Query psy1084
Match_columns 110
No_of_seqs 114 out of 1024
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 19:47:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01720 Sm_D2 The eukaryotic S 99.9 7.3E-27 1.6E-31 154.3 10.8 87 18-105 1-87 (87)
2 cd01730 LSm3 The eukaryotic Sm 99.9 6E-25 1.3E-29 143.3 9.9 82 19-103 1-82 (82)
3 cd01732 LSm5 The eukaryotic Sm 99.9 3.2E-24 6.9E-29 138.5 10.2 74 18-104 2-75 (76)
4 PRK00737 small nuclear ribonuc 99.9 5.3E-24 1.1E-28 135.8 9.3 71 17-103 2-72 (72)
5 cd01731 archaeal_Sm1 The archa 99.9 1.9E-23 4E-28 131.7 9.1 68 20-103 1-68 (68)
6 cd01718 Sm_E The eukaryotic Sm 99.9 1.5E-22 3.2E-27 131.6 9.8 75 16-103 3-79 (79)
7 cd01729 LSm7 The eukaryotic Sm 99.9 3.6E-22 7.8E-27 130.2 10.2 77 21-105 4-80 (81)
8 cd01726 LSm6 The eukaryotic Sm 99.9 3.5E-22 7.6E-27 125.6 9.0 67 20-102 1-67 (67)
9 cd01719 Sm_G The eukaryotic Sm 99.9 7.5E-22 1.6E-26 126.1 8.9 70 20-105 1-70 (72)
10 cd01727 LSm8 The eukaryotic Sm 99.9 1E-21 2.2E-26 125.8 9.3 72 22-105 2-73 (74)
11 cd01722 Sm_F The eukaryotic Sm 99.9 7.9E-22 1.7E-26 124.4 8.5 68 19-102 1-68 (68)
12 cd01728 LSm1 The eukaryotic Sm 99.9 1.8E-21 3.8E-26 125.1 10.2 71 20-103 3-73 (74)
13 cd01717 Sm_B The eukaryotic Sm 99.9 1.4E-21 3E-26 126.5 9.6 76 22-103 3-78 (79)
14 PTZ00138 small nuclear ribonuc 99.9 1.8E-21 3.9E-26 129.0 10.0 79 13-104 8-88 (89)
15 COG1958 LSM1 Small nuclear rib 99.9 3.7E-21 8E-26 124.3 9.6 76 16-103 4-79 (79)
16 cd01721 Sm_D3 The eukaryotic S 99.8 2E-20 4.4E-25 118.7 9.5 70 20-105 1-70 (70)
17 cd01723 LSm4 The eukaryotic Sm 99.8 2.5E-20 5.3E-25 120.0 8.9 74 19-107 1-74 (76)
18 PF01423 LSM: LSM domain ; In 99.8 6.3E-20 1.4E-24 114.3 9.3 67 22-103 1-67 (67)
19 smart00651 Sm snRNP Sm protein 99.8 6.7E-20 1.5E-24 114.0 8.9 66 23-103 2-67 (67)
20 cd06168 LSm9 The eukaryotic Sm 99.8 1.7E-19 3.8E-24 116.1 9.8 72 22-103 3-74 (75)
21 KOG3460|consensus 99.8 7E-21 1.5E-25 123.9 1.5 87 17-106 3-89 (91)
22 KOG1774|consensus 99.8 3.1E-19 6.7E-24 115.7 5.6 78 15-105 8-87 (88)
23 cd01724 Sm_D1 The eukaryotic S 99.8 2E-18 4.3E-23 114.6 9.5 72 20-107 2-73 (90)
24 cd00600 Sm_like The eukaryotic 99.8 2E-18 4.2E-23 106.0 8.4 63 24-102 1-63 (63)
25 cd01725 LSm2 The eukaryotic Sm 99.8 3.6E-18 7.9E-23 111.2 9.0 75 20-108 2-76 (81)
26 cd01733 LSm10 The eukaryotic S 99.8 4.6E-18 1E-22 110.1 9.2 72 17-104 7-78 (78)
27 KOG3482|consensus 99.7 1.5E-17 3.3E-22 105.8 6.1 74 16-105 5-78 (79)
28 KOG3459|consensus 99.7 1.4E-18 3.1E-23 118.0 1.2 95 11-106 16-110 (114)
29 KOG1780|consensus 99.7 3.1E-17 6.8E-22 104.6 6.6 69 19-105 6-74 (77)
30 KOG1781|consensus 99.7 7.7E-18 1.7E-22 112.6 0.5 76 24-107 22-97 (108)
31 KOG1775|consensus 99.6 7.3E-16 1.6E-20 99.0 4.8 78 15-105 3-80 (84)
32 KOG3168|consensus 99.5 5.1E-15 1.1E-19 107.3 1.6 75 24-104 9-83 (177)
33 KOG1784|consensus 99.5 2.4E-14 5.2E-19 94.7 4.5 74 22-107 3-76 (96)
34 KOG1783|consensus 99.5 6.6E-15 1.4E-19 93.7 1.7 72 18-105 5-76 (77)
35 KOG1782|consensus 99.5 5.5E-15 1.2E-19 102.3 0.4 72 24-108 14-85 (129)
36 KOG3293|consensus 99.3 3.2E-12 7E-17 88.7 6.4 75 18-107 1-75 (134)
37 KOG3172|consensus 99.2 1.8E-11 3.9E-16 83.3 6.3 76 16-107 2-77 (119)
38 cd01739 LSm11_C The eukaryotic 99.2 6.6E-12 1.4E-16 78.6 2.5 45 24-68 1-49 (66)
39 KOG3448|consensus 99.1 3.2E-10 6.8E-15 74.8 8.2 72 21-106 4-75 (96)
40 KOG3428|consensus 98.6 4.1E-07 8.9E-12 62.1 8.5 69 21-106 4-72 (109)
41 cd01716 Hfq Hfq, an abundant, 97.4 0.00048 1.1E-08 42.7 5.0 39 23-61 3-41 (61)
42 TIGR02383 Hfq RNA chaperone Hf 97.3 0.0007 1.5E-08 42.0 5.1 40 22-61 6-45 (61)
43 PRK00395 hfq RNA-binding prote 97.1 0.0014 3.1E-08 42.6 5.0 40 22-61 10-49 (79)
44 PF14438 SM-ATX: Ataxin 2 SM d 97.0 0.0038 8.1E-08 39.6 6.4 69 22-99 5-76 (77)
45 COG1923 Hfq Uncharacterized ho 96.7 0.0048 1E-07 39.9 4.7 36 23-58 11-46 (77)
46 PRK14091 RNA-binding protein H 95.7 0.026 5.7E-07 41.3 5.0 40 22-61 95-134 (165)
47 PRK14091 RNA-binding protein H 95.7 0.027 5.9E-07 41.2 5.0 40 22-61 15-54 (165)
48 PF12701 LSM14: Scd6-like Sm d 95.6 0.21 4.5E-06 33.5 8.7 72 25-103 4-76 (96)
49 PF02237 BPL_C: Biotin protein 95.1 0.14 3E-06 29.7 5.9 33 31-64 3-35 (48)
50 cd01735 LSm12_N LSm12 belongs 94.9 0.07 1.5E-06 33.0 4.4 31 31-61 6-36 (61)
51 cd01736 LSm14_N LSm14 (also kn 91.7 2.1 4.5E-05 27.5 7.4 69 26-100 3-72 (74)
52 PRK14638 hypothetical protein; 90.9 0.45 9.8E-06 34.1 4.3 33 24-59 95-127 (150)
53 PF11095 Gemin7: Gem-associate 89.9 3.5 7.6E-05 26.8 7.4 64 20-104 15-79 (80)
54 PRK14639 hypothetical protein; 89.6 0.69 1.5E-05 32.7 4.3 33 24-59 83-115 (140)
55 PRK02001 hypothetical protein; 89.4 0.7 1.5E-05 33.3 4.2 33 24-59 85-117 (152)
56 PF03614 Flag1_repress: Repres 88.2 0.87 1.9E-05 33.2 4.0 34 21-54 110-143 (165)
57 PF06372 Gemin6: Gemin6 protei 87.4 1.7 3.8E-05 31.8 5.2 40 18-61 7-47 (166)
58 PRK14644 hypothetical protein; 84.0 2.3 5.1E-05 30.0 4.4 33 24-59 80-116 (136)
59 PF03614 Flag1_repress: Repres 82.9 2.7 5.8E-05 30.7 4.3 34 29-62 27-60 (165)
60 PRK14640 hypothetical protein; 82.4 2.9 6.3E-05 29.9 4.4 33 24-59 92-128 (152)
61 cd01734 YlxS_C YxlS is a Bacil 82.1 3.4 7.5E-05 26.3 4.3 32 25-59 21-56 (83)
62 PRK14636 hypothetical protein; 81.8 2.9 6.2E-05 30.8 4.3 33 24-59 93-129 (176)
63 PRK14642 hypothetical protein; 81.4 3.1 6.7E-05 31.3 4.4 29 24-54 95-136 (197)
64 COG0779 Uncharacterized protei 81.1 3.4 7.3E-05 29.9 4.4 34 23-59 93-130 (153)
65 PRK14633 hypothetical protein; 80.7 3.6 7.8E-05 29.4 4.4 33 24-59 89-125 (150)
66 PF02576 DUF150: Uncharacteris 80.5 3 6.5E-05 29.0 3.9 34 23-59 81-118 (141)
67 PRK14645 hypothetical protein; 80.1 3.5 7.6E-05 29.7 4.2 32 24-59 97-128 (154)
68 PRK14643 hypothetical protein; 79.1 4.1 8.9E-05 29.6 4.3 34 24-59 99-137 (164)
69 PRK14632 hypothetical protein; 78.5 4.4 9.5E-05 29.6 4.3 33 24-59 93-132 (172)
70 PRK14646 hypothetical protein; 77.9 4.9 0.00011 28.9 4.4 33 24-59 95-131 (155)
71 PRK14634 hypothetical protein; 77.6 5.1 0.00011 28.8 4.4 33 24-59 95-131 (155)
72 PF10842 DUF2642: Protein of u 77.5 7.4 0.00016 24.4 4.5 59 16-103 6-66 (66)
73 PRK00092 ribosome maturation p 75.7 6.2 0.00013 28.0 4.4 28 24-53 93-124 (154)
74 PRK14647 hypothetical protein; 74.3 6.9 0.00015 28.1 4.3 28 24-53 94-130 (159)
75 PRK14631 hypothetical protein; 72.2 7.8 0.00017 28.4 4.3 27 24-52 112-142 (174)
76 PF11607 DUF3247: Protein of u 72.1 9.8 0.00021 25.6 4.3 26 24-49 21-46 (101)
77 PRK10898 serine endoprotease; 71.3 8.9 0.00019 30.7 4.8 33 30-62 100-132 (353)
78 PRK14637 hypothetical protein; 70.1 8.5 0.00018 27.6 4.0 33 24-59 93-126 (151)
79 TIGR02038 protease_degS peripl 69.0 10 0.00023 30.2 4.7 32 31-62 101-132 (351)
80 PRK14641 hypothetical protein; 68.8 9.4 0.0002 28.0 4.1 27 24-52 99-129 (173)
81 PRK10139 serine endoprotease; 67.4 11 0.00025 31.2 4.8 34 29-62 112-145 (455)
82 PRK10942 serine endoprotease; 66.2 12 0.00026 31.3 4.7 32 30-61 134-165 (473)
83 PRK06955 biotin--protein ligas 65.4 20 0.00043 28.1 5.6 34 28-61 246-279 (300)
84 PF14563 DUF4444: Domain of un 63.8 8.3 0.00018 22.2 2.3 22 44-65 10-31 (42)
85 TIGR02037 degP_htrA_DO peripla 59.3 18 0.00038 29.5 4.4 33 30-62 80-112 (428)
86 PF08863 YolD: YolD-like prote 56.7 46 0.001 20.7 5.5 37 23-59 34-73 (92)
87 KOG3382|consensus 53.2 7.3 0.00016 27.9 1.1 23 40-62 41-63 (151)
88 PRK11886 bifunctional biotin-- 52.5 42 0.00091 26.1 5.4 31 29-60 270-300 (319)
89 KOG1073|consensus 52.0 49 0.0011 27.2 5.8 79 24-108 4-83 (361)
90 TIGR00121 birA_ligase birA, bi 49.9 55 0.0012 24.4 5.5 30 30-60 192-221 (237)
91 PTZ00275 biotin-acetyl-CoA-car 49.5 53 0.0012 25.6 5.5 31 30-61 236-266 (285)
92 PF05071 NDUFA12: NADH ubiquin 49.4 7.2 0.00016 26.1 0.6 17 46-62 1-17 (105)
93 PRK14630 hypothetical protein; 47.4 36 0.00078 24.1 3.9 28 24-54 92-119 (143)
94 PRK14635 hypothetical protein; 47.3 39 0.00084 24.3 4.1 33 24-59 94-131 (162)
95 PF02604 PhdYeFM_antitox: Anti 44.6 24 0.00053 21.2 2.4 43 13-57 6-48 (75)
96 PF07073 ROF: Modulator of Rho 42.8 40 0.00086 21.7 3.2 24 24-47 10-33 (80)
97 PRK13325 bifunctional biotin-- 42.8 68 0.0015 27.8 5.6 32 30-61 277-308 (592)
98 COG0340 BirA Biotin-(acetyl-Co 40.3 1E+02 0.0022 23.6 5.6 33 30-62 189-221 (238)
99 PRK08330 biotin--protein ligas 39.4 1.1E+02 0.0025 22.7 5.8 31 30-61 187-218 (236)
100 PF14153 Spore_coat_CotO: Spor 36.7 51 0.0011 24.5 3.4 34 21-54 123-157 (185)
101 COG4771 FepA Outer membrane re 35.0 42 0.00092 29.8 3.1 44 7-50 132-176 (699)
102 TIGR02603 CxxCH_TIGR02603 puta 31.7 54 0.0012 22.4 2.8 36 14-52 43-78 (133)
103 PF09465 LBR_tudor: Lamin-B re 30.4 97 0.0021 18.7 3.3 26 29-54 7-33 (55)
104 PF09196 DUF1953: Domain of un 28.6 78 0.0017 19.5 2.7 17 91-107 13-29 (66)
105 PRK06630 hypothetical protein; 28.2 30 0.00064 23.4 0.9 19 44-62 11-29 (99)
106 PF11743 DUF3301: Protein of u 28.1 61 0.0013 21.3 2.4 21 85-105 76-96 (97)
107 PF06257 DUF1021: Protein of u 27.8 1.3E+02 0.0028 19.3 3.8 26 23-50 11-40 (76)
108 smart00333 TUDOR Tudor domain. 26.8 1.3E+02 0.0027 16.9 4.4 24 31-54 6-29 (57)
109 PRK10708 hypothetical protein; 26.7 73 0.0016 19.6 2.3 25 31-55 4-28 (62)
110 COG0048 RpsL Ribosomal protein 25.9 77 0.0017 22.4 2.7 24 25-50 52-75 (129)
111 PRK09618 flgD flagellar basal 25.9 2.4E+02 0.0051 20.2 5.2 26 25-52 88-113 (142)
112 PRK08477 biotin--protein ligas 25.9 2.6E+02 0.0056 20.9 5.7 32 29-61 173-204 (211)
113 COG0265 DegQ Trypsin-like seri 25.5 1.3E+02 0.0028 23.6 4.2 31 31-61 95-125 (347)
114 PF07317 YcgR: Flagellar regul 25.4 2E+02 0.0044 18.9 4.8 41 21-61 11-51 (108)
115 PLN03095 NADH:ubiquinone oxido 23.8 43 0.00093 23.2 1.1 18 45-62 9-26 (115)
116 PF10781 DSRB: Dextransucrase 23.6 83 0.0018 19.3 2.2 25 31-55 4-28 (62)
117 PRK11625 Rho-binding antitermi 23.2 2.2E+02 0.0048 18.5 7.1 58 24-103 16-73 (84)
118 cd03367 Ribosomal_S23 S12-like 22.9 1.2E+02 0.0026 21.0 3.1 26 25-52 38-64 (115)
119 COG2131 ComEB Deoxycytidylate 22.1 1E+02 0.0022 22.6 2.8 25 85-109 27-51 (164)
120 TIGR03170 flgA_cterm flagella 21.9 1.2E+02 0.0027 19.9 3.1 20 31-50 96-116 (122)
No 1
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.94 E-value=7.3e-27 Score=154.30 Aligned_cols=87 Identities=89% Similarity=1.386 Sum_probs=72.0
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCc
Q psy1084 18 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 97 (110)
Q Consensus 18 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~ 97 (110)
.+|+++|..++.++++|.|+|++|+.+.|+|.|||+||||+|+||+|++...++++... +..+..+.+++|.+|||||+
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~ 79 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDS 79 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCE
Confidence 48999999999889999999999999999999999999999999999987644332111 11123356789999999999
Q ss_pred EEEEeeCC
Q psy1084 98 VILILKNP 105 (110)
Q Consensus 98 Vv~I~~~~ 105 (110)
|++|+++|
T Consensus 80 Vv~Is~~~ 87 (87)
T cd01720 80 VILVLRNP 87 (87)
T ss_pred EEEEecCC
Confidence 99999874
No 2
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.92 E-value=6e-25 Score=143.31 Aligned_cols=82 Identities=33% Similarity=0.533 Sum_probs=66.2
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 19 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 19 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
.|+++|+.++ +++|.|.|++||.+.|+|+|||+||||+|+||+|++.....+.+.. ........|.+|.+|||||+|
T Consensus 1 ~pl~~l~~~~--~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~-~~~~~~~~r~lg~~~iRGd~V 77 (82)
T cd01730 1 EPLDLIRLSL--DERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETY-EEIVKTTKRNIPMLFVRGDSV 77 (82)
T ss_pred CchHHHHHhC--CCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeeccccccccc-ccccceeEEEcCeEEEeCCEE
Confidence 5999999999 9999999999999999999999999999999999986533221100 001112467899999999999
Q ss_pred EEEee
Q psy1084 99 ILILK 103 (110)
Q Consensus 99 v~I~~ 103 (110)
++|++
T Consensus 78 v~i~~ 82 (82)
T cd01730 78 ILVSP 82 (82)
T ss_pred EEECC
Confidence 99974
No 3
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=3.2e-24 Score=138.47 Aligned_cols=74 Identities=26% Similarity=0.545 Sum_probs=64.9
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCc
Q psy1084 18 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 97 (110)
Q Consensus 18 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~ 97 (110)
..|+++|.+++ +++|.|.+++|+.+.|+|+|||+||||+|+||+|++.. +. +. ..+.+|.++|||||
T Consensus 2 ~~P~~~L~~~~--~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~-~~-~~---------~~~~lg~v~iRG~n 68 (76)
T cd01732 2 LLPLELIDKCI--GSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEIT-PE-GR---------KITKLDQILLNGNN 68 (76)
T ss_pred cChHHHHHHhC--CCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEc-CC-Cc---------eeeEcCeEEEeCCe
Confidence 57999999999 99999999999999999999999999999999998742 11 11 24679999999999
Q ss_pred EEEEeeC
Q psy1084 98 VILILKN 104 (110)
Q Consensus 98 Vv~I~~~ 104 (110)
|++|+|.
T Consensus 69 V~~i~p~ 75 (76)
T cd01732 69 ICMLVPG 75 (76)
T ss_pred EEEEECC
Confidence 9999974
No 4
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.91 E-value=5.3e-24 Score=135.81 Aligned_cols=71 Identities=31% Similarity=0.637 Sum_probs=63.1
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCC
Q psy1084 17 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGD 96 (110)
Q Consensus 17 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 96 (110)
+..|+++|++++ +++|.|+|++|+.|.|+|+|||+||||+|+||+|.+. ++ ..+.+|.+||||+
T Consensus 2 ~~~P~~~L~~~~--~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----~~---------~~~~lg~v~iRG~ 65 (72)
T PRK00737 2 AQRPLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-----GE---------VVRKLGKVVIRGD 65 (72)
T ss_pred CcchHHHHHHhC--CCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-----CC---------eEeEcCcEEEeCC
Confidence 368999999999 9999999999999999999999999999999999752 11 1357999999999
Q ss_pred cEEEEee
Q psy1084 97 SVILILK 103 (110)
Q Consensus 97 ~Vv~I~~ 103 (110)
+|++|++
T Consensus 66 ~V~~i~~ 72 (72)
T PRK00737 66 NVVYVSP 72 (72)
T ss_pred EEEEEcC
Confidence 9999974
No 5
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.90 E-value=1.9e-23 Score=131.66 Aligned_cols=68 Identities=37% Similarity=0.659 Sum_probs=61.5
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
|+++|+.++ +++|.|.|++|+.|.|+|.|||+||||+|+||+|++.. + ..+.+|.+||||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~----~----------~~~~lg~~~iRG~~I~ 64 (68)
T cd01731 1 PLDVLKDSL--NKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDG----E----------PVRKYGRVVIRGDNVL 64 (68)
T ss_pred ChHHHHHhc--CCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecC----C----------eEeEcCcEEEeCCEEE
Confidence 899999999 99999999999999999999999999999999998632 1 1457899999999999
Q ss_pred EEee
Q psy1084 100 LILK 103 (110)
Q Consensus 100 ~I~~ 103 (110)
+|++
T Consensus 65 ~i~~ 68 (68)
T cd01731 65 FISP 68 (68)
T ss_pred EEcC
Confidence 9975
No 6
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=1.5e-22 Score=131.64 Aligned_cols=75 Identities=21% Similarity=0.432 Sum_probs=64.7
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEec--CCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEE
Q psy1084 16 FATGPLSILTDSVKHNTQVLINCR--NNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFL 93 (110)
Q Consensus 16 ~~~~Pl~~L~~~~~~~krV~V~l~--~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~I 93 (110)
....|++.|++++....+|.||++ +|+.+.|+|.|||+||||+|+||+|+... +. ..+.+|.++|
T Consensus 3 ~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~----~~---------~~~~lG~ili 69 (79)
T cd01718 3 VMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK----TK---------TRKPLGRILL 69 (79)
T ss_pred cccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC----Cc---------eEeEcCcEEE
Confidence 456899999999966669999998 89999999999999999999999998642 11 2456899999
Q ss_pred eCCcEEEEee
Q psy1084 94 RGDSVILILK 103 (110)
Q Consensus 94 RGd~Vv~I~~ 103 (110)
|||||++|++
T Consensus 70 RGnnV~~I~p 79 (79)
T cd01718 70 KGDNITLIQN 79 (79)
T ss_pred eCCEEEEEcC
Confidence 9999999984
No 7
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=3.6e-22 Score=130.16 Aligned_cols=77 Identities=23% Similarity=0.378 Sum_probs=62.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEE
Q psy1084 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 100 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~ 100 (110)
+.-|.+++ +++|+|.|++||.+.|+|+|||+||||+|+||+|+......+ . ......+.+|.++|||+||++
T Consensus 4 ~~~L~~~i--~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~-~-----~~~~~~~~lG~v~iRG~nV~~ 75 (81)
T cd01729 4 ILDLSKYV--DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDP-Y-----KLTDKTRQLGLVVCRGTSVVL 75 (81)
T ss_pred hhhHHHhc--CCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcc-c-----ccccceeEccEEEEcCCEEEE
Confidence 34488999 999999999999999999999999999999999987531110 0 011135679999999999999
Q ss_pred EeeCC
Q psy1084 101 ILKNP 105 (110)
Q Consensus 101 I~~~~ 105 (110)
|++.+
T Consensus 76 i~~~~ 80 (81)
T cd01729 76 ISPVD 80 (81)
T ss_pred EecCC
Confidence 99764
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=99.88 E-value=3.5e-22 Score=125.64 Aligned_cols=67 Identities=22% Similarity=0.393 Sum_probs=59.6
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
|+++|++++ +++|+|.|++|++|+|+|.|||.||||+|+||+|... +. ....+|.++|||++|+
T Consensus 1 p~~~L~~~~--~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-----~~---------~~~~~~~v~IRG~~I~ 64 (67)
T cd01726 1 PSEFLKAII--GRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-----GQ---------LKNKYGDAFIRGNNVL 64 (67)
T ss_pred CHHHHHhhC--CCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-----Cc---------eeeEeCCEEEECCEEE
Confidence 899999999 9999999999999999999999999999999988632 11 1346899999999999
Q ss_pred EEe
Q psy1084 100 LIL 102 (110)
Q Consensus 100 ~I~ 102 (110)
+|+
T Consensus 65 ~I~ 67 (67)
T cd01726 65 YIS 67 (67)
T ss_pred EEC
Confidence 985
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=7.5e-22 Score=126.08 Aligned_cols=70 Identities=21% Similarity=0.414 Sum_probs=61.1
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
|-+.|.+++ +++|.|.|++|+.+.|+|.|||+||||+|+||+|+... . ..+.+|.++|||++|+
T Consensus 1 ~~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~----~----------~~~~lg~v~IRG~~I~ 64 (72)
T cd01719 1 HPPELKKYM--DKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG----G----------EKNNIGMVVIRGNSIV 64 (72)
T ss_pred CchhhHHhC--CCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC----C----------ceeEeceEEECCCEEE
Confidence 446889999 99999999999999999999999999999999998521 1 1356899999999999
Q ss_pred EEeeCC
Q psy1084 100 LILKNP 105 (110)
Q Consensus 100 ~I~~~~ 105 (110)
+|++.+
T Consensus 65 ~i~~~~ 70 (72)
T cd01719 65 MLEALE 70 (72)
T ss_pred EEEccc
Confidence 999764
No 10
>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=99.87 E-value=1e-21 Score=125.75 Aligned_cols=72 Identities=22% Similarity=0.404 Sum_probs=61.2
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I 101 (110)
+-|.+++ +++|+|.+++||.+.|+|+|||+|||++|+||+|+...... + ...+.+|.++|||+||++|
T Consensus 2 ~~L~~~l--~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~-~---------~~~~~lG~~~iRG~~I~~i 69 (74)
T cd01727 2 STLEDYL--NKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDE-G---------VEQVVLGLYIIRGDNIAVV 69 (74)
T ss_pred hhHHHhc--CCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCC-C---------ceeeEeceEEECCCEEEEE
Confidence 4688999 99999999999999999999999999999999998643111 1 1245789999999999999
Q ss_pred eeCC
Q psy1084 102 LKNP 105 (110)
Q Consensus 102 ~~~~ 105 (110)
++.+
T Consensus 70 ~~~d 73 (74)
T cd01727 70 GEID 73 (74)
T ss_pred EccC
Confidence 9865
No 11
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.87 E-value=7.9e-22 Score=124.44 Aligned_cols=68 Identities=22% Similarity=0.372 Sum_probs=59.9
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 19 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 19 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
.|+++|++++ +++|+|.|++|+.|.|+|.|||+|||++|+||+|+.. +. ....+|.++|||++|
T Consensus 1 ~p~~~L~~~~--g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~-----~~---------~~~~lg~~~IRG~~I 64 (68)
T cd01722 1 NPKPFLNDLT--GKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-----GK---------STGNLGEVLIRCNNV 64 (68)
T ss_pred CHHHHHHHcC--CCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-----Cc---------cccCcCcEEEECCEE
Confidence 4899999999 9999999999999999999999999999999998742 11 124589999999999
Q ss_pred EEEe
Q psy1084 99 ILIL 102 (110)
Q Consensus 99 v~I~ 102 (110)
++|+
T Consensus 65 ~~i~ 68 (68)
T cd01722 65 LYIR 68 (68)
T ss_pred EEEC
Confidence 9984
No 12
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=1.8e-21 Score=125.12 Aligned_cols=71 Identities=27% Similarity=0.444 Sum_probs=61.3
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
++..|.+++ +++|.|.|++||.+.|+|.|||+||||+|+||+|+..... . ..++.+|.++||||||+
T Consensus 3 ~~~~L~~~l--~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~---~--------~~~~~lG~~viRG~~V~ 69 (74)
T cd01728 3 GTASLVDDL--DKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD---K--------YGDIPRGIFIIRGENVV 69 (74)
T ss_pred chHHHHHhc--CCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC---c--------cceeEeeEEEEECCEEE
Confidence 567899999 9999999999999999999999999999999999875311 0 11457999999999999
Q ss_pred EEee
Q psy1084 100 LILK 103 (110)
Q Consensus 100 ~I~~ 103 (110)
+|+.
T Consensus 70 ~ig~ 73 (74)
T cd01728 70 LLGE 73 (74)
T ss_pred EEEc
Confidence 9985
No 13
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=1.4e-21 Score=126.49 Aligned_cols=76 Identities=21% Similarity=0.461 Sum_probs=61.3
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I 101 (110)
+-|..++ +++|.|.|+|||.+.|+|+|||+||||+|+||+|++...+.... .......+++|.+||||++|++|
T Consensus 3 ~~l~~~l--~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~----~~~~~~~r~lG~v~iRG~~Vv~i 76 (79)
T cd01717 3 SKMLQLI--NYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK----NSEREEKRTLGLVLLRGENIVSM 76 (79)
T ss_pred chhHHHc--CCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc----cccCcceeEeeeEEEcCCEEEEE
Confidence 3478888 99999999999999999999999999999999998865322110 00112467899999999999999
Q ss_pred ee
Q psy1084 102 LK 103 (110)
Q Consensus 102 ~~ 103 (110)
+.
T Consensus 77 ~v 78 (79)
T cd01717 77 TV 78 (79)
T ss_pred EE
Confidence 74
No 14
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.87 E-value=1.8e-21 Score=129.05 Aligned_cols=79 Identities=24% Similarity=0.465 Sum_probs=67.8
Q ss_pred hhhcCCCcHHHHHhhhhCCcEEEEEecCC--eEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCe
Q psy1084 13 EESFATGPLSILTDSVKHNTQVLINCRNN--KKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90 (110)
Q Consensus 13 ~~~~~~~Pl~~L~~~~~~~krV~V~l~~g--r~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~ 90 (110)
..+....|+.+++++++...+|.||+.++ +++.|+|.|||+||||+|+||+|++.. +. ..+.+|.
T Consensus 8 ~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~----~~---------~~~~lG~ 74 (89)
T PTZ00138 8 LQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTK----KN---------TRKDLGR 74 (89)
T ss_pred cceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecC----Cc---------eeeEcCe
Confidence 34566799999999999999999999875 889999999999999999999998632 11 2457999
Q ss_pred EEEeCCcEEEEeeC
Q psy1084 91 MFLRGDSVILILKN 104 (110)
Q Consensus 91 i~IRGd~Vv~I~~~ 104 (110)
++||||||++|++.
T Consensus 75 ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 75 ILLKGDNITLIMAA 88 (89)
T ss_pred EEEcCCEEEEEEcC
Confidence 99999999999875
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.86 E-value=3.7e-21 Score=124.31 Aligned_cols=76 Identities=33% Similarity=0.610 Sum_probs=62.8
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeC
Q psy1084 16 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 95 (110)
Q Consensus 16 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRG 95 (110)
....|+++|+.++ +++|.|+|++|++|.|+|+|||+||||+|+||+|+... ++. . ...+..+.++|||
T Consensus 4 ~~~~~~~~l~~~~--~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~---~~~--~-----~~~~~~~~~~IRG 71 (79)
T COG1958 4 LGPLPLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH---DGE--K-----NVRRLGGEVLIRG 71 (79)
T ss_pred ccCCcHHHHHHhh--CCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc---CCc--c-----ccceeccEEEEEC
Confidence 4557899999999 99999999999999999999999999999999998741 111 0 0123455999999
Q ss_pred CcEEEEee
Q psy1084 96 DSVILILK 103 (110)
Q Consensus 96 d~Vv~I~~ 103 (110)
++|++|++
T Consensus 72 ~~I~~I~~ 79 (79)
T COG1958 72 DNIVLISP 79 (79)
T ss_pred CcEEEEeC
Confidence 99999964
No 16
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=2e-20 Score=118.71 Aligned_cols=70 Identities=14% Similarity=0.335 Sum_probs=61.4
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
|+++|+.+. +++|.|.|++|..|+|+|.+||.|||++|+||.+... +++ ...+|.+||||+||.
T Consensus 1 P~~~L~~~~--g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~----~g~----------~~~~~~v~IRG~nI~ 64 (70)
T cd01721 1 PIKLLHEAE--GHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTAR----DGR----------VSQLEQVYIRGSKIR 64 (70)
T ss_pred ChHHHhhCC--CCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECC----CCc----------EeEcCcEEEeCCEEE
Confidence 889999998 9999999999999999999999999999999987531 121 235799999999999
Q ss_pred EEeeCC
Q psy1084 100 LILKNP 105 (110)
Q Consensus 100 ~I~~~~ 105 (110)
+|..|+
T Consensus 65 ~v~lPd 70 (70)
T cd01721 65 FFILPD 70 (70)
T ss_pred EEEeCC
Confidence 998875
No 17
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=2.5e-20 Score=119.97 Aligned_cols=74 Identities=22% Similarity=0.305 Sum_probs=63.2
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 19 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 19 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
-|+.+|+.+. +++|.|.|++|+.+.|+|.+||.|||++|+||+|... +|+ ....++.+||||++|
T Consensus 1 ~Pl~~L~~~~--g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~----~g~---------~~~~~~~v~IRG~~I 65 (76)
T cd01723 1 LPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSK----DGD---------KFWKMPECYIRGNTI 65 (76)
T ss_pred CchHHHHhcC--CCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECC----CCc---------EeeeCCcEEEeCCEE
Confidence 3999999998 9999999999999999999999999999999998621 121 123478999999999
Q ss_pred EEEeeCCcc
Q psy1084 99 ILILKNPLA 107 (110)
Q Consensus 99 v~I~~~~~~ 107 (110)
.+|+.++..
T Consensus 66 ~~i~~p~~~ 74 (76)
T cd01723 66 KYLRVPDEI 74 (76)
T ss_pred EEEEcCHHH
Confidence 999987654
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.83 E-value=6.3e-20 Score=114.31 Aligned_cols=67 Identities=25% Similarity=0.488 Sum_probs=59.4
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I 101 (110)
.+|++++ +++|+|.|++|+.++|+|.+||+||||+|+||.|++...+ ..+.+|.+||||++|++|
T Consensus 1 ~~L~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~-------------~~~~~~~~~irG~~I~~I 65 (67)
T PF01423_consen 1 NFLQKLI--GKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP-------------EKRSLGLVFIRGSNIRYI 65 (67)
T ss_dssp HHHHHTT--TSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES-------------EEEEEEEEEEEGGGEEEE
T ss_pred ChhHHhC--CcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC-------------cEeECcEEEEECCEEEEE
Confidence 3688999 9999999999999999999999999999999999864310 256799999999999999
Q ss_pred ee
Q psy1084 102 LK 103 (110)
Q Consensus 102 ~~ 103 (110)
++
T Consensus 66 ~~ 67 (67)
T PF01423_consen 66 SL 67 (67)
T ss_dssp EE
T ss_pred EC
Confidence 75
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.82 E-value=6.7e-20 Score=114.05 Aligned_cols=66 Identities=30% Similarity=0.613 Sum_probs=58.3
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEe
Q psy1084 23 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 102 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~ 102 (110)
+|..++ +++|+|.|++|+.+.|+|.+||+||||+|+||+|++... ...+++|.+||||++|++|+
T Consensus 2 ~L~~~~--~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~-------------~~~~~~~~~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLI--GKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG-------------EKKRKLGLVFIRGNNIVYII 66 (67)
T ss_pred hhHHhC--CcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC-------------cEEeEeCCEEEcCCEEEEEe
Confidence 678888 999999999999999999999999999999999986420 12567999999999999997
Q ss_pred e
Q psy1084 103 K 103 (110)
Q Consensus 103 ~ 103 (110)
+
T Consensus 67 ~ 67 (67)
T smart00651 67 L 67 (67)
T ss_pred C
Confidence 4
No 20
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=1.7e-19 Score=116.09 Aligned_cols=72 Identities=18% Similarity=0.337 Sum_probs=60.6
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I 101 (110)
+-|..++ +++|+|.|+|||.|.|+|.+||+||||+|+||.|++....... ....|.+|.++|||++|++|
T Consensus 3 ~~L~~~l--~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~--------~~~~r~lGlv~IrG~~Iv~i 72 (75)
T cd06168 3 QKLRSLL--GRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFS--------PTEPRVLGLVMIPGHHIVSI 72 (75)
T ss_pred hHHHHhc--CCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccC--------CccEEEeeeEEEeCCeEEEE
Confidence 4578899 9999999999999999999999999999999999975422111 01357899999999999998
Q ss_pred ee
Q psy1084 102 LK 103 (110)
Q Consensus 102 ~~ 103 (110)
..
T Consensus 73 ~v 74 (75)
T cd06168 73 EV 74 (75)
T ss_pred EE
Confidence 74
No 21
>KOG3460|consensus
Probab=99.80 E-value=7e-21 Score=123.86 Aligned_cols=87 Identities=31% Similarity=0.469 Sum_probs=69.5
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCC
Q psy1084 17 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGD 96 (110)
Q Consensus 17 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 96 (110)
...|+.+|+-++ +.||.|+++++|+++|+|.|||+|.||+|.||+|+++....+.....+.- ...+|.+.-+|+|||
T Consensus 3 v~ePldllrlsL--dErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~-k~~~r~~emlFvRGd 79 (91)
T KOG3460|consen 3 VEEPLDLLRLSL--DERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIV-KTTKRTVEMLFVRGD 79 (91)
T ss_pred ccccHHHHhhcc--cceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHH-hhhhcceeEEEEeCC
Confidence 347999999999 99999999999999999999999999999999998876432211111111 123567899999999
Q ss_pred cEEEEeeCCc
Q psy1084 97 SVILILKNPL 106 (110)
Q Consensus 97 ~Vv~I~~~~~ 106 (110)
+|++|+++-.
T Consensus 80 ~Vilvspp~~ 89 (91)
T KOG3460|consen 80 GVILVSPPLR 89 (91)
T ss_pred eEEEEcCccc
Confidence 9999998744
No 22
>KOG1774|consensus
Probab=99.78 E-value=3.1e-19 Score=115.72 Aligned_cols=78 Identities=23% Similarity=0.453 Sum_probs=66.3
Q ss_pred hcCCCcHHHHHhhhhCCcEEEEEecC--CeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEE
Q psy1084 15 SFATGPLSILTDSVKHNTQVLINCRN--NKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMF 92 (110)
Q Consensus 15 ~~~~~Pl~~L~~~~~~~krV~V~l~~--gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~ 92 (110)
+..+.|+.+++++++...+|.|||.. +-.+.|.++|||+|||+||+||+|..... + ..+.+|+++
T Consensus 8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~----~---------~rk~lGRil 74 (88)
T KOG1774|consen 8 KVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKT----K---------SRKELGRIL 74 (88)
T ss_pred ceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccc----c---------CCCccccEE
Confidence 34579999999999999999999987 57899999999999999999999985431 0 123699999
Q ss_pred EeCCcEEEEeeCC
Q psy1084 93 LRGDSVILILKNP 105 (110)
Q Consensus 93 IRGd~Vv~I~~~~ 105 (110)
++||||.+|....
T Consensus 75 LKGDnItli~~~~ 87 (88)
T KOG1774|consen 75 LKGDNITLIQSAG 87 (88)
T ss_pred EcCCcEEEEeecC
Confidence 9999999998653
No 23
>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=99.78 E-value=2e-18 Score=114.59 Aligned_cols=72 Identities=19% Similarity=0.244 Sum_probs=62.8
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
++.+|+++. |++|+|.|++|..|+|+|.++|.|||++|+||+++... + ....+|.++|||++|.
T Consensus 2 ~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~----~----------~~~~~~~v~IRG~nI~ 65 (90)
T cd01724 2 LVRFLMKLT--NETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKG----R----------NPVPLDTLSIRGNNIR 65 (90)
T ss_pred HhHHHHhCC--CCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCC----C----------ceeEcceEEEeCCEEE
Confidence 678999998 99999999999999999999999999999999987421 1 1346899999999999
Q ss_pred EEeeCCcc
Q psy1084 100 LILKNPLA 107 (110)
Q Consensus 100 ~I~~~~~~ 107 (110)
+|..++..
T Consensus 66 yi~lPd~l 73 (90)
T cd01724 66 YFILPDSL 73 (90)
T ss_pred EEEcCCcC
Confidence 99998653
No 24
>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=99.77 E-value=2e-18 Score=105.99 Aligned_cols=63 Identities=37% Similarity=0.608 Sum_probs=55.2
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 102 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~ 102 (110)
|+.++ +++|+|.|++|+.+.|+|.|||+|||++|+||.|.+.. . ..+.+|.+||||++|.+|.
T Consensus 1 l~~~~--g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~----~----------~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLV--GKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE----G----------KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHC--CCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC----C----------cEEECCeEEEECCEEEEEC
Confidence 45677 99999999999999999999999999999999998642 1 2467999999999999874
No 25
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=3.6e-18 Score=111.21 Aligned_cols=75 Identities=19% Similarity=0.233 Sum_probs=62.4
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv 99 (110)
|+++|+++. |++|+|.|++|..|+|+|.++|.|||++|+||++.... +.. ....++.++|||++|.
T Consensus 2 ~~~fL~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~----~~~--------~~~~~~~v~IRG~~I~ 67 (81)
T cd01725 2 FFSFFKTLV--GKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPE----KYP--------HMLSVKNCFIRGSVVR 67 (81)
T ss_pred hhHHHHhCC--CCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCC----Ccc--------cccccCeEEEECCEEE
Confidence 789999998 99999999999999999999999999999999875211 100 1124689999999999
Q ss_pred EEeeCCccC
Q psy1084 100 LILKNPLAL 108 (110)
Q Consensus 100 ~I~~~~~~~ 108 (110)
+|..++...
T Consensus 68 ~I~lp~~~i 76 (81)
T cd01725 68 YVQLPADEV 76 (81)
T ss_pred EEEeChhHc
Confidence 999987643
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.76 E-value=4.6e-18 Score=110.14 Aligned_cols=72 Identities=18% Similarity=0.291 Sum_probs=60.7
Q ss_pred CCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCC
Q psy1084 17 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGD 96 (110)
Q Consensus 17 ~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd 96 (110)
...+..+|+.+. |++|.|.|++|..|.|+|.++|.|||++|+||++... ++. ...+|.+||||+
T Consensus 7 ~~tl~~~L~~l~--g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~----~~~----------~~~~~~v~IRG~ 70 (78)
T cd01733 7 ENTLIILLQGLQ--GKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDR----NGK----------QVQVEEIMVTGR 70 (78)
T ss_pred hchHHHHHHHCC--CCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcC----CCc----------eeECCcEEEECC
Confidence 345677889998 9999999999999999999999999999999987631 111 235899999999
Q ss_pred cEEEEeeC
Q psy1084 97 SVILILKN 104 (110)
Q Consensus 97 ~Vv~I~~~ 104 (110)
+|.+|..|
T Consensus 71 nI~yI~lP 78 (78)
T cd01733 71 NIRYVHIP 78 (78)
T ss_pred EEEEEEcC
Confidence 99999864
No 27
>KOG3482|consensus
Probab=99.72 E-value=1.5e-17 Score=105.78 Aligned_cols=74 Identities=19% Similarity=0.301 Sum_probs=64.9
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeC
Q psy1084 16 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 95 (110)
Q Consensus 16 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRG 95 (110)
...+|..||+... +++|.|.|+.|.+|.|+|++.|.||||.|.+|+|++.. . ....+|.++||.
T Consensus 5 ~PvNPKpFL~~l~--gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-----~---------~~g~lGEilIRC 68 (79)
T KOG3482|consen 5 QPVNPKPFLNGLT--GKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-----V---------STGNLGEILIRC 68 (79)
T ss_pred ccCCchHHHhhcc--CCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-----c---------ccccceeEEEEe
Confidence 3468999999999 99999999999999999999999999999999998743 1 134699999999
Q ss_pred CcEEEEeeCC
Q psy1084 96 DSVILILKNP 105 (110)
Q Consensus 96 d~Vv~I~~~~ 105 (110)
+||.+|.-.|
T Consensus 69 NNvlyi~gv~ 78 (79)
T KOG3482|consen 69 NNVLYIRGVP 78 (79)
T ss_pred ccEEEEecCC
Confidence 9999996543
No 28
>KOG3459|consensus
Probab=99.71 E-value=1.4e-18 Score=118.03 Aligned_cols=95 Identities=84% Similarity=1.315 Sum_probs=85.4
Q ss_pred hhhhhcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCe
Q psy1084 11 EEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90 (110)
Q Consensus 11 ~e~~~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~ 90 (110)
-|++++..||++++..++.+..+|.|.+|+++.+-|.+.|||.|+|++|+++.|.|+..++.+++.+ +++..+.|++|.
T Consensus 16 ~e~~ef~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk-~~~~~~~r~isK 94 (114)
T KOG3459|consen 16 PEEEEFNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKK-AKPVNKDRFISK 94 (114)
T ss_pred ccccccCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCccc-CCccchhhhhhe
Confidence 3677889999999999999999999999999999999999999999999999999999887776654 566777899999
Q ss_pred EEEeCCcEEEEeeCCc
Q psy1084 91 MFLRGDSVILILKNPL 106 (110)
Q Consensus 91 i~IRGd~Vv~I~~~~~ 106 (110)
+|||||+|+++-..|.
T Consensus 95 ~flRGdsvI~v~r~pl 110 (114)
T KOG3459|consen 95 MFLRGDSVILVLRNPL 110 (114)
T ss_pred eeecCCeEEEEEecch
Confidence 9999999999986554
No 29
>KOG1780|consensus
Probab=99.71 E-value=3.1e-17 Score=104.63 Aligned_cols=69 Identities=20% Similarity=0.443 Sum_probs=59.3
Q ss_pred CcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 19 GPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 19 ~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
.| -|++++ +|++.+.|.+||.+.|.|+|||.|||+||+||+|.-.. +. ...+|.++|||++|
T Consensus 6 ~P--eLkkym--dKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~----~~----------~~~ig~~vIrgnsi 67 (77)
T KOG1780|consen 6 HP--ELKKYM--DKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGD----GD----------KNNIGMVVIRGNSI 67 (77)
T ss_pred Cc--hHHHhh--hheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCc----CC----------cceeeeEEEeccEE
Confidence 56 789999 99999999999999999999999999999999997422 11 23589999999999
Q ss_pred EEEeeCC
Q psy1084 99 ILILKNP 105 (110)
Q Consensus 99 v~I~~~~ 105 (110)
+.+.+-+
T Consensus 68 v~~eaL~ 74 (77)
T KOG1780|consen 68 VMVEALE 74 (77)
T ss_pred EEEeecc
Confidence 9987644
No 30
>KOG1781|consensus
Probab=99.67 E-value=7.7e-18 Score=112.61 Aligned_cols=76 Identities=18% Similarity=0.328 Sum_probs=62.6
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEee
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 103 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~~ 103 (110)
|.+++ +++|+|++.+||++.|+|+|||+.|||||+|++|+...+..+. +.....|.+|++++||..+++|++
T Consensus 22 Lsky~--Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~------~~~~~tR~LGLvV~RGTalvlisp 93 (108)
T KOG1781|consen 22 LSKYL--DKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPY------KLTDETRKLGLVVCRGTALVLISP 93 (108)
T ss_pred HHHhh--ccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCcc------chhhhhheeeeEEEcccEEEEEcC
Confidence 45555 9999999999999999999999999999999999976533211 122335889999999999999999
Q ss_pred CCcc
Q psy1084 104 NPLA 107 (110)
Q Consensus 104 ~~~~ 107 (110)
.+..
T Consensus 94 ~dG~ 97 (108)
T KOG1781|consen 94 ADGS 97 (108)
T ss_pred Ccch
Confidence 8753
No 31
>KOG1775|consensus
Probab=99.61 E-value=7.3e-16 Score=98.99 Aligned_cols=78 Identities=23% Similarity=0.514 Sum_probs=66.3
Q ss_pred hcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEe
Q psy1084 15 SFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLR 94 (110)
Q Consensus 15 ~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IR 94 (110)
-+...|+.++.+++ +++|.|.+++++++.|+|+|||.|.|++|+||+|+-.. +. ++ +-.+++++++.
T Consensus 3 ~~~llPlEliDkcI--gski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~-~e-gr---------~~tk~~~iLLn 69 (84)
T KOG1775|consen 3 PSTLLPLELIDKCI--GSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEIT-PE-GR---------RMTKLDQILLN 69 (84)
T ss_pred hhhcccHHHHHHhc--CceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeC-CC-cc---------eeeeeeeeeec
Confidence 35568999999999 99999999999999999999999999999999997432 21 11 23468999999
Q ss_pred CCcEEEEeeCC
Q psy1084 95 GDSVILILKNP 105 (110)
Q Consensus 95 Gd~Vv~I~~~~ 105 (110)
|++|.+..|.-
T Consensus 70 GNni~mLvPGG 80 (84)
T KOG1775|consen 70 GNNITMLVPGG 80 (84)
T ss_pred CCcEEEEecCC
Confidence 99999998764
No 32
>KOG3168|consensus
Probab=99.50 E-value=5.1e-15 Score=107.31 Aligned_cols=75 Identities=23% Similarity=0.537 Sum_probs=59.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEee
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 103 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~~ 103 (110)
|-.++ |++++|.++|||.|.|.+++||+||||+|.||+|.....++.++ ... ..+.|.+|++++||+||++.+.
T Consensus 9 ml~~i--Nyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~---~~~-~eEkr~lgLvllRgenIvs~tV 82 (177)
T KOG3168|consen 9 MLQHI--NYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRK---MTD-GEEKRVLGLVLLRGENIVSMTV 82 (177)
T ss_pred HHHhh--cceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhcccccccc---ccc-cceeeEEEEEEecCCcEEEEec
Confidence 34455 99999999999999999999999999999999998655443321 011 1246789999999999999976
Q ss_pred C
Q psy1084 104 N 104 (110)
Q Consensus 104 ~ 104 (110)
.
T Consensus 83 e 83 (177)
T KOG3168|consen 83 E 83 (177)
T ss_pred c
Confidence 5
No 33
>KOG1784|consensus
Probab=99.50 E-value=2.4e-14 Score=94.66 Aligned_cols=74 Identities=22% Similarity=0.393 Sum_probs=62.0
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I 101 (110)
+-|..++ +++|.|.+.|||.+.|.|+|||+-.||+|+|+.|++..... +. ..-.+|..+|||+||.+|
T Consensus 3 s~L~~y~--n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~-gv---------~q~~lGlyiirgeNva~i 70 (96)
T KOG1784|consen 3 STLEDYM--NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETE-GV---------EQIVLGLYIIRGENVAVI 70 (96)
T ss_pred hhHHHHh--hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhc-ch---------hheeeEEEEEecCcccee
Confidence 4588999 99999999999999999999999999999999998754221 11 134589999999999999
Q ss_pred eeCCcc
Q psy1084 102 LKNPLA 107 (110)
Q Consensus 102 ~~~~~~ 107 (110)
++.+-.
T Consensus 71 g~iDEe 76 (96)
T KOG1784|consen 71 GEIDEE 76 (96)
T ss_pred eecchh
Confidence 987644
No 34
>KOG1783|consensus
Probab=99.50 E-value=6.6e-15 Score=93.74 Aligned_cols=72 Identities=21% Similarity=0.353 Sum_probs=63.4
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCc
Q psy1084 18 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 97 (110)
Q Consensus 18 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~ 97 (110)
..|-++|.... |++|.|+|.+|-.|+|+|.+.|.|||+.|+.++|+.. |+ ..+..|..||||++
T Consensus 5 ~~~~~fl~~ii--Gr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-----gq---------l~n~ygdaFirGnn 68 (77)
T KOG1783|consen 5 SMPGEFLKAII--GRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-----GQ---------LKNKYGDAFIRGNN 68 (77)
T ss_pred cCcHHHHHHHh--CCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-----Cc---------ccccccceeecccc
Confidence 46889999999 9999999999999999999999999999999999752 32 13468999999999
Q ss_pred EEEEeeCC
Q psy1084 98 VILILKNP 105 (110)
Q Consensus 98 Vv~I~~~~ 105 (110)
|.+|+...
T Consensus 69 VlyIs~~~ 76 (77)
T KOG1783|consen 69 VLYISTQK 76 (77)
T ss_pred EEEEEecc
Confidence 99998753
No 35
>KOG1782|consensus
Probab=99.48 E-value=5.5e-15 Score=102.30 Aligned_cols=72 Identities=26% Similarity=0.403 Sum_probs=61.3
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEee
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 103 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~~ 103 (110)
|..++ ++++.|-|||||...|.|++||||-|++|++|+|++.... ..++...|..+|||+||++++.
T Consensus 14 l~~~~--dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-----------~Y~di~~glfiIRGENVvllGe 80 (129)
T KOG1782|consen 14 LVEYL--DKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-----------KYCDIPRGLFIIRGENVVLLGE 80 (129)
T ss_pred HHHHh--cceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-----------eecccCceEEEEecCcEEEEec
Confidence 56666 9999999999999999999999999999999999876521 1235567999999999999998
Q ss_pred CCccC
Q psy1084 104 NPLAL 108 (110)
Q Consensus 104 ~~~~~ 108 (110)
.|...
T Consensus 81 id~dk 85 (129)
T KOG1782|consen 81 IDLDK 85 (129)
T ss_pred CCcch
Confidence 87543
No 36
>KOG3293|consensus
Probab=99.33 E-value=3.2e-12 Score=88.71 Aligned_cols=75 Identities=21% Similarity=0.294 Sum_probs=63.6
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCc
Q psy1084 18 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDS 97 (110)
Q Consensus 18 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~ 97 (110)
+.|+++|+.+- +.++.|.|++|..|.|.|+..|.+|||.|.+|+++..+ +. + --.+..++|||++
T Consensus 1 mlPLsLL~~aq--~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~D----gd--k-------f~r~pEcYirGtt 65 (134)
T KOG3293|consen 1 MLPLSLLKTAQ--NHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSED----GD--K-------FFRMPECYIRGTT 65 (134)
T ss_pred CcchhHHHhcC--CCeEEEEecCCCEecceeecchhhhhcchheeEEeccC----CC--c-------eeecceeEEecce
Confidence 36999999998 99999999999999999999999999999999987432 21 1 1237899999999
Q ss_pred EEEEeeCCcc
Q psy1084 98 VILILKNPLA 107 (110)
Q Consensus 98 Vv~I~~~~~~ 107 (110)
|-++..++..
T Consensus 66 Ikylri~d~i 75 (134)
T KOG3293|consen 66 IKYLRIPDEI 75 (134)
T ss_pred eEEEeccHHH
Confidence 9999877643
No 37
>KOG3172|consensus
Probab=99.25 E-value=1.8e-11 Score=83.28 Aligned_cols=76 Identities=13% Similarity=0.298 Sum_probs=65.3
Q ss_pred cCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeC
Q psy1084 16 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRG 95 (110)
Q Consensus 16 ~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRG 95 (110)
+..-|+.+|+++- +.-|++.+..|..|+|+|+..|.+||++|+|++-+.. ++. ..++.++||||
T Consensus 2 s~gvpiKlLhEaq--GhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~----dg~----------vs~le~V~IRG 65 (119)
T KOG3172|consen 2 SVGVPIKLLHEAQ--GHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTAR----DGR----------VSQLEQVFIRG 65 (119)
T ss_pred ccccceeeeeccc--CcEEEEEecCCceeeeeeEEeccccccEEEEEEEEcc----CCc----------ceeeeeEEEec
Confidence 3457999999997 9999999999999999999999999999999886642 221 24689999999
Q ss_pred CcEEEEeeCCcc
Q psy1084 96 DSVILILKNPLA 107 (110)
Q Consensus 96 d~Vv~I~~~~~~ 107 (110)
+.|.++..+|..
T Consensus 66 S~IRFlvlPdmL 77 (119)
T KOG3172|consen 66 SKIRFLVLPDML 77 (119)
T ss_pred CeEEEEECchHh
Confidence 999999987754
No 38
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.21 E-value=6.6e-12 Score=78.60 Aligned_cols=45 Identities=29% Similarity=0.400 Sum_probs=38.5
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEeccccceEeceeEEEeec
Q psy1084 24 LTDSVKHNTQVLINCRNN----KKLLGRVKAFDRHCNMVLENVKEMWTE 68 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~g----r~i~G~L~~fD~~mNlvL~d~~E~~~~ 68 (110)
|.+++.++.||+|.++.- ..+.|.|+|||+||||+|.||+|.|..
T Consensus 1 ~~~~~~er~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 1 LHRCVQERIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CchhhhCCcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 356777899999999853 367899999999999999999999854
No 39
>KOG3448|consensus
Probab=99.15 E-value=3.2e-10 Score=74.85 Aligned_cols=72 Identities=18% Similarity=0.311 Sum_probs=57.6
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEE
Q psy1084 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 100 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~ 100 (110)
.++++.++ |++|.|.|+++-.|.|+|.+.|+|.||-|.|..-. .+.+ .+. --.+..+||||+.|.+
T Consensus 4 ysfFkslv--g~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~k--------yPh--m~Sv~ncfIRGSvvrY 69 (96)
T KOG3448|consen 4 YSFFKSLV--GKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDK--------YPH--MLSVKNCFIRGSVVRY 69 (96)
T ss_pred HHHHHHhc--CCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--Cccc--------CCC--eeeeeeEEEeccEEEE
Confidence 47888999 99999999999999999999999999999996643 2111 111 1246789999999999
Q ss_pred EeeCCc
Q psy1084 101 ILKNPL 106 (110)
Q Consensus 101 I~~~~~ 106 (110)
|..+..
T Consensus 70 v~l~kd 75 (96)
T KOG3448|consen 70 VQLPKD 75 (96)
T ss_pred EEeChh
Confidence 988643
No 40
>KOG3428|consensus
Probab=98.60 E-value=4.1e-07 Score=62.06 Aligned_cols=69 Identities=20% Similarity=0.322 Sum_probs=57.4
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEE
Q psy1084 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 100 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~ 100 (110)
..+|..+. +.+|+|.|++|..+.|++.+.|-+||..|.++.=. .. ++ ...+..+.|||+||.+
T Consensus 4 vr~L~kl~--~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t--~~---~~----------pv~l~~lsirgnniRy 66 (109)
T KOG3428|consen 4 VRFLKKLL--NERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMT--VK---GE----------PVRLDTLSIRGNNIRY 66 (109)
T ss_pred HHHHHHhh--CCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEe--cC---CC----------ceeEEEEEeecceEEE
Confidence 45788888 99999999999999999999999999999997743 21 11 1247789999999999
Q ss_pred EeeCCc
Q psy1084 101 ILKNPL 106 (110)
Q Consensus 101 I~~~~~ 106 (110)
+..++.
T Consensus 67 ~~lpD~ 72 (109)
T KOG3428|consen 67 YILPDS 72 (109)
T ss_pred EEccCC
Confidence 988765
No 41
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=97.39 E-value=0.00048 Score=42.74 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=34.0
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 23 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
+|..+...+.+|+|.|.+|-.++|.+.|||+|+=|+-.+
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 677787889999999999999999999999998665543
No 42
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=97.32 E-value=0.0007 Score=42.04 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=34.2
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.+|..+...+.+|+|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 3677777789999999999999999999999998665533
No 43
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=97.09 E-value=0.0014 Score=42.58 Aligned_cols=40 Identities=25% Similarity=0.344 Sum_probs=34.4
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.+|..+...+..|+|.|.+|-.++|.+.|||+|+=|+-.+
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 3677777789999999999999999999999998666544
No 44
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.01 E-value=0.0038 Score=39.57 Aligned_cols=69 Identities=13% Similarity=0.224 Sum_probs=40.6
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEecc---ccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDR---HCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~---~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
.++..++ |++|.|.+++|..|.|.|.+++. -+.++|.-|...-.... .. ...........++|.++.|
T Consensus 5 ~l~~~lv--G~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~---~~----~~~~~~~~~~tlii~~~dv 75 (77)
T PF14438_consen 5 YLLTNLV--GQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQ---SN----SDPLSSEIVETLIIPAKDV 75 (77)
T ss_dssp HHHHTTT--TSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-------------EEEEEEE-GGGEEE----
T ss_pred HHHHhCc--CCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccccc---cc----CCccCCCCCceEEEecccc
Confidence 4567777 99999999999999999999999 89999988776532100 00 0111223356788888776
Q ss_pred E
Q psy1084 99 I 99 (110)
Q Consensus 99 v 99 (110)
+
T Consensus 76 v 76 (77)
T PF14438_consen 76 V 76 (77)
T ss_dssp -
T ss_pred C
Confidence 5
No 45
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=96.66 E-value=0.0048 Score=39.85 Aligned_cols=36 Identities=31% Similarity=0.361 Sum_probs=32.0
Q ss_pred HHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceE
Q psy1084 23 ILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMV 58 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlv 58 (110)
+|..+..++.+|.|.|.+|-..+|.+.|||+|.=|+
T Consensus 11 fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 11 FLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred HHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 677787889999999999999999999999997433
No 46
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.68 E-value=0.026 Score=41.31 Aligned_cols=40 Identities=23% Similarity=0.329 Sum_probs=34.8
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.+|..+...+.+|+|.|.+|-.++|.+.|||+|+=|+..+
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 4678888889999999999999999999999998666544
No 47
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=95.66 E-value=0.027 Score=41.24 Aligned_cols=40 Identities=23% Similarity=0.228 Sum_probs=34.4
Q ss_pred HHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 22 SILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 22 ~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.+|..+...+.+|.|.|.+|-.++|.+.+||+|.=|+-.+
T Consensus 15 ~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 15 IFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 4678888889999999999999999999999998555544
No 48
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.56 E-value=0.21 Score=33.48 Aligned_cols=72 Identities=14% Similarity=0.250 Sum_probs=51.7
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEEEEecc-ccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEee
Q psy1084 25 TDSVKHNTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 103 (110)
Q Consensus 25 ~~~~~~~krV~V~l~~gr~i~G~L~~fD~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~~ 103 (110)
..|+ |++|.+..+.+-.|.|+|...|. -.++.|.+|.-+-++.++... .-.........+.+||..|--+..
T Consensus 4 ~~~I--Gs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~-----~ipp~~~v~~~I~Fr~sDIkdL~v 76 (96)
T PF12701_consen 4 DPYI--GSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDR-----EIPPSDEVYDYIVFRGSDIKDLKV 76 (96)
T ss_dssp CCCT--TCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS--------C-CSSSSEEEEETTTEEEEEE
T ss_pred cccc--CCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCc-----ccCCCCceeeEEEEEccccceEEE
Confidence 3567 99999999999999999999998 789999998876443211110 000112346889999999987754
No 49
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=95.08 E-value=0.14 Score=29.67 Aligned_cols=33 Identities=9% Similarity=0.245 Sum_probs=28.6
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEeceeEE
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKE 64 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E 64 (110)
+++|++.+ ++..+.|+..+.|..-.|+++....
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 89999999 6777899999999999999966433
No 50
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=94.90 E-value=0.07 Score=33.05 Aligned_cols=31 Identities=29% Similarity=0.372 Sum_probs=28.4
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
|..|.+.+-.|.+|+|.+.+||.-.+|++=.
T Consensus 6 Gs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 6 GSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 8999999999999999999999999887643
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=91.70 E-value=2.1 Score=27.50 Aligned_cols=69 Identities=13% Similarity=0.214 Sum_probs=47.6
Q ss_pred hhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEE
Q psy1084 26 DSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 100 (110)
Q Consensus 26 ~~~~~~krV~V~l~~gr~i~G~L~~fD~~m-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~ 100 (110)
.++ |++|.+..+.+-.|.|.|..+|..= -+.|.||.-+-++..+.+. . .-.....-...++.||+.|--
T Consensus 3 ~~I--G~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~-~---~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYI--GSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDG-P---EIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccc--CceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCC-C---ccCCCCcceeEEEEcCCcccc
Confidence 456 9999999999999999999999876 5668998766554322110 0 000112346889999998754
No 52
>PRK14638 hypothetical protein; Provisional
Probab=90.92 E-value=0.45 Score=34.06 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=27.1
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|+|.+++++.+.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 95 YVRFT--GKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 45666 999999999999999999999963 3444
No 53
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=89.92 E-value=3.5 Score=26.82 Aligned_cols=64 Identities=25% Similarity=0.258 Sum_probs=45.9
Q ss_pred cHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcE
Q psy1084 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSV 98 (110)
Q Consensus 20 Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~m-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~V 98 (110)
-+.+|.... |++|.+.+.++..+.|...|+|-.. |+.+++=. .|- ......+||..-|
T Consensus 15 fLr~l~~~~--gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-----TPl--------------Gv~~eAlLR~~DV 73 (80)
T PF11095_consen 15 FLRSLLAMV--GKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-----TPL--------------GVQPEALLRCSDV 73 (80)
T ss_dssp HHHHHHHCT--TSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-----TTT--------------TEEEEEEEEGGGE
T ss_pred HHHHHHHhc--CCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-----CCc--------------ccChhheeecCCE
Confidence 355566666 9999999999999999999999876 66665411 111 1257899999999
Q ss_pred EEEeeC
Q psy1084 99 ILILKN 104 (110)
Q Consensus 99 v~I~~~ 104 (110)
++++..
T Consensus 74 i~~~f~ 79 (80)
T PF11095_consen 74 ISISFD 79 (80)
T ss_dssp EEEEE-
T ss_pred EEEEec
Confidence 999763
No 54
>PRK14639 hypothetical protein; Provisional
Probab=89.59 E-value=0.69 Score=32.74 Aligned_cols=33 Identities=24% Similarity=0.456 Sum_probs=27.6
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|+|.+.+++.+.|+|.++|.- ++.|
T Consensus 83 f~r~~--G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 83 FAKSI--GELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHhC--CCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 45666 999999999999999999999983 4444
No 55
>PRK02001 hypothetical protein; Validated
Probab=89.43 E-value=0.7 Score=33.28 Aligned_cols=33 Identities=21% Similarity=0.447 Sum_probs=27.5
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL 59 (110)
..+++ |+.|+|.+.+++.+.|+|.++|.- ++.|
T Consensus 85 f~r~~--G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 85 YKKNI--GRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHhC--CCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 35666 999999999999999999999974 4444
No 56
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=88.22 E-value=0.87 Score=33.16 Aligned_cols=34 Identities=9% Similarity=0.260 Sum_probs=30.7
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccc
Q psy1084 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRH 54 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~ 54 (110)
+++...+.++++-|+|.+.|||++.|.=.|.|..
T Consensus 110 F~Icrka~qqg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 110 FSICRKAHQQGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred HHHHHHHHHCCCeEEEEEcCCcEEEeeecccceE
Confidence 6788889999999999999999999999888754
No 57
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=87.42 E-value=1.7 Score=31.81 Aligned_cols=40 Identities=30% Similarity=0.410 Sum_probs=29.9
Q ss_pred CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecccc-ceEece
Q psy1084 18 TGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHC-NMVLEN 61 (110)
Q Consensus 18 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~m-NlvL~d 61 (110)
.+|+.+ ..++ +|.|+|.+.+ +++.|.|..+|--. |+||-+
T Consensus 7 ~~p~~~-~~yv--~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~ 47 (166)
T PF06372_consen 7 KSPLEW-QDYV--GKEVKVTLSD-KEYKGWVYTIDPVSASIVLVN 47 (166)
T ss_dssp S-HHHH-HCTT--T-EEEEEETT-EEEEEEEEEE-TTT--EEEEE
T ss_pred CCHHHH-HHhh--CcEEEEEEec-cEEEEEEEEeCCCCCeEEEEE
Confidence 356655 6677 9999999999 99999999999866 888864
No 58
>PRK14644 hypothetical protein; Provisional
Probab=84.01 E-value=2.3 Score=29.97 Aligned_cols=33 Identities=9% Similarity=0.224 Sum_probs=27.1
Q ss_pred HHhhhhCCcEEEEEecCC----eEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNN----KKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~g----r~i~G~L~~fD~~mNlvL 59 (110)
+.+++ |+.|.|.|++. +.+.|.|.++|.. ++.|
T Consensus 80 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l 116 (136)
T PRK14644 80 LENHI--GEIIDVSLNKEVNKTDFITGELLENNPE-TITL 116 (136)
T ss_pred HHHhC--CCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEE
Confidence 56777 99999999876 8899999999983 4555
No 59
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=82.90 E-value=2.7 Score=30.65 Aligned_cols=34 Identities=18% Similarity=0.122 Sum_probs=30.8
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 29 ~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
..+-+|+|.+.||..|.|++-+|+.--|++|.-+
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~ 60 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD 60 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence 3489999999999999999999999999998653
No 60
>PRK14640 hypothetical protein; Provisional
Probab=82.35 E-value=2.9 Score=29.89 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=26.2
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~~mNlvL 59 (110)
+.+++ |+.|.|.++ +++.+.|.|.++|.. ++.|
T Consensus 92 f~r~~--G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 92 FEKYV--GQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 45666 999999994 668999999999984 4444
No 61
>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=82.13 E-value=3.4 Score=26.31 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=25.0
Q ss_pred HhhhhCCcEEEEEec---CC-eEEEEEEEEeccccceEe
Q psy1084 25 TDSVKHNTQVLINCR---NN-KKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 25 ~~~~~~~krV~V~l~---~g-r~i~G~L~~fD~~mNlvL 59 (110)
.++. |+.|.|.++ +| +.+.|.|.++|.- ++.|
T Consensus 21 ~r~~--G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 21 ERAV--GKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHhC--CCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 5566 999999997 55 6899999999983 3444
No 62
>PRK14636 hypothetical protein; Provisional
Probab=81.80 E-value=2.9 Score=30.77 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEec---CC-eEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCR---NN-KKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~---~g-r~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.|+ +| +.+.|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 93 FADWA--GHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHhC--CCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 45666 999999997 45 6999999999883 4444
No 63
>PRK14642 hypothetical protein; Provisional
Probab=81.36 E-value=3.1 Score=31.30 Aligned_cols=29 Identities=17% Similarity=0.236 Sum_probs=24.6
Q ss_pred HHhhhhCCcEEEEEec-------------CCeEEEEEEEEeccc
Q psy1084 24 LTDSVKHNTQVLINCR-------------NNKKLLGRVKAFDRH 54 (110)
Q Consensus 24 L~~~~~~~krV~V~l~-------------~gr~i~G~L~~fD~~ 54 (110)
+.++. |+.|.|.|+ +.+.|+|+|.++|..
T Consensus 95 f~rfi--G~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~ 136 (197)
T PRK14642 95 FERFA--GEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG 136 (197)
T ss_pred HHHhC--CCeEEEEEeccccccccccccCCceEEEEEEEEEcCC
Confidence 35566 999999998 678999999999884
No 64
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.13 E-value=3.4 Score=29.89 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=28.2
Q ss_pred HHHhhhhCCcEEEEEe----cCCeEEEEEEEEeccccceEe
Q psy1084 23 ILTDSVKHNTQVLINC----RNNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l----~~gr~i~G~L~~fD~~mNlvL 59 (110)
-+.++. |+.|.|+| .+++.++|+|.++|.-. +.+
T Consensus 93 ~f~r~~--G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 93 HFARFI--GEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred HHHHhc--CcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 356677 99999999 67899999999999987 444
No 65
>PRK14633 hypothetical protein; Provisional
Probab=80.72 E-value=3.6 Score=29.37 Aligned_cols=33 Identities=18% Similarity=0.220 Sum_probs=25.9
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.++ +++.+.|+|.++|+. ++.|
T Consensus 89 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 89 AQALV--GFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHhC--CCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 35666 999999984 568999999999984 4444
No 66
>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=80.49 E-value=3 Score=29.05 Aligned_cols=34 Identities=15% Similarity=0.285 Sum_probs=24.6
Q ss_pred HHHhhhhCCcEEEEEec----CCeEEEEEEEEeccccceEe
Q psy1084 23 ILTDSVKHNTQVLINCR----NNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~----~gr~i~G~L~~fD~~mNlvL 59 (110)
-+.+++ |+.|.|+++ +.+.+.|+|.++|. -+++|
T Consensus 81 ~~~~~i--G~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 81 DFERFI--GRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHH---SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHhc--CCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 457777 999999994 45789999999999 34444
No 67
>PRK14645 hypothetical protein; Provisional
Probab=80.06 E-value=3.5 Score=29.66 Aligned_cols=32 Identities=13% Similarity=0.266 Sum_probs=24.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.+ +++.+.|+|.++|.- ++.|
T Consensus 97 f~r~~--G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 97 FERFA--GLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHhC--CCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 35666 99999976 789999999999984 3444
No 68
>PRK14643 hypothetical protein; Provisional
Probab=79.15 E-value=4.1 Score=29.61 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=26.3
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEeccc-cceEe
Q psy1084 24 LTDSVKHNTQVLINCRN----NKKLLGRVKAFDRH-CNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~----gr~i~G~L~~fD~~-mNlvL 59 (110)
+.++. |+.|.|.|+. .+.+.|+|.++|.- ..+.|
T Consensus 99 f~r~~--G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 99 LVKAL--NQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHhc--CCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 45677 9999999974 58899999999864 34433
No 69
>PRK14632 hypothetical protein; Provisional
Probab=78.52 E-value=4.4 Score=29.62 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=25.8
Q ss_pred HHhhhhCCcEEEEEecC-------CeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRN-------NKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~-------gr~i~G~L~~fD~~mNlvL 59 (110)
+.+++ |+.|.|.+++ .+.|.|+|.++|.- ++.|
T Consensus 93 f~r~i--G~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 93 MSPYV--GRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHhC--CCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 45666 9999999975 57999999999863 4444
No 70
>PRK14646 hypothetical protein; Provisional
Probab=77.91 E-value=4.9 Score=28.87 Aligned_cols=33 Identities=12% Similarity=0.102 Sum_probs=25.7
Q ss_pred HHhhhhCCcEEEEEecC---C-eEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRN---N-KKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~---g-r~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.|++ | +.+.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 95 FKTFK--GFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHhC--CCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 46666 9999999964 2 6789999999984 4554
No 71
>PRK14634 hypothetical protein; Provisional
Probab=77.56 E-value=5.1 Score=28.76 Aligned_cols=33 Identities=12% Similarity=0.213 Sum_probs=25.3
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRN----NKKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~----gr~i~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.+.+ .+.|.|+|.++|.- ++.|
T Consensus 95 f~r~~--G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 95 FQTFR--GFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHhC--CCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 35666 9999999973 37899999999984 3444
No 72
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=77.45 E-value=7.4 Score=24.35 Aligned_cols=59 Identities=15% Similarity=0.311 Sum_probs=40.0
Q ss_pred cCCCc--HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEE
Q psy1084 16 FATGP--LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFL 93 (110)
Q Consensus 16 ~~~~P--l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~I 93 (110)
+..+| ...|++++ |++|.|.+-.|. ++|+|.+...- .++|+. .-..+||
T Consensus 6 s~vdpyvyq~lq~li--G~~vvV~T~~g~-v~G~L~~V~pD-hIvl~~-------------------------~~~~~~I 56 (66)
T PF10842_consen 6 SLVDPYVYQTLQSLI--GQRVVVQTTRGS-VRGILVDVKPD-HIVLEE-------------------------NGTPFFI 56 (66)
T ss_pred eccCHHHHHHHHHhc--CCEEEEEEcCCc-EEEEEEeecCC-EEEEEe-------------------------CCcEEEE
Confidence 44567 56689999 999999996655 49999876421 123311 1245889
Q ss_pred eCCcEEEEee
Q psy1084 94 RGDSVILILK 103 (110)
Q Consensus 94 RGd~Vv~I~~ 103 (110)
|=..|++|.|
T Consensus 57 R~~~IV~v~p 66 (66)
T PF10842_consen 57 RIAQIVWVMP 66 (66)
T ss_pred EeeeEEEEcC
Confidence 9888888754
No 73
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=75.67 E-value=6.2 Score=28.02 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=23.9
Q ss_pred HHhhhhCCcEEEEEe----cCCeEEEEEEEEecc
Q psy1084 24 LTDSVKHNTQVLINC----RNNKKLLGRVKAFDR 53 (110)
Q Consensus 24 L~~~~~~~krV~V~l----~~gr~i~G~L~~fD~ 53 (110)
+.+++ |+.|.|.+ .+++.+.|+|.++|.
T Consensus 93 f~r~~--G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 93 FRRFI--GREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHhC--CCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 46677 99999997 467899999999998
No 74
>PRK14647 hypothetical protein; Provisional
Probab=74.27 E-value=6.9 Score=28.11 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=23.3
Q ss_pred HHhhhhCCcEEEEEec---------CCeEEEEEEEEecc
Q psy1084 24 LTDSVKHNTQVLINCR---------NNKKLLGRVKAFDR 53 (110)
Q Consensus 24 L~~~~~~~krV~V~l~---------~gr~i~G~L~~fD~ 53 (110)
+.+++ |+.|.|.++ +.+.+.|+|.++|.
T Consensus 94 f~r~~--G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 94 YERYA--GRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHhC--CcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 45666 999999995 34899999999997
No 75
>PRK14631 hypothetical protein; Provisional
Probab=72.23 E-value=7.8 Score=28.43 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=23.1
Q ss_pred HHhhhhCCcEEEEEec----CCeEEEEEEEEec
Q psy1084 24 LTDSVKHNTQVLINCR----NNKKLLGRVKAFD 52 (110)
Q Consensus 24 L~~~~~~~krV~V~l~----~gr~i~G~L~~fD 52 (110)
+.++. |+.|.|.+. +.+.|.|+|.++|
T Consensus 112 f~r~~--G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 112 LQGYI--GQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHhC--CCeEEEEEecccCCceEEEEEEEEee
Confidence 46666 999999996 4589999999998
No 76
>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=72.09 E-value=9.8 Score=25.64 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=19.0
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEE
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVK 49 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~ 49 (110)
|-..+.-+.+|.+.|+||+.+.|++.
T Consensus 21 lv~~L~ge~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 21 LVSELDGEERVELELDDGSMLRGTVA 46 (101)
T ss_dssp HHHCTTTT-EEEEEETTS-EEEEEEC
T ss_pred HHhhcCCcceEEEEEcCCCeeeeeec
Confidence 33444568899999999999999874
No 77
>PRK10898 serine endoprotease; Provisional
Probab=71.29 E-value=8.9 Score=30.73 Aligned_cols=33 Identities=6% Similarity=0.209 Sum_probs=28.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
....+.|.+.||+.+.+.++++|...+|.|=.+
T Consensus 100 ~a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 100 DADQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CCCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 356789999999999999999999999988443
No 78
>PRK14637 hypothetical protein; Provisional
Probab=70.05 E-value=8.5 Score=27.56 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=24.6
Q ss_pred HHhhhhCCcEEEEEecCCeEE-EEEEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKL-LGRVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i-~G~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.+.+...+ .|+|.++|.- ++.|
T Consensus 93 f~r~~--G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 93 FSIFV--GETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHhC--CCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 45666 99999999544556 7999999885 4444
No 79
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=69.01 E-value=10 Score=30.22 Aligned_cols=32 Identities=9% Similarity=0.271 Sum_probs=27.9
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
...+.|.+.+|+.+.+.++++|...+|.|=.+
T Consensus 101 ~~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 101 ADQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 45688999999999999999999999998443
No 80
>PRK14641 hypothetical protein; Provisional
Probab=68.81 E-value=9.4 Score=28.04 Aligned_cols=27 Identities=11% Similarity=0.302 Sum_probs=22.2
Q ss_pred HHhhhhCCcEEEEEecC----CeEEEEEEEEec
Q psy1084 24 LTDSVKHNTQVLINCRN----NKKLLGRVKAFD 52 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~----gr~i~G~L~~fD 52 (110)
..++. |+.|.|.|.+ .+.+.|.|.++|
T Consensus 99 f~r~~--G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 99 YGRHV--GRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHhC--CCEEEEEEecccCCeEEEEEEEEeee
Confidence 45666 9999999975 468999999995
No 81
>PRK10139 serine endoprotease; Provisional
Probab=67.40 E-value=11 Score=31.24 Aligned_cols=34 Identities=9% Similarity=0.279 Sum_probs=29.6
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 29 ~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
.....+.|.+.||+.+.+.++++|....|.+=.+
T Consensus 112 ~~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 112 NQAQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 3567899999999999999999999999988443
No 82
>PRK10942 serine endoprotease; Provisional
Probab=66.18 E-value=12 Score=31.27 Aligned_cols=32 Identities=16% Similarity=0.292 Sum_probs=28.4
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
....|.|.+.||+++.+.++++|...+|.|=.
T Consensus 134 ~a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 134 NATKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CCCEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 45678999999999999999999999998854
No 83
>PRK06955 biotin--protein ligase; Provisional
Probab=65.44 E-value=20 Score=28.08 Aligned_cols=34 Identities=12% Similarity=0.185 Sum_probs=28.5
Q ss_pred hhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 28 VKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 28 ~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
+..+++|+|...+++.+.|+.+|+|..-.|++++
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 3458999997666778999999999999999953
No 84
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=63.81 E-value=8.3 Score=22.15 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=14.8
Q ss_pred EEEEEEEeccccceEeceeEEE
Q psy1084 44 LLGRVKAFDRHCNMVLENVKEM 65 (110)
Q Consensus 44 i~G~L~~fD~~mNlvL~d~~E~ 65 (110)
..|+..|.|+.+.|+|++....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6799999999999999886654
No 85
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=59.34 E-value=18 Score=29.49 Aligned_cols=33 Identities=3% Similarity=0.226 Sum_probs=28.6
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
....+.|.+.+|+.+.+.++++|...+|.|=.+
T Consensus 80 ~~~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CCCeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 346788999999999999999999999988443
No 86
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=56.65 E-value=46 Score=20.74 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=29.6
Q ss_pred HHHhhhhCCcEEEEEecC-C--eEEEEEEEEeccccceEe
Q psy1084 23 ILTDSVKHNTQVLINCRN-N--KKLLGRVKAFDRHCNMVL 59 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~~-g--r~i~G~L~~fD~~mNlvL 59 (110)
.|..++..+..|+|..-+ | ..+.|++..+|..-+.+.
T Consensus 34 ~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~ 73 (92)
T PF08863_consen 34 KLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLK 73 (92)
T ss_pred HHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEE
Confidence 477777788999998764 4 468999999999987665
No 87
>KOG3382|consensus
Probab=53.18 E-value=7.3 Score=27.89 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=18.1
Q ss_pred CCeEEEEEEEEeccccceEecee
Q psy1084 40 NNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 40 ~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
.+..=.|+|+|.|+|-|=.-+|-
T Consensus 41 td~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 41 TDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred cccccceeeeeecccccchhccc
Confidence 33445799999999999887765
No 88
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=52.55 E-value=42 Score=26.15 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=26.5
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEec
Q psy1084 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 60 (110)
Q Consensus 29 ~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~ 60 (110)
..|++|++.. ++..+.|++.|.|..-.|++.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 3589999987 445799999999999999995
No 89
>KOG1073|consensus
Probab=52.01 E-value=49 Score=27.22 Aligned_cols=79 Identities=16% Similarity=0.323 Sum_probs=51.9
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEecc-ccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEe
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDR-HCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILIL 102 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~-~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~ 102 (110)
...++ |+.|.++-+..-.|.|+|--.|- -.-|-|.+|--+-++..+.. +.. .+.. .+...-|+.||+.|-.+.
T Consensus 4 ~t~yI--GS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~-~pq--~p~~-~kVy~YIlFRGSDIKDL~ 77 (361)
T KOG1073|consen 4 VTSYI--GSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTD-GPQ--VPPD-DKVYDYILFRGSDIKDLI 77 (361)
T ss_pred ccccc--cceeEEeecccceeeeEEEeccccccceehhheeecccccCCCC-CCc--CCCC-ccceeeEEecCcccceee
Confidence 35567 99999999999999999987773 34677888654433321111 110 1111 124688999999999777
Q ss_pred eCCccC
Q psy1084 103 KNPLAL 108 (110)
Q Consensus 103 ~~~~~~ 108 (110)
..+.++
T Consensus 78 V~~~p~ 83 (361)
T KOG1073|consen 78 VQETPA 83 (361)
T ss_pred eccCcc
Confidence 665544
No 90
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=49.93 E-value=55 Score=24.42 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=26.1
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEec
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 60 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~ 60 (110)
.+++|+|...+ ..+.|+..|.|..-.|+|+
T Consensus 192 ~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 192 IGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred cCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 58999998644 5689999999999999995
No 91
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=49.54 E-value=53 Score=25.56 Aligned_cols=31 Identities=19% Similarity=0.409 Sum_probs=26.8
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.+++|+|.. ++..+.|++.|.|..-.|+|+.
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 589999875 5688999999999999999964
No 92
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=49.38 E-value=7.2 Score=26.15 Aligned_cols=17 Identities=29% Similarity=0.290 Sum_probs=14.8
Q ss_pred EEEEEeccccceEecee
Q psy1084 46 GRVKAFDRHCNMVLENV 62 (110)
Q Consensus 46 G~L~~fD~~mNlvL~d~ 62 (110)
|+|+|.|.|-|.--.+-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999988554
No 93
>PRK14630 hypothetical protein; Provisional
Probab=47.36 E-value=36 Score=24.07 Aligned_cols=28 Identities=7% Similarity=-0.058 Sum_probs=22.0
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccc
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRH 54 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~ 54 (110)
..++. |+.|.|.+.+. ...|+|.++|.-
T Consensus 92 f~r~~--G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 92 FKIFE--GKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred HHHhC--CCEEEEEEcCc-ceEEEEEEEeCC
Confidence 35666 99999999654 359999999883
No 94
>PRK14635 hypothetical protein; Provisional
Probab=47.34 E-value=39 Score=24.30 Aligned_cols=33 Identities=21% Similarity=0.175 Sum_probs=24.4
Q ss_pred HHhhhhCCcEEEEEec--CCeEEEE---EEEEeccccceEe
Q psy1084 24 LTDSVKHNTQVLINCR--NNKKLLG---RVKAFDRHCNMVL 59 (110)
Q Consensus 24 L~~~~~~~krV~V~l~--~gr~i~G---~L~~fD~~mNlvL 59 (110)
+.++. |+.|.|.+. ++..+.| .|.++|.- ++.|
T Consensus 94 ~~r~~--G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 94 LDRFR--GIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHhC--CCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 45666 999999886 4577877 99999874 4444
No 95
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=44.61 E-value=24 Score=21.22 Aligned_cols=43 Identities=14% Similarity=0.166 Sum_probs=30.2
Q ss_pred hhhcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccce
Q psy1084 13 EESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNM 57 (110)
Q Consensus 13 ~~~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNl 57 (110)
..++..++-.+|+.....+.+| +.+++|+. .+.|+.++.|=++
T Consensus 6 ~~e~r~~~~~~l~~v~~~~~pv-~It~~g~~-~~vli~~~~ye~l 48 (75)
T PF02604_consen 6 ITEFRNNFSELLDEVEEGEEPV-IITKNGKP-VAVLISVEDYERL 48 (75)
T ss_dssp HHHHHHTHHHHHHHHHHCT-EE-EEEETTEE-EEEEEEHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCeE-EEEECCCC-CeecccHHHHHHH
Confidence 3455567788888887655567 55677776 8888888877554
No 96
>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=42.84 E-value=40 Score=21.71 Aligned_cols=24 Identities=8% Similarity=0.210 Sum_probs=15.0
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEE
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGR 47 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~ 47 (110)
|.-+-..+.+|++.|+||..+.|+
T Consensus 10 iEiAC~~~~~v~L~l~dG~~~~g~ 33 (80)
T PF07073_consen 10 IEIACMYRYPVKLTLKDGEQIEGK 33 (80)
T ss_dssp HHHHHTTTT-EEEE-TTT--EEES
T ss_pred HHHHHhcCCeEEEEEeCCCEEEEE
Confidence 333334588899999999999996
No 97
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=42.83 E-value=68 Score=27.79 Aligned_cols=32 Identities=28% Similarity=0.346 Sum_probs=27.7
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
.|++|++...++..+.|+..|.|..-.|+|+.
T Consensus 277 ~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 277 HGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred CCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 48999987667778999999999999999953
No 98
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=40.28 E-value=1e+02 Score=23.58 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=29.9
Q ss_pred CCcEEEEEecCCeEEEEEEEEeccccceEecee
Q psy1084 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 30 ~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~ 62 (110)
.+++|++...++..+.|+..+.|..-.|+|+..
T Consensus 189 ~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 189 LGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred CCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 699999999888888889999999999999665
No 99
>PRK08330 biotin--protein ligase; Provisional
Probab=39.37 E-value=1.1e+02 Score=22.75 Aligned_cols=31 Identities=19% Similarity=0.214 Sum_probs=25.6
Q ss_pred CCcEEEEEecCCeEE-EEEEEEeccccceEece
Q psy1084 30 HNTQVLINCRNNKKL-LGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 30 ~~krV~V~l~~gr~i-~G~L~~fD~~mNlvL~d 61 (110)
.+++|++.. ++..+ .|+..|.|..-.|++..
T Consensus 187 ~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 187 LGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred cCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 589999875 55565 69999999999999964
No 100
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=36.66 E-value=51 Score=24.49 Aligned_cols=34 Identities=15% Similarity=0.278 Sum_probs=22.5
Q ss_pred HHHHHhhhhCCcEEEEEe-cCCeEEEEEEEEeccc
Q psy1084 21 LSILTDSVKHNTQVLINC-RNNKKLLGRVKAFDRH 54 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l-~~gr~i~G~L~~fD~~ 54 (110)
++||..+--+--+|.+.+ .++..|+|+|++||.=
T Consensus 123 I~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~ 157 (185)
T PF14153_consen 123 IDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG 157 (185)
T ss_pred HHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC
Confidence 345555443344555555 4678999999999975
No 101
>COG4771 FepA Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]
Probab=34.96 E-value=42 Score=29.81 Aligned_cols=44 Identities=27% Similarity=0.252 Sum_probs=36.4
Q ss_pred ccchhhhhhcCCCcHHHHHhhhhCCcEEEEEec-CCeEEEEEEEE
Q psy1084 7 PKQQEEEESFATGPLSILTDSVKHNTQVLINCR-NNKKLLGRVKA 50 (110)
Q Consensus 7 ~~~~~e~~~~~~~Pl~~L~~~~~~~krV~V~l~-~gr~i~G~L~~ 50 (110)
||+.+|..+...+||+-|..+=..+-.|.|++| .+.+-.|.+..
T Consensus 132 Pp~~IERIEViRGPmSslYGSdA~GGVVNIITkK~~d~W~GSv~~ 176 (699)
T COG4771 132 PPESIERIEVIRGPMSSLYGSDALGGVVNIITKKVGDKWHGSVTL 176 (699)
T ss_pred ChhHeEEEEEeecchhhhcccccccceEEEEeeccCCeeEEEEEe
Confidence 778899999999999999987666999999997 45667776543
No 102
>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=31.71 E-value=54 Score=22.39 Aligned_cols=36 Identities=11% Similarity=0.082 Sum_probs=24.8
Q ss_pred hhcCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEec
Q psy1084 14 ESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFD 52 (110)
Q Consensus 14 ~~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD 52 (110)
......|-..+..-. ....|.++||+.+.|.+++=|
T Consensus 43 l~~I~~P~~~i~~~y---~~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 43 LEAILDPSREVAPGF---EAYRVTLKDGRILSGIVASET 78 (133)
T ss_pred HHHHhCchhhhCccc---ccEEEEECCCCEEEEEEEecC
Confidence 334445655555443 337889999999999998844
No 103
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=30.41 E-value=97 Score=18.72 Aligned_cols=26 Identities=15% Similarity=0.259 Sum_probs=18.0
Q ss_pred hCCcEEEEEecCC-eEEEEEEEEeccc
Q psy1084 29 KHNTQVLINCRNN-KKLLGRVKAFDRH 54 (110)
Q Consensus 29 ~~~krV~V~l~~g-r~i~G~L~~fD~~ 54 (110)
..|.+|.++=-++ ..|.|.+.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 3588999987765 4569999999973
No 104
>PF09196 DUF1953: Domain of unknown function (DUF1953); InterPro: IPR015279 This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. ; PDB: 3HJE_A 1IV8_A.
Probab=28.64 E-value=78 Score=19.50 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=12.9
Q ss_pred EEEeCCcEEEEeeCCcc
Q psy1084 91 MFLRGDSVILILKNPLA 107 (110)
Q Consensus 91 i~IRGd~Vv~I~~~~~~ 107 (110)
=|+|||.|..|.....+
T Consensus 13 gf~r~~kilviiktkgs 29 (66)
T PF09196_consen 13 GFIRFNKILVIIKTKGS 29 (66)
T ss_dssp EEEETTTEEEEEES-TT
T ss_pred eEEecCEEEEEEecccc
Confidence 38999999999876443
No 105
>PRK06630 hypothetical protein; Provisional
Probab=28.18 E-value=30 Score=23.40 Aligned_cols=19 Identities=16% Similarity=0.111 Sum_probs=16.2
Q ss_pred EEEEEEEeccccceEecee
Q psy1084 44 LLGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 44 i~G~L~~fD~~mNlvL~d~ 62 (110)
..|.|+|-|+|-|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999888763
No 106
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=28.08 E-value=61 Score=21.31 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=18.8
Q ss_pred eeeeCeEEEeCCcEEEEeeCC
Q psy1084 85 DRFISKMFLRGDSVILILKNP 105 (110)
Q Consensus 85 ~r~lg~i~IRGd~Vv~I~~~~ 105 (110)
.|+-|.+.++|..+..|..+|
T Consensus 76 ~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred hcceEEEEEECCeeeEEEcCC
Confidence 567899999999999998876
No 107
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=27.84 E-value=1.3e+02 Score=19.25 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=18.8
Q ss_pred HHHhhhhCCcEEEEEecCCe----EEEEEEEE
Q psy1084 23 ILTDSVKHNTQVLINCRNNK----KLLGRVKA 50 (110)
Q Consensus 23 ~L~~~~~~~krV~V~l~~gr----~i~G~L~~ 50 (110)
-|..++ |++|.+..+.|| +-.|.|..
T Consensus 11 ~l~~~v--G~~V~l~a~~GRkK~~~r~GvL~~ 40 (76)
T PF06257_consen 11 ELESHV--GKRVKLKANKGRKKIIEREGVLEE 40 (76)
T ss_dssp HHHHTT--TSEEEEEE--SSS--S-EEEEEEE
T ss_pred HHHHcC--CCEEEEEEcCCceEEEEEEEEEEe
Confidence 467777 999999999997 46898864
No 108
>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=26.78 E-value=1.3e+02 Score=16.87 Aligned_cols=24 Identities=13% Similarity=0.156 Sum_probs=19.8
Q ss_pred CcEEEEEecCCeEEEEEEEEeccc
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRH 54 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~ 54 (110)
|..+.+...+|..++|++.+++.-
T Consensus 6 G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 6 GDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCEEEEEeCCCCEEEEEEEEECCC
Confidence 666666667899999999999964
No 109
>PRK10708 hypothetical protein; Provisional
Probab=26.73 E-value=73 Score=19.58 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=21.5
Q ss_pred CcEEEEEecCCeEEEEEEEEecccc
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHC 55 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~m 55 (110)
+.+|+|++.++-.=.|++.+...|-
T Consensus 4 nD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 4 NDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred ccEEEEecCCCccccceEEEEeecc
Confidence 7899999999988889888887775
No 110
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=25.95 E-value=77 Score=22.38 Aligned_cols=24 Identities=8% Similarity=0.155 Sum_probs=18.2
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEEEE
Q psy1084 25 TDSVKHNTQVLINCRNNKKLLGRVKA 50 (110)
Q Consensus 25 ~~~~~~~krV~V~l~~gr~i~G~L~~ 50 (110)
.+++ .|-++|.|-+|+++..++=|
T Consensus 52 NSAl--RK~~RVrL~NG~~VtAyiPg 75 (129)
T COG0048 52 NSAL--RKVARVRLINGKEVTAYIPG 75 (129)
T ss_pred Chhh--heeEEEEeeCCcEEEEEcCC
Confidence 4455 67789999999999876643
No 111
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=25.91 E-value=2.4e+02 Score=20.15 Aligned_cols=26 Identities=12% Similarity=0.239 Sum_probs=22.4
Q ss_pred HhhhhCCcEEEEEecCCeEEEEEEEEec
Q psy1084 25 TDSVKHNTQVLINCRNNKKLLGRVKAFD 52 (110)
Q Consensus 25 ~~~~~~~krV~V~l~~gr~i~G~L~~fD 52 (110)
..++ |+.|.+...+|..+.|++.+..
T Consensus 88 ~slV--Gk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELI--GKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHh--CCEEEEEeCCCCEEEEEEEEEE
Confidence 4567 9999999899999999998875
No 112
>PRK08477 biotin--protein ligase; Provisional
Probab=25.89 E-value=2.6e+02 Score=20.90 Aligned_cols=32 Identities=3% Similarity=0.058 Sum_probs=27.1
Q ss_pred hCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 29 KHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 29 ~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
..++.|+|. .+++.+.|+.++.|+.--|++..
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~ 204 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILING 204 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECC
Confidence 458999986 57889999999999999888865
No 113
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.49 E-value=1.3e+02 Score=23.57 Aligned_cols=31 Identities=3% Similarity=0.192 Sum_probs=26.9
Q ss_pred CcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
-.++.|.+.+|+.+.+.++|+|...-+.+-.
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlk 125 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLK 125 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEE
Confidence 5678888999999999999999998877744
No 114
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=25.44 E-value=2e+02 Score=18.87 Aligned_cols=41 Identities=15% Similarity=0.298 Sum_probs=30.1
Q ss_pred HHHHHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEece
Q psy1084 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLEN 61 (110)
Q Consensus 21 l~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d 61 (110)
..+|+...+.+..|+|...+|..|.=.|.+.|.--|.++=|
T Consensus 11 ~~~Lr~L~~~~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD 51 (108)
T PF07317_consen 11 LAVLRDLAKQRSPLTVRHPRGQSFITSILAVDPDRGTLVLD 51 (108)
T ss_dssp HHHHHHHHHTT--EEEETT-SSEEEE-EEEEETTTTEEEEE
T ss_pred HHHHHHHHhCCCeEEEEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence 45688888889999999888887999999999988766633
No 115
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=23.81 E-value=43 Score=23.16 Aligned_cols=18 Identities=33% Similarity=0.311 Sum_probs=15.7
Q ss_pred EEEEEEeccccceEecee
Q psy1084 45 LGRVKAFDRHCNMVLENV 62 (110)
Q Consensus 45 ~G~L~~fD~~mNlvL~d~ 62 (110)
.|.|+|-|+|-|---++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 699999999999888654
No 116
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=23.59 E-value=83 Score=19.32 Aligned_cols=25 Identities=16% Similarity=0.221 Sum_probs=21.3
Q ss_pred CcEEEEEecCCeEEEEEEEEecccc
Q psy1084 31 NTQVLINCRNNKKLLGRVKAFDRHC 55 (110)
Q Consensus 31 ~krV~V~l~~gr~i~G~L~~fD~~m 55 (110)
+.+|+|++.++-.=.|++.+...|-
T Consensus 4 nD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 4 NDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred ccEEEEecCCcccccceEEEEeecc
Confidence 7899999999988889888887775
No 117
>PRK11625 Rho-binding antiterminator; Provisional
Probab=23.17 E-value=2.2e+02 Score=18.46 Aligned_cols=58 Identities=14% Similarity=0.082 Sum_probs=36.5
Q ss_pred HHhhhhCCcEEEEEecCCeEEEEEEEEeccccceEeceeEEEeeccCCCCCCcccCCCcceeeeeCeEEEeCCcEEEEee
Q psy1084 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILILK 103 (110)
Q Consensus 24 L~~~~~~~krV~V~l~~gr~i~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~i~IRGd~Vv~I~~ 103 (110)
|.-+...+.+|.+.+++|..+.|+. .|-+.+ +-+|+..-.. .-+.-.||=|.|+.++.
T Consensus 16 LElAC~~~~~l~l~l~dGe~~~g~A--~D~~~~----~k~EyL~l~~----------------~g~~~~iRLD~I~s~~~ 73 (84)
T PRK11625 16 LELACQHHLMLTLELKDGEVLQAKA--SDLVSR----KNVEYLVVEA----------------AGETRELRLDKIASFSH 73 (84)
T ss_pred HHHHHhcCCeEEEEECCCCEEEEEE--EeeecC----CceEEEEEEc----------------CCCEEEEEeeeEeeccC
Confidence 4455556889999999999999875 454433 4455543210 11345667777777763
No 118
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=22.89 E-value=1.2e+02 Score=21.02 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=19.4
Q ss_pred HhhhhCCcEEEEEe-cCCeEEEEEEEEec
Q psy1084 25 TDSVKHNTQVLINC-RNNKKLLGRVKAFD 52 (110)
Q Consensus 25 ~~~~~~~krV~V~l-~~gr~i~G~L~~fD 52 (110)
.+++ .+.++|.| ++|+.+..++=|-.
T Consensus 38 NSA~--RK~~rV~L~~ngk~itAyIPG~G 64 (115)
T cd03367 38 NSAI--RKCVRVQLIKNGKKITAFVPGDG 64 (115)
T ss_pred Chhh--ceEEEEEEccCCeEEEEEeCCCC
Confidence 4555 78899999 69999987765533
No 119
>COG2131 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism]
Probab=22.09 E-value=1e+02 Score=22.61 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=20.7
Q ss_pred eeeeCeEEEeCCcEEEEeeCCccCC
Q psy1084 85 DRFISKMFLRGDSVILILKNPLALK 109 (110)
Q Consensus 85 ~r~lg~i~IRGd~Vv~I~~~~~~~~ 109 (110)
++++|-+++|+..|+..+.+..+.+
T Consensus 27 r~~VGAvIvkd~rIiatGYNG~p~g 51 (164)
T COG2131 27 RRQVGAVIVKDGRIIATGYNGAPSG 51 (164)
T ss_pred ccceeEEEEeCCeEEEeecCCCCcc
Confidence 3568999999999999998876543
No 120
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=21.89 E-value=1.2e+02 Score=19.92 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=12.9
Q ss_pred CcEEEEE-ecCCeEEEEEEEE
Q psy1084 31 NTQVLIN-CRNNKKLLGRVKA 50 (110)
Q Consensus 31 ~krV~V~-l~~gr~i~G~L~~ 50 (110)
|..|+|. +..|+.+.|++.+
T Consensus 96 G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 96 GDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCEEEEEECCCCCEEEEEEeC
Confidence 6666666 5666677776654
Done!