Query psy9158
Match_columns 133
No_of_seqs 130 out of 642
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 20:24:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9158.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9158hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01733 LSm10 The eukaryotic S 99.9 6.7E-28 1.4E-32 166.5 8.6 69 9-77 1-78 (78)
2 cd01724 Sm_D1 The eukaryotic S 99.9 2.2E-26 4.8E-31 162.8 9.5 77 18-95 2-87 (90)
3 cd01721 Sm_D3 The eukaryotic S 99.9 2.6E-23 5.6E-28 140.4 8.1 60 19-78 2-70 (70)
4 cd01725 LSm2 The eukaryotic Sm 99.9 1.1E-22 2.4E-27 141.0 8.0 62 19-80 3-75 (81)
5 cd01723 LSm4 The eukaryotic Sm 99.9 6.2E-22 1.3E-26 135.4 7.5 63 18-80 2-74 (76)
6 KOG3172|consensus 99.8 3.9E-20 8.4E-25 135.5 5.1 73 19-91 7-88 (119)
7 KOG3428|consensus 99.8 3.4E-19 7.3E-24 130.2 6.2 76 16-91 1-84 (109)
8 cd01726 LSm6 The eukaryotic Sm 99.8 1.7E-18 3.6E-23 115.7 7.6 57 19-75 2-67 (67)
9 cd01722 Sm_F The eukaryotic Sm 99.7 6.1E-18 1.3E-22 113.4 8.1 58 18-75 2-68 (68)
10 KOG3293|consensus 99.7 1.9E-18 4.1E-23 129.1 5.5 71 19-91 4-84 (134)
11 KOG3448|consensus 99.7 2.4E-17 5.3E-22 117.2 6.9 71 19-89 4-85 (96)
12 PF01423 LSM: LSM domain ; In 99.7 1.2E-16 2.6E-21 105.0 7.8 57 20-76 1-67 (67)
13 smart00651 Sm snRNP Sm protein 99.7 1.2E-16 2.6E-21 104.9 7.5 56 21-76 2-67 (67)
14 KOG3482|consensus 99.7 1.2E-16 2.5E-21 110.2 6.5 58 18-75 9-75 (79)
15 PRK00737 small nuclear ribonuc 99.7 2.4E-16 5.2E-21 106.8 7.9 59 17-75 4-71 (72)
16 cd01731 archaeal_Sm1 The archa 99.6 7E-16 1.5E-20 103.0 7.5 57 19-75 2-67 (68)
17 cd00600 Sm_like The eukaryotic 99.6 8.8E-16 1.9E-20 99.3 6.5 54 22-75 1-63 (63)
18 KOG1783|consensus 99.6 7.1E-16 1.5E-20 106.2 3.1 63 16-78 5-76 (77)
19 COG1958 LSM1 Small nuclear rib 99.6 1.1E-14 2.4E-19 99.7 7.4 59 17-75 7-78 (79)
20 cd01732 LSm5 The eukaryotic Sm 99.5 5.9E-14 1.3E-18 96.6 8.0 58 18-75 4-73 (76)
21 cd01719 Sm_G The eukaryotic Sm 99.5 5.5E-14 1.2E-18 95.6 7.6 59 20-78 3-70 (72)
22 cd01730 LSm3 The eukaryotic Sm 99.4 1.5E-12 3.2E-17 90.2 7.3 57 19-75 3-81 (82)
23 cd01720 Sm_D2 The eukaryotic S 99.4 2.7E-12 5.9E-17 90.6 7.8 57 19-75 4-84 (87)
24 cd01729 LSm7 The eukaryotic Sm 99.4 2.7E-12 5.9E-17 89.0 7.5 57 22-78 7-80 (81)
25 cd01718 Sm_E The eukaryotic Sm 99.3 1.5E-11 3.3E-16 85.6 8.0 60 16-75 6-78 (79)
26 cd01717 Sm_B The eukaryotic Sm 99.3 1.2E-11 2.5E-16 85.0 7.0 55 22-76 5-78 (79)
27 cd01728 LSm1 The eukaryotic Sm 99.2 5.6E-11 1.2E-15 81.5 7.8 59 17-76 3-73 (74)
28 cd01727 LSm8 The eukaryotic Sm 99.2 7.8E-11 1.7E-15 80.0 7.4 58 21-78 3-73 (74)
29 cd06168 LSm9 The eukaryotic Sm 99.1 1.9E-10 4.1E-15 79.1 7.2 56 21-76 4-74 (75)
30 PTZ00138 small nuclear ribonuc 99.1 3.4E-10 7.3E-15 80.5 8.2 66 11-76 9-87 (89)
31 KOG3460|consensus 98.7 1.1E-08 2.3E-13 72.5 2.5 64 17-80 5-90 (91)
32 KOG1780|consensus 98.4 6.1E-07 1.3E-11 62.2 4.6 53 22-74 9-70 (77)
33 KOG1774|consensus 97.9 3E-05 6.5E-10 54.8 5.0 61 16-76 12-85 (88)
34 KOG1775|consensus 97.8 1.2E-05 2.6E-10 56.3 2.7 59 19-78 9-79 (84)
35 PF14438 SM-ATX: Ataxin 2 SM d 97.6 0.00022 4.9E-09 48.1 5.9 40 18-57 3-45 (77)
36 KOG1781|consensus 97.2 0.00014 3.1E-09 53.1 1.6 60 22-81 22-98 (108)
37 KOG1782|consensus 97.0 0.00028 6E-09 53.2 1.0 55 21-76 14-80 (129)
38 KOG3168|consensus 96.7 0.00087 1.9E-08 52.9 1.6 61 23-83 10-89 (177)
39 KOG1784|consensus 96.0 0.017 3.8E-07 41.7 5.0 65 22-87 5-82 (96)
40 PF11095 Gemin7: Gem-associate 95.9 0.071 1.5E-06 37.4 7.6 59 19-77 16-79 (80)
41 PF12701 LSM14: Scd6-like Sm d 95.6 0.093 2E-06 37.7 7.5 55 24-78 5-78 (96)
42 TIGR02383 Hfq RNA chaperone Hf 94.4 0.066 1.4E-06 35.8 3.8 37 21-57 7-45 (61)
43 cd01716 Hfq Hfq, an abundant, 94.4 0.068 1.5E-06 35.7 3.8 37 21-57 3-41 (61)
44 PRK00395 hfq RNA-binding prote 93.5 0.11 2.5E-06 36.4 3.7 60 20-82 10-71 (79)
45 KOG3459|consensus 93.3 0.052 1.1E-06 40.4 1.8 60 15-74 23-105 (114)
46 PF02237 BPL_C: Biotin protein 91.9 0.95 2.1E-05 28.0 6.0 41 26-67 2-48 (48)
47 cd01739 LSm11_C The eukaryotic 91.4 0.34 7.5E-06 33.0 3.8 32 26-57 7-42 (66)
48 COG1923 Hfq Uncharacterized ho 91.3 0.32 7E-06 34.0 3.6 38 19-57 9-48 (77)
49 PF10842 DUF2642: Protein of u 90.6 2.6 5.6E-05 28.5 7.5 54 18-75 12-65 (66)
50 PRK14091 RNA-binding protein H 83.7 1.5 3.4E-05 34.6 3.7 39 19-57 94-134 (165)
51 cd01736 LSm14_N LSm14 (also kn 83.6 4.5 9.7E-05 28.1 5.5 34 24-57 3-37 (74)
52 PRK14638 hypothetical protein; 83.3 2.4 5.1E-05 32.4 4.5 36 19-56 93-128 (150)
53 PRK14091 RNA-binding protein H 82.7 1.8 3.8E-05 34.2 3.6 39 19-57 14-54 (165)
54 PRK14639 hypothetical protein; 82.0 7.8 0.00017 29.2 6.8 34 22-56 83-116 (140)
55 PF11607 DUF3247: Protein of u 81.6 2.9 6.3E-05 30.5 4.1 30 16-45 16-46 (101)
56 PRK02001 hypothetical protein; 78.7 4.2 9.1E-05 31.3 4.5 31 19-50 83-113 (152)
57 PF07073 ROF: Modulator of Rho 78.6 1.9 4E-05 30.1 2.3 23 22-44 12-34 (80)
58 cd01734 YlxS_C YxlS is a Bacil 77.5 5.4 0.00012 27.1 4.3 33 23-56 21-57 (83)
59 PRK14644 hypothetical protein; 74.1 6.5 0.00014 29.7 4.4 34 22-56 80-117 (136)
60 PRK14640 hypothetical protein; 70.8 8.7 0.00019 29.3 4.4 33 23-56 93-129 (152)
61 COG0779 Uncharacterized protei 70.5 12 0.00026 29.0 5.2 35 19-55 92-130 (153)
62 cd01735 LSm12_N LSm12 belongs 70.5 13 0.00028 24.7 4.6 30 25-54 4-33 (61)
63 PRK11625 Rho-binding antitermi 70.2 9.5 0.00021 26.9 4.2 25 23-47 19-43 (84)
64 PRK09618 flgD flagellar basal 69.1 7.9 0.00017 29.8 3.8 26 23-48 88-113 (142)
65 PF06372 Gemin6: Gemin6 protei 67.6 30 0.00064 27.3 6.9 68 21-91 11-82 (166)
66 PRK14642 hypothetical protein; 67.2 10 0.00022 30.6 4.3 61 19-81 93-183 (197)
67 PRK14632 hypothetical protein; 64.5 13 0.00028 29.0 4.3 53 23-76 94-159 (172)
68 PRK14636 hypothetical protein; 64.2 13 0.00029 29.1 4.4 34 22-56 93-130 (176)
69 PRK00092 ribosome maturation p 64.0 14 0.00031 27.9 4.4 29 22-50 93-125 (154)
70 PRK14634 hypothetical protein; 64.0 14 0.0003 28.4 4.3 35 19-55 93-131 (155)
71 PRK14645 hypothetical protein; 63.3 14 0.00031 28.4 4.3 30 19-50 95-124 (154)
72 PRK14633 hypothetical protein; 62.2 16 0.00035 27.8 4.4 33 23-56 90-126 (150)
73 PRK14647 hypothetical protein; 60.0 17 0.00038 27.8 4.3 29 22-50 94-131 (159)
74 TIGR00567 3mg DNA-3-methyladen 59.1 25 0.00054 28.2 5.1 38 15-52 7-44 (192)
75 PRK14643 hypothetical protein; 58.3 19 0.00041 28.0 4.2 36 19-55 97-137 (164)
76 PF02576 DUF150: Uncharacteris 56.0 18 0.00039 26.7 3.7 28 22-49 82-113 (141)
77 PF02245 Pur_DNA_glyco: Methyl 56.0 25 0.00055 27.9 4.7 38 14-52 5-42 (184)
78 PRK14646 hypothetical protein; 55.3 24 0.00051 27.1 4.3 35 19-55 93-131 (155)
79 PRK14637 hypothetical protein; 54.0 25 0.00054 26.9 4.2 36 19-56 91-127 (151)
80 KOG1073|consensus 52.5 28 0.00061 30.6 4.8 56 23-78 5-80 (361)
81 PRK14631 hypothetical protein; 49.2 33 0.00071 26.9 4.3 27 22-48 112-142 (174)
82 PRK11911 flgD flagellar basal 49.2 40 0.00088 25.8 4.7 27 23-49 89-115 (140)
83 smart00333 TUDOR Tudor domain. 47.7 61 0.0013 19.5 4.9 25 26-50 5-29 (57)
84 PF05037 DUF669: Protein of un 47.5 15 0.00033 27.2 2.1 30 14-43 90-120 (141)
85 PRK14641 hypothetical protein; 47.3 32 0.0007 27.0 4.0 27 22-48 99-129 (173)
86 PRK11886 bifunctional biotin-- 46.8 59 0.0013 26.9 5.7 32 25-57 270-301 (319)
87 PRK06955 biotin--protein ligas 44.4 68 0.0015 26.7 5.7 33 25-57 247-279 (300)
88 cd00540 AAG Alkyladenine DNA g 43.1 66 0.0014 25.5 5.2 38 15-53 3-40 (179)
89 PRK14635 hypothetical protein; 42.2 68 0.0015 24.6 5.1 32 23-55 95-131 (162)
90 PRK14630 hypothetical protein; 40.4 52 0.0011 24.9 4.1 30 19-50 90-119 (143)
91 cd06526 metazoan_ACD Alpha-cry 36.2 1.2E+02 0.0027 19.9 5.1 45 29-85 22-67 (83)
92 TIGR00121 birA_ligase birA, bi 34.2 1.1E+02 0.0023 24.4 5.2 32 25-57 191-222 (237)
93 COG2094 Mpg 3-methyladenine DN 33.3 97 0.0021 25.2 4.8 42 10-52 7-48 (200)
94 PRK13325 bifunctional biotin-- 32.1 1.2E+02 0.0026 28.0 5.8 45 25-69 276-325 (592)
95 COG4568 Rof Transcriptional an 30.9 66 0.0014 22.8 3.0 19 26-44 22-40 (84)
96 PRK08330 biotin--protein ligas 30.4 1.6E+02 0.0034 23.4 5.6 33 24-57 185-218 (236)
97 PF00560 LRR_1: Leucine Rich R 30.4 36 0.00079 17.4 1.3 18 61-80 2-19 (22)
98 PRK06792 flgD flagellar basal 29.6 80 0.0017 25.5 3.7 26 24-49 115-140 (190)
99 cd06479 ACD_HspB7_like Alpha c 29.1 1.6E+02 0.0034 20.0 4.7 42 29-85 23-65 (81)
100 TIGR02603 CxxCH_TIGR02603 puta 28.8 80 0.0017 23.0 3.4 20 29-48 59-78 (133)
101 cd05694 S1_Rrp5_repeat_hs2_sc2 28.2 55 0.0012 21.6 2.2 18 33-50 1-18 (74)
102 TIGR00999 8a0102 Membrane Fusi 24.9 1.3E+02 0.0029 23.3 4.2 27 26-52 141-167 (265)
103 PF08169 RBB1NT: RBB1NT (NUC16 24.6 1.4E+02 0.0031 21.5 4.0 42 23-68 5-48 (96)
104 PF13437 HlyD_3: HlyD family s 23.0 1.8E+02 0.0039 19.4 4.1 24 26-49 53-78 (105)
105 PF05954 Phage_GPD: Phage late 22.9 1E+02 0.0023 24.0 3.3 27 22-48 23-49 (292)
106 PRK00802 3-methyladenine DNA g 21.5 1.7E+02 0.0038 23.3 4.3 36 14-53 10-45 (188)
107 PRK06789 flagellar motor switc 21.2 1.8E+02 0.0039 20.0 3.7 34 23-56 37-70 (74)
108 PRK10898 serine endoprotease; 20.8 2E+02 0.0043 24.5 4.8 31 27-57 101-131 (353)
109 PF13861 FLgD_tudor: FlgD Tudo 20.3 1.6E+02 0.0035 18.5 3.2 25 24-48 9-35 (61)
110 PRK02649 ppnK inorganic polyph 20.3 4.5E+02 0.0098 22.2 6.8 68 28-102 232-302 (305)
No 1
>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=99.95 E-value=6.7e-28 Score=166.54 Aligned_cols=69 Identities=42% Similarity=0.749 Sum_probs=66.8
Q ss_pred hhhhcccCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcC
Q psy9158 9 KEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIP 77 (133)
Q Consensus 9 ~Ek~~~~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lP 77 (133)
||+++.+|||+|||++++|+.|+||||||.+|+|+|.+||+|||++|+| ..+++++||||++|+|||||
T Consensus 1 ~e~~~~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 1 KERTLLENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred CccchhhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 6999999999999999999999999999999999999999999999999 35789999999999999999
No 2
>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=99.94 E-value=2.2e-26 Score=162.81 Aligned_cols=77 Identities=22% Similarity=0.415 Sum_probs=71.2
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCCCCCchhHHHH
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPRHVSIVNKVED 88 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~~ 88 (133)
|.+||++++|++|+||||||++|+|+|.+||+||||+|+| ...++++||||++|+||||||++|+++.+.+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~~ 81 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLVD 81 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhhh
Confidence 6799999999999999999999999999999999999999 5678999999999999999999999999988
Q ss_pred HHhcCCC
Q psy9158 89 ALQSKPR 95 (133)
Q Consensus 89 ~l~~~~r 95 (133)
. +..||
T Consensus 82 ~-~~~~~ 87 (90)
T cd01724 82 S-TPKPK 87 (90)
T ss_pred c-CCccc
Confidence 6 33444
No 3
>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=99.89 E-value=2.6e-23 Score=140.42 Aligned_cols=60 Identities=22% Similarity=0.375 Sum_probs=56.8
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCC
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd 78 (133)
..||+++.|+.|+||||||.+|+|+|.+||+|||++|+| ..+++++||||++|+||||||
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 468999999999999999999999999999999999999 457899999999999999997
No 4
>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=99.88 E-value=1.1e-22 Score=141.02 Aligned_cols=62 Identities=31% Similarity=0.559 Sum_probs=57.3
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-----------ccccccEEEecCeeEEEEcCCCC
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-----------ELTFESLFIQSRNVMFIHIPRHV 80 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-----------~~~l~~ifIRGsnIryI~lPd~l 80 (133)
..||++++|+.|+||||||++|+|+|.+||+|||++|+| ...++++||||++|+|||+||++
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhH
Confidence 578999999999999999999999999999999999998 13467899999999999999975
No 5
>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=99.86 E-value=6.2e-22 Score=135.45 Aligned_cols=63 Identities=21% Similarity=0.405 Sum_probs=58.7
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEcCCCC
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHIPRHV 80 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~lPd~l 80 (133)
..+||+++.|++|+||||||.+|+|+|.+||+|||++|+| ...++++||||++|+||++||++
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 4689999999999999999999999999999999999999 24578999999999999999986
No 6
>KOG3172|consensus
Probab=99.80 E-value=3.9e-20 Score=135.53 Aligned_cols=73 Identities=18% Similarity=0.285 Sum_probs=68.9
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCCCCCchhHHHHH
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPRHVSIVNKVEDA 89 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~~~ 89 (133)
.-||++.+|+.|++|+.+|..|+|.|.++|++|||+|.| ...++++|||||.|||+.+||.+..+|+++..
T Consensus 7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnAPmFkk~ 86 (119)
T KOG3172|consen 7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNAPMFKKG 86 (119)
T ss_pred eeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcCcccccc
Confidence 458999999999999999999999999999999999999 78899999999999999999999999999975
Q ss_pred Hh
Q psy9158 90 LQ 91 (133)
Q Consensus 90 l~ 91 (133)
-.
T Consensus 87 ~~ 88 (119)
T KOG3172|consen 87 KS 88 (119)
T ss_pred cC
Confidence 44
No 7
>KOG3428|consensus
Probab=99.78 E-value=3.4e-19 Score=130.22 Aligned_cols=76 Identities=21% Similarity=0.362 Sum_probs=72.0
Q ss_pred CcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec--------ccccccEEEecCeeEEEEcCCCCCchhHHH
Q psy9158 16 NTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR--------ELTFESLFIQSRNVMFIHIPRHVSIVNKVE 87 (133)
Q Consensus 16 nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n--------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~ 87 (133)
++|+.||+.+.+..|+||||||+.++|+|++||-.||..|.+ +.+++.++|||++|||+++||++++++.+.
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~~pv~l~~lsirgnniRy~~lpD~l~ld~Llv 80 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKGEPVRLDTLSIRGNNIRYYILPDSLNLDTLLV 80 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCCCceeEEEEEeecceEEEEEccCCcCcceeee
Confidence 579999999999999999999999999999999999999999 347899999999999999999999999999
Q ss_pred HHHh
Q psy9158 88 DALQ 91 (133)
Q Consensus 88 ~~l~ 91 (133)
++..
T Consensus 81 d~~~ 84 (109)
T KOG3428|consen 81 DDAP 84 (109)
T ss_pred ehhh
Confidence 8776
No 8
>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=99.77 E-value=1.7e-18 Score=115.67 Aligned_cols=57 Identities=28% Similarity=0.535 Sum_probs=53.6
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
..||+++.|++|+|+|+||.+|+|+|.++|+|||+.|+| ...++.+||||++|+||+
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 478999999999999999999999999999999999999 457899999999999984
No 9
>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=99.75 E-value=6.1e-18 Score=113.37 Aligned_cols=58 Identities=24% Similarity=0.391 Sum_probs=54.1
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
...+|+++.|++|+|+|+||.+|+|+|.++|+|||+.|+| ...++.+||||++|+||.
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 4568999999999999999999999999999999999999 468899999999999983
No 10
>KOG3293|consensus
Probab=99.74 E-value=1.9e-18 Score=129.11 Aligned_cols=71 Identities=21% Similarity=0.438 Sum_probs=63.3
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEcCCCCCchhHHHH
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHIPRHVSIVNKVED 88 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~~ 88 (133)
+.||...+|+++.||||||.+|.|.|.+||.|||++|.+ .+.++++||||++|+|+.|||.| ....++
T Consensus 4 LsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~i--id~vke 81 (134)
T KOG3293|consen 4 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEI--IDKVKE 81 (134)
T ss_pred hhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHH--HHHHHH
Confidence 579999999999999999999999999999999999999 68889999999999999999965 444444
Q ss_pred HHh
Q psy9158 89 ALQ 91 (133)
Q Consensus 89 ~l~ 91 (133)
+..
T Consensus 82 e~~ 84 (134)
T KOG3293|consen 82 ECV 84 (134)
T ss_pred HHH
Confidence 444
No 11
>KOG3448|consensus
Probab=99.71 E-value=2.4e-17 Score=117.20 Aligned_cols=71 Identities=30% Similarity=0.533 Sum_probs=62.9
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-----------ccccccEEEecCeeEEEEcCCCCCchhHHH
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-----------ELTFESLFIQSRNVMFIHIPRHVSIVNKVE 87 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-----------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~ 87 (133)
-.|++++.|+.|+||||||.++.|+|.+||.|+|+.|.| -.....+||||+.||||++|.+-...+.+.
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtqll~ 83 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQLLQ 83 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHHHH
Confidence 479999999999999999999999999999999999999 244678999999999999999876666665
Q ss_pred HH
Q psy9158 88 DA 89 (133)
Q Consensus 88 ~~ 89 (133)
++
T Consensus 84 da 85 (96)
T KOG3448|consen 84 DA 85 (96)
T ss_pred HH
Confidence 54
No 12
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.69 E-value=1.2e-16 Score=105.04 Aligned_cols=57 Identities=28% Similarity=0.519 Sum_probs=52.7
Q ss_pred HHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEc
Q psy9158 20 CLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 20 ~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~l 76 (133)
.+|+.+.|++|+|+|+||.+|+|+|.++|+|||+.|+| ...++.+||||++|+||++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 37899999999999999999999999999999999999 3457899999999999985
No 13
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.68 E-value=1.2e-16 Score=104.91 Aligned_cols=56 Identities=29% Similarity=0.548 Sum_probs=52.4
Q ss_pred HHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEc
Q psy9158 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 21 lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~l 76 (133)
+|+++.|+.|+|+|+||.++.|+|.++|.|||+.|+| ...++.+||||++|+||+.
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 6889999999999999999999999999999999999 3478999999999999974
No 14
>KOG3482|consensus
Probab=99.67 E-value=1.2e-16 Score=110.16 Aligned_cols=58 Identities=24% Similarity=0.403 Sum_probs=55.2
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
...||+.+.|++|.|.||+|.+|+|+|+++|+|||+.|.+ ..++++++||++||.||.
T Consensus 9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEe
Confidence 4679999999999999999999999999999999999999 688999999999999994
No 15
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.67 E-value=2.4e-16 Score=106.78 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=54.4
Q ss_pred cHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 17 sL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
....+|+.+.|++|+|+|+||..|.|+|.++|+|||++|+| ...++.+||||++|.||.
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEc
Confidence 45678999999999999999999999999999999999999 347899999999999985
No 16
>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=99.64 E-value=7e-16 Score=103.00 Aligned_cols=57 Identities=26% Similarity=0.398 Sum_probs=52.8
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
..+|+.+.|++|+|+|+||..|.|+|.++|.|||+.|+| ...++.+||||++|.||.
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEc
Confidence 457888999999999999999999999999999999999 357899999999999985
No 17
>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=99.63 E-value=8.8e-16 Score=99.32 Aligned_cols=54 Identities=26% Similarity=0.449 Sum_probs=50.0
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEE
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~ 75 (133)
|+++.|++|+|+|+||..|.|+|.++|+|||+.|+| ...++.+||||++|+||+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 457789999999999999999999999999999999 366999999999999985
No 18
>KOG1783|consensus
Probab=99.59 E-value=7.1e-16 Score=106.20 Aligned_cols=63 Identities=25% Similarity=0.484 Sum_probs=59.0
Q ss_pred CcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCC
Q psy9158 16 NTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 16 nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd 78 (133)
.+...|+.+..|++|.|+|.+|..|+|+|.+.|+|||+.|+. ..+++..||||++|.||+..+
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence 567899999999999999999999999999999999999998 788999999999999998754
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.56 E-value=1.1e-14 Score=99.72 Aligned_cols=59 Identities=22% Similarity=0.348 Sum_probs=52.5
Q ss_pred cHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---c---------cccc-cEEEecCeeEEEE
Q psy9158 17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---E---------LTFE-SLFIQSRNVMFIH 75 (133)
Q Consensus 17 sL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---~---------~~l~-~ifIRGsnIryI~ 75 (133)
....+|+.+.|++|.|+|+||..|+|+|.++|.|||+.|+| . ..++ .+||||++|.||.
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEe
Confidence 45788999999999999999999999999999999999999 1 1234 9999999999996
No 20
>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=99.52 E-value=5.9e-14 Score=96.60 Aligned_cols=58 Identities=12% Similarity=0.305 Sum_probs=53.5
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec------------ccccccEEEecCeeEEEE
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------------~~~l~~ifIRGsnIryI~ 75 (133)
...+|+.+.|++|.|+|+||..|.|+|.++|.|||+.|+| ...++.++|||++|.+|+
T Consensus 4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 3578888999999999999999999999999999999999 246899999999999997
No 21
>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=99.52 E-value=5.5e-14 Score=95.62 Aligned_cols=59 Identities=19% Similarity=0.285 Sum_probs=53.4
Q ss_pred HHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCC
Q psy9158 20 CLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 20 ~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd 78 (133)
.+|.++.|++|.|+|+||..|.|+|.++|.|||+.|+| ...++.++|||++|.+|..=|
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~ 70 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALE 70 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEccc
Confidence 46788899999999999999999999999999999999 357899999999999997543
No 22
>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=99.38 E-value=1.5e-12 Score=90.16 Aligned_cols=57 Identities=21% Similarity=0.389 Sum_probs=51.5
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------------------ccccccEEEecCeeEEEE
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------------------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------------------~~~l~~ifIRGsnIryI~ 75 (133)
..||+...|++|.|.|+||..|.|+|.++|.|||+.|+| ...++.+||||++|.+|+
T Consensus 3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred hHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 468888899999999999999999999999999999998 115689999999999985
No 23
>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=99.37 E-value=2.7e-12 Score=90.60 Aligned_cols=57 Identities=18% Similarity=0.338 Sum_probs=49.3
Q ss_pred HHHHHhc--CCCeEEEEecCCcEEEEEEEEeccccceEEec------c-c---------------ccccEEEecCeeEEE
Q psy9158 19 ACLAKSL--VGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------E-L---------------TFESLFIQSRNVMFI 74 (133)
Q Consensus 19 ~~lL~~l--~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------~-~---------------~l~~ifIRGsnIryI 74 (133)
..+|+.. .|++|.|.|++|..|.|+|.++|.|||+.|+| . . .++.+||||++|.||
T Consensus 4 l~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~I 83 (87)
T cd01720 4 LSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILV 83 (87)
T ss_pred HHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEE
Confidence 3455555 49999999999999999999999999999999 1 1 479999999999998
Q ss_pred E
Q psy9158 75 H 75 (133)
Q Consensus 75 ~ 75 (133)
+
T Consensus 84 s 84 (87)
T cd01720 84 L 84 (87)
T ss_pred e
Confidence 5
No 24
>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=99.36 E-value=2.7e-12 Score=89.03 Aligned_cols=57 Identities=16% Similarity=0.242 Sum_probs=50.8
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec------c-----------cccccEEEecCeeEEEEcCC
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------E-----------LTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------~-----------~~l~~ifIRGsnIryI~lPd 78 (133)
|..+.|++|.|.|++|..|.|+|.++|.|||+.|++ . ..++.++|||+||.+|.-.|
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 566789999999999999999999999999999999 1 34799999999999997543
No 25
>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=99.29 E-value=1.5e-11 Score=85.59 Aligned_cols=60 Identities=13% Similarity=0.282 Sum_probs=49.9
Q ss_pred CcHHHHHHhcCCC-eEEEEec--CCcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEE
Q psy9158 16 NTLACLAKSLVGM-ITCVDLR--NESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 16 nsL~~lL~~l~G~-~VtVELK--Ng~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~ 75 (133)
.++..+.+-+..+ +|+|.|+ +|..+.|+|.++|.|||+.|+| ...+|.++|||+||.+|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 4455555555444 8999998 8999999999999999999999 246789999999999987
No 26
>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=99.28 E-value=1.2e-11 Score=84.95 Aligned_cols=55 Identities=18% Similarity=0.324 Sum_probs=50.0
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-------c------------cccccEEEecCeeEEEEc
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-------E------------LTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-------~------------~~l~~ifIRGsnIryI~l 76 (133)
|..+.|++|.|.|++|..+.|+|.++|.|||+.|+| . ..++.+||||++|.+|.+
T Consensus 5 l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 5 MLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 566789999999999999999999999999999999 0 357999999999999975
No 27
>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=99.22 E-value=5.6e-11 Score=81.48 Aligned_cols=59 Identities=20% Similarity=0.266 Sum_probs=50.0
Q ss_pred cHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec------------ccccccEEEecCeeEEEEc
Q psy9158 17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 17 sL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------------~~~l~~ifIRGsnIryI~l 76 (133)
++.+ |.+..+++|.|.|++|..|.|+|.++|.|||+.|+| ...++.++|||++|.+|..
T Consensus 3 ~~~~-L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTAS-LVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHH-HHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 3444 455679999999999999999999999999999999 1235789999999999853
No 28
>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=99.20 E-value=7.8e-11 Score=80.04 Aligned_cols=58 Identities=12% Similarity=0.173 Sum_probs=50.9
Q ss_pred HHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-------------ccccccEEEecCeeEEEEcCC
Q psy9158 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-------------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 21 lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-------------~~~l~~ifIRGsnIryI~lPd 78 (133)
-|....|++|.|.|++|..|.|+|.++|.|||+.|++ ...++.++|||++|.+|..-|
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 3566789999999999999999999999999999999 234799999999999997533
No 29
>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=99.14 E-value=1.9e-10 Score=79.07 Aligned_cols=56 Identities=16% Similarity=0.267 Sum_probs=51.0
Q ss_pred HHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------------ccccccEEEecCeeEEEEc
Q psy9158 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 21 lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------------~~~l~~ifIRGsnIryI~l 76 (133)
-|.++.|++|.|.|+||..+.|+|.++|.+||+.|+| ...+|.++|||++|..|++
T Consensus 4 ~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 4 KLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 4667789999999999999999999999999999999 2368999999999999975
No 30
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.12 E-value=3.4e-10 Score=80.49 Aligned_cols=66 Identities=12% Similarity=0.238 Sum_probs=53.2
Q ss_pred hhcccCcHHHHHHhcCCC-eEEEEecCC--cEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEc
Q psy9158 11 QFLSFNTLACLAKSLVGM-ITCVDLRNE--SSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 11 k~~~~nsL~~lL~~l~G~-~VtVELKNg--~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~l 76 (133)
+.....++.+++.-++.+ .|.|-|.++ ..+.|+|.++|.|||++|+| ...++.++|||+||.+|+-
T Consensus 9 ~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 9 QKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred ceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 334456667777666554 688888774 78999999999999999999 2478999999999999964
No 31
>KOG3460|consensus
Probab=98.68 E-value=1.1e-08 Score=72.48 Aligned_cols=64 Identities=22% Similarity=0.366 Sum_probs=57.0
Q ss_pred cHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec----------------------ccccccEEEecCeeEEE
Q psy9158 17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------------------ELTFESLFIQSRNVMFI 74 (133)
Q Consensus 17 sL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------------------~~~l~~ifIRGsnIryI 74 (133)
...||++---...|-|+|++|..++|+|..+|.|+|+.|.| ...++.+||||.+|.+|
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv 84 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV 84 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence 45788888889999999999999999999999999999977 46678999999999999
Q ss_pred EcCCCC
Q psy9158 75 HIPRHV 80 (133)
Q Consensus 75 ~lPd~l 80 (133)
+-|-..
T Consensus 85 spp~~~ 90 (91)
T KOG3460|consen 85 SPPLRL 90 (91)
T ss_pred cCcccC
Confidence 877543
No 32
>KOG1780|consensus
Probab=98.37 E-value=6.1e-07 Score=62.22 Aligned_cols=53 Identities=21% Similarity=0.363 Sum_probs=47.3
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEE
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFI 74 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI 74 (133)
|+..-.+.+.+.|..|-.+.|+|..+|.|||++|++ ....+.++|||+.|--+
T Consensus 9 LkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~ 70 (77)
T KOG1780|consen 9 LKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMV 70 (77)
T ss_pred HHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEE
Confidence 455567899999999999999999999999999999 56788999999998765
No 33
>KOG1774|consensus
Probab=97.87 E-value=3e-05 Score=54.83 Aligned_cols=61 Identities=15% Similarity=0.281 Sum_probs=50.1
Q ss_pred CcHHHHHHhcCCC-eEEEEecC--CcEEEEEEEEeccccceEEec----------ccccccEEEecCeeEEEEc
Q psy9158 16 NTLACLAKSLVGM-ITCVDLRN--ESSVSGRLEHVDGFMNIYMSR----------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 16 nsL~~lL~~l~G~-~VtVELKN--g~~~~G~L~~vD~~MNl~L~n----------~~~l~~ifIRGsnIryI~l 76 (133)
-++.+.+.=|+++ +|.|=|.. |..+.|.+..+|.|||++|++ ...++.+.++|.||-.|+-
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 3455666666554 79999987 678999999999999999998 4489999999999988863
No 34
>KOG1775|consensus
Probab=97.84 E-value=1.2e-05 Score=56.28 Aligned_cols=59 Identities=15% Similarity=0.397 Sum_probs=52.8
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec------------ccccccEEEecCeeEEEEcCC
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------------~~~l~~ifIRGsnIryI~lPd 78 (133)
..++....|.+|-|-+|++.++.|+|..+|+|.|+.|+| ..+++++.+-||||-.. +|-
T Consensus 9 lEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mL-vPG 79 (84)
T KOG1775|consen 9 LELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITML-VPG 79 (84)
T ss_pred HHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEE-ecC
Confidence 467778899999999999999999999999999999999 57889999999999754 553
No 35
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.59 E-value=0.00022 Score=48.12 Aligned_cols=40 Identities=23% Similarity=0.280 Sum_probs=33.2
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEecc---ccceEEec
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDG---FMNIYMSR 57 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~---~MNl~L~n 57 (133)
|..++.++.|+.|+|.++||..|.|++.+++. -+.+.|+.
T Consensus 3 l~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~ 45 (77)
T PF14438_consen 3 LVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKM 45 (77)
T ss_dssp -HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEE
T ss_pred HHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEe
Confidence 56788999999999999999999999999999 89999988
No 36
>KOG1781|consensus
Probab=97.25 E-value=0.00014 Score=53.06 Aligned_cols=60 Identities=12% Similarity=0.166 Sum_probs=52.8
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-----------------ccccccEEEecCeeEEEEcCCCCC
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-----------------ELTFESLFIQSRNVMFIHIPRHVS 81 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-----------------~~~l~~ifIRGsnIryI~lPd~ld 81 (133)
|.....+.|.|.+-.|..+.|+|..+|..||++|++ .++++-+.+||..+..|+-.|-.+
T Consensus 22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 344568999999999999999999999999999998 588999999999999987666554
No 37
>KOG1782|consensus
Probab=96.97 E-value=0.00028 Score=53.22 Aligned_cols=55 Identities=24% Similarity=0.336 Sum_probs=46.3
Q ss_pred HHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec------------ccccccEEEecCeeEEEEc
Q psy9158 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------------ELTFESLFIQSRNVMFIHI 76 (133)
Q Consensus 21 lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------------~~~l~~ifIRGsnIryI~l 76 (133)
++..+ .+.+.|=|++|...-|.|-|+|.|=|+.|.+ ....+-+.|||-||..+-.
T Consensus 14 l~~~~-dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYL-DKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHh-cceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEec
Confidence 33334 6789999999999999999999999999998 3445788999999988754
No 38
>KOG3168|consensus
Probab=96.65 E-value=0.00087 Score=52.92 Aligned_cols=61 Identities=11% Similarity=0.225 Sum_probs=51.3
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-------------------ccccccEEEecCeeEEEEcCCCCCch
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-------------------ELTFESLFIQSRNVMFIHIPRHVSIV 83 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-------------------~~~l~~ifIRGsnIryI~lPd~ld~~ 83 (133)
-.+.++.+.|-+.+|.++-|.+..+|.|||+.|.+ ..-|+-+.+||.||.-...-+-.-.+
T Consensus 10 l~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s 89 (177)
T KOG3168|consen 10 LQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPS 89 (177)
T ss_pred HHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCc
Confidence 34568999999999999999999999999999988 45578899999999988775544333
No 39
>KOG1784|consensus
Probab=95.97 E-value=0.017 Score=41.65 Aligned_cols=65 Identities=14% Similarity=0.226 Sum_probs=52.0
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec-------------ccccccEEEecCeeEEEEcCCCCCchhHHH
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-------------ELTFESLFIQSRNVMFIHIPRHVSIVNKVE 87 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-------------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~ 87 (133)
|....++.|.|-..+|..+-|.|..+|..-|+.+++ ..-++-..|||.||-.|-.-|+ ..++.|+
T Consensus 5 L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDE-e~d~~ld 82 (96)
T KOG1784|consen 5 LEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDE-ELDSRLD 82 (96)
T ss_pred HHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecch-hhhhhhh
Confidence 445568999999999999999999999999999999 4557788999999988765443 2344443
No 40
>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=95.87 E-value=0.071 Score=37.43 Aligned_cols=59 Identities=19% Similarity=0.158 Sum_probs=48.8
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEecccc-ceEEec----ccccccEEEecCeeEEEEcC
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFM-NIYMSR----ELTFESLFIQSRNVMFIHIP 77 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~M-Nl~L~n----~~~l~~ifIRGsnIryI~lP 77 (133)
+.++..+.|++|.+.|+.++.+.|+...+|..- |+..++ ....++..+|++-|-.+++.
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLGVQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTTEEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcccChhheeecCCEEEEEec
Confidence 345778899999999999999999999999775 898888 55668899999999888764
No 41
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.59 E-value=0.093 Score=37.74 Aligned_cols=55 Identities=9% Similarity=0.198 Sum_probs=47.6
Q ss_pred hcCCCeEEEEecCCcEEEEEEEEecc-ccceEEec------------------ccccccEEEecCeeEEEEcCC
Q psy9158 24 SLVGMITCVDLRNESSVSGRLEHVDG-FMNIYMSR------------------ELTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 24 ~l~G~~VtVELKNg~~~~G~L~~vD~-~MNl~L~n------------------~~~l~~ifIRGsnIryI~lPd 78 (133)
...|..|.+..+++..|.|+|.++|. .=++.|.| ..-++.+..||+-|.-+++=+
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e 78 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIE 78 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEc
Confidence 46799999999999999999999998 66899999 124788999999999988744
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=94.42 E-value=0.066 Score=35.82 Aligned_cols=37 Identities=24% Similarity=0.301 Sum_probs=29.3
Q ss_pred HHHhc--CCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 21 LAKSL--VGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 21 lL~~l--~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
||..+ .+.+|+|-|.||..+.|.+.++|.|+=+.-.+
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 44444 36789999999999999999999998554443
No 43
>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=94.39 E-value=0.068 Score=35.71 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=29.2
Q ss_pred HHHhc--CCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 21 LAKSL--VGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 21 lL~~l--~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
||..+ .+.+|+|-|.||..++|.+.++|.|+=+.-.+
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 44444 35689999999999999999999998554443
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=93.52 E-value=0.11 Score=36.37 Aligned_cols=60 Identities=18% Similarity=0.266 Sum_probs=40.9
Q ss_pred HHHHhc--CCCeEEEEecCCcEEEEEEEEeccccceEEecccccccEEEecCeeEEEEcCCCCCc
Q psy9158 20 CLAKSL--VGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSI 82 (133)
Q Consensus 20 ~lL~~l--~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRGsnIryI~lPd~ld~ 82 (133)
.||..+ .+.+|+|-|.||..++|.+.++|.|.=+...+. ..-+|-=.-|-.|.-...+++
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g---kqqLIYKHAISTI~p~~~i~~ 71 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG---KSQLVYKHAISTVVPARPVSL 71 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC---cEEEEEEeeeEEEecCCcccc
Confidence 444444 367899999999999999999999986555442 122555556666654444443
No 45
>KOG3459|consensus
Probab=93.34 E-value=0.052 Score=40.36 Aligned_cols=60 Identities=18% Similarity=0.382 Sum_probs=49.0
Q ss_pred cCcHHHHHHhcC-CCeEEEEecCCcEEEEEEEEeccccceEEec----------------------ccccccEEEecCee
Q psy9158 15 FNTLACLAKSLV-GMITCVDLRNESSVSGRLEHVDGFMNIYMSR----------------------ELTFESLFIQSRNV 71 (133)
Q Consensus 15 ~nsL~~lL~~l~-G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n----------------------~~~l~~ifIRGsnI 71 (133)
...|..+-++.. ...|.|-++|...+-|.+...|.|-|+.|+| ....+..||||..|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 356666666665 4589999999999999999999999999999 23467899999886
Q ss_pred EEE
Q psy9158 72 MFI 74 (133)
Q Consensus 72 ryI 74 (133)
-.+
T Consensus 103 I~v 105 (114)
T KOG3459|consen 103 ILV 105 (114)
T ss_pred EEE
Confidence 555
No 46
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=91.94 E-value=0.95 Score=27.98 Aligned_cols=41 Identities=12% Similarity=0.225 Sum_probs=32.2
Q ss_pred CCCeEEEEecCCcEEEEEEEEeccccceEEec------ccccccEEEe
Q psy9158 26 VGMITCVDLRNESSVSGRLEHVDGFMNIYMSR------ELTFESLFIQ 67 (133)
Q Consensus 26 ~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n------~~~l~~ifIR 67 (133)
.|+.|+|++ ++..+.|+...+|+.=.+.++. ...-+++++|
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~~~~i~sGdv~~r 48 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGSIRTISSGDVSLR 48 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEEEEEESSSEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCCEEEEEEEEEEeC
Confidence 489999999 6677799999999999998877 3334555544
No 47
>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=91.44 E-value=0.34 Score=32.97 Aligned_cols=32 Identities=25% Similarity=0.289 Sum_probs=25.5
Q ss_pred CCCeEEEEecC--C--cEEEEEEEEeccccceEEec
Q psy9158 26 VGMITCVDLRN--E--SSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 26 ~G~~VtVELKN--g--~~~~G~L~~vD~~MNl~L~n 57 (133)
.+..|.|-++. | -.+.|.|..+|.|||+.|.|
T Consensus 7 er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~D 42 (66)
T cd01739 7 ERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVD 42 (66)
T ss_pred CCcEEEEEEecccCcccEEEEEEEeeeeehhheehh
Confidence 45667766665 3 35789999999999999999
No 48
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.28 E-value=0.32 Score=34.01 Aligned_cols=38 Identities=18% Similarity=0.317 Sum_probs=30.1
Q ss_pred HHHHHhc--CCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 19 ACLAKSL--VGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 19 ~~lL~~l--~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
..||.++ .+.+|+|-|-||...+|.+.++|.|- +.|++
T Consensus 9 D~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 9 DPFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred hHHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 4556655 47799999999999999999999884 44444
No 49
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=90.63 E-value=2.6 Score=28.52 Aligned_cols=54 Identities=20% Similarity=0.266 Sum_probs=39.6
Q ss_pred HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEecccccccEEEecCeeEEEE
Q psy9158 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIH 75 (133)
Q Consensus 18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRGsnIryI~ 75 (133)
+...|+++.|+.|+|+.--|+. +|+|.+|... .+.|+.. -..+|||=..|-+|.
T Consensus 12 vyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~--~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN--GTPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--CcEEEEEeeeEEEEc
Confidence 3567899999999999966655 9999998643 1233322 356789988888873
No 50
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=83.67 E-value=1.5 Score=34.56 Aligned_cols=39 Identities=15% Similarity=0.158 Sum_probs=31.3
Q ss_pred HHHHHhcC--CCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 19 ACLAKSLV--GMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 19 ~~lL~~l~--G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
..||..+. +.+|+|-|.||..++|.+.++|.|.=+...+
T Consensus 94 d~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 94 DVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 55666664 5689999999999999999999997555444
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=83.56 E-value=4.5 Score=28.07 Aligned_cols=34 Identities=12% Similarity=0.133 Sum_probs=28.9
Q ss_pred hcCCCeEEEEecCCcEEEEEEEEecccc-ceEEec
Q psy9158 24 SLVGMITCVDLRNESSVSGRLEHVDGFM-NIYMSR 57 (133)
Q Consensus 24 ~l~G~~VtVELKNg~~~~G~L~~vD~~M-Nl~L~n 57 (133)
...|+.+.+--+++..|.|+|.++|..= .+.|.|
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~n 37 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKN 37 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeee
Confidence 4679999999999999999999998754 456766
No 52
>PRK14638 hypothetical protein; Provisional
Probab=83.28 E-value=2.4 Score=32.44 Aligned_cols=36 Identities=17% Similarity=0.223 Sum_probs=28.6
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEe
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~ 56 (133)
..|. ...|+.|.|.++++..+.|+|.++|+. ++.+.
T Consensus 93 ~~f~-r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYV-RFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHH-HhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3444 467999999999999999999999975 34443
No 53
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=82.74 E-value=1.8 Score=34.25 Aligned_cols=39 Identities=15% Similarity=0.126 Sum_probs=30.8
Q ss_pred HHHHHhcC--CCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 19 ACLAKSLV--GMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 19 ~~lL~~l~--G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
..||..+. ..+|+|-|.||..++|.+.++|.|.=+...+
T Consensus 14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 45666664 5589999999999999999999997554444
No 54
>PRK14639 hypothetical protein; Provisional
Probab=81.98 E-value=7.8 Score=29.25 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=28.5
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEeccccceEEe
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~ 56 (133)
++...|+.|.|.|.++..+.|+|.++|+. ++.|.
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 45577999999999999999999999984 55553
No 55
>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=81.59 E-value=2.9 Score=30.52 Aligned_cols=30 Identities=23% Similarity=0.303 Sum_probs=24.0
Q ss_pred CcHHHHHHhcCCC-eEEEEecCCcEEEEEEE
Q psy9158 16 NTLACLAKSLVGM-ITCVDLRNESSVSGRLE 45 (133)
Q Consensus 16 nsL~~lL~~l~G~-~VtVELKNg~~~~G~L~ 45 (133)
.+|-.|+..|-|. .|.++|++|+.+.|++.
T Consensus 16 a~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 16 ARLEHLVSELDGEERVELELDDGSMLRGTVA 46 (101)
T ss_dssp HHHHHHHHCTTTT-EEEEEETTS-EEEEEEC
T ss_pred HHHHHHHhhcCCcceEEEEEcCCCeeeeeec
Confidence 3567777778776 79999999999999974
No 56
>PRK02001 hypothetical protein; Validated
Probab=78.70 E-value=4.2 Score=31.31 Aligned_cols=31 Identities=19% Similarity=0.162 Sum_probs=26.3
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccc
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGF 50 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~ 50 (133)
..|- ...|+.|.|.|.++..+.|+|.++|+.
T Consensus 83 ~~f~-r~~G~~v~V~l~~~~~~~G~L~~~~~~ 113 (152)
T PRK02001 83 RQYK-KNIGRELEVLTKNGKKIEGELKSADEN 113 (152)
T ss_pred HHHH-HhCCCEEEEEECCCCEEEEEEEEEeCC
Confidence 3444 456999999999999999999999985
No 57
>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=78.62 E-value=1.9 Score=30.07 Aligned_cols=23 Identities=9% Similarity=0.229 Sum_probs=16.2
Q ss_pred HHhcCCCeEEEEecCCcEEEEEE
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRL 44 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L 44 (133)
+..+.+.+|.++|+||..+.|+-
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~A 34 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGKA 34 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEESS
T ss_pred HHHhcCCeEEEEEeCCCEEEEEE
Confidence 45678899999999999999983
No 58
>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=77.49 E-value=5.4 Score=27.14 Aligned_cols=33 Identities=24% Similarity=0.295 Sum_probs=25.6
Q ss_pred HhcCCCeEEEEec---CC-cEEEEEEEEeccccceEEe
Q psy9158 23 KSLVGMITCVDLR---NE-SSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 23 ~~l~G~~VtVELK---Ng-~~~~G~L~~vD~~MNl~L~ 56 (133)
....|+.|.|.++ +| ..+.|.|.++|+. ++.|.
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l~ 57 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTLE 57 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEEE
Confidence 4567999999998 56 5799999999885 44443
No 59
>PRK14644 hypothetical protein; Provisional
Probab=74.13 E-value=6.5 Score=29.66 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=27.5
Q ss_pred HHhcCCCeEEEEecCC----cEEEEEEEEeccccceEEe
Q psy9158 22 AKSLVGMITCVDLRNE----SSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 22 L~~l~G~~VtVELKNg----~~~~G~L~~vD~~MNl~L~ 56 (133)
+....|+.|.|.|++. ..+.|.|.++|+. ++.|.
T Consensus 80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 4456799999999987 8899999999985 45553
No 60
>PRK14640 hypothetical protein; Provisional
Probab=70.76 E-value=8.7 Score=29.28 Aligned_cols=33 Identities=27% Similarity=0.396 Sum_probs=26.0
Q ss_pred HhcCCCeEEEEe----cCCcEEEEEEEEeccccceEEe
Q psy9158 23 KSLVGMITCVDL----RNESSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 23 ~~l~G~~VtVEL----KNg~~~~G~L~~vD~~MNl~L~ 56 (133)
....|+.|.|.| .+...+.|+|.++|+. ++.|.
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 446699999999 4668999999999985 34443
No 61
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.51 E-value=12 Score=28.97 Aligned_cols=35 Identities=23% Similarity=0.391 Sum_probs=28.4
Q ss_pred HHHHHhcCCCeEEEEe----cCCcEEEEEEEEeccccceEE
Q psy9158 19 ACLAKSLVGMITCVDL----RNESSVSGRLEHVDGFMNIYM 55 (133)
Q Consensus 19 ~~lL~~l~G~~VtVEL----KNg~~~~G~L~~vD~~MNl~L 55 (133)
..|- ...|+.|.|.| .+...+.|+|..+|+.. +++
T Consensus 92 ~~f~-r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 92 EHFA-RFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHH-HhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 4444 46699999999 78899999999999987 444
No 62
>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=70.48 E-value=13 Score=24.72 Aligned_cols=30 Identities=17% Similarity=0.096 Sum_probs=27.2
Q ss_pred cCCCeEEEEecCCcEEEEEEEEeccccceE
Q psy9158 25 LVGMITCVDLRNESSVSGRLEHVDGFMNIY 54 (133)
Q Consensus 25 l~G~~VtVELKNg~~~~G~L~~vD~~MNl~ 54 (133)
..|..|.+...+|..++|.+..+|..-++.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~l 33 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKML 33 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEE
Confidence 369999999999999999999999987765
No 63
>PRK11625 Rho-binding antiterminator; Provisional
Probab=70.20 E-value=9.5 Score=26.86 Aligned_cols=25 Identities=4% Similarity=0.220 Sum_probs=20.7
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEe
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHV 47 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~v 47 (133)
..+.+.+|.++|+||..+.|+....
T Consensus 19 AC~~~~~l~l~l~dGe~~~g~A~D~ 43 (84)
T PRK11625 19 ACQHHLMLTLELKDGEVLQAKASDL 43 (84)
T ss_pred HHhcCCeEEEEECCCCEEEEEEEee
Confidence 3447899999999999999998543
No 64
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=69.08 E-value=7.9 Score=29.77 Aligned_cols=26 Identities=23% Similarity=0.261 Sum_probs=24.1
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEec
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHVD 48 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~vD 48 (133)
.++.|+.|+++.-+|..+.|++.+|.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 47899999999999999999999996
No 65
>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=67.61 E-value=30 Score=27.25 Aligned_cols=68 Identities=18% Similarity=0.146 Sum_probs=46.8
Q ss_pred HHHhcCCCeEEEEecCCcEEEEEEEEecccc-ceEEec---ccccccEEEecCeeEEEEcCCCCCchhHHHHHHh
Q psy9158 21 LAKSLVGMITCVDLRNESSVSGRLEHVDGFM-NIYMSR---ELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQ 91 (133)
Q Consensus 21 lL~~l~G~~VtVELKNg~~~~G~L~~vD~~M-Nl~L~n---~~~l~~ifIRGsnIryI~lPd~ld~~~~l~~~l~ 91 (133)
.+..+.|+.|.|.+.| .++.|.|-.+|.-= |+.|-+ .....--+|-|..|+.|-+=++- +....+.+.
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~~~~sv~~I~ghaVk~vevl~~~--~~~~~e~l~ 82 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQEDGKRSVKVIMGHAVKSVEVLSEG--DQEVPEKLQ 82 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TTS-EEEEEE-GGGEEEEEEEE-----HHHHHHHH
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccCCceeEEEEEccceEEEEEccCC--chhhHHHHH
Confidence 3456889999999999 99999999999865 788877 22334568999999999886643 344445564
No 66
>PRK14642 hypothetical protein; Provisional
Probab=67.23 E-value=10 Score=30.55 Aligned_cols=61 Identities=15% Similarity=0.207 Sum_probs=43.2
Q ss_pred HHHHHhcCCCeEEEEec-------------CCcEEEEEEEEeccccceEEe--cc---------------cccccEEEec
Q psy9158 19 ACLAKSLVGMITCVDLR-------------NESSVSGRLEHVDGFMNIYMS--RE---------------LTFESLFIQS 68 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELK-------------Ng~~~~G~L~~vD~~MNl~L~--n~---------------~~l~~ifIRG 68 (133)
..|.+ ..|+.|.|.|+ +...++|+|.++|+. +++|. +. .-...+-+-=
T Consensus 93 ~df~r-fiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~k~g~~~~k~~~~~~~~~~~~~~ 170 (197)
T PRK14642 93 QDFER-FAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPVKPGQRVSKKRVPAPLQALGFTL 170 (197)
T ss_pred HHHHH-hCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccCCCccccccccccccceeEEeeh
Confidence 44444 56999999999 778999999999885 66563 20 1123466667
Q ss_pred CeeEEEEcCCCCC
Q psy9158 69 RNVMFIHIPRHVS 81 (133)
Q Consensus 69 snIryI~lPd~ld 81 (133)
+.|++.++-..+|
T Consensus 171 ~eik~a~l~p~~~ 183 (197)
T PRK14642 171 DELREARLAPIVD 183 (197)
T ss_pred hheeeEEEEEEEe
Confidence 7788888776665
No 67
>PRK14632 hypothetical protein; Provisional
Probab=64.51 E-value=13 Score=29.04 Aligned_cols=53 Identities=19% Similarity=0.151 Sum_probs=35.3
Q ss_pred HhcCCCeEEEEecC-------CcEEEEEEEEeccccceEEeccc------ccccEEEecCeeEEEEc
Q psy9158 23 KSLVGMITCVDLRN-------ESSVSGRLEHVDGFMNIYMSREL------TFESLFIQSRNVMFIHI 76 (133)
Q Consensus 23 ~~l~G~~VtVELKN-------g~~~~G~L~~vD~~MNl~L~n~~------~l~~ifIRGsnIryI~l 76 (133)
....|+.|.|.|++ ...+.|+|.++|+. ++.|.... .-+.+-|-=+.|..+.+
T Consensus 94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~~~~~~~~~~~~~~~~i~~~~I~ka~l 159 (172)
T PRK14632 94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLRPEGAPAPEAEEAVLRTSWQGVRKANL 159 (172)
T ss_pred HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEEEcCcccccCCceeEEEEhHHccEEEE
Confidence 45679999999986 46899999999974 45554311 11245555566665554
No 68
>PRK14636 hypothetical protein; Provisional
Probab=64.24 E-value=13 Score=29.15 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=26.3
Q ss_pred HHhcCCCeEEEEec---CC-cEEEEEEEEeccccceEEe
Q psy9158 22 AKSLVGMITCVDLR---NE-SSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 22 L~~l~G~~VtVELK---Ng-~~~~G~L~~vD~~MNl~L~ 56 (133)
+....|+.|.|.|+ +| ..+.|+|.++|+. ++.|.
T Consensus 93 f~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l~ 130 (176)
T PRK14636 93 FADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTIA 130 (176)
T ss_pred HHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEEE
Confidence 34567999999998 55 6899999999884 45553
No 69
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=63.99 E-value=14 Score=27.88 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=24.0
Q ss_pred HHhcCCCeEEEEe----cCCcEEEEEEEEeccc
Q psy9158 22 AKSLVGMITCVDL----RNESSVSGRLEHVDGF 50 (133)
Q Consensus 22 L~~l~G~~VtVEL----KNg~~~~G~L~~vD~~ 50 (133)
+....|+.|.|.| .++..+.|.|.++|+.
T Consensus 93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred HHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 3456799999997 4667899999999984
No 70
>PRK14634 hypothetical protein; Provisional
Probab=63.96 E-value=14 Score=28.36 Aligned_cols=35 Identities=14% Similarity=0.206 Sum_probs=26.2
Q ss_pred HHHHHhcCCCeEEEEecCC----cEEEEEEEEeccccceEE
Q psy9158 19 ACLAKSLVGMITCVDLRNE----SSVSGRLEHVDGFMNIYM 55 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg----~~~~G~L~~vD~~MNl~L 55 (133)
..|- ...|+.|.|+|++. ..+.|+|.++|+. ++.|
T Consensus 93 ~~f~-r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 93 RDFQ-TFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHH-HhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 4444 46699999999853 5899999999985 3444
No 71
>PRK14645 hypothetical protein; Provisional
Probab=63.32 E-value=14 Score=28.40 Aligned_cols=30 Identities=20% Similarity=0.305 Sum_probs=24.4
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccc
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGF 50 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~ 50 (133)
..|. ...|+.|.|.+ ++..+.|+|.++|+.
T Consensus 95 ~df~-r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFE-RFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHH-HhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 3444 45699999986 789999999999985
No 72
>PRK14633 hypothetical protein; Provisional
Probab=62.25 E-value=16 Score=27.82 Aligned_cols=33 Identities=27% Similarity=0.435 Sum_probs=25.8
Q ss_pred HhcCCCeEEEEec----CCcEEEEEEEEeccccceEEe
Q psy9158 23 KSLVGMITCVDLR----NESSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 23 ~~l~G~~VtVELK----Ng~~~~G~L~~vD~~MNl~L~ 56 (133)
....|+.|.|.++ +...++|+|.++|+. ++.|.
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 4567999999984 558899999999985 44443
No 73
>PRK14647 hypothetical protein; Provisional
Probab=60.01 E-value=17 Score=27.79 Aligned_cols=29 Identities=17% Similarity=0.149 Sum_probs=23.5
Q ss_pred HHhcCCCeEEEEec---------CCcEEEEEEEEeccc
Q psy9158 22 AKSLVGMITCVDLR---------NESSVSGRLEHVDGF 50 (133)
Q Consensus 22 L~~l~G~~VtVELK---------Ng~~~~G~L~~vD~~ 50 (133)
+....|+.|.|.|+ +...+.|+|.++|+.
T Consensus 94 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 94 YERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred HHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 34567999999996 347899999999973
No 74
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=59.13 E-value=25 Score=28.22 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=32.9
Q ss_pred cCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccc
Q psy9158 15 FNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMN 52 (133)
Q Consensus 15 ~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MN 52 (133)
.++-..+-+.|.|+....++.+|..+.|.|++++.|+-
T Consensus 7 ~~~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 7 QQDAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred cCCHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 45566788999999999999989888999999999974
No 75
>PRK14643 hypothetical protein; Provisional
Probab=58.35 E-value=19 Score=27.99 Aligned_cols=36 Identities=14% Similarity=0.103 Sum_probs=26.8
Q ss_pred HHHHHhcCCCeEEEEecC----CcEEEEEEEEeccc-cceEE
Q psy9158 19 ACLAKSLVGMITCVDLRN----ESSVSGRLEHVDGF-MNIYM 55 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKN----g~~~~G~L~~vD~~-MNl~L 55 (133)
..|. ...|+.|.|.|+. ...+.|+|.++|+. ..+.|
T Consensus 97 ~df~-r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 97 EELV-KALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHH-HhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 3444 4569999999976 58899999999864 34443
No 76
>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=56.01 E-value=18 Score=26.73 Aligned_cols=28 Identities=25% Similarity=0.406 Sum_probs=21.0
Q ss_pred HHhcCCCeEEEEec----CCcEEEEEEEEecc
Q psy9158 22 AKSLVGMITCVDLR----NESSVSGRLEHVDG 49 (133)
Q Consensus 22 L~~l~G~~VtVELK----Ng~~~~G~L~~vD~ 49 (133)
+....|+.|.|.++ +...+.|+|.++|+
T Consensus 82 ~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 82 FERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 44566999999995 44679999999998
No 77
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=55.98 E-value=25 Score=27.90 Aligned_cols=38 Identities=16% Similarity=0.322 Sum_probs=30.4
Q ss_pred ccCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccc
Q psy9158 14 SFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMN 52 (133)
Q Consensus 14 ~~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MN 52 (133)
...+-..+-+.|.|+....++.+|. +.|.|++++.|+-
T Consensus 5 f~r~~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 5 FDRDTVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HSSBHHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred hccCHHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 3677788899999999999999888 9999999999986
No 78
>PRK14646 hypothetical protein; Provisional
Probab=55.32 E-value=24 Score=27.07 Aligned_cols=35 Identities=14% Similarity=0.161 Sum_probs=26.0
Q ss_pred HHHHHhcCCCeEEEEecCC----cEEEEEEEEeccccceEE
Q psy9158 19 ACLAKSLVGMITCVDLRNE----SSVSGRLEHVDGFMNIYM 55 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg----~~~~G~L~~vD~~MNl~L 55 (133)
..|. ...|+.|.|.|++. ..+.|+|.++|+. +++|
T Consensus 93 ~df~-r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFK-TFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHH-HhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 4444 46699999999653 5689999999985 4444
No 79
>PRK14637 hypothetical protein; Provisional
Probab=54.00 E-value=25 Score=26.90 Aligned_cols=36 Identities=17% Similarity=0.174 Sum_probs=25.4
Q ss_pred HHHHHhcCCCeEEEEecCCcEE-EEEEEEeccccceEEe
Q psy9158 19 ACLAKSLVGMITCVDLRNESSV-SGRLEHVDGFMNIYMS 56 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~-~G~L~~vD~~MNl~L~ 56 (133)
..|- ...|+.|.|.|.+...+ .|+|.++|+. ++.|.
T Consensus 91 ~~f~-r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 91 AEFS-IFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHH-HhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 3444 46699999999444445 7999999986 44443
No 80
>KOG1073|consensus
Probab=52.52 E-value=28 Score=30.61 Aligned_cols=56 Identities=9% Similarity=0.212 Sum_probs=44.1
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEeccc-cceEEec------------------c-cccccEEEecCeeEEEEcCC
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHVDGF-MNIYMSR------------------E-LTFESLFIQSRNVMFIHIPR 78 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~vD~~-MNl~L~n------------------~-~~l~~ifIRGsnIryI~lPd 78 (133)
...+|..|.+--|+|..|.|+|-.+|-. =-|-|.+ . .-++.|.-||+.|+=+.+-+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 3567999999999999999999988753 2455555 1 25789999999999776655
No 81
>PRK14631 hypothetical protein; Provisional
Probab=49.25 E-value=33 Score=26.93 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=22.5
Q ss_pred HHhcCCCeEEEEec----CCcEEEEEEEEec
Q psy9158 22 AKSLVGMITCVDLR----NESSVSGRLEHVD 48 (133)
Q Consensus 22 L~~l~G~~VtVELK----Ng~~~~G~L~~vD 48 (133)
+....|+.|.|.|+ +...+.|+|.++|
T Consensus 112 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 112 LQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34466999999996 4588999999998
No 82
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=49.19 E-value=40 Score=25.84 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=23.2
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEecc
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHVDG 49 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~vD~ 49 (133)
.++.|+.|+....+|..+.|++.+|..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 368999999888899999999997763
No 83
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=47.73 E-value=61 Score=19.52 Aligned_cols=25 Identities=24% Similarity=0.250 Sum_probs=21.5
Q ss_pred CCCeEEEEecCCcEEEEEEEEeccc
Q psy9158 26 VGMITCVDLRNESSVSGRLEHVDGF 50 (133)
Q Consensus 26 ~G~~VtVELKNg~~~~G~L~~vD~~ 50 (133)
.|..+.+...+|.-|+|++.++++.
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5788888887889999999999963
No 84
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=47.47 E-value=15 Score=27.24 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=26.3
Q ss_pred ccCcHHHHHHhcCCCeEEEEecCC-cEEEEE
Q psy9158 14 SFNTLACLAKSLVGMITCVDLRNE-SSVSGR 43 (133)
Q Consensus 14 ~~nsL~~lL~~l~G~~VtVELKNg-~~~~G~ 43 (133)
..+++..|+..+.|+.+.|.++++ ..+.|.
T Consensus 90 ~~~sl~~~~~~l~gk~l~V~v~~~~~e~nGk 120 (141)
T PF05037_consen 90 DFESLEQFLNQLLGKPLRVTVKWEENEYNGK 120 (141)
T ss_pred CcccHHHHHHHHcCCeeEEEecccccCCCCc
Confidence 367899999999999999999999 778884
No 85
>PRK14641 hypothetical protein; Provisional
Probab=47.31 E-value=32 Score=27.01 Aligned_cols=27 Identities=33% Similarity=0.473 Sum_probs=21.9
Q ss_pred HHhcCCCeEEEEecC----CcEEEEEEEEec
Q psy9158 22 AKSLVGMITCVDLRN----ESSVSGRLEHVD 48 (133)
Q Consensus 22 L~~l~G~~VtVELKN----g~~~~G~L~~vD 48 (133)
+....|+.|.|.|++ ...+.|+|.++|
T Consensus 99 f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 344679999999976 457999999995
No 86
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=46.78 E-value=59 Score=26.88 Aligned_cols=32 Identities=13% Similarity=0.219 Sum_probs=27.5
Q ss_pred cCCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 25 LVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 25 l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
+.|+.|++.. ++..+.|++..+|+.=.+.+.+
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~ 301 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLED 301 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEe
Confidence 5699999987 4457999999999999998875
No 87
>PRK06955 biotin--protein ligase; Provisional
Probab=44.44 E-value=68 Score=26.67 Aligned_cols=33 Identities=9% Similarity=0.060 Sum_probs=28.4
Q ss_pred cCCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 25 LVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 25 l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
..|+.|+|...++..+.|++..+|..=.+.+..
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 579999997666778999999999998888875
No 88
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=43.09 E-value=66 Score=25.47 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=30.6
Q ss_pred cCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccce
Q psy9158 15 FNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNI 53 (133)
Q Consensus 15 ~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl 53 (133)
.++-..+-+.|.|+.+..++. |..+.|.|++++.|+--
T Consensus 3 ~~~~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G~ 40 (179)
T cd00540 3 NRDTVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLGP 40 (179)
T ss_pred CCCHHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCCC
Confidence 345667888999998887775 66899999999999743
No 89
>PRK14635 hypothetical protein; Provisional
Probab=42.23 E-value=68 Score=24.62 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=23.9
Q ss_pred HhcCCCeEEEEec--CCcEEEE---EEEEeccccceEE
Q psy9158 23 KSLVGMITCVDLR--NESSVSG---RLEHVDGFMNIYM 55 (133)
Q Consensus 23 ~~l~G~~VtVELK--Ng~~~~G---~L~~vD~~MNl~L 55 (133)
....|+.|.|.+. ++..+.| .|.++|+. ++.|
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3466999999886 4567887 99999885 4444
No 90
>PRK14630 hypothetical protein; Provisional
Probab=40.41 E-value=52 Score=24.90 Aligned_cols=30 Identities=13% Similarity=0.012 Sum_probs=23.0
Q ss_pred HHHHHhcCCCeEEEEecCCcEEEEEEEEeccc
Q psy9158 19 ACLAKSLVGMITCVDLRNESSVSGRLEHVDGF 50 (133)
Q Consensus 19 ~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~ 50 (133)
..|- ...|+.|.|.|.... ..|+|.++|+.
T Consensus 90 ~df~-r~~G~~v~V~l~~~~-~~G~L~~~~d~ 119 (143)
T PRK14630 90 REFK-IFEGKKIKLMLDNDF-EEGFILEAKAD 119 (143)
T ss_pred HHHH-HhCCCEEEEEEcCcc-eEEEEEEEeCC
Confidence 3444 467999999996654 59999999884
No 91
>cd06526 metazoan_ACD Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=36.19 E-value=1.2e+02 Score=19.92 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=28.2
Q ss_pred eEEEEecCC-cEEEEEEEEeccccceEEecccccccEEEecCeeEEEEcCCCCCchhH
Q psy9158 29 ITCVDLRNE-SSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNK 85 (133)
Q Consensus 29 ~VtVELKNg-~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRGsnIryI~lPd~ld~~~~ 85 (133)
.|.|++.++ .++.|.=...+. +.-+..|+.-|-+.||+.+|...+
T Consensus 22 dI~v~v~~~~L~I~g~~~~~~~------------~~~~~~~~f~r~~~LP~~vd~~~i 67 (83)
T cd06526 22 ELKVKVSDNKLVVEGKHEERED------------EHGYVSREFTRRYQLPEGVDPDSV 67 (83)
T ss_pred HcEEEEECCEEEEEEEEeeecc------------CCCEEEEEEEEEEECCCCCChHHe
Confidence 355555555 346666544332 122466888999999999987653
No 92
>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=34.23 E-value=1.1e+02 Score=24.35 Aligned_cols=32 Identities=13% Similarity=0.175 Sum_probs=27.0
Q ss_pred cCCCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 25 LVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 25 l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
..|+.|+|...+ ..+.|++..+|..=.+.+++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~~ 222 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLED 222 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEEe
Confidence 569999998755 56899999999998888875
No 93
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=33.26 E-value=97 Score=25.25 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=35.1
Q ss_pred hhhcccCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccc
Q psy9158 10 EQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMN 52 (133)
Q Consensus 10 Ek~~~~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MN 52 (133)
.+.+..++-..+-+.|.|+.+.=+ -+|..+.|.|++++.|+=
T Consensus 7 p~~F~~rd~~~vAr~LLG~~lv~~-~~g~~~~g~IVEtEAY~G 48 (200)
T COG2094 7 PRSFFARDTLVVARELLGKTLVRR-IGGLTTSGRIVETEAYLG 48 (200)
T ss_pred CHhhhccCHHHHHHHhcCcEEEEe-cCCcEEEEEEEEEeEecC
Confidence 355677788889999999976655 778899999999999995
No 94
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=32.07 E-value=1.2e+02 Score=27.98 Aligned_cols=45 Identities=16% Similarity=0.145 Sum_probs=34.6
Q ss_pred cCCCeEEEEecCCcEEEEEEEEeccccceEEec-----ccccccEEEecC
Q psy9158 25 LVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR-----ELTFESLFIQSR 69 (133)
Q Consensus 25 l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n-----~~~l~~ifIRGs 69 (133)
..|+.|.|...++..+.|+...+|..=.+.|+. ...-+++.+|..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~~~g~~~~~sGEVslr~~ 325 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLETAEGKQTVVSGEISLRSD 325 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEECCCeEEEEEEeEEEeec
Confidence 679999987556677999999999999998875 334466666653
No 95
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=30.85 E-value=66 Score=22.78 Aligned_cols=19 Identities=5% Similarity=0.191 Sum_probs=16.2
Q ss_pred CCCeEEEEecCCcEEEEEE
Q psy9158 26 VGMITCVDLRNESSVSGRL 44 (133)
Q Consensus 26 ~G~~VtVELKNg~~~~G~L 44 (133)
.--+++.+||+|..+.|.-
T Consensus 22 ~hl~l~L~lkdGev~~a~A 40 (84)
T COG4568 22 HHLPLTLELKDGEVLQAKA 40 (84)
T ss_pred hhceEEEEEcCCeEEEEEe
Confidence 3468999999999999974
No 96
>PRK08330 biotin--protein ligase; Provisional
Probab=30.45 E-value=1.6e+02 Score=23.37 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=26.0
Q ss_pred hcCCCeEEEEecCCcE-EEEEEEEeccccceEEec
Q psy9158 24 SLVGMITCVDLRNESS-VSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 24 ~l~G~~VtVELKNg~~-~~G~L~~vD~~MNl~L~n 57 (133)
...|+.|++.. ++.. +.|+...+|+.=.+.+..
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 36799999976 4555 479999999988887764
No 97
>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....
Probab=30.40 E-value=36 Score=17.37 Aligned_cols=18 Identities=28% Similarity=0.427 Sum_probs=14.1
Q ss_pred cccEEEecCeeEEEEcCCCC
Q psy9158 61 FESLFIQSRNVMFIHIPRHV 80 (133)
Q Consensus 61 l~~ifIRGsnIryI~lPd~l 80 (133)
+..+.++|++|. .||+.+
T Consensus 2 L~~Ldls~n~l~--~ip~~~ 19 (22)
T PF00560_consen 2 LEYLDLSGNNLT--SIPSSF 19 (22)
T ss_dssp ESEEEETSSEES--EEGTTT
T ss_pred ccEEECCCCcCE--eCChhh
Confidence 567889999887 688864
No 98
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=29.57 E-value=80 Score=25.53 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=22.9
Q ss_pred hcCCCeEEEEecCCcEEEEEEEEecc
Q psy9158 24 SLVGMITCVDLRNESSVSGRLEHVDG 49 (133)
Q Consensus 24 ~l~G~~VtVELKNg~~~~G~L~~vD~ 49 (133)
+++|+.|++.--+|..+.|++.+|.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 67999999888889999999998863
No 99
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=29.12 E-value=1.6e+02 Score=20.00 Aligned_cols=42 Identities=17% Similarity=0.105 Sum_probs=27.6
Q ss_pred eEEEEecCC-cEEEEEEEEeccccceEEecccccccEEEecCeeEEEEcCCCCCchhH
Q psy9158 29 ITCVDLRNE-SSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNK 85 (133)
Q Consensus 29 ~VtVELKNg-~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRGsnIryI~lPd~ld~~~~ 85 (133)
-|.|++.++ .+++|.-...++ ..-|+.-|-+.||+++|...+
T Consensus 23 di~V~v~~~~L~I~ger~~~~~---------------~~~g~F~R~~~LP~~vd~e~v 65 (81)
T cd06479 23 DIIVTTSNNQIEVHAEKLASDG---------------TVMNTFTHKCQLPEDVDPTSV 65 (81)
T ss_pred HeEEEEECCEEEEEEEEeccCC---------------CEEEEEEEEEECCCCcCHHHe
Confidence 466666665 447776433221 136888899999999987654
No 100
>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=28.79 E-value=80 Score=22.98 Aligned_cols=20 Identities=20% Similarity=0.210 Sum_probs=17.7
Q ss_pred eEEEEecCCcEEEEEEEEec
Q psy9158 29 ITCVDLRNESSVSGRLEHVD 48 (133)
Q Consensus 29 ~VtVELKNg~~~~G~L~~vD 48 (133)
.+.|.++||.++.|.+.+=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 58999999999999998844
No 101
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.25 E-value=55 Score=21.59 Aligned_cols=18 Identities=28% Similarity=0.385 Sum_probs=15.7
Q ss_pred EecCCcEEEEEEEEeccc
Q psy9158 33 DLRNESSVSGRLEHVDGF 50 (133)
Q Consensus 33 ELKNg~~~~G~L~~vD~~ 50 (133)
+|+.|..+.|.+.++++|
T Consensus 1 dl~~G~~v~g~V~si~d~ 18 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDH 18 (74)
T ss_pred CCCCCCEEEEEEEEEeCC
Confidence 478899999999999887
No 102
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=24.87 E-value=1.3e+02 Score=23.29 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=23.9
Q ss_pred CCCeEEEEecCCcEEEEEEEEeccccc
Q psy9158 26 VGMITCVDLRNESSVSGRLEHVDGFMN 52 (133)
Q Consensus 26 ~G~~VtVELKNg~~~~G~L~~vD~~MN 52 (133)
.|..|+|.+.+|..+.|.+..++...+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 599999999999999999999997654
No 103
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family [].; PDB: 2YRV_A.
Probab=24.58 E-value=1.4e+02 Score=21.53 Aligned_cols=42 Identities=14% Similarity=0.304 Sum_probs=24.0
Q ss_pred HhcCCCeEEEEecCC--cEEEEEEEEeccccceEEecccccccEEEec
Q psy9158 23 KSLVGMITCVDLRNE--SSVSGRLEHVDGFMNIYMSRELTFESLFIQS 68 (133)
Q Consensus 23 ~~l~G~~VtVELKNg--~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRG 68 (133)
.++.|+.|.|+-... .-|-+.+++-+.+.++.... +++.||.
T Consensus 5 dellGkVV~V~~~~~k~~W~PALVVsPsc~ddv~VkK----D~~lVRS 48 (96)
T PF08169_consen 5 DELLGKVVCVESTKKKTSWFPALVVSPSCNDDVTVKK----DQCLVRS 48 (96)
T ss_dssp -SSTTSEEEEE-SS-SS-EEEEEEE--SS-SS----T----T-EEEEE
T ss_pred HhhcCcEEEEEcCCCCCceeeEEEEcCCccceeeecc----ceEEEEE
Confidence 467899999988664 55999999999998886543 5555554
No 104
>PF13437 HlyD_3: HlyD family secretion protein
Probab=23.00 E-value=1.8e+02 Score=19.43 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=21.4
Q ss_pred CCCeEEEEecCC--cEEEEEEEEecc
Q psy9158 26 VGMITCVDLRNE--SSVSGRLEHVDG 49 (133)
Q Consensus 26 ~G~~VtVELKNg--~~~~G~L~~vD~ 49 (133)
.|..|++.+.++ ..+.|++.+++.
T Consensus 53 ~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 53 PGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred CCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 699999999865 589999999998
No 105
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=22.87 E-value=1e+02 Score=24.03 Aligned_cols=27 Identities=30% Similarity=0.412 Sum_probs=22.6
Q ss_pred HHhcCCCeEEEEecCCcEEEEEEEEec
Q psy9158 22 AKSLVGMITCVDLRNESSVSGRLEHVD 48 (133)
Q Consensus 22 L~~l~G~~VtVELKNg~~~~G~L~~vD 48 (133)
+..+.|..|+|.+.....+.|.+.+++
T Consensus 23 ~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 23 LKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 344889999999998889999999984
No 106
>PRK00802 3-methyladenine DNA glycosylase; Reviewed
Probab=21.47 E-value=1.7e+02 Score=23.31 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=29.2
Q ss_pred ccCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccce
Q psy9158 14 SFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNI 53 (133)
Q Consensus 14 ~~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl 53 (133)
..++-..+-+.|.|+.+..+ | .+.|.|++++.|+--
T Consensus 10 f~~~~~~vA~~LLGk~Lv~~---~-~~~grIvETEAY~G~ 45 (188)
T PRK00802 10 FARDALEVARDLLGKVLVHE---G-GVSGRIVETEAYIGA 45 (188)
T ss_pred HCCCHHHHHHHhCCCEEEEC---C-EEEEEEEEEecccCC
Confidence 34566688999999988876 4 799999999999743
No 107
>PRK06789 flagellar motor switch protein; Validated
Probab=21.17 E-value=1.8e+02 Score=19.96 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=26.6
Q ss_pred HhcCCCeEEEEecCCcEEEEEEEEeccccceEEe
Q psy9158 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS 56 (133)
Q Consensus 23 ~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~ 56 (133)
....|.+|.|-+.+-..-+|.+..+|+.+=+.+.
T Consensus 37 dk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIt 70 (74)
T PRK06789 37 ENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIV 70 (74)
T ss_pred CCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEE
Confidence 3455777888888888899999999998766654
No 108
>PRK10898 serine endoprotease; Provisional
Probab=20.80 E-value=2e+02 Score=24.47 Aligned_cols=31 Identities=13% Similarity=0.137 Sum_probs=27.1
Q ss_pred CCeEEEEecCCcEEEEEEEEeccccceEEec
Q psy9158 27 GMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57 (133)
Q Consensus 27 G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n 57 (133)
...+.|.+.+|..|.+.+...|...++.+-.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~ 131 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLK 131 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEE
Confidence 3568999999999999999999999986655
No 109
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=20.34 E-value=1.6e+02 Score=18.54 Aligned_cols=25 Identities=40% Similarity=0.517 Sum_probs=17.3
Q ss_pred hcCCCeEEEE--ecCCcEEEEEEEEec
Q psy9158 24 SLVGMITCVD--LRNESSVSGRLEHVD 48 (133)
Q Consensus 24 ~l~G~~VtVE--LKNg~~~~G~L~~vD 48 (133)
++.|+.|++. ..-.....|++.+|+
T Consensus 9 ~lIGk~V~~~~~~~~~~~~~g~V~sV~ 35 (61)
T PF13861_consen 9 SLIGKEVLVPKSVAATTLVSGRVESVT 35 (61)
T ss_dssp CTTTSEEEEEEEEEE-EEEEEEEEEEE
T ss_pred HhcCCEEEECCcEeeeeEEEEEEEEEE
Confidence 5789999995 334456777777765
No 110
>PRK02649 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=20.33 E-value=4.5e+02 Score=22.16 Aligned_cols=68 Identities=16% Similarity=0.173 Sum_probs=45.8
Q ss_pred CeEEEEecCCcEEEEEEEEeccccceEEecccccccEEEecC--eeEEEEcCCCCCchhHHHHHHh-cCCCCCCchhh
Q psy9158 28 MITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSR--NVMFIHIPRHVSIVNKVEDALQ-SKPRQSSSAGR 102 (133)
Q Consensus 28 ~~VtVELKNg~~~~G~L~~vD~~MNl~L~n~~~l~~ifIRGs--nIryI~lPd~ld~~~~l~~~l~-~~~r~~~~~~~ 102 (133)
..|.|++... ......+|+.-.+.|.. -+.+.|+.+ .+++|++++. +.-+.|++.|. +.+.-+||...
T Consensus 232 ~~I~i~~~~~---~~~~l~~DG~~~~~l~~---gd~i~I~~s~~~~~lv~~~~~-~f~~~Lr~KL~wg~~~~~~~~~~ 302 (305)
T PRK02649 232 EPVTVFPATP---ERLVMVVDGNAGCYVWP---EDRVLIRRSPYPVRFIRLQDP-EFFRVLREKLGWGLPHIAKPTSV 302 (305)
T ss_pred CEEEEEecCC---CcEEEEEecceeEecCC---CCEEEEEECCCEEEEEEcCCC-CHHHHHHHHcCCCCCcccCCCcc
Confidence 3456655442 35667888887777754 244667655 4888988864 78999999898 66655566543
Done!