rib 99.9 7.8E-21 1.7E-25 122.9 9.7 76 17-104 4-79 (79)
16 cd01721 Sm_D3 The eukaryotic S 99.8 1.1E-20 2.3E-25 120.0 9.3 70 21-106 1-70 (70)
17 cd01723 LSm4 The eukaryotic Sm 99.8 1.3E-20 2.8E-25 121.3 8.6 74 20-108 1-74 (76)
18 PF01423 LSM: LSM domain ; In 99.8 6.4E-20 1.4E-24 114.3 9.2 66 24-104 2-67 (67)
19 smart00651 Sm snRNP Sm protein 99.8 6.7E-20 1.4E-24 114.1 9.1 66 24-104 2-67 (67)
20 cd06168 LSm9 The eukaryotic Sm 99.8 1.3E-19 2.7E-24 116.8 9.9 72 23-104 3-74 (75)
21 KOG3460|consensus 99.8 3.7E-21 8E-26 125.1 2.1 88 18-108 3-90 (91)
22 cd01724 Sm_D1 The eukaryotic S 99.8 9.8E-19 2.1E-23 116.1 9.5 72 21-108 2-73 (90)
23 cd00600 Sm_like The eukaryotic 99.8 1.6E-18 3.5E-23 106.4 8.5 63 25-103 1-63 (63)
24 cd01733 LSm10 The eukaryotic S 99.8 1.9E-18 4.1E-23 112.0 9.1 74 16-105 5-78 (78)
25 cd01725 LSm2 The eukaryotic Sm 99.8 4.9E-18 1.1E-22 110.6 9.0 75 20-108 1-75 (81)
26 KOG3482|consensus 99.7 3E-18 6.4E-23 109.0 6.4 74 17-106 5-78 (79)
27 KOG3459|consensus 99.7 9.5E-19 2.1E-23 118.9 1.5 99 9-108 13-111 (114)
28 KOG1780|consensus 99.7 2.1E-17 4.6E-22 105.4 6.5 69 19-105 5-73 (77)
29 KOG1774|consensus 99.7 1.7E-17 3.6E-22 107.6 6.0 76 17-105 9-86 (88)
30 KOG1781|consensus 99.6 3.6E-17 7.9E-22 109.4 0.8 81 22-108 17-97 (108)
31 KOG1775|consensus 99.6 1.3E-15 2.9E-20 97.7 4.9 78 16-106 3-80 (84)
32 KOG1783|consensus 99.5 2.3E-15 5E-20 95.8 1.7 71 19-105 5-75 (77)
33 KOG3168|consensus 99.5 4.4E-15 9.6E-20 107.6 1.2 74 25-104 9-82 (177)
34 KOG1784|consensus 99.5 3.9E-14 8.4E-19 93.6 4.7 73 24-108 4-76 (96)
35 KOG1782|consensus 99.5 8E-15 1.7E-19 101.5 0.4 70 25-107 14-83 (129)
36 KOG3293|consensus 99.4 5.3E-13 1.2E-17 92.6 5.7 75 19-108 1-75 (134)
37 cd01739 LSm11_C The eukaryotic 99.3 1.8E-12 3.8E-17 81.1 2.6 44 26-69 2-49 (66)
38 KOG3448|consensus 99.2 3.3E-10 7.1E-15 74.7 8.4 71 22-106 4-74 (96)
39 KOG3172|consensus 99.1 1.6E-10 3.4E-15 78.7 6.3 76 17-108 2-77 (119)
40 KOG3428|consensus 98.7 2.2E-07 4.9E-12 63.3 8.7 71 22-109 4-74 (109)
41 cd01716 Hfq Hfq, an abundant, 97.3 0.00059 1.3E-08 42.4 5.0 39 24-62 3-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.3 0.00081 1.7E-08 41.8 5.1 39 24-62 7-45 (61)
43 PRK00395 hfq RNA-binding prote 97.0 0.0017 3.7E-08 42.3 5.0 40 24-63 11-50 (79)
44 PF14438 SM-ATX: Ataxin 2 SM d 97.0 0.0042 9E-08 39.4 6.2 68 24-100 6-76 (77)
45 COG1923 Hfq Uncharacterized ho 96.7 0.0046 9.9E-08 39.9 4.8 36 24-59 11-46 (77)
46 PF12701 LSM14: Scd6-like Sm d 95.9 0.12 2.6E-06 34.6 8.6 72 27-105 5-77 (96)
47 PRK14091 RNA-binding protein H 95.6 0.031 6.7E-07 40.9 5.0 41 23-63 95-135 (165)
48 PRK14091 RNA-binding protein H 95.5 0.033 7.1E-07 40.8 5.0 40 24-63 16-55 (165)
49 PF02237 BPL_C: Biotin protein 95.1 0.12 2.7E-06 29.9 5.7 32 32-64 3-34 (48)
50 cd01735 LSm12_N LSm12 belongs 94.7 0.089 1.9E-06 32.6 4.5 34 32-65 6-39 (61)
51 cd01736 LSm14_N LSm14 (also kn 92.7 1.2 2.7E-05 28.6 7.3 69 27-101 3-72 (74)
52 PRK14638 hypothetical protein; 90.4 0.54 1.2E-05 33.7 4.3 33 25-60 95-127 (150)
53 PF11095 Gemin7: Gem-associate 89.3 4 8.7E-05 26.5 7.3 63 22-105 16-79 (80)
54 PRK02001 hypothetical protein; 89.0 0.8 1.7E-05 33.0 4.3 33 25-60 85-117 (152)
55 PRK14639 hypothetical protein; 88.9 0.84 1.8E-05 32.3 4.3 33 25-60 83-115 (140)
56 PF03614 Flag1_repress: Repres 87.1 1.1 2.4E-05 32.6 4.0 34 22-55 110-143 (165)
57 PF06372 Gemin6: Gemin6 protei 85.8 1.7 3.7E-05 31.9 4.5 41 19-63 7-48 (166)
58 PRK14644 hypothetical protein; 83.0 2.7 5.9E-05 29.6 4.4 33 25-60 80-116 (136)
59 PRK14640 hypothetical protein; 81.2 3.4 7.4E-05 29.5 4.4 33 25-60 92-128 (152)
60 cd01734 YlxS_C YxlS is a Bacil 80.9 4.1 8.8E-05 26.0 4.3 33 25-60 20-56 (83)
61 PRK14642 hypothetical protein; 80.4 3.5 7.6E-05 31.0 4.4 29 25-55 95-136 (197)
62 PRK14636 hypothetical protein; 80.4 3.5 7.5E-05 30.3 4.3 33 25-60 93-129 (176)
63 COG0779 Uncharacterized protei 79.8 4 8.7E-05 29.5 4.4 33 25-60 94-130 (153)
64 PF02576 DUF150: Uncharacteris 79.4 3.5 7.6E-05 28.7 3.9 34 24-60 81-118 (141)
65 PRK14633 hypothetical protein; 79.4 4.3 9.3E-05 29.0 4.4 33 25-60 89-125 (150)
66 PRK14645 hypothetical protein; 78.3 4.3 9.4E-05 29.2 4.2 32 25-60 97-128 (154)
67 PRK14643 hypothetical protein; 78.2 4.6 0.0001 29.3 4.3 29 25-55 99-131 (164)
68 PF03614 Flag1_repress: Repres 77.8 5.1 0.00011 29.2 4.4 35 30-64 27-61 (165)
69 PRK14632 hypothetical protein; 77.2 5.1 0.00011 29.3 4.4 33 25-60 93-132 (172)
70 PRK14646 hypothetical protein; 77.0 5.4 0.00012 28.6 4.4 33 25-60 95-131 (155)
71 PRK14634 hypothetical protein; 75.7 6.2 0.00013 28.3 4.4 33 25-60 95-131 (155)
72 PRK00092 ribosome maturation p 74.0 7.3 0.00016 27.7 4.4 28 25-54 93-124 (154)
73 PF10842 DUF2642: Protein of u 74.0 11 0.00023 23.7 4.6 59 17-104 6-66 (66)
74 PRK14647 hypothetical protein; 72.9 7.8 0.00017 27.8 4.4 28 25-54 94-130 (159)
75 PF11607 DUF3247: Protein of u 71.1 11 0.00023 25.4 4.3 24 26-49 22-45 (101)
76 PRK10898 serine endoprotease; 70.7 9.4 0.0002 30.6 4.8 34 31-64 100-133 (353)
77 PRK14637 hypothetical protein; 70.1 8.6 0.00019 27.5 4.0 33 25-60 93-126 (151)
78 PRK14631 hypothetical protein; 69.7 9.3 0.0002 28.0 4.2 27 25-53 112-142 (174)
79 PRK06955 biotin--protein ligas 67.9 16 0.00035 28.6 5.5 33 29-61 246-278 (300)
80 PRK14641 hypothetical protein; 67.5 10 0.00023 27.8 4.1 27 25-53 99-129 (173)
81 TIGR02038 protease_degS peripl 67.4 12 0.00026 29.9 4.7 33 32-64 101-133 (351)
82 PF08863 YolD: YolD-like prote 66.0 23 0.00049 22.2 5.0 37 24-60 34-73 (92)
83 PRK10139 serine endoprotease; 65.6 13 0.00029 30.9 4.8 35 30-64 112-146 (455)
84 PRK10942 serine endoprotease; 65.0 13 0.00029 31.1 4.7 33 31-63 134-166 (473)
85 TIGR02037 degP_htrA_DO peripla 58.7 18 0.0004 29.4 4.4 34 31-64 80-113 (428)
86 PF14563 DUF4444: Domain of un 57.1 12 0.00025 21.5 2.1 22 45-66 10-31 (42)
87 PRK11886 bifunctional biotin-- 54.0 37 0.00081 26.5 5.3 31 30-61 270-300 (319)
88 TIGR00121 birA_ligase birA, bi 51.5 49 0.0011 24.7 5.4 31 30-61 191-221 (237)
89 PTZ00275 biotin-acetyl-CoA-car 51.1 48 0.001 25.9 5.5 32 30-62 235-266 (285)
90 KOG1073|consensus 50.1 54 0.0012 27.0 5.7 75 26-106 5-80 (361)
91 KOG3382|consensus 48.7 9.6 0.00021 27.3 1.1 25 41-65 41-65 (151)
92 PRK14635 hypothetical protein; 46.1 42 0.00091 24.1 4.2 33 25-60 94-131 (162)
93 PRK14630 hypothetical protein; 45.9 39 0.00085 23.9 3.9 32 25-60 92-123 (143)
94 PRK13325 bifunctional biotin-- 44.5 59 0.0013 28.2 5.5 32 31-62 277-308 (592)
95 PF09196 DUF1953: Domain of un 44.3 33 0.00071 21.1 2.8 19 92-110 13-31 (66)
96 PF05071 NDUFA12: NADH ubiquin 43.6 13 0.00029 24.9 1.2 17 47-63 1-17 (105)
97 PF07073 ROF: Modulator of Rho 43.5 38 0.00083 21.8 3.2 19 30-48 15-33 (80)
98 COG0340 BirA Biotin-(acetyl-Co 42.1 1.5E+02 0.0034 22.5 7.0 33 31-63 189-221 (238)
99 PRK08330 biotin--protein ligas 40.9 1E+02 0.0022 23.1 5.7 32 30-62 186-218 (236)
100 PF14153 Spore_coat_CotO: Spor 40.3 42 0.0009 25.0 3.4 34 22-55 123-157 (185)
101 PF02604 PhdYeFM_antitox: Anti 34.4 86 0.0019 18.7 3.8 40 17-58 9-48 (75)
102 PRK11625 Rho-binding antitermi 32.7 1.2E+02 0.0025 19.8 4.3 58 25-104 16-73 (84)
103 PF11743 DUF3301: Protein of u 29.2 58 0.0013 21.4 2.4 21 86-106 76-96 (97)
104 PF09465 LBR_tudor: Lamin-B re 28.8 1.1E+02 0.0024 18.5 3.3 26 30-55 7-33 (55)
105 TIGR02603 CxxCH_TIGR02603 puta 26.9 87 0.0019 21.4 3.1 27 33-59 58-85 (133)
106 PRK08477 biotin--protein ligas 26.3 2.5E+02 0.0055 21.0 5.7 32 30-62 173-204 (211)
107 PRK06630 hypothetical protein; 25.7 36 0.00077 23.0 0.9 19 45-63 11-29 (99)
108 PF07317 YcgR: Flagellar regul 25.0 2.1E+02 0.0045 18.8 4.8 41 22-62 11-51 (108)
109 cd01737 LSm16_N LSm16 belongs 24.6 1.5E+02 0.0033 18.3 3.5 28 27-56 3-31 (62)
110 PRK10708 hypothetical protein; 24.4 86 0.0019 19.2 2.3 25 32-56 4-28 (62)
111 COG0265 DegQ Trypsin-like seri 24.4 1.4E+02 0.0031 23.4 4.3 33 32-64 95-127 (347)
112 PLN03095 NADH:ubiquinone oxido 21.7 51 0.0011 22.8 1.1 19 46-64 9-27 (115)
113 PF10781 DSRB: Dextransucrase 21.5 98 0.0021 19.0 2.2 25 32-56 4-28 (62)
114 TIGR03170 flgA_cterm flagella 21.2 1.3E+02 0.0028 19.9 3.0 20 32-51 96-116 (122)
115 PRK09618 flgD flagellar basal 21.0 3.2E+02 0.0069 19.5 5.3 26 26-53 88-113 (142)
116 PF06257 DUF1021: Protein of u 20.4 2.2E+02 0.0048 18.1 3.8 25 25-51 12-40 (76)
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=5.8e-27 Score=154.81 Aligned_cols=87 Identities=89% Similarity=1.386 Sum_probs=71.8
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCc
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 98 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdn 98 (111)
.||+++|+.++..+++|.|+|++|+++.|+|.|||+||||+|+||+|++...++++... +..+..+.+++|.+|||||+
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 48999999999779999999999999999999999999999999999987644332211 11122346789999999999
Q ss_pred EEEEeeCC
Q psy11157 99 VILILKNP 106 (111)
Q Consensus 99 Vv~I~~~~ 106 (111)
|++|++.|
T Consensus 80 Vv~Is~~~ 87 (87)
T cd01720 80 VILVLRNP 87 (87)
T ss_pred EEEEecCC
Confidence 99999864
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=3.2e-25 Score=144.63 Aligned_cols=82 Identities=33% Similarity=0.533 Sum_probs=66.3
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcE
Q psy11157 20 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 99 (111)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnV 99 (111)
.|+++|+.++ +++|.|+|+|||++.|+|+|||+||||+|+||+|++...+++.+..+ .......|.+|.+|||||+|
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--DERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYE-EIVKTTKRNIPMLFVRGDSV 77 (82)
T ss_pred CchHHHHHhC--CCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccc-cccceeEEEcCeEEEeCCEE
Confidence 5999999999 99999999999999999999999999999999999875432211000 00112357899999999999
Q ss_pred EEEee
Q psy11157 100 ILILK 104 (111)
Q Consensus 100 v~I~~ 104 (111)
++|++
T Consensus 78 v~i~~ 82 (82)
T cd01730 78 ILVSP 82 (82)
T ss_pred EEECC
Confidence 99974
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=3.1e-24 Score=138.52 Aligned_cols=74 Identities=26% Similarity=0.545 Sum_probs=64.7
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCc
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 98 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdn 98 (111)
..|+++|++++ +++|.|++++|+++.|+|+|||+||||+|+||+|++.. ++ ++ ..+++|.++|||||
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--GSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PE-GR---------KITKLDQILLNGNN 68 (76)
T ss_pred cChHHHHHHhC--CCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CC-Cc---------eeeEcCeEEEeCCe
Confidence 47999999999 99999999999999999999999999999999999732 21 11 24679999999999
Q ss_pred EEEEeeC
Q psy11157 99 VILILKN 105 (111)
Q Consensus 99 Vv~I~~~ 105 (111)
|++|+|.
T Consensus 69 V~~i~p~ 75 (76)
T cd01732 69 ICMLVPG 75 (76)
T ss_pred EEEEECC
Confidence 9999964
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=3.3e-24 Score=136.79 Aligned_cols=71 Identities=31% Similarity=0.637 Sum_probs=63.4
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCC
Q psy11157 18 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGD 97 (111)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (111)
+..|+++|++++ +++|.|+|++|+.|+|+|.|||+|||++|+||+|.+. ++ ..+.+|.+||||+
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--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-----GE---------VVRKLGKVVIRGD 65 (72)
T ss_pred CcchHHHHHHhC--CCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-----CC---------eEeEcCcEEEeCC
Confidence 468999999999 9999999999999999999999999999999999753 11 1357999999999
Q ss_pred cEEEEee
Q psy11157 98 SVILILK 104 (111)
Q Consensus 98 nVv~I~~ 104 (111)
+|++|++
T Consensus 66 ~V~~i~~ 72 (72)
T PRK00737 66 NVVYVSP 72 (72)
T ss_pred EEEEEcC
Confidence 9999974
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=99.90 E-value=1.3e-23 Score=132.46 Aligned_cols=68 Identities=37% Similarity=0.659 Sum_probs=61.6
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|+++|+.++ +++|+|+|++|+.|.|+|.|||+||||+|+||+|++.. + ..+.+|.+||||++|+
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 1357999999999999
Q ss_pred EEee
Q psy11157 101 LILK 104 (111)
Q Consensus 101 ~I~~ 104 (111)
+|++
T Consensus 65 ~i~~ 68 (68)
T cd01731 65 FISP 68 (68)
T ss_pred EEcC
Confidence 9975
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=99.88 E-value=2.2e-22 Score=130.80 Aligned_cols=75 Identities=21% Similarity=0.432 Sum_probs=64.4
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEec--CCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEE
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCR--NNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFL 94 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk--~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I 94 (111)
....|++.|.+++....+|.|+++ +|++++|+|.|||+||||+|+||+|+... ++ ..+.+|.++|
T Consensus 3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~----~~---------~~~~lG~ili 69 (79)
T cd01718 3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK----TK---------TRKPLGRILL 69 (79)
T ss_pred cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC----Cc---------eEeEcCcEEE
Confidence 346899999999966669999998 89999999999999999999999998642 11 2457999999
Q ss_pred eCCcEEEEee
Q psy11157 95 RGDSVILILK 104 (111)
Q Consensus 95 RGdnVv~I~~ 104 (111)
|||||++|+|
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999984
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=2.1e-22 Score=126.71 Aligned_cols=67 Identities=22% Similarity=0.393 Sum_probs=59.8
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|+++|+.++ +++|+|+|++|++|+|+|.|||.||||+|+||+|... +. ..+.+|.++|||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-----~~---------~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 1 PSEFLKAII--GRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-----GQ---------LKNKYGDAFIRGNNVL 64 (67)
T ss_pred CHHHHHhhC--CCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-----Cc---------eeeEeCCEEEECCEEE
Confidence 899999999 9999999999999999999999999999999998642 11 1356999999999999
Q ss_pred EEe
Q psy11157 101 LIL 103 (111)
Q Consensus 101 ~I~ 103 (111)
+|+
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=4.4e-22 Score=129.76 Aligned_cols=75 Identities=24% Similarity=0.385 Sum_probs=61.0
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
-|.+++ +++|+|.|++||++.|+|+|||+||||+|+||+|+....... . +.....+.+|.++|||+||++|+
T Consensus 6 ~L~~~i--~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~-~-----~~~~~~~~lG~v~iRG~nV~~i~ 77 (81)
T cd01729 6 DLSKYV--DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP-Y-----KLTDKTRQLGLVVCRGTSVVLIS 77 (81)
T ss_pred hHHHhc--CCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc-c-----ccccceeEccEEEEcCCEEEEEe
Confidence 378888 999999999999999999999999999999999987532110 0 00113467999999999999999
Q ss_pred eCC
Q psy11157 104 KNP 106 (111)
Q Consensus 104 ~~~ 106 (111)
+.+
T Consensus 78 ~~~ 80 (81)
T cd01729 78 PVD 80 (81)
T ss_pred cCC
Confidence 764
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=8.2e-22 Score=125.95 Aligned_cols=71 Identities=20% Similarity=0.362 Sum_probs=61.5
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|-..|.+++ +++|.|.|++|+++.|+|.|||+||||+|+||+|+... . ..+.+|.++|||++|+
T Consensus 1 ~~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-----~---------~~~~lg~v~IRG~~I~ 64 (72)
T cd01719 1 HPPELKKYM--DKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-----G---------EKNNIGMVVIRGNSIV 64 (72)
T ss_pred CchhhHHhC--CCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-----C---------ceeEeceEEECCCEEE
Confidence 445789999 99999999999999999999999999999999998521 1 1357999999999999
Q ss_pred EEeeCCC
Q psy11157 101 LILKNPL 107 (111)
Q Consensus 101 ~I~~~~~ 107 (111)
+|++-+.
T Consensus 65 ~i~~~~~ 71 (72)
T cd01719 65 MLEALER 71 (72)
T ss_pred EEEcccc
Confidence 9997653
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=5.7e-22 Score=125.13 Aligned_cols=68 Identities=22% Similarity=0.372 Sum_probs=60.0
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcE
Q psy11157 20 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 99 (111)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnV 99 (111)
.|+.+|++++ +++|+|+|++|++|+|+|.|||+|||++|+||+|+.. +. ....+|.++|||++|
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--GKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-----GK---------STGNLGEVLIRCNNV 64 (68)
T ss_pred CHHHHHHHcC--CCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-----Cc---------cccCcCcEEEECCEE
Confidence 4899999999 9999999999999999999999999999999998742 11 124589999999999
Q ss_pred EEEe
Q psy11157 100 ILIL 103 (111)
Q Consensus 100 v~I~ 103 (111)
++|+
T Consensus 65 ~~i~ 68 (68)
T cd01722 65 LYIR 68 (68)
T ss_pred EEEC
Confidence 9984
No 11
>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=1.3e-21 Score=126.65 Aligned_cols=75 Identities=20% Similarity=0.457 Sum_probs=60.8
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
-|..++ +++|.|.++|||.+.|+|.|||+||||+|+||+|++...+.... .......+++|.+||||++|++|+
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--NYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK----NSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred hhHHHc--CCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc----cccCcceeEeeeEEEcCCEEEEEE
Confidence 477888 99999999999999999999999999999999999865322100 001123578999999999999997
Q ss_pred e
Q psy11157 104 K 104 (111)
Q Consensus 104 ~ 104 (111)
.
T Consensus 78 v 78 (79)
T cd01717 78 V 78 (79)
T ss_pred E
Confidence 4
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=99.87 E-value=2e-21 Score=124.86 Aligned_cols=71 Identities=27% Similarity=0.447 Sum_probs=60.9
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
++..|.+++ +++|.|.+++||++.|+|.|||+||||+|+||.|+.... .+ ..++.+|.++||||||+
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--DKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVG---DK--------YGDIPRGIFIIRGENVV 69 (74)
T ss_pred chHHHHHhc--CCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecC---Cc--------cceeEeeEEEEECCEEE
Confidence 456788998 999999999999999999999999999999999987531 11 11367999999999999
Q ss_pred EEee
Q psy11157 101 LILK 104 (111)
Q Consensus 101 ~I~~ 104 (111)
+|+.
T Consensus 70 ~ig~ 73 (74)
T cd01728 70 LLGE 73 (74)
T ss_pred EEEc
Confidence 9985
No 13
>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=99.86 E-value=2e-21 Score=124.51 Aligned_cols=72 Identities=22% Similarity=0.404 Sum_probs=60.9
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEE
Q psy11157 23 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 102 (111)
Q Consensus 23 ~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I 102 (111)
+.|..++ +++|+|.+++||.+.|+|+|||+|||++|++|+|+....+. + ..++.+|.++|||+||++|
T Consensus 2 ~~L~~~l--~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~-~---------~~~~~lG~~~iRG~~I~~i 69 (74)
T cd01727 2 STLEDYL--NKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE-G---------VEQVVLGLYIIRGDNIAVV 69 (74)
T ss_pred hhHHHhc--CCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC-C---------ceeeEeceEEECCCEEEEE
Confidence 4578888 99999999999999999999999999999999998643111 1 1246799999999999999
Q ss_pred eeCC
Q psy11157 103 LKNP 106 (111)
Q Consensus 103 ~~~~ 106 (111)
++.+
T Consensus 70 ~~~d 73 (74)
T cd01727 70 GEID 73 (74)
T ss_pred EccC
Confidence 9875
No 14
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=3.7e-21 Score=127.57 Aligned_cols=77 Identities=25% Similarity=0.482 Sum_probs=66.9
Q ss_pred hcCCCcHHHHHhhhhCCcEEEEEecCC--eEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEE
Q psy11157 16 SFATGPLSILTDSVKHNTQVLINCRNN--KKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMF 93 (111)
Q Consensus 16 ~~~~~Pl~~L~~~~~~~krV~V~lk~g--r~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~ 93 (111)
+....|+..++++++...+|.||+.++ ++++|+|.|||+||||+|+||+|++.. ++ ..+.+|.++
T Consensus 10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~~---------~~~~lG~il 76 (89)
T PTZ00138 10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----KN---------TRKDLGRIL 76 (89)
T ss_pred eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----Cc---------eeeEcCeEE
Confidence 356789999999999999999999874 889999999999999999999998642 11 245799999
Q ss_pred EeCCcEEEEeeC
Q psy11157 94 LRGDSVILILKN 105 (111)
Q Consensus 94 IRGdnVv~I~~~ 105 (111)
||||||++|++.
T Consensus 77 IRGnnV~~I~~~ 88 (89)
T PTZ00138 77 LKGDNITLIMAA 88 (89)
T ss_pred EcCCEEEEEEcC
Confidence 999999999865
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.85 E-value=7.8e-21 Score=122.85 Aligned_cols=76 Identities=32% Similarity=0.591 Sum_probs=62.8
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeC
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 96 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (111)
....|+++|+.++ +++|.|+|++|++|.|+|.|||+||||+|+||+|++.. ++.. ...+..+.++|||
T Consensus 4 ~~~~~~~~l~~~~--~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~~-------~~~~~~~~~~IRG 71 (79)
T COG1958 4 LGPLPLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGEK-------NVRRLGGEVLIRG 71 (79)
T ss_pred ccCCcHHHHHHhh--CCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCcc-------ccceeccEEEEEC
Confidence 4567899999999 99999999999999999999999999999999998741 0110 0123455999999
Q ss_pred CcEEEEee
Q psy11157 97 DSVILILK 104 (111)
Q Consensus 97 dnVv~I~~ 104 (111)
++|++|++
T Consensus 72 ~~I~~I~~ 79 (79)
T COG1958 72 DNIVLISP 79 (79)
T ss_pred CcEEEEeC
Confidence 99999973
No 16
>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=99.85 E-value=1.1e-20 Score=120.04 Aligned_cols=70 Identities=14% Similarity=0.349 Sum_probs=61.6
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|+++|+.+. +++|.|+||+|.+|+|+|.+||.|||++|+||++.... ++ ...+|.+||||+||.
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 889999998 99999999999999999999999999999999875321 21 245899999999999
Q ss_pred EEeeCC
Q psy11157 101 LILKNP 106 (111)
Q Consensus 101 ~I~~~~ 106 (111)
+|..|+
T Consensus 65 ~v~lPd 70 (70)
T cd01721 65 FFILPD 70 (70)
T ss_pred EEEeCC
Confidence 999875
No 17
>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=99.84 E-value=1.3e-20 Score=121.29 Aligned_cols=74 Identities=22% Similarity=0.319 Sum_probs=63.4
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcE
Q psy11157 20 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 99 (111)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnV 99 (111)
-|+.+|+.+. +++|.|.|++|++++|+|.+||.|||++|+||+|.... |+ ....++.+||||++|
T Consensus 1 ~Pl~~L~~~~--g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~----g~---------~~~~~~~v~IRG~~I 65 (76)
T cd01723 1 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKD----GD---------KFWKMPECYIRGNTI 65 (76)
T ss_pred CchHHHHhcC--CCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCC----Cc---------EeeeCCcEEEeCCEE
Confidence 3999999998 99999999999999999999999999999999986221 22 123478999999999
Q ss_pred EEEeeCCCC
Q psy11157 100 ILILKNPLA 108 (111)
Q Consensus 100 v~I~~~~~~ 108 (111)
.+|+.++..
T Consensus 66 ~~i~~p~~~ 74 (76)
T cd01723 66 KYLRVPDEI 74 (76)
T ss_pred EEEEcCHHH
Confidence 999987754
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.83 E-value=6.4e-20 Score=114.33 Aligned_cols=66 Identities=26% Similarity=0.491 Sum_probs=58.9
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
+|++++ +++|+|.+++|+.++|+|.+||+|||++|+||.|++...+ ..+++|.+||||++|++|+
T Consensus 2 ~L~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I~ 66 (67)
T PF01423_consen 2 FLQKLI--GKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYIS 66 (67)
T ss_dssp HHHHTT--TSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEEE
T ss_pred hhHHhC--CcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEEE
Confidence 688998 9999999999999999999999999999999999864310 2467999999999999998
Q ss_pred e
Q psy11157 104 K 104 (111)
Q Consensus 104 ~ 104 (111)
+
T Consensus 67 ~ 67 (67)
T PF01423_consen 67 L 67 (67)
T ss_dssp E
T ss_pred C
Confidence 5
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.83 E-value=6.7e-20 Score=114.14 Aligned_cols=66 Identities=30% Similarity=0.614 Sum_probs=58.2
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
+|..++ +++|+|.|+||+.+.|+|.+||+||||+|+||+|++... . ..+++|.+||||++|++|+
T Consensus 2 ~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~----~---------~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLI--GKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG----E---------KKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hhHHhC--CcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC----c---------EEeEeCCEEEcCCEEEEEe
Confidence 578888 999999999999999999999999999999999986420 1 2467999999999999997
Q ss_pred e
Q psy11157 104 K 104 (111)
Q Consensus 104 ~ 104 (111)
+
T Consensus 67 ~ 67 (67)
T smart00651 67 L 67 (67)
T ss_pred C
Confidence 4
No 20
>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=99.82 E-value=1.3e-19 Score=116.79 Aligned_cols=72 Identities=18% Similarity=0.342 Sum_probs=60.4
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEE
Q psy11157 23 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 102 (111)
Q Consensus 23 ~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I 102 (111)
+-|..++ +++|+|.|+|||.|.|+|.+||+||||+|+||.|+......... ...|.+|.++|||++|++|
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 99999999999999999999999999999999999754221111 1357899999999999999
Q ss_pred ee
Q psy11157 103 LK 104 (111)
Q Consensus 103 ~~ 104 (111)
..
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 74
No 21
>KOG3460|consensus
Probab=99.82 E-value=3.7e-21 Score=125.12 Aligned_cols=88 Identities=31% Similarity=0.459 Sum_probs=70.2
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCC
Q psy11157 18 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGD 97 (111)
Q Consensus 18 ~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGd 97 (111)
...|+++|+-++ +.||.|++|++|+++|+|.|||+|.||+|.||+|+++....+....++. -...+|.+..+|+|||
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 457999999999 9999999999999999999999999999999999987533211111100 0123577899999999
Q ss_pred cEEEEeeCCCC
Q psy11157 98 SVILILKNPLA 108 (111)
Q Consensus 98 nVv~I~~~~~~ 108 (111)
+|++|+++-..
T Consensus 80 ~Vilvspp~~~ 90 (91)
T KOG3460|consen 80 GVILVSPPLRL 90 (91)
T ss_pred eEEEEcCcccC
Confidence 99999988653
No 22
>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=99.79 E-value=9.8e-19 Score=116.11 Aligned_cols=72 Identities=19% Similarity=0.244 Sum_probs=63.4
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 21 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 21 Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|+.+|+++. |++|+|+|++|..|+|+|.++|.|||++|+||+++... +. ...+|.++|||+||.
T Consensus 2 ~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~----~~----------~~~~~~v~IRG~nI~ 65 (90)
T cd01724 2 LVRFLMKLT--NETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG----RN----------PVPLDTLSIRGNNIR 65 (90)
T ss_pred HhHHHHhCC--CCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC----Cc----------eeEcceEEEeCCEEE
Confidence 678899998 99999999999999999999999999999999987432 11 346899999999999
Q ss_pred EEeeCCCC
Q psy11157 101 LILKNPLA 108 (111)
Q Consensus 101 ~I~~~~~~ 108 (111)
+|..|+..
T Consensus 66 yi~lPd~l 73 (90)
T cd01724 66 YFILPDSL 73 (90)
T ss_pred EEEcCCcC
Confidence 99998764
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=1.6e-18 Score=106.45 Aligned_cols=63 Identities=37% Similarity=0.608 Sum_probs=55.1
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
|+.++ +++|+|.|+||+.+.|+|.+||+|||++|+||.|++.. + ..+.+|.+||||++|.+|.
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 99999999999999999999999999999999998642 1 2467999999999999984
No 24
>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=99.78 E-value=1.9e-18 Score=111.98 Aligned_cols=74 Identities=18% Similarity=0.288 Sum_probs=62.1
Q ss_pred hcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEe
Q psy11157 16 SFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLR 95 (111)
Q Consensus 16 ~~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IR 95 (111)
.....+..+|+.+. |+.|.|+||+|..|+|+|.++|.|||++|+||++.... +. ...+|.+|||
T Consensus 5 ~~~~tl~~~L~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~----~~----------~~~~~~v~IR 68 (78)
T cd01733 5 LLENTLIILLQGLQ--GKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRN----GK----------QVQVEEIMVT 68 (78)
T ss_pred hhhchHHHHHHHCC--CCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCC----Cc----------eeECCcEEEE
Confidence 34456778889998 99999999999999999999999999999999876311 11 2368999999
Q ss_pred CCcEEEEeeC
Q psy11157 96 GDSVILILKN 105 (111)
Q Consensus 96 GdnVv~I~~~ 105 (111)
|++|.+|..|
T Consensus 69 G~nI~yI~lP 78 (78)
T cd01733 69 GRNIRYVHIP 78 (78)
T ss_pred CCEEEEEEcC
Confidence 9999999865
No 25
>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=99.76 E-value=4.9e-18 Score=110.62 Aligned_cols=75 Identities=19% Similarity=0.205 Sum_probs=62.5
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcE
Q psy11157 20 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 99 (111)
Q Consensus 20 ~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnV 99 (111)
.|+++|+++. |++|.|+|++|..++|+|.++|.|||++|+||++.... +.. ....++.++|||++|
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 3788999997 99999999999999999999999999999999876211 110 123479999999999
Q ss_pred EEEeeCCCC
Q psy11157 100 ILILKNPLA 108 (111)
Q Consensus 100 v~I~~~~~~ 108 (111)
.+|..|+..
T Consensus 67 ~~I~lp~~~ 75 (81)
T cd01725 67 RYVQLPADE 75 (81)
T ss_pred EEEEeChhH
Confidence 999988764
No 26
>KOG3482|consensus
Probab=99.75 E-value=3e-18 Score=109.01 Aligned_cols=74 Identities=19% Similarity=0.301 Sum_probs=65.3
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeC
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 96 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (111)
...+|..+|+... +++|.|.|++|.+|+|+|++.|.||||.|.+|+|+++. . ....+|.++||+
T Consensus 5 ~PvNPKpFL~~l~--gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-----~---------~~g~lGEilIRC 68 (79)
T KOG3482|consen 5 QPVNPKPFLNGLT--GKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-----V---------STGNLGEILIRC 68 (79)
T ss_pred ccCCchHHHhhcc--CCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-----c---------ccccceeEEEEe
Confidence 4568999999999 99999999999999999999999999999999998753 2 134699999999
Q ss_pred CcEEEEeeCC
Q psy11157 97 DSVILILKNP 106 (111)
Q Consensus 97 dnVv~I~~~~ 106 (111)
+||.+|.-.|
T Consensus 69 NNvlyi~gv~ 78 (79)
T KOG3482|consen 69 NNVLYIRGVP 78 (79)
T ss_pred ccEEEEecCC
Confidence 9999997543
No 27
>KOG3459|consensus
Probab=99.72 E-value=9.5e-19 Score=118.87 Aligned_cols=99 Identities=81% Similarity=1.243 Sum_probs=87.5
Q ss_pred chhhhhhhcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeee
Q psy11157 9 KQQEEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRF 88 (111)
Q Consensus 9 ~~~~~~~~~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~ 88 (111)
.+..|++++..||++++..++....+|.|.+|+++.+-|.+.|||.|+|++|+|+.|.|+..++.+++.+ .+++...|.
T Consensus 13 ~~~~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~ 91 (114)
T KOG3459|consen 13 LEVPEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRF 91 (114)
T ss_pred cccccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhh
Confidence 3555788999999999999999999999999999999999999999999999999999998887766644 566667889
Q ss_pred eCeEEEeCCcEEEEeeCCCC
Q psy11157 89 ISKMFLRGDSVILILKNPLA 108 (111)
Q Consensus 89 lg~v~IRGdnVv~I~~~~~~ 108 (111)
+|.+|||||+|+++-..|..
T Consensus 92 isK~flRGdsvI~v~r~pl~ 111 (114)
T KOG3459|consen 92 ISKMFLRGDSVILVLRNPLW 111 (114)
T ss_pred hheeeecCCeEEEEEecchh
Confidence 99999999999999866643
No 28
>KOG1780|consensus
Probab=99.71 E-value=2.1e-17 Score=105.35 Aligned_cols=69 Identities=20% Similarity=0.440 Sum_probs=59.1
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCc
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 98 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdn 98 (111)
..| -|++++ +|++.+.|.+||.+.|.|+|||.|||++|+||+|.... +. ...+|.++|||++
T Consensus 5 g~P--eLkkym--dKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~~----------~~~ig~~vIrgns 66 (77)
T KOG1780|consen 5 GHP--ELKKYM--DKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----GD----------KNNIGMVVIRGNS 66 (77)
T ss_pred cCc--hHHHhh--hheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----CC----------cceeeeEEEeccE
Confidence 356 689999 99999999999999999999999999999999997432 11 2358999999999
Q ss_pred EEEEeeC
Q psy11157 99 VILILKN 105 (111)
Q Consensus 99 Vv~I~~~ 105 (111)
|+++.+-
T Consensus 67 iv~~eaL 73 (77)
T KOG1780|consen 67 IVMVEAL 73 (77)
T ss_pred EEEEeec
Confidence 9998754
No 29
>KOG1774|consensus
Probab=99.71 E-value=1.7e-17 Score=107.63 Aligned_cols=76 Identities=24% Similarity=0.471 Sum_probs=65.2
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecC--CeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEE
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFL 94 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk~--gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I 94 (111)
..+.|+.+++++++...+|.|||.. +-.++|.++|||+|||+||+||+|..... + ..+.+|.+++
T Consensus 9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~----~---------~rk~lGRilL 75 (88)
T KOG1774|consen 9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT----K---------SRKELGRILL 75 (88)
T ss_pred eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc----c---------CCCccccEEE
Confidence 3489999999999999999999997 67899999999999999999999975321 1 1236999999
Q ss_pred eCCcEEEEeeC
Q psy11157 95 RGDSVILILKN 105 (111)
Q Consensus 95 RGdnVv~I~~~ 105 (111)
+||||.+|...
T Consensus 76 KGDnItli~~~ 86 (88)
T KOG1774|consen 76 KGDNITLIQSA 86 (88)
T ss_pred cCCcEEEEeec
Confidence 99999999864
No 30
>KOG1781|consensus
Probab=99.64 E-value=3.6e-17 Score=109.35 Aligned_cols=81 Identities=21% Similarity=0.283 Sum_probs=64.2
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEE
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 101 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~ 101 (111)
-++|.-+.+.+++|+|++.+||+..|+|+|||+.|||||+||+|+...+..+. +.....|.+|++++||..+++
T Consensus 17 EsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~------~~~~~tR~LGLvV~RGTalvl 90 (108)
T KOG1781|consen 17 ESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDETRKLGLVVCRGTALVL 90 (108)
T ss_pred hHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc------chhhhhheeeeEEEcccEEEE
Confidence 34555444559999999999999999999999999999999999976532211 111234789999999999999
Q ss_pred EeeCCCC
Q psy11157 102 ILKNPLA 108 (111)
Q Consensus 102 I~~~~~~ 108 (111)
|++.+.+
T Consensus 91 isp~dG~ 97 (108)
T KOG1781|consen 91 ISPADGS 97 (108)
T ss_pred EcCCcch
Confidence 9988753
No 31
>KOG1775|consensus
Probab=99.60 E-value=1.3e-15 Score=97.71 Aligned_cols=78 Identities=23% Similarity=0.513 Sum_probs=66.0
Q ss_pred hcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEe
Q psy11157 16 SFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLR 95 (111)
Q Consensus 16 ~~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IR 95 (111)
-+...|+.++.+++ +.+|.|.+++++++.|+|+|||.|.|++|+||+|+-. .++ ++ +..+++++++.
T Consensus 3 ~~~llPlEliDkcI--gski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~-~~e-gr---------~~tk~~~iLLn 69 (84)
T KOG1775|consen 3 PSTLLPLELIDKCI--GSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEI-TPE-GR---------RMTKLDQILLN 69 (84)
T ss_pred hhhcccHHHHHHhc--CceEEEEEccCceeeeEEechHHHHHHHHHhhhheee-CCC-cc---------eeeeeeeeeec
Confidence 35678999999999 9999999999999999999999999999999999743 222 11 12468999999
Q ss_pred CCcEEEEeeCC
Q psy11157 96 GDSVILILKNP 106 (111)
Q Consensus 96 GdnVv~I~~~~ 106 (111)
|+||.+..|.-
T Consensus 70 GNni~mLvPGG 80 (84)
T KOG1775|consen 70 GNNITMLVPGG 80 (84)
T ss_pred CCcEEEEecCC
Confidence 99999987653
No 32
>KOG1783|consensus
Probab=99.53 E-value=2.3e-15 Score=95.80 Aligned_cols=71 Identities=21% Similarity=0.361 Sum_probs=63.4
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCc
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 98 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdn 98 (111)
..|-++|...+ +++|.|+|.+|-.|+|+|.+.|.|||+.|+.++|+.. |+ ..+..|..||||+|
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 9999999999999999999999999999999999853 33 23568999999999
Q ss_pred EEEEeeC
Q psy11157 99 VILILKN 105 (111)
Q Consensus 99 Vv~I~~~ 105 (111)
|.+|+..
T Consensus 69 VlyIs~~ 75 (77)
T KOG1783|consen 69 VLYISTQ 75 (77)
T ss_pred EEEEEec
Confidence 9999864
No 33
>KOG3168|consensus
Probab=99.50 E-value=4.4e-15 Score=107.65 Aligned_cols=74 Identities=23% Similarity=0.526 Sum_probs=59.3
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEee
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 104 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~~ 104 (111)
|-.++ |.+++|.++|||.|.|.+++||+||||+|.||+|+....++.++. . .-++.|-+|++++||+||++.+.
T Consensus 9 ml~~i--Nyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~---~-~~eEkr~lgLvllRgenIvs~tV 82 (177)
T KOG3168|consen 9 MLQHI--NYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKM---T-DGEEKRVLGLVLLRGENIVSMTV 82 (177)
T ss_pred HHHhh--cceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccc---c-ccceeeEEEEEEecCCcEEEEec
Confidence 34455 999999999999999999999999999999999986654433211 1 11346789999999999999884
No 34
>KOG1784|consensus
Probab=99.48 E-value=3.9e-14 Score=93.64 Aligned_cols=73 Identities=21% Similarity=0.388 Sum_probs=61.7
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEe
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 103 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~ 103 (111)
-|..++ +++|.|++.|||.+.|.|.|||+-.||+|+++.|++..... + . ....+|..+|||+||.+|+
T Consensus 4 ~L~~y~--n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~-g--v-------~q~~lGlyiirgeNva~ig 71 (96)
T KOG1784|consen 4 TLEDYM--NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE-G--V-------EQIVLGLYIIRGENVAVIG 71 (96)
T ss_pred hHHHHh--hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc-c--h-------hheeeEEEEEecCccceee
Confidence 478898 99999999999999999999999999999999998754221 1 1 1345899999999999999
Q ss_pred eCCCC
Q psy11157 104 KNPLA 108 (111)
Q Consensus 104 ~~~~~ 108 (111)
+.+..
T Consensus 72 ~iDEe 76 (96)
T KOG1784|consen 72 EIDEE 76 (96)
T ss_pred ecchh
Confidence 88764
No 35
>KOG1782|consensus
Probab=99.47 E-value=8e-15 Score=101.48 Aligned_cols=70 Identities=27% Similarity=0.446 Sum_probs=59.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEee
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 104 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~~ 104 (111)
|..++ ++++.|.|||||.+.|.|++||+|-|++|.+|+|++.-..+ .+.+..|..+|||+||++++.
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 56666 99999999999999999999999999999999998765211 245668999999999999997
Q ss_pred CCC
Q psy11157 105 NPL 107 (111)
Q Consensus 105 ~~~ 107 (111)
.+.
T Consensus 81 id~ 83 (129)
T KOG1782|consen 81 IDL 83 (129)
T ss_pred CCc
Confidence 653
No 36
>KOG3293|consensus
Probab=99.40 E-value=5.3e-13 Score=92.58 Aligned_cols=75 Identities=21% Similarity=0.294 Sum_probs=64.1
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCc
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 98 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdn 98 (111)
+.||++|+.+- +.+|.|+|++|.+|.|.|+..|.+|||.|.+|+++..+ +. +--.+..++|||++
T Consensus 1 mlPLsLL~~aq--~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----gd---------kf~r~pEcYirGtt 65 (134)
T KOG3293|consen 1 MLPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED----GD---------KFFRMPECYIRGTT 65 (134)
T ss_pred CcchhHHHhcC--CCeEEEEecCCCEecceeecchhhhhcchheeEEeccC----CC---------ceeecceeEEecce
Confidence 46999999998 99999999999999999999999999999999987532 22 01237899999999
Q ss_pred EEEEeeCCCC
Q psy11157 99 VILILKNPLA 108 (111)
Q Consensus 99 Vv~I~~~~~~ 108 (111)
|.++-.++..
T Consensus 66 Ikylri~d~i 75 (134)
T KOG3293|consen 66 IKYLRIPDEI 75 (134)
T ss_pred eEEEeccHHH
Confidence 9999877654
No 37
>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=99.28 E-value=1.8e-12 Score=81.14 Aligned_cols=44 Identities=27% Similarity=0.404 Sum_probs=38.8
Q ss_pred HhhhhCCcEEEEEecC----CeEEEEEEEEeccccceEecceEEEeec
Q psy11157 26 TDSVKHNTQVLINCRN----NKKLLGRVKAFDRHCNMVLENVKEMWTE 69 (111)
Q Consensus 26 ~~~~~~~krV~V~lk~----gr~i~G~L~~fD~~mNLvL~d~~E~~~~ 69 (111)
.+++.++.||+|.++. +..++|.|+|||+||||+|.||+|.|..
T Consensus 2 ~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 2 HRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred chhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 5677789999999996 3578899999999999999999999864
No 38
>KOG3448|consensus
Probab=99.15 E-value=3.3e-10 Score=74.75 Aligned_cols=71 Identities=20% Similarity=0.328 Sum_probs=57.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEE
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 101 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~ 101 (111)
.++++.++ |++|.|.|+++-.+.|+|.+.|+|.|+-|.|..-. ... +. |. --.+..+||||..|.+
T Consensus 4 ysfFkslv--g~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~---ky-----Ph--m~Sv~ncfIRGSvvrY 69 (96)
T KOG3448|consen 4 YSFFKSLV--GKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPD---KY-----PH--MLSVKNCFIRGSVVRY 69 (96)
T ss_pred HHHHHHhc--CCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--Ccc---cC-----CC--eeeeeeEEEeccEEEE
Confidence 46788888 99999999999999999999999999999996643 211 11 11 1347899999999999
Q ss_pred EeeCC
Q psy11157 102 ILKNP 106 (111)
Q Consensus 102 I~~~~ 106 (111)
|..+.
T Consensus 70 v~l~k 74 (96)
T KOG3448|consen 70 VQLPK 74 (96)
T ss_pred EEeCh
Confidence 98765
No 39
>KOG3172|consensus
Probab=99.13 E-value=1.6e-10 Score=78.71 Aligned_cols=76 Identities=13% Similarity=0.311 Sum_probs=65.4
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeC
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 96 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG 96 (111)
+..-|+.+|+++- +.-|++++..|..|+|.|+..|.+||++|+|++-+..+ +. ..++.++||||
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 4567999999997 99999999999999999999999999999998866432 22 24689999999
Q ss_pred CcEEEEeeCCCC
Q psy11157 97 DSVILILKNPLA 108 (111)
Q Consensus 97 dnVv~I~~~~~~ 108 (111)
+.|.++..++..
T Consensus 66 S~IRFlvlPdmL 77 (119)
T KOG3172|consen 66 SKIRFLVLPDML 77 (119)
T ss_pred CeEEEEECchHh
Confidence 999999988754
No 40
>KOG3428|consensus
Probab=98.67 E-value=2.2e-07 Score=63.32 Aligned_cols=71 Identities=20% Similarity=0.288 Sum_probs=58.9
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEE
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 101 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~ 101 (111)
..+|+.+. +.+|+|.|++|..+.|++.+.|-+||..|.++.=... ++ .-++..+.|||+||.+
T Consensus 4 vr~L~kl~--~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-----~~----------pv~l~~lsirgnniRy 66 (109)
T KOG3428|consen 4 VRFLKKLL--NERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-----GE----------PVRLDTLSIRGNNIRY 66 (109)
T ss_pred HHHHHHhh--CCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-----CC----------ceeEEEEEeecceEEE
Confidence 35788888 9999999999999999999999999999999774321 21 1247889999999999
Q ss_pred EeeCCCCC
Q psy11157 102 ILKNPLAL 109 (111)
Q Consensus 102 I~~~~~~~ 109 (111)
+..++...
T Consensus 67 ~~lpD~l~ 74 (109)
T KOG3428|consen 67 YILPDSLN 74 (109)
T ss_pred EEccCCcC
Confidence 99887653
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=97.35 E-value=0.00059 Score=42.37 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=33.7
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
+|..+..++.+|.|.|.+|-.++|.+.+||+|+=|+-.+
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 567777789999999999999999999999998665544
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=97.29 E-value=0.00081 Score=41.76 Aligned_cols=39 Identities=21% Similarity=0.266 Sum_probs=33.5
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
+|..+..++.+|.|.|.+|-.++|.+.|||+|+=|+-.+
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 567777778999999999999999999999998666544
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.05 E-value=0.0017 Score=42.26 Aligned_cols=40 Identities=25% Similarity=0.313 Sum_probs=34.0
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecce
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~ 63 (111)
+|..+..++..|.|.|.+|-.++|.+.|||+|+=|+-.+.
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 5666777789999999999999999999999986665453
No 44
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.96 E-value=0.0042 Score=39.38 Aligned_cols=68 Identities=13% Similarity=0.232 Sum_probs=39.5
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEecc---ccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDR---HCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~---~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
++..++ |++|.|.++||..|+|.|.+++. -+-++|+-|...-... ... ...........++|.++.|+
T Consensus 6 l~~~lv--G~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~---~~~----~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLV--GQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSD---QSN----SDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTT--TSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE-----
T ss_pred HHHhCc--CCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccc---ccc----CCccCCCCCceEEEeccccC
Confidence 456677 99999999999999999999999 8999998877642210 000 01112233567888887765
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.68 E-value=0.0046 Score=39.95 Aligned_cols=36 Identities=31% Similarity=0.361 Sum_probs=31.2
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceE
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMV 59 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLv 59 (111)
+|.....++.+|.|.|.+|-.++|.+.+||+|.=|+
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 566777778999999999999999999999997443
No 46
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.91 E-value=0.12 Score=34.63 Aligned_cols=72 Identities=15% Similarity=0.276 Sum_probs=51.6
Q ss_pred hhhhCCcEEEEEecCCeEEEEEEEEecc-ccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEeeC
Q psy11157 27 DSVKHNTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILKN 105 (111)
Q Consensus 27 ~~~~~~krV~V~lk~gr~i~G~L~~fD~-~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~~~ 105 (111)
.++ |++|.+..+.+-.|+|+|...|. -..+.|.||.-+-++....+.. ..+ .......+.+||..|.-+...
T Consensus 5 ~~I--Gs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~---ipp--~~~v~~~I~Fr~sDIkdL~v~ 77 (96)
T PF12701_consen 5 PYI--GSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDRE---IPP--SDEVYDYIVFRGSDIKDLKVI 77 (96)
T ss_dssp CCT--TCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS------C---CSSSSEEEEETTTEEEEEEC
T ss_pred ccc--CCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcc---cCC--CCceeeEEEEEccccceEEEE
Confidence 466 99999999999999999999998 6799999988765432111110 001 122468999999999876643
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.57 E-value=0.031 Score=40.95 Aligned_cols=41 Identities=22% Similarity=0.294 Sum_probs=34.9
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecce
Q psy11157 23 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 23 ~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~ 63 (111)
.+|..+..++.+|.|.|.+|-.++|.+.+||+|+=|+-.+.
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 35777777899999999999999999999999986665554
No 48
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.54 E-value=0.033 Score=40.83 Aligned_cols=40 Identities=23% Similarity=0.216 Sum_probs=34.2
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecce
Q psy11157 24 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~ 63 (111)
+|..+..++.+|.|.|.+|-.++|.+.+||+|.=|+-.+.
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 5777777889999999999999999999999986655443
No 49
>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=95.09 E-value=0.12 Score=29.91 Aligned_cols=32 Identities=9% Similarity=0.261 Sum_probs=28.3
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
+++|+|.+ ++..++|...+.|..-.|+++...
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence 89999999 777889999999999999996533
No 50
>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=94.66 E-value=0.089 Score=32.58 Aligned_cols=34 Identities=26% Similarity=0.336 Sum_probs=29.9
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEecceEE
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKE 65 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E 65 (111)
|..|++++..|.+|+|.+.+||.-.+|++-.|.+
T Consensus 6 Gs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 6 GSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 8999999999999999999999999988654433
No 51
>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=92.75 E-value=1.2 Score=28.56 Aligned_cols=69 Identities=14% Similarity=0.265 Sum_probs=47.6
Q ss_pred hhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEE
Q psy11157 27 DSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 101 (111)
Q Consensus 27 ~~~~~~krV~V~lk~gr~i~G~L~~fD~~m-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~ 101 (111)
.++ ++++.+..+.+-.|+|.|...|..= -+.|.||.-+-++..+.+. ....+ ...-...++.||+.|.-
T Consensus 3 ~~I--G~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~--~~ipp--~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYI--GSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDG--PEIPP--SDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccc--CceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCC--CccCC--CCcceeEEEEcCCcccc
Confidence 345 9999999999999999999999876 5668998876554222110 00111 12236889999998753
No 52
>PRK14638 hypothetical protein; Provisional
Probab=90.42 E-value=0.54 Score=33.68 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=27.1
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.+++++.++|.|.++|.- ++.|
T Consensus 95 f~r~~--G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 95 YVRFT--GKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 45666 999999999999999999999963 3444
No 53
>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=89.30 E-value=4 Score=26.53 Aligned_cols=63 Identities=25% Similarity=0.283 Sum_probs=44.3
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEE
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 100 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~m-NLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv 100 (111)
|.+|.... +++|.+.+.++.++.|...|+|... |+..+|= ..|- .....-++|+.-|+
T Consensus 16 Lr~l~~~~--gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L-----~TPl--------------Gv~~eAlLR~~DVi 74 (80)
T PF11095_consen 16 LRSLLAMV--GKPVEFTLHENTTVSARFGACDIDVSNFQVSNL-----QTPL--------------GVQPEALLRCSDVI 74 (80)
T ss_dssp HHHHHHCT--TSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE-----ETTT--------------TEEEEEEEEGGGEE
T ss_pred HHHHHHhc--CCceEEEEeCCeEEEEEEEEecCchheEEhhhc-----CCCc--------------ccChhheeecCCEE
Confidence 34444554 9999999999999999999999765 6665541 1111 12578999999999
Q ss_pred EEeeC
Q psy11157 101 LILKN 105 (111)
Q Consensus 101 ~I~~~ 105 (111)
+++..
T Consensus 75 ~~~f~ 79 (80)
T PF11095_consen 75 SISFD 79 (80)
T ss_dssp EEEE-
T ss_pred EEEec
Confidence 99863
No 54
>PRK02001 hypothetical protein; Validated
Probab=89.00 E-value=0.8 Score=33.01 Aligned_cols=33 Identities=21% Similarity=0.447 Sum_probs=27.5
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|+|.+.+++.+.|.|.++|.- ++.|
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 35666 999999999999999999999974 4444
No 55
>PRK14639 hypothetical protein; Provisional
Probab=88.88 E-value=0.84 Score=32.31 Aligned_cols=33 Identities=24% Similarity=0.456 Sum_probs=27.6
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.+++++.+.|.|.++|.- ++.|
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 45666 999999999999999999999983 4544
No 56
>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=87.07 E-value=1.1 Score=32.61 Aligned_cols=34 Identities=9% Similarity=0.260 Sum_probs=30.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccc
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRH 55 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~ 55 (111)
+++.+.+-++++-|+|++.|||+++|.=.|.|..
T Consensus 110 F~Icrka~qqg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 110 FSICRKAHQQGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred HHHHHHHHHCCCeEEEEEcCCcEEEeeecccceE
Confidence 6677888889999999999999999998888754
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=85.79 E-value=1.7 Score=31.87 Aligned_cols=41 Identities=29% Similarity=0.401 Sum_probs=30.0
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEecce
Q psy11157 19 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLENV 63 (111)
Q Consensus 19 ~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~m-NLvL~d~ 63 (111)
.+|+.+ ..++ +|.|+|.+.+ +++.|.|..+|--. |++|-+-
T Consensus 7 ~~p~~~-~~yv--~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~ 48 (166)
T PF06372_consen 7 KSPLEW-QDYV--GKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNF 48 (166)
T ss_dssp S-HHHH-HCTT--T-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE
T ss_pred CCHHHH-HHhh--CcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEc
Confidence 456554 5666 9999999999 99999999999865 8888643
No 58
>PRK14644 hypothetical protein; Provisional
Probab=83.03 E-value=2.7 Score=29.64 Aligned_cols=33 Identities=9% Similarity=0.224 Sum_probs=27.3
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNN----KKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~g----r~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.+++. +.+.|.|.++|.. ++.|
T Consensus 80 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l 116 (136)
T PRK14644 80 LENHI--GEIIDVSLNKEVNKTDFITGELLENNPE-TITL 116 (136)
T ss_pred HHHhC--CCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEE
Confidence 56777 99999999876 8999999999983 4555
No 59
>PRK14640 hypothetical protein; Provisional
Probab=81.23 E-value=3.4 Score=29.54 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=26.2
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk----~gr~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.++ +.+.+.|.|.++|.. ++.|
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 45666 999999994 569999999999984 4444
No 60
>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=80.94 E-value=4.1 Score=25.98 Aligned_cols=33 Identities=18% Similarity=0.313 Sum_probs=25.5
Q ss_pred HHhhhhCCcEEEEEec---CC-eEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCR---NN-KKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk---~g-r~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.++ +| +.+.|.|.++|.- ++.|
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 45 6899999999983 3444
No 61
>PRK14642 hypothetical protein; Provisional
Probab=80.41 E-value=3.5 Score=31.01 Aligned_cols=29 Identities=17% Similarity=0.236 Sum_probs=24.6
Q ss_pred HHhhhhCCcEEEEEec-------------CCeEEEEEEEEeccc
Q psy11157 25 LTDSVKHNTQVLINCR-------------NNKKLLGRVKAFDRH 55 (111)
Q Consensus 25 L~~~~~~~krV~V~lk-------------~gr~i~G~L~~fD~~ 55 (111)
+.++. |+.|.|.|+ +.+.|+|+|.++|..
T Consensus 95 f~rfi--G~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 95 FERFA--GEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HHHhC--CCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 35555 999999998 679999999999884
No 62
>PRK14636 hypothetical protein; Provisional
Probab=80.35 E-value=3.5 Score=30.34 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEec---CC-eEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCR---NN-KKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk---~g-r~i~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.++ +| +.++|.|.++|.- ++.|
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 45666 999999998 44 7999999999883 4444
No 63
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.85 E-value=4 Score=29.52 Aligned_cols=33 Identities=21% Similarity=0.377 Sum_probs=27.6
Q ss_pred HHhhhhCCcEEEEEe----cCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINC----RNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~l----k~gr~i~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|+| .+++.++|+|.++|.-+ +++
T Consensus 94 f~r~~--G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 94 FARFI--GEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHhc--CcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 45666 99999999 67899999999999987 444
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=79.41 E-value=3.5 Score=28.72 Aligned_cols=34 Identities=15% Similarity=0.285 Sum_probs=24.6
Q ss_pred HHHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy11157 24 ILTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk----~gr~i~G~L~~fD~~mNLvL 60 (111)
-+.+++ |+.|.|+++ +.+.+.|+|.++|. -.++|
T Consensus 81 ~~~~~i--G~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 81 DFERFI--GRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHH---SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHhc--CCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 356777 999999995 45789999999999 34444
No 65
>PRK14633 hypothetical protein; Provisional
Probab=79.37 E-value=4.3 Score=29.00 Aligned_cols=33 Identities=18% Similarity=0.220 Sum_probs=26.0
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk----~gr~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.++ +.+.++|+|.++|.. ++.|
T Consensus 89 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 89 AQALV--GFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHhC--CCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 45666 999999995 568999999999984 4444
No 66
>PRK14645 hypothetical protein; Provisional
Probab=78.34 E-value=4.3 Score=29.21 Aligned_cols=32 Identities=13% Similarity=0.266 Sum_probs=24.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.+ +++.+.|+|.++|.- .+.|
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 35566 99999976 789999999999884 3444
No 67
>PRK14643 hypothetical protein; Provisional
Probab=78.16 E-value=4.6 Score=29.35 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=24.5
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEeccc
Q psy11157 25 LTDSVKHNTQVLINCRN----NKKLLGRVKAFDRH 55 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~----gr~i~G~L~~fD~~ 55 (111)
+.+++ |+.|.|.++. .+.+.|+|.++|.-
T Consensus 99 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 99 LVKAL--NQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHhc--CCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 45666 9999999975 58999999999864
No 68
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=77.81 E-value=5.1 Score=29.22 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=31.3
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
..+-+|+|.+.||..|.|++-+|+.--|++|.-+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 45799999999999999999999999999986543
No 69
>PRK14632 hypothetical protein; Provisional
Probab=77.15 E-value=5.1 Score=29.28 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEecC-------CeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRN-------NKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~-------gr~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.+++ .+.+.|+|.++|.- ++.|
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 45666 9999999986 57999999999863 4444
No 70
>PRK14646 hypothetical protein; Provisional
Probab=76.96 E-value=5.4 Score=28.64 Aligned_cols=33 Identities=12% Similarity=0.102 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNN----KKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~g----r~i~G~L~~fD~~mNLvL 60 (111)
+.+++ |+.|.|.|++. +.+.|.|.++|.- ++.|
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 46666 99999999752 7889999999984 4555
No 71
>PRK14634 hypothetical protein; Provisional
Probab=75.70 E-value=6.2 Score=28.33 Aligned_cols=33 Identities=12% Similarity=0.213 Sum_probs=25.6
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRN----NKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~----gr~i~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.+++ .+.|.|.|.++|.- ++.|
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 35666 9999999974 37999999999984 4444
No 72
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=74.00 E-value=7.3 Score=27.67 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=23.9
Q ss_pred HHhhhhCCcEEEEEe----cCCeEEEEEEEEecc
Q psy11157 25 LTDSVKHNTQVLINC----RNNKKLLGRVKAFDR 54 (111)
Q Consensus 25 L~~~~~~~krV~V~l----k~gr~i~G~L~~fD~ 54 (111)
+.+++ |+.|.|.+ .+++.+.|.|.++|.
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 46666 99999997 467899999999998
No 73
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=74.00 E-value=11 Score=23.66 Aligned_cols=59 Identities=15% Similarity=0.311 Sum_probs=39.4
Q ss_pred cCCCc--HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEE
Q psy11157 17 FATGP--LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFL 94 (111)
Q Consensus 17 ~~~~P--l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~I 94 (111)
+..+| ...|++++ |++|.|.+-.|. ++|.|.+...= .++|+. .-..+||
T Consensus 6 s~vdpyvyq~lq~li--G~~vvV~T~~g~-v~G~L~~V~pD-hIvl~~-------------------------~~~~~~I 56 (66)
T PF10842_consen 6 SLVDPYVYQTLQSLI--GQRVVVQTTRGS-VRGILVDVKPD-HIVLEE-------------------------NGTPFFI 56 (66)
T ss_pred eccCHHHHHHHHHhc--CCEEEEEEcCCc-EEEEEEeecCC-EEEEEe-------------------------CCcEEEE
Confidence 45566 45688898 999999996554 59999875321 112211 1245789
Q ss_pred eCCcEEEEee
Q psy11157 95 RGDSVILILK 104 (111)
Q Consensus 95 RGdnVv~I~~ 104 (111)
|=..|++|.|
T Consensus 57 R~~~IV~v~p 66 (66)
T PF10842_consen 57 RIAQIVWVMP 66 (66)
T ss_pred EeeeEEEEcC
Confidence 9899988854
No 74
>PRK14647 hypothetical protein; Provisional
Probab=72.89 E-value=7.8 Score=27.83 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=23.3
Q ss_pred HHhhhhCCcEEEEEec---------CCeEEEEEEEEecc
Q psy11157 25 LTDSVKHNTQVLINCR---------NNKKLLGRVKAFDR 54 (111)
Q Consensus 25 L~~~~~~~krV~V~lk---------~gr~i~G~L~~fD~ 54 (111)
+.+++ |+.|.|.++ +.+.+.|.|.++|.
T Consensus 94 f~r~~--G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 94 YERYA--GRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHhC--CcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 45666 999999996 35899999999997
No 75
>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=71.06 E-value=11 Score=25.44 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=18.1
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEE
Q psy11157 26 TDSVKHNTQVLINCRNNKKLLGRV 49 (111)
Q Consensus 26 ~~~~~~~krV~V~lk~gr~i~G~L 49 (111)
-..+..+.+|.+.|+||+.+.|++
T Consensus 22 v~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 22 VSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HhhcCCcceEEEEEcCCCeeeeee
Confidence 344456799999999999999987
No 76
>PRK10898 serine endoprotease; Provisional
Probab=70.67 E-value=9.4 Score=30.61 Aligned_cols=34 Identities=6% Similarity=0.211 Sum_probs=29.5
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 31 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 31 ~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
....+.|.+.||+.+.+.++++|...+|.|=.+.
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 3567999999999999999999999999885543
No 77
>PRK14637 hypothetical protein; Provisional
Probab=70.06 E-value=8.6 Score=27.55 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=24.7
Q ss_pred HHhhhhCCcEEEEEecCCeEE-EEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKL-LGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i-~G~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.+.+.+.+ +|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 93 FSIFV--GETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHhC--CCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 45566 99999999555566 7999999884 4444
No 78
>PRK14631 hypothetical protein; Provisional
Probab=69.70 E-value=9.3 Score=28.04 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=23.1
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEec
Q psy11157 25 LTDSVKHNTQVLINCR----NNKKLLGRVKAFD 53 (111)
Q Consensus 25 L~~~~~~~krV~V~lk----~gr~i~G~L~~fD 53 (111)
+.+++ |+.|.|.++ +.+.|+|.|.++|
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 45666 999999996 4599999999998
No 79
>PRK06955 biotin--protein ligase; Provisional
Probab=67.85 E-value=16 Score=28.62 Aligned_cols=33 Identities=12% Similarity=0.186 Sum_probs=28.2
Q ss_pred hhCCcEEEEEecCCeEEEEEEEEeccccceEec
Q psy11157 29 VKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 61 (111)
Q Consensus 29 ~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~ 61 (111)
...+++|+|...+++.+.|+..|.|..-.|+++
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 346899999766677899999999999999995
No 80
>PRK14641 hypothetical protein; Provisional
Probab=67.46 E-value=10 Score=27.80 Aligned_cols=27 Identities=11% Similarity=0.302 Sum_probs=22.3
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEec
Q psy11157 25 LTDSVKHNTQVLINCRN----NKKLLGRVKAFD 53 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~----gr~i~G~L~~fD 53 (111)
+.++. |+.|.|.+++ .+.++|.|.++|
T Consensus 99 f~r~~--G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHV--GRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhC--CCEEEEEEecccCCeEEEEEEEEeee
Confidence 45666 9999999976 468999999995
No 81
>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=67.43 E-value=12 Score=29.93 Aligned_cols=33 Identities=9% Similarity=0.275 Sum_probs=28.8
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
...+.|.+.||+.+.+.++++|...+|.|=.+.
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 457899999999999999999999999985543
No 82
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=65.97 E-value=23 Score=22.24 Aligned_cols=37 Identities=16% Similarity=0.293 Sum_probs=29.7
Q ss_pred HHHhhhhCCcEEEEEecCC---eEEEEEEEEeccccceEe
Q psy11157 24 ILTDSVKHNTQVLINCRNN---KKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 24 ~L~~~~~~~krV~V~lk~g---r~i~G~L~~fD~~mNLvL 60 (111)
.|..++..+..|+|..-++ ..+.|++..+|..-+.+.
T Consensus 34 ~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~ 73 (92)
T PF08863_consen 34 KLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLK 73 (92)
T ss_pred HHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEE
Confidence 3777777789999888754 567899999999987665
No 83
>PRK10139 serine endoprotease; Provisional
Probab=65.56 E-value=13 Score=30.91 Aligned_cols=35 Identities=9% Similarity=0.285 Sum_probs=30.4
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
....++.|.+.||+++.+.++++|....|.+=.+.
T Consensus 112 ~~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 112 NQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 35678999999999999999999999999985543
No 84
>PRK10942 serine endoprotease; Provisional
Probab=65.03 E-value=13 Score=31.07 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=29.0
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecce
Q psy11157 31 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 31 ~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~ 63 (111)
....+.|.+.||+++.+.++++|...+|.|=.+
T Consensus 134 ~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 134 NATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 356799999999999999999999999988643
No 85
>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=58.66 E-value=18 Score=29.39 Aligned_cols=34 Identities=3% Similarity=0.224 Sum_probs=29.5
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 31 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 31 ~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
.-..+.|.+.+++.+.+.++++|...+|.|=.+.
T Consensus 80 ~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 3468899999999999999999999999985543
No 86
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=57.12 E-value=12 Score=21.55 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=14.8
Q ss_pred EEEEEEEeccccceEecceEEE
Q psy11157 45 LLGRVKAFDRHCNMVLENVKEM 66 (111)
Q Consensus 45 i~G~L~~fD~~mNLvL~d~~E~ 66 (111)
..|+..|.|+.+.|+|.+....
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 6799999999999999886654
No 87
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=53.97 E-value=37 Score=26.47 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=26.6
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEec
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 61 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~ 61 (111)
..+++|++.. ++..++|++.+.|....|++.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 4589999986 446799999999999999995
No 88
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=51.53 E-value=49 Score=24.75 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=26.5
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEec
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 61 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~ 61 (111)
..+++|+|... +..+.|+..|.|..-.|+++
T Consensus 191 ~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTG-NGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeC-CcEEEEEEEeECCCceEEEE
Confidence 35899999864 46799999999999999995
No 89
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=51.06 E-value=48 Score=25.86 Aligned_cols=32 Identities=19% Similarity=0.374 Sum_probs=27.1
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
..+++|+|.. ++..+.|++.+.|....|+|+.
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 3589999875 5688999999999999999953
No 90
>KOG1073|consensus
Probab=50.11 E-value=54 Score=26.98 Aligned_cols=75 Identities=16% Similarity=0.297 Sum_probs=49.0
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEEEEeccc-cceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEee
Q psy11157 26 TDSVKHNTQVLINCRNNKKLLGRVKAFDRH-CNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 104 (111)
Q Consensus 26 ~~~~~~~krV~V~lk~gr~i~G~L~~fD~~-mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~~ 104 (111)
..++ |+.|.++-+.+-.|+|+|--.|-- .-|-|.+|--+-++..+... .. .-+. ..-...|+.||..|.-+..
T Consensus 5 t~yI--GS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~-pq-~p~~--~kVy~YIlFRGSDIKDL~V 78 (361)
T KOG1073|consen 5 TSYI--GSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDG-PQ-VPPD--DKVYDYILFRGSDIKDLIV 78 (361)
T ss_pred cccc--cceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCC-Cc-CCCC--ccceeeEEecCcccceeee
Confidence 4566 999999999999999999877643 46788887555443221110 00 0011 1136889999999986665
Q ss_pred CC
Q psy11157 105 NP 106 (111)
Q Consensus 105 ~~ 106 (111)
.+
T Consensus 79 ~~ 80 (361)
T KOG1073|consen 79 QE 80 (361)
T ss_pred cc
Confidence 44
No 91
>KOG3382|consensus
Probab=48.74 E-value=9.6 Score=27.29 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=19.2
Q ss_pred CCeEEEEEEEEeccccceEecceEE
Q psy11157 41 NNKKLLGRVKAFDRHCNMVLENVKE 65 (111)
Q Consensus 41 ~gr~i~G~L~~fD~~mNLvL~d~~E 65 (111)
.+-.=.|+|+|.|+|-|=.-+|-.-
T Consensus 41 td~~kiGTLVG~DkfGNkYyen~~~ 65 (151)
T KOG3382|consen 41 TDDHKIGTLVGVDKFGNKYYENNDY 65 (151)
T ss_pred cccccceeeeeecccccchhcccce
Confidence 3344569999999999988877643
No 92
>PRK14635 hypothetical protein; Provisional
Probab=46.13 E-value=42 Score=24.14 Aligned_cols=33 Identities=21% Similarity=0.175 Sum_probs=24.4
Q ss_pred HHhhhhCCcEEEEEec--CCeEEEE---EEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCR--NNKKLLG---RVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk--~gr~i~G---~L~~fD~~mNLvL 60 (111)
+.++. |+.|.|.+. ++..+.| .|.++|.- ++.|
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 35666 999999886 4578887 99999874 4444
No 93
>PRK14630 hypothetical protein; Provisional
Probab=45.91 E-value=39 Score=23.87 Aligned_cols=32 Identities=6% Similarity=0.028 Sum_probs=23.6
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 60 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL 60 (111)
+.++. |++|.|.+.+. ..+|+|.++|.- ++.|
T Consensus 92 f~r~~--G~~v~V~l~~~-~~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 92 FKIFE--GKKIKLMLDND-FEEGFILEAKAD-SFIF 123 (143)
T ss_pred HHHhC--CCEEEEEEcCc-ceEEEEEEEeCC-EEEE
Confidence 35666 99999999654 359999999883 3434
No 94
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=44.54 E-value=59 Score=28.18 Aligned_cols=32 Identities=28% Similarity=0.346 Sum_probs=27.7
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 31 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 31 ~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
.+++|++...+++.+.|+..|.|..-.|+|+.
T Consensus 277 ~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 277 HGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 58999987667778999999999999999963
No 95
>PF09196 DUF1953: Domain of unknown function (DUF1953); InterPro: IPR015279 This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. ; PDB: 3HJE_A 1IV8_A.
Probab=44.29 E-value=33 Score=21.13 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=14.7
Q ss_pred EEEeCCcEEEEeeCCCCCC
Q psy11157 92 MFLRGDSVILILKNPLALN 110 (111)
Q Consensus 92 v~IRGdnVv~I~~~~~~~~ 110 (111)
=|||||.|..|.....+.|
T Consensus 13 gf~r~~kilviiktkgs~n 31 (66)
T PF09196_consen 13 GFIRFNKILVIIKTKGSVN 31 (66)
T ss_dssp EEEETTTEEEEEES-TTSS
T ss_pred eEEecCEEEEEEecccccc
Confidence 3899999999987766554
No 96
>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=43.58 E-value=13 Score=24.85 Aligned_cols=17 Identities=29% Similarity=0.290 Sum_probs=15.1
Q ss_pred EEEEEeccccceEecce
Q psy11157 47 GRVKAFDRHCNMVLENV 63 (111)
Q Consensus 47 G~L~~fD~~mNLvL~d~ 63 (111)
|+|+|.|.|-|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998664
No 97
>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=43.46 E-value=38 Score=21.78 Aligned_cols=19 Identities=11% Similarity=0.265 Sum_probs=13.1
Q ss_pred hCCcEEEEEecCCeEEEEE
Q psy11157 30 KHNTQVLINCRNNKKLLGR 48 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~ 48 (111)
..+.+|++.|+||..++|+
T Consensus 15 ~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 15 MYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp TTTT-EEEE-TTT--EEES
T ss_pred hcCCeEEEEEeCCCEEEEE
Confidence 3588999999999999996
No 98
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=42.09 E-value=1.5e+02 Score=22.54 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=29.9
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecce
Q psy11157 31 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 31 ~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~ 63 (111)
.+++|++...++..+.|+..+.|..-.|+|+..
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 699999999888888889999999999999664
No 99
>PRK08330 biotin--protein ligase; Provisional
Probab=40.88 E-value=1e+02 Score=23.07 Aligned_cols=32 Identities=19% Similarity=0.185 Sum_probs=26.0
Q ss_pred hCCcEEEEEecCCeEE-EEEEEEeccccceEecc
Q psy11157 30 KHNTQVLINCRNNKKL-LGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i-~G~L~~fD~~mNLvL~d 62 (111)
..+++|++.. ++..+ .|+..+.|..-.|+++.
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 3589999875 55565 79999999999999964
No 100
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=40.28 E-value=42 Score=24.97 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=21.7
Q ss_pred HHHHHhhhhCCcEEEEEec-CCeEEEEEEEEeccc
Q psy11157 22 LSILTDSVKHNTQVLINCR-NNKKLLGRVKAFDRH 55 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk-~gr~i~G~L~~fD~~ 55 (111)
++||-.+--.--+|.+.+. ++..|+|+|.+||+=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 3445444322344555444 789999999999975
No 101
>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=34.43 E-value=86 Score=18.70 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=27.7
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccce
Q psy11157 17 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNM 58 (111)
Q Consensus 17 ~~~~Pl~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNL 58 (111)
+..++-.+++.....+.+| +++++|+. .+.|+.++.|=++
T Consensus 9 ~r~~~~~~l~~v~~~~~pv-~It~~g~~-~~vli~~~~ye~l 48 (75)
T PF02604_consen 9 FRNNFSELLDEVEEGEEPV-IITKNGKP-VAVLISVEDYERL 48 (75)
T ss_dssp HHHTHHHHHHHHHHCT-EE-EEEETTEE-EEEEEEHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeE-EEEECCCC-CeecccHHHHHHH
Confidence 4556777888887545557 55677766 8889988887554
No 102
>PRK11625 Rho-binding antiterminator; Provisional
Probab=32.73 E-value=1.2e+02 Score=19.80 Aligned_cols=58 Identities=14% Similarity=0.082 Sum_probs=35.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecceEEEeeccCCCCCCcccCCccceeeeeCeEEEeCCcEEEEee
Q psy11157 25 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 104 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRGdnVv~I~~ 104 (111)
|.-+...+.+|.+.+++|..+.|+. .|-+.+ +-.|+..-.. .=+.-.||=|.|+.++.
T Consensus 16 LElAC~~~~~l~l~l~dGe~~~g~A--~D~~~~----~k~EyL~l~~----------------~g~~~~iRLD~I~s~~~ 73 (84)
T PRK11625 16 LELACQHHLMLTLELKDGEVLQAKA--SDLVSR----KNVEYLVVEA----------------AGETRELRLDKIASFSH 73 (84)
T ss_pred HHHHHhcCCeEEEEECCCCEEEEEE--EeeecC----CceEEEEEEc----------------CCCEEEEEeeeEeeccC
Confidence 4444446889999999999999975 555533 4445443210 01345667777777763
No 103
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=29.22 E-value=58 Score=21.43 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=18.7
Q ss_pred eeeeCeEEEeCCcEEEEeeCC
Q psy11157 86 DRFISKMFLRGDSVILILKNP 106 (111)
Q Consensus 86 ~r~lg~v~IRGdnVv~I~~~~ 106 (111)
.|+-|.+.++|..+..|..+|
T Consensus 76 ~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hcceEEEEEECCeeeEEEcCC
Confidence 478899999999999998876
No 104
>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=28.80 E-value=1.1e+02 Score=18.50 Aligned_cols=26 Identities=15% Similarity=0.259 Sum_probs=18.0
Q ss_pred hCCcEEEEEecCC-eEEEEEEEEeccc
Q psy11157 30 KHNTQVLINCRNN-KKLLGRVKAFDRH 55 (111)
Q Consensus 30 ~~~krV~V~lk~g-r~i~G~L~~fD~~ 55 (111)
..|.+|.++=-++ .-|.|.+.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 3588899888866 4569999999973
No 105
>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=26.90 E-value=87 Score=21.37 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=19.8
Q ss_pred cEEEEEecCCeEEEEEEEEec-cccceE
Q psy11157 33 TQVLINCRNNKKLLGRVKAFD-RHCNMV 59 (111)
Q Consensus 33 krV~V~lk~gr~i~G~L~~fD-~~mNLv 59 (111)
....|.++||+.+.|.++.=| ....|.
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~~~~~l~ 85 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETADGVTVK 85 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCCCeEEEE
Confidence 347899999999999998843 333443
No 106
>PRK08477 biotin--protein ligase; Provisional
Probab=26.30 E-value=2.5e+02 Score=20.96 Aligned_cols=32 Identities=3% Similarity=0.058 Sum_probs=27.2
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 30 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 30 ~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
..++.|+|. .+++.++|+.++.|+.--|++..
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECC
Confidence 468999986 57899999999999999888855
No 107
>PRK06630 hypothetical protein; Provisional
Probab=25.72 E-value=36 Score=23.02 Aligned_cols=19 Identities=16% Similarity=0.111 Sum_probs=16.5
Q ss_pred EEEEEEEeccccceEecce
Q psy11157 45 LLGRVKAFDRHCNMVLENV 63 (111)
Q Consensus 45 i~G~L~~fD~~mNLvL~d~ 63 (111)
..|.|+|-|+|-|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999988774
No 108
>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=25.02 E-value=2.1e+02 Score=18.83 Aligned_cols=41 Identities=15% Similarity=0.298 Sum_probs=29.6
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEecc
Q psy11157 22 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 62 (111)
Q Consensus 22 l~~L~~~~~~~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d 62 (111)
..+|+.....+..|+|...+|..+.=.|.+.|.--|.++=|
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 34578888888999999888887999999999988776644
No 109
>cd01737 LSm16_N LSm16 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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=24.62 E-value=1.5e+02 Score=18.32 Aligned_cols=28 Identities=32% Similarity=0.440 Sum_probs=23.3
Q ss_pred hhhhCCcEEEEEecCC-eEEEEEEEEecccc
Q psy11157 27 DSVKHNTQVLINCRNN-KKLLGRVKAFDRHC 56 (111)
Q Consensus 27 ~~~~~~krV~V~lk~g-r~i~G~L~~fD~~m 56 (111)
.|+ |+-|.|.+.+. ..|+|.+...|+--
T Consensus 3 dWi--Gs~VSI~C~~~lGVyQG~i~~V~~~~ 31 (62)
T cd01737 3 DWL--GSIVSINCGETLGVYQGLVSAVDQES 31 (62)
T ss_pred ccc--ceEEEEecCCceEEEEEEEEEeCccc
Confidence 466 89999999876 78999999998753
No 110
>PRK10708 hypothetical protein; Provisional
Probab=24.39 E-value=86 Score=19.25 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=21.2
Q ss_pred CcEEEEEecCCeEEEEEEEEecccc
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHC 56 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~m 56 (111)
+.+|.|++.++-.=.|++.+...|-
T Consensus 4 nD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 4 NDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred ccEEEEecCCCccccceEEEEeecc
Confidence 7899999999988889888877764
No 111
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.39 E-value=1.4e+02 Score=23.39 Aligned_cols=33 Identities=3% Similarity=0.217 Sum_probs=28.2
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEecceE
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~mNLvL~d~~ 64 (111)
-.++.|.+.+|+++.+.++++|...-+.+-...
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki~ 127 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKID 127 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEec
Confidence 578889999999999999999999988775443
No 112
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=21.68 E-value=51 Score=22.78 Aligned_cols=19 Identities=32% Similarity=0.296 Sum_probs=16.4
Q ss_pred EEEEEEeccccceEecceE
Q psy11157 46 LGRVKAFDRHCNMVLENVK 64 (111)
Q Consensus 46 ~G~L~~fD~~mNLvL~d~~ 64 (111)
.|.|+|-|+|-|-.-++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6899999999999887643
No 113
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=21.47 E-value=98 Score=19.00 Aligned_cols=25 Identities=16% Similarity=0.221 Sum_probs=21.0
Q ss_pred CcEEEEEecCCeEEEEEEEEecccc
Q psy11157 32 NTQVLINCRNNKKLLGRVKAFDRHC 56 (111)
Q Consensus 32 ~krV~V~lk~gr~i~G~L~~fD~~m 56 (111)
+.+|.|++.++-.=.|++.+...|-
T Consensus 4 nD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 4 NDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred ccEEEEecCCcccccceEEEEeecc
Confidence 7899999999888889888877764
No 114
>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=21.20 E-value=1.3e+02 Score=19.87 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=10.3
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q psy11157 32 NTQVLIN-CRNNKKLLGRVKA 51 (111)
Q Consensus 32 ~krV~V~-lk~gr~i~G~L~~ 51 (111)
|..|+|. +..++.+.|++.+
T Consensus 96 G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 96 GDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCEEEEEECCCCCEEEEEEeC
Confidence 4555555 4455555555443
No 115
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=21.01 E-value=3.2e+02 Score=19.48 Aligned_cols=26 Identities=12% Similarity=0.239 Sum_probs=22.0
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEEEEec
Q psy11157 26 TDSVKHNTQVLINCRNNKKLLGRVKAFD 53 (111)
Q Consensus 26 ~~~~~~~krV~V~lk~gr~i~G~L~~fD 53 (111)
..++ |+.|.+...+|..+.|++.+..
T Consensus 88 ~slV--Gk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELI--GKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHh--CCEEEEEeCCCCEEEEEEEEEE
Confidence 3556 9999999889999999998875
No 116
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=20.36 E-value=2.2e+02 Score=18.15 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=17.9
Q ss_pred HHhhhhCCcEEEEEecCCe----EEEEEEEE
Q psy11157 25 LTDSVKHNTQVLINCRNNK----KLLGRVKA 51 (111)
Q Consensus 25 L~~~~~~~krV~V~lk~gr----~i~G~L~~ 51 (111)
|..++ |++|.+..+.|| +-+|.|..
T Consensus 12 l~~~v--G~~V~l~a~~GRkK~~~r~GvL~~ 40 (76)
T PF06257_consen 12 LESHV--GKRVKLKANKGRKKIIEREGVLEE 40 (76)
T ss_dssp HHHTT--TSEEEEEE--SSS--S-EEEEEEE
T ss_pred HHHcC--CCEEEEEEcCCceEEEEEEEEEEe
Confidence 66777 999999999986 45798864
Done!