Query psy17123
Match_columns 105
No_of_seqs 126 out of 1019
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 22:27:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17123.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17123hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.9 6.3E-25 1.4E-29 142.8 10.1 77 20-96 1-81 (81)
2 cd01719 Sm_G The eukaryotic Sm 99.9 1.1E-23 2.5E-28 134.2 9.7 70 23-96 2-71 (72)
3 cd01727 LSm8 The eukaryotic Sm 99.9 1.5E-23 3.3E-28 133.9 9.9 73 24-96 2-74 (74)
4 cd01728 LSm1 The eukaryotic Sm 99.9 3.3E-23 7.2E-28 132.9 10.2 73 21-94 2-74 (74)
5 cd01731 archaeal_Sm1 The archa 99.9 4.3E-23 9.2E-28 129.6 9.0 68 22-93 1-68 (68)
6 PRK00737 small nuclear ribonuc 99.9 7.1E-23 1.5E-27 130.2 8.9 69 21-93 4-72 (72)
7 cd01732 LSm5 The eukaryotic Sm 99.9 1.7E-22 3.7E-27 130.1 9.8 72 22-94 4-75 (76)
8 cd01730 LSm3 The eukaryotic Sm 99.9 1.5E-22 3.2E-27 131.7 9.1 72 22-93 2-82 (82)
9 cd01717 Sm_B The eukaryotic Sm 99.9 4.2E-22 9.1E-27 128.5 9.8 69 24-92 3-77 (79)
10 cd01726 LSm6 The eukaryotic Sm 99.9 4.8E-22 1E-26 124.7 8.7 67 22-92 1-67 (67)
11 cd06168 LSm9 The eukaryotic Sm 99.9 1E-21 2.3E-26 126.2 10.0 70 23-92 2-73 (75)
12 cd01722 Sm_F The eukaryotic Sm 99.9 7.8E-22 1.7E-26 124.1 7.7 67 22-92 2-68 (68)
13 smart00651 Sm snRNP Sm protein 99.9 3.9E-21 8.5E-26 119.2 9.5 66 25-93 2-67 (67)
14 PF01423 LSM: LSM domain ; In 99.9 3.8E-21 8.3E-26 119.3 8.8 66 25-93 2-67 (67)
15 cd01718 Sm_E The eukaryotic Sm 99.9 5.9E-21 1.3E-25 123.9 9.2 74 17-93 2-79 (79)
16 cd01720 Sm_D2 The eukaryotic S 99.8 1.1E-20 2.3E-25 124.7 9.5 72 22-93 3-85 (87)
17 cd01721 Sm_D3 The eukaryotic S 99.8 1.2E-20 2.5E-25 119.5 9.1 69 23-95 2-70 (70)
18 COG1958 LSM1 Small nuclear rib 99.8 4.1E-20 8.9E-25 119.0 9.4 72 20-92 6-78 (79)
19 KOG1781|consensus 99.8 4.3E-22 9.3E-27 133.1 -0.5 87 12-98 8-98 (108)
20 cd00600 Sm_like The eukaryotic 99.8 5.1E-20 1.1E-24 112.6 8.8 63 26-92 1-63 (63)
21 cd01723 LSm4 The eukaryotic Sm 99.8 4.8E-20 1E-24 118.3 8.9 72 22-96 2-73 (76)
22 cd01724 Sm_D1 The eukaryotic S 99.8 2.1E-19 4.6E-24 119.0 9.4 73 22-98 2-74 (90)
23 KOG1780|consensus 99.8 5.7E-20 1.2E-24 117.3 6.1 69 24-96 7-75 (77)
24 PTZ00138 small nuclear ribonuc 99.8 5.8E-19 1.3E-23 116.9 9.7 76 16-94 9-88 (89)
25 cd01733 LSm10 The eukaryotic S 99.8 1.4E-18 3E-23 112.4 8.8 70 20-93 8-77 (78)
26 cd01725 LSm2 The eukaryotic Sm 99.8 1.9E-18 4.1E-23 112.3 8.6 73 23-97 3-75 (81)
27 KOG3482|consensus 99.7 3.2E-17 7E-22 104.5 6.0 71 21-95 8-78 (79)
28 KOG1784|consensus 99.7 3.5E-17 7.7E-22 108.1 4.4 76 23-98 2-77 (96)
29 KOG1782|consensus 99.6 1.6E-16 3.5E-21 109.9 -0.2 76 23-99 11-86 (129)
30 KOG1783|consensus 99.6 4.1E-16 8.8E-21 99.4 0.9 72 19-94 4-75 (77)
31 KOG3460|consensus 99.5 1.5E-15 3.2E-20 99.1 2.0 75 20-94 4-87 (91)
32 KOG3168|consensus 99.5 7.5E-16 1.6E-20 111.6 0.5 79 24-102 7-91 (177)
33 KOG1775|consensus 99.5 3E-14 6.6E-19 91.6 3.9 71 24-95 10-80 (84)
34 KOG1774|consensus 99.4 8.1E-14 1.8E-18 90.6 4.0 78 15-95 6-87 (88)
35 KOG3293|consensus 99.4 7E-13 1.5E-17 92.0 5.6 72 22-96 3-74 (134)
36 KOG3448|consensus 99.4 4.2E-12 9.2E-17 83.8 7.9 70 23-94 4-73 (96)
37 KOG3172|consensus 99.0 1E-09 2.2E-14 74.8 7.1 72 21-96 5-76 (119)
38 KOG3428|consensus 98.9 2.2E-08 4.8E-13 68.2 8.4 71 23-98 4-74 (109)
39 KOG3459|consensus 98.3 4.8E-08 1E-12 66.7 -1.4 72 21-92 24-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.1 7.8E-06 1.7E-10 51.9 5.7 69 21-89 2-76 (77)
41 cd01739 LSm11_C The eukaryotic 97.9 7.8E-06 1.7E-10 51.4 2.7 38 31-68 8-49 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.3 0.001 2.2E-08 44.6 6.1 72 27-98 4-81 (96)
43 PF06372 Gemin6: Gemin6 protei 96.8 0.0036 7.8E-08 45.8 5.6 65 21-96 7-72 (166)
44 PF02237 BPL_C: Biotin protein 96.7 0.0062 1.4E-07 35.4 5.3 33 29-62 1-33 (48)
45 cd01736 LSm14_N LSm14 (also kn 96.6 0.011 2.3E-07 38.0 6.3 65 27-91 2-73 (74)
46 cd01716 Hfq Hfq, an abundant, 96.4 0.0066 1.4E-07 37.7 4.1 32 30-61 10-41 (61)
47 TIGR02383 Hfq RNA chaperone Hf 96.3 0.0084 1.8E-07 37.2 4.1 32 30-61 14-45 (61)
48 PRK00395 hfq RNA-binding prote 95.9 0.016 3.4E-07 37.7 4.1 34 29-62 17-50 (79)
49 PF11095 Gemin7: Gem-associate 95.6 0.075 1.6E-06 34.6 6.5 63 21-92 14-77 (80)
50 PRK14638 hypothetical protein; 95.3 0.046 1E-06 39.1 5.3 45 13-59 83-127 (150)
51 COG1923 Hfq Uncharacterized ho 95.1 0.036 7.8E-07 35.8 3.7 29 30-58 18-46 (77)
52 PRK14639 hypothetical protein; 94.8 0.085 1.8E-06 37.3 5.2 45 13-59 71-115 (140)
53 PRK02001 hypothetical protein; 94.7 0.091 2E-06 37.8 5.3 45 13-59 73-117 (152)
54 cd01735 LSm12_N LSm12 belongs 94.5 0.12 2.7E-06 31.9 4.8 35 29-63 4-38 (61)
55 PF10842 DUF2642: Protein of u 94.2 0.59 1.3E-05 29.3 7.4 56 21-93 11-66 (66)
56 PRK14644 hypothetical protein; 93.7 0.23 4.9E-06 35.0 5.5 47 11-60 67-117 (136)
57 PRK14091 RNA-binding protein H 93.2 0.19 4.2E-06 36.8 4.6 33 30-62 103-135 (165)
58 PRK14091 RNA-binding protein H 93.1 0.23 5E-06 36.4 4.9 33 30-62 23-55 (165)
59 cd01734 YlxS_C YxlS is a Bacil 93.0 0.38 8.3E-06 30.7 5.4 43 15-59 10-56 (83)
60 PRK14640 hypothetical protein; 92.9 0.43 9.3E-06 34.1 6.0 45 14-60 81-129 (152)
61 PRK14633 hypothetical protein; 92.3 0.45 9.6E-06 34.0 5.4 44 15-60 79-126 (150)
62 KOG1073|consensus 92.0 0.57 1.2E-05 38.2 6.2 71 27-97 5-82 (361)
63 PRK14645 hypothetical protein; 91.5 0.53 1.1E-05 33.8 5.1 42 15-59 87-128 (154)
64 PRK14642 hypothetical protein; 91.3 0.57 1.2E-05 35.1 5.3 42 16-59 86-140 (197)
65 PRK14636 hypothetical protein; 91.1 0.62 1.3E-05 34.2 5.2 45 13-59 81-129 (176)
66 PF02576 DUF150: Uncharacteris 91.0 0.51 1.1E-05 32.8 4.6 36 23-59 79-118 (141)
67 PRK00092 ribosome maturation p 90.8 0.75 1.6E-05 32.6 5.3 31 23-53 90-124 (154)
68 PRK14632 hypothetical protein; 90.5 0.79 1.7E-05 33.4 5.3 44 15-60 83-133 (172)
69 PRK14634 hypothetical protein; 90.5 0.8 1.7E-05 32.8 5.2 45 13-59 83-131 (155)
70 PRK14643 hypothetical protein; 90.5 0.84 1.8E-05 33.1 5.4 41 13-54 87-131 (164)
71 COG0779 Uncharacterized protei 90.2 1.3 2.8E-05 32.0 6.0 42 16-59 85-130 (153)
72 PRK14647 hypothetical protein; 89.8 1 2.2E-05 32.3 5.4 40 13-53 82-130 (159)
73 PRK14646 hypothetical protein; 89.3 1.2 2.6E-05 31.9 5.4 45 13-59 83-131 (155)
74 PRK14631 hypothetical protein; 88.5 1.4 2.9E-05 32.4 5.3 39 13-52 100-142 (174)
75 PRK06955 biotin--protein ligas 87.7 2.5 5.5E-05 32.9 6.7 32 29-60 247-278 (300)
76 PRK14637 hypothetical protein; 87.4 1.6 3.6E-05 31.2 5.0 45 13-59 81-126 (151)
77 PRK14641 hypothetical protein; 87.3 1.6 3.4E-05 32.1 5.0 36 16-52 90-129 (173)
78 PRK11886 bifunctional biotin-- 84.3 5.4 0.00012 31.0 7.0 49 29-86 270-318 (319)
79 PRK13325 bifunctional biotin-- 82.1 5.8 0.00012 34.1 6.8 32 29-60 276-307 (592)
80 TIGR00121 birA_ligase birA, bi 81.9 9.3 0.0002 28.5 7.2 32 28-60 190-221 (237)
81 PRK14635 hypothetical protein; 79.0 6.4 0.00014 28.3 5.3 45 13-59 82-131 (162)
82 PRK08330 biotin--protein ligas 78.3 9.7 0.00021 28.4 6.3 33 28-61 185-218 (236)
83 PF03614 Flag1_repress: Repres 78.3 3.6 7.8E-05 30.0 3.7 34 30-63 28-61 (165)
84 PRK14630 hypothetical protein; 75.5 8.1 0.00017 27.3 4.9 41 16-59 83-123 (143)
85 PF03614 Flag1_repress: Repres 74.9 5.2 0.00011 29.2 3.8 24 30-53 119-142 (165)
86 PTZ00275 biotin-acetyl-CoA-car 73.3 8.5 0.00018 29.9 5.0 31 30-61 236-266 (285)
87 PRK10898 serine endoprotease; 72.7 8.4 0.00018 30.7 4.9 32 31-62 101-132 (353)
88 COG0340 BirA Biotin-(acetyl-Co 72.1 16 0.00034 27.9 6.1 36 27-62 186-221 (238)
89 TIGR02038 protease_degS peripl 70.9 9.6 0.00021 30.3 4.8 31 32-62 102-132 (351)
90 PRK10942 serine endoprotease; 65.4 13 0.00029 30.8 4.8 31 31-61 135-165 (473)
91 PRK10139 serine endoprotease; 65.3 14 0.00031 30.6 4.9 32 31-62 114-145 (455)
92 PF07073 ROF: Modulator of Rho 65.1 8.9 0.00019 24.7 2.9 61 25-96 11-71 (80)
93 PF14563 DUF4444: Domain of un 64.1 10 0.00022 21.8 2.7 21 44-64 10-30 (42)
94 PF06257 DUF1021: Protein of u 62.4 20 0.00044 23.0 4.2 29 23-51 9-41 (76)
95 PF11607 DUF3247: Protein of u 62.3 12 0.00027 25.2 3.3 27 23-49 15-46 (101)
96 PF05071 NDUFA12: NADH ubiquin 57.1 6.9 0.00015 26.2 1.4 17 46-62 1-17 (105)
97 TIGR02037 degP_htrA_DO peripla 56.8 24 0.00052 28.5 4.8 31 32-62 82-112 (428)
98 PRK09618 flgD flagellar basal 56.3 28 0.0006 24.9 4.5 28 25-52 86-113 (142)
99 KOG3382|consensus 53.5 7.5 0.00016 27.8 1.2 25 38-62 39-63 (151)
100 PRK08477 biotin--protein ligas 52.2 55 0.0012 24.4 5.8 34 29-63 173-206 (211)
101 TIGR02603 CxxCH_TIGR02603 puta 50.2 27 0.00058 23.9 3.5 20 33-52 59-78 (133)
102 PF14485 DUF4431: Domain of un 43.9 21 0.00046 20.7 1.9 18 20-37 8-25 (48)
103 TIGR03170 flgA_cterm flagella 41.9 35 0.00075 22.6 3.0 22 29-50 94-116 (122)
104 PF11743 DUF3301: Protein of u 41.1 42 0.00092 22.0 3.3 27 63-93 68-94 (97)
105 PRK11911 flgD flagellar basal 39.9 56 0.0012 23.3 3.9 27 27-53 89-115 (140)
106 smart00333 TUDOR Tudor domain. 39.6 71 0.0015 17.9 4.2 25 30-54 5-29 (57)
107 PF09465 LBR_tudor: Lamin-B re 38.3 68 0.0015 19.4 3.6 26 30-55 8-34 (55)
108 PRK06630 hypothetical protein; 38.2 19 0.00041 24.3 1.2 19 44-62 11-29 (99)
109 COG0265 DegQ Trypsin-like seri 36.3 76 0.0016 24.8 4.6 31 31-61 95-125 (347)
110 PLN02732 Probable NADH dehydro 35.5 31 0.00067 25.1 2.1 18 45-62 48-65 (159)
111 smart00166 UBX Domain present 33.4 42 0.0009 20.7 2.2 22 32-53 5-26 (80)
112 PRK07018 flgA flagellar basal 33.2 51 0.0011 24.8 3.0 22 29-50 205-227 (235)
113 KOG3493|consensus 32.9 37 0.00079 21.5 1.8 19 25-43 5-23 (73)
114 PF14153 Spore_coat_CotO: Spor 32.9 41 0.00089 24.9 2.4 51 30-94 133-183 (185)
115 COG4466 Veg Uncharacterized pr 32.7 38 0.00083 22.0 1.9 24 20-43 8-31 (80)
116 PF03122 Herpes_MCP: Herpes vi 32.6 15 0.00032 34.8 0.0 58 32-91 248-305 (1354)
117 PRK11625 Rho-binding antitermi 31.5 86 0.0019 20.4 3.5 55 26-92 18-72 (84)
118 PF00789 UBX: UBX domain; Int 31.0 59 0.0013 19.9 2.6 22 32-53 7-28 (82)
119 PF01887 SAM_adeno_trans: S-ad 30.4 72 0.0016 24.6 3.5 19 43-61 169-187 (258)
120 cd01767 UBX UBX (ubiquitin reg 30.1 58 0.0013 19.8 2.4 22 32-53 3-24 (77)
121 PLN03095 NADH:ubiquinone oxido 26.8 50 0.0011 22.8 1.8 19 44-62 8-26 (115)
122 cd00319 Ribosomal_S12_like Rib 26.7 72 0.0016 21.4 2.5 40 11-50 11-54 (95)
123 KOG1719|consensus 26.2 51 0.0011 24.4 1.9 60 6-65 82-145 (183)
124 PF05954 Phage_GPD: Phage late 25.9 1E+02 0.0022 22.6 3.6 27 26-52 23-49 (292)
125 cd03367 Ribosomal_S23 S12-like 25.7 98 0.0021 21.4 3.1 42 10-51 17-63 (115)
126 PRK12617 flgA flagellar basal 25.5 86 0.0019 23.6 3.1 21 30-50 185-206 (214)
127 PRK06792 flgD flagellar basal 24.9 1.2E+02 0.0027 22.7 3.8 26 27-52 114-139 (190)
128 PRK06005 flgA flagellar basal 24.8 95 0.0021 22.2 3.1 21 30-50 130-151 (160)
129 cd01737 LSm16_N LSm16 belongs 24.8 1.3E+02 0.0029 18.6 3.3 36 28-63 3-40 (62)
130 KOG4401|consensus 24.6 77 0.0017 23.7 2.6 35 29-63 9-43 (184)
131 cd04479 RPA3 RPA3: A subfamily 24.4 1.7E+02 0.0036 19.1 4.0 14 24-37 8-21 (101)
132 PRK08183 NADH dehydrogenase; V 24.4 42 0.00092 23.7 1.2 20 44-63 24-43 (133)
133 TIGR03361 VI_Rhs_Vgr type VI s 23.9 1.4E+02 0.003 24.7 4.3 29 24-52 40-72 (513)
134 COG3466 ISA1214 Putative trans 23.9 77 0.0017 19.0 2.0 18 23-40 34-51 (52)
135 PRK08515 flgA flagellar basal 23.3 1.2E+02 0.0027 22.6 3.6 22 29-50 194-215 (222)
136 PRK10708 hypothetical protein; 23.0 1E+02 0.0022 19.0 2.5 26 30-55 3-28 (62)
137 COG5316 Uncharacterized conser 23.0 1.7E+02 0.0037 24.5 4.5 43 24-67 75-117 (421)
138 cd01772 SAKS1_UBX SAKS1-like U 22.9 65 0.0014 20.0 1.7 24 30-53 3-26 (79)
139 PRK05163 rpsL 30S ribosomal pr 22.8 97 0.0021 21.7 2.7 32 21-52 40-71 (124)
140 TIGR00981 rpsL_bact ribosomal 21.9 1E+02 0.0022 21.7 2.6 31 21-51 40-70 (124)
141 PTZ00276 biotin/lipoate protei 21.3 1.3E+02 0.0028 22.7 3.3 23 39-61 209-231 (245)
142 PHA00672 hypothetical protein 21.0 3.2E+02 0.007 19.5 6.0 46 35-85 51-96 (152)
143 PF12869 tRNA_anti-like: tRNA_ 20.8 87 0.0019 21.0 2.2 21 43-63 124-144 (144)
144 PRK04211 rps12P 30S ribosomal 20.8 1.3E+02 0.0027 21.7 3.0 41 10-50 43-88 (145)
145 TIGR00982 S23_S12_E_A ribosoma 20.5 1.4E+02 0.003 21.4 3.1 41 10-50 37-82 (139)
146 CHL00051 rps12 ribosomal prote 20.1 1.1E+02 0.0023 21.5 2.5 32 21-52 40-71 (123)
No 1
>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=99.92 E-value=6.3e-25 Score=142.81 Aligned_cols=77 Identities=56% Similarity=0.770 Sum_probs=67.5
Q ss_pred ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce----eeeeeEEeeEEEcCCcEEEEEecC
Q psy17123 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ----SVQVRSWCSIVRRQESRRNVHRRD 95 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~----~~~~~~lg~vlIRG~~I~~i~~~d 95 (105)
++++..|.++++|+|+|+|+|||.|+|+|.|||+||||+|++|+|+...++. ....+.+|.++|||++|++|++.|
T Consensus 1 ~~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred CcchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 3578899999999999999999999999999999999999999999764321 124688999999999999999876
Q ss_pred C
Q psy17123 96 H 96 (105)
Q Consensus 96 ~ 96 (105)
+
T Consensus 81 ~ 81 (81)
T cd01729 81 G 81 (81)
T ss_pred C
Confidence 4
No 2
>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=99.91 E-value=1.1e-23 Score=134.19 Aligned_cols=70 Identities=34% Similarity=0.535 Sum_probs=63.8
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
.++|+++++|+|+|+|++||.++|+|.|||+||||+|++|.|+..+. ..+.+|.++|||++|++|++.|.
T Consensus 2 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~----~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 2 PPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGG----EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred chhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCC----ceeEeceEEECCCEEEEEEcccc
Confidence 46899999999999999999999999999999999999999986432 36889999999999999998875
No 3
>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=99.90 E-value=1.5e-23 Score=133.89 Aligned_cols=73 Identities=29% Similarity=0.380 Sum_probs=64.9
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
+.|+++++++|+|+++|||.|.|+|+|||+||||+|++|.|+....++....+.+|.++|||++|++|+++|.
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 5799999999999999999999999999999999999999987643323346789999999999999999874
No 4
>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=99.90 E-value=3.3e-23 Score=132.87 Aligned_cols=73 Identities=29% Similarity=0.289 Sum_probs=65.2
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR 94 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~ 94 (105)
.+++.|+++++|+|.|.++|||.|.|+|.|||+||||+|+||.|+...++ ++..+.+|.++|||++|++|+++
T Consensus 2 ~~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~-~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 2 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGD-KYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCC-ccceeEeeEEEEECCEEEEEEcC
Confidence 46889999999999999999999999999999999999999999876542 23468899999999999999853
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=99.89 E-value=4.3e-23 Score=129.62 Aligned_cols=68 Identities=31% Similarity=0.433 Sum_probs=61.6
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
|...|+++++++|+|+|++|+.|.|+|.|||+||||+|++|.|...++ ..+.+|.++|||++|++|++
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~----~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE----PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC----eEeEcCcEEEeCCEEEEEcC
Confidence 356789999999999999999999999999999999999999987654 36789999999999999974
No 6
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.89 E-value=7.1e-23 Score=130.25 Aligned_cols=69 Identities=33% Similarity=0.433 Sum_probs=61.8
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
.|...|+++++++|+|+|+||+.|+|+|.|||+||||+|+||.|...+ + ..+.+|.++|||++|++|.+
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~---~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDG-E---VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCC-C---eEeEcCcEEEeCCEEEEEcC
Confidence 467789999999999999999999999999999999999999997533 2 36789999999999999863
No 7
>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=99.89 E-value=1.7e-22 Score=130.10 Aligned_cols=72 Identities=21% Similarity=0.275 Sum_probs=62.6
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR 94 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~ 94 (105)
|...|+++++++|+|++++||++.|+|.|||+|||++|+||.|++..+++ ...+.+|.++|||++|++|++.
T Consensus 4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~-~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEG-RKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCC-ceeeEcCeEEEeCCeEEEEECC
Confidence 45568999999999999999999999999999999999999999743321 1467899999999999999863
No 8
>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=99.88 E-value=1.5e-22 Score=131.65 Aligned_cols=72 Identities=25% Similarity=0.289 Sum_probs=61.7
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---------eeeeeEEeeEEEcCCcEEEEE
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---------SVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---------~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|...|+.+++++|.|+|+|||.|.|+|+|||+||||+|+||.|++..... ....+.+|.++|||++|++|+
T Consensus 2 pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~ 81 (82)
T cd01730 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVS 81 (82)
T ss_pred chHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEEC
Confidence 44567888999999999999999999999999999999999999864211 124689999999999999986
Q ss_pred e
Q psy17123 93 R 93 (105)
Q Consensus 93 ~ 93 (105)
+
T Consensus 82 ~ 82 (82)
T cd01730 82 P 82 (82)
T ss_pred C
Confidence 3
No 9
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=4.2e-22 Score=128.52 Aligned_cols=69 Identities=23% Similarity=0.399 Sum_probs=60.8
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEE
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
..|.+|++++|+|.|+|||.|.|+|.|||+||||+|+||.|++.... ...+.+.+|+++|||++|++|+
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 46899999999999999999999999999999999999999875321 1234688999999999999997
No 10
>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=99.87 E-value=4.8e-22 Score=124.69 Aligned_cols=67 Identities=21% Similarity=0.312 Sum_probs=59.5
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|...|+++++++|+|+|++|++|+|+|.|||+||||+|++|.|....+ ..+.+|.++|||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~----~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQ----LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCc----eeeEeCCEEEECCEEEEEC
Confidence 356789999999999999999999999999999999999999865332 3678999999999999884
No 11
>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=99.87 E-value=1e-21 Score=126.22 Aligned_cols=70 Identities=17% Similarity=0.258 Sum_probs=62.5
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc--eeeeeeEEeeEEEcCCcEEEEE
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY--QSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~--~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
...|++|++++|+|+|+|||.|.|+|.|||++|||+|++|.|+...+. ...+.|.+|+++|||++|++|+
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 356899999999999999999999999999999999999999986432 2235799999999999999997
No 12
>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=99.86 E-value=7.8e-22 Score=124.13 Aligned_cols=67 Identities=25% Similarity=0.290 Sum_probs=59.8
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|...|+++++++|+|+|+||++|+|+|.|||+||||+|+||.|+.... ....+|.++|||++|++|.
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~----~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGK----STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCc----cccCcCcEEEECCEEEEEC
Confidence 567899999999999999999999999999999999999999985332 2577999999999999983
No 13
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.86 E-value=3.9e-21 Score=119.15 Aligned_cols=66 Identities=30% Similarity=0.431 Sum_probs=60.5
Q ss_pred hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
.|+++++++|+|.|+||+.+.|+|.+||+||||+|++|.|+..++. +.+.+|.++|||++|++|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~---~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE---KKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc---EEeEeCCEEEcCCEEEEEeC
Confidence 5889999999999999999999999999999999999999876532 47899999999999999974
No 14
>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=99.86 E-value=3.8e-21 Score=119.35 Aligned_cols=66 Identities=32% Similarity=0.452 Sum_probs=61.0
Q ss_pred hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
.|++++|++|+|+|+||+.++|+|.+||+||||+|++|.|....+. +.+.+|.++|||++|++|++
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~---~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP---EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES---EEEEEEEEEEEGGGEEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC---cEeECcEEEEECCEEEEEEC
Confidence 5899999999999999999999999999999999999999976542 47889999999999999985
No 15
>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=99.85 E-value=5.9e-21 Score=123.93 Aligned_cols=74 Identities=20% Similarity=0.301 Sum_probs=63.2
Q ss_pred cccccchhhHHhhcCC--EEEEEEc--CCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 17 RKRKESILDLSKFLDK--VIRVKFA--GGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 17 ~~~~~~~~~L~~~i~k--~V~V~Lk--dGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|..-.|...|.+++++ +|.|.++ +|+.++|+|.|||+||||+|+||+|+...++ ..+.+|.++|||++|++|+
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~---~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK---TRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc---eEeEcCcEEEeCCEEEEEc
Confidence 4456788889999998 6777766 9999999999999999999999999975332 3678999999999999997
Q ss_pred e
Q psy17123 93 R 93 (105)
Q Consensus 93 ~ 93 (105)
+
T Consensus 79 p 79 (79)
T cd01718 79 N 79 (79)
T ss_pred C
Confidence 4
No 16
>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=99.85 E-value=1.1e-20 Score=124.67 Aligned_cols=72 Identities=21% Similarity=0.229 Sum_probs=61.2
Q ss_pred chhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCce---------eeeeeEEeeEEEcCCcEEE
Q psy17123 22 SILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQ---------SVQVRSWCSIVRRQESRRN 90 (105)
Q Consensus 22 ~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~---------~~~~~~lg~vlIRG~~I~~ 90 (105)
|...|.+.+ +++|.|+|++|+.+.|+|.|||+||||+|+||.|++..... ....+.+|.+||||++|++
T Consensus 3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 455678886 89999999999999999999999999999999998764221 1346789999999999999
Q ss_pred EEe
Q psy17123 91 VHR 93 (105)
Q Consensus 91 i~~ 93 (105)
|.+
T Consensus 83 Is~ 85 (87)
T cd01720 83 VLR 85 (87)
T ss_pred Eec
Confidence 974
No 17
>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=1.2e-20 Score=119.54 Aligned_cols=69 Identities=20% Similarity=0.124 Sum_probs=61.7
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD 95 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d 95 (105)
...|++..|++|+|+||||.+|+|+|.++|+|||++|++|.+...+++ ...+|.++|||++|.+|+.+|
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~----~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR----VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc----EeEcCcEEEeCCEEEEEEeCC
Confidence 456899999999999999999999999999999999999988655543 466899999999999999775
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.83 E-value=4.1e-20 Score=119.02 Aligned_cols=72 Identities=31% Similarity=0.379 Sum_probs=60.6
Q ss_pred ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEe-cCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR-VTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~-~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
..+...|+++++++|.|+|++|++|.|+|+|||+||||+|+||.|+.. ++.. ...+..|.++|||++|++|.
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~-~~~~~~~~~~IRG~~I~~I~ 78 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEK-NVRRLGGEVLIRGDNIVLIS 78 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCcc-ccceeccEEEEECCcEEEEe
Confidence 456788999999999999999999999999999999999999999874 2221 02344459999999999986
No 19
>KOG1781|consensus
Probab=99.83 E-value=4.3e-22 Score=133.15 Aligned_cols=87 Identities=52% Similarity=0.727 Sum_probs=78.6
Q ss_pred CCccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCcee----eeeeEEeeEEEcCCc
Q psy17123 12 AETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQS----VQVRSWCSIVRRQES 87 (105)
Q Consensus 12 ~~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~----~~~~~lg~vlIRG~~ 87 (105)
....+|++++++.+|.+|++|+|+|++.+||...|+|+|||+.|||||++++|+..+++++ .+.|.+|++++||..
T Consensus 8 ~~~~e~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTa 87 (108)
T KOG1781|consen 8 RKKFEKPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTA 87 (108)
T ss_pred cccccccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccE
Confidence 3455789999999999999999999999999999999999999999999999999877642 245999999999999
Q ss_pred EEEEEecCCcc
Q psy17123 88 RRNVHRRDHKE 98 (105)
Q Consensus 88 I~~i~~~d~~~ 98 (105)
++.|++.|+..
T Consensus 88 lvlisp~dG~e 98 (108)
T KOG1781|consen 88 LVLISPADGSE 98 (108)
T ss_pred EEEEcCCcchh
Confidence 99999998754
No 20
>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=99.83 E-value=5.1e-20 Score=112.62 Aligned_cols=63 Identities=32% Similarity=0.518 Sum_probs=57.9
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 26 L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|++++|++|+|+|+||+.|.|+|.+||+|||++|++|.|..... ..+.+|.++|||++|.+|+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~----~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEG----KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCC----cEEECCeEEEECCEEEEEC
Confidence 57899999999999999999999999999999999999987653 3788999999999999884
No 21
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.83 E-value=4.8e-20 Score=118.28 Aligned_cols=72 Identities=14% Similarity=0.111 Sum_probs=62.7
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
|...|++++|++|.|+|++|+.++|+|.+||+|||++|+||.|...+++ ....++.++|||++|.+|+..|.
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~---~~~~~~~v~IRG~~I~~i~~p~~ 73 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGD---KFWKMPECYIRGNTIKYLRVPDE 73 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCc---EeeeCCcEEEeCCEEEEEEcCHH
Confidence 4567899999999999999999999999999999999999998755543 24567899999999999986653
No 22
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.81 E-value=2.1e-19 Score=119.00 Aligned_cols=73 Identities=19% Similarity=0.228 Sum_probs=64.9
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE 98 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~ 98 (105)
++..|+++.|++|+|+|++|..|+|+|.++|+|||++|+||.+...++. ...+|.++|||++|.+|+..|...
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~----~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN----PVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc----eeEcceEEEeCCEEEEEEcCCcCC
Confidence 3567899999999999999999999999999999999999998855443 567999999999999999988753
No 23
>KOG1780|consensus
Probab=99.81 E-value=5.7e-20 Score=117.30 Aligned_cols=69 Identities=36% Similarity=0.541 Sum_probs=62.7
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
++|++|++|++.++|..||.+.|+|+|||.||||||++++|...+++ ...+|.++|||++|+.+...|.
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~----~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD----KNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC----cceeeeEEEeccEEEEEeeccc
Confidence 49999999999999999999999999999999999999999866554 5788999999999999987653
No 24
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.80 E-value=5.8e-19 Score=116.89 Aligned_cols=76 Identities=16% Similarity=0.288 Sum_probs=63.6
Q ss_pred ccccccchhhHHhhcCC--EEEEEEcC--CeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEE
Q psy17123 16 DRKRKESILDLSKFLDK--VIRVKFAG--GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNV 91 (105)
Q Consensus 16 ~~~~~~~~~~L~~~i~k--~V~V~Lkd--Gr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i 91 (105)
.|....|+..+.+++.+ +|.|.+.+ ++.++|+|+|||+||||+|+||.|+..+++ ..+.+|.++|||++|++|
T Consensus 9 ~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~---~~~~lG~ilIRGnnV~~I 85 (89)
T PTZ00138 9 QKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN---TRKDLGRILLKGDNITLI 85 (89)
T ss_pred ceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc---eeeEcCeEEEcCCEEEEE
Confidence 35567888889999875 66777667 589999999999999999999999865433 367899999999999999
Q ss_pred Eec
Q psy17123 92 HRR 94 (105)
Q Consensus 92 ~~~ 94 (105)
++.
T Consensus 86 ~~~ 88 (89)
T PTZ00138 86 MAA 88 (89)
T ss_pred EcC
Confidence 864
No 25
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.78 E-value=1.4e-18 Score=112.35 Aligned_cols=70 Identities=21% Similarity=0.214 Sum_probs=60.6
Q ss_pred ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
......|+.+.|+.|.|+||||..|.|+|.++|+|||++|+||.+...++. ...+|.++|||++|.+|+.
T Consensus 8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~----~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGK----QVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCc----eeECCcEEEECCEEEEEEc
Confidence 344556799999999999999999999999999999999999988754433 4578999999999999985
No 26
>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=1.9e-18 Score=112.26 Aligned_cols=73 Identities=19% Similarity=0.179 Sum_probs=61.8
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHK 97 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~ 97 (105)
...|+++.|++|+|+||+|..|.|+|.++|+|||++|+||.+...++. .....++.++|||++|.+|+..|..
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~--~~~~~~~~v~IRG~~I~~I~lp~~~ 75 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY--PHMLSVKNCFIRGSVVRYVQLPADE 75 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc--ccccccCeEEEECCEEEEEEeChhH
Confidence 456889999999999999999999999999999999999987643322 1245678999999999999987654
No 27
>KOG3482|consensus
Probab=99.70 E-value=3.2e-17 Score=104.48 Aligned_cols=71 Identities=24% Similarity=0.258 Sum_probs=63.5
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD 95 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d 95 (105)
-+.+.|+.+.+|.|.|+||.|.+|+|+|.+.|.||||.|.+|+|++... ....+|.++||.+||.+|..++
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~----~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGV----STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhccc----ccccceeEEEEeccEEEEecCC
Confidence 3567899999999999999999999999999999999999999986543 3678999999999999997654
No 28
>KOG1784|consensus
Probab=99.68 E-value=3.5e-17 Score=108.15 Aligned_cols=76 Identities=24% Similarity=0.314 Sum_probs=69.6
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE 98 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~ 98 (105)
...|..|++++|.|.+.|||.+.|.|+||||-.||+|+++.|++.+..+..+...+|+.+|||+||..|+++|++.
T Consensus 2 ts~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~ 77 (96)
T KOG1784|consen 2 TSTLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEEL 77 (96)
T ss_pred chhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhh
Confidence 3568999999999999999999999999999999999999999876655667789999999999999999999864
No 29
>KOG1782|consensus
Probab=99.58 E-value=1.6e-16 Score=109.93 Aligned_cols=76 Identities=26% Similarity=0.296 Sum_probs=67.8
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCccc
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKEY 99 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~~ 99 (105)
...|.++++|++.|.|+|||.+.|.|++||||-|++|..|+|++.-++ .+-.+..|..+|||+||+.++.+|....
T Consensus 11 t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~-~Y~di~~glfiIRGENVvllGeid~dkE 86 (129)
T KOG1782|consen 11 TTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGN-KYCDIPRGLFIIRGENVVLLGEIDLDKE 86 (129)
T ss_pred hhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecc-eecccCceEEEEecCcEEEEecCCcchh
Confidence 445899999999999999999999999999999999999999987654 4566788999999999999999887654
No 30
>KOG1783|consensus
Probab=99.57 E-value=4.1e-16 Score=99.40 Aligned_cols=72 Identities=18% Similarity=0.253 Sum_probs=64.5
Q ss_pred cccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123 19 RKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR 94 (105)
Q Consensus 19 ~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~ 94 (105)
.+.+-..|++.+||+|.|+|.+|-.|+|+|.|.|.||||-|+.+.|+.... ..+++|..||||++|.+|+..
T Consensus 4 ~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngq----l~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 4 GSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQ----LKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred ccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCc----ccccccceeeccccEEEEEec
Confidence 455667899999999999999999999999999999999999999997543 378899999999999999864
No 31
>KOG3460|consensus
Probab=99.55 E-value=1.5e-15 Score=99.09 Aligned_cols=75 Identities=27% Similarity=0.290 Sum_probs=62.2
Q ss_pred ccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEec--Cc-e------eeeeeEEeeEEEcCCcEEE
Q psy17123 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV--TY-Q------SVQVRSWCSIVRRQESRRN 90 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~--~~-~------~~~~~~lg~vlIRG~~I~~ 90 (105)
.+|...|.=+++.+|.|+++++|.+.|+|.+||+|.|++|+++.|.... .+ + +...|.+..+|+||++|+.
T Consensus 4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil 83 (91)
T KOG3460|consen 4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL 83 (91)
T ss_pred cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence 3445556667999999999999999999999999999999999997752 11 1 1356888999999999999
Q ss_pred EEec
Q psy17123 91 VHRR 94 (105)
Q Consensus 91 i~~~ 94 (105)
|++.
T Consensus 84 vspp 87 (91)
T KOG3460|consen 84 VSPP 87 (91)
T ss_pred EcCc
Confidence 9875
No 32
>KOG3168|consensus
Probab=99.55 E-value=7.5e-16 Score=111.60 Aligned_cols=79 Identities=23% Similarity=0.347 Sum_probs=67.3
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCc------eeeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTY------QSVQVRSWCSIVRRQESRRNVHRRDHK 97 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~------~~~~~~~lg~vlIRG~~I~~i~~~d~~ 97 (105)
..|-+++|.+++|.++|||.|.|.|++||+||||+|.+|+|+.+-+. +..+.|.+|++++||++|++....+..
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 34678899999999999999999999999999999999999875221 245789999999999999999877666
Q ss_pred ccccc
Q psy17123 98 EYEDS 102 (105)
Q Consensus 98 ~~~~~ 102 (105)
.-+|+
T Consensus 87 p~s~s 91 (177)
T KOG3168|consen 87 PPSDS 91 (177)
T ss_pred CCccc
Confidence 65554
No 33
>KOG1775|consensus
Probab=99.48 E-value=3e-14 Score=91.65 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=62.0
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecC
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRD 95 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d 95 (105)
..+.+.++++|+|.+|+.|+|.|+|.|||.|.|++|+|+.||...++. ....+++.+++.|++|..+.+..
T Consensus 10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~eg-r~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEG-RRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCc-ceeeeeeeeeecCCcEEEEecCC
Confidence 345778999999999999999999999999999999999999775543 35678999999999999887654
No 34
>KOG1774|consensus
Probab=99.45 E-value=8.1e-14 Score=90.61 Aligned_cols=78 Identities=21% Similarity=0.296 Sum_probs=62.5
Q ss_pred cccccccchhhHHhhcCC--EEEEEEcC--CeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEE
Q psy17123 15 KDRKRKESILDLSKFLDK--VIRVKFAG--GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRN 90 (105)
Q Consensus 15 ~~~~~~~~~~~L~~~i~k--~V~V~Lkd--Gr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~ 90 (105)
-+|..-+|+..+.+|+.. +|.|.|.+ |-.++|.+.|||+|||+||++|+|....++ ..+.+|.++++|++|..
T Consensus 6 v~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~---~rk~lGRilLKGDnItl 82 (88)
T KOG1774|consen 6 VQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK---SRKELGRILLKGDNITL 82 (88)
T ss_pred ccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc---CCCccccEEEcCCcEEE
Confidence 345567788888888764 56666655 789999999999999999999999865443 24589999999999999
Q ss_pred EEecC
Q psy17123 91 VHRRD 95 (105)
Q Consensus 91 i~~~d 95 (105)
|...+
T Consensus 83 i~~~~ 87 (88)
T KOG1774|consen 83 IQSAG 87 (88)
T ss_pred EeecC
Confidence 98654
No 35
>KOG3293|consensus
Probab=99.38 E-value=7e-13 Score=92.04 Aligned_cols=72 Identities=15% Similarity=0.091 Sum_probs=64.0
Q ss_pred chhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 22 ~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
|...|+...+.++.|+||+|.+|.|.|...|.||||.|.+++++..+++ ....+..++|||++|.++...|.
T Consensus 3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgd---kf~r~pEcYirGttIkylri~d~ 74 (134)
T KOG3293|consen 3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGD---KFFRMPECYIRGTTIKYLRIPDE 74 (134)
T ss_pred chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCC---ceeecceeEEecceeEEEeccHH
Confidence 3455777899999999999999999999999999999999999987765 46778899999999999988765
No 36
>KOG3448|consensus
Probab=99.36 E-value=4.2e-12 Score=83.76 Aligned_cols=70 Identities=19% Similarity=0.129 Sum_probs=60.0
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR 94 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~ 94 (105)
+...++++|++|.|+||++-.+.|+|.|.|||+|+.|.|.... +++.-++...+..++|||+.|.+|...
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLP 73 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeC
Confidence 4557888999999999999999999999999999999998765 333335677888999999999999853
No 37
>KOG3172|consensus
Probab=99.03 E-value=1e-09 Score=74.82 Aligned_cols=72 Identities=19% Similarity=0.100 Sum_probs=63.7
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
-++-.|++.-+.-|++++..|..|+|.|...+++||++|.|.+-...++. ...+..|+|||+.|.++...|-
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~----vs~le~V~IRGS~IRFlvlPdm 76 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR----VSQLEQVFIRGSKIRFLVLPDM 76 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc----ceeeeeEEEecCeEEEEECchH
Confidence 35667899999999999999999999999999999999999998776664 5678899999999999987764
No 38
>KOG3428|consensus
Probab=98.86 E-value=2.2e-08 Score=68.23 Aligned_cols=71 Identities=15% Similarity=0.166 Sum_probs=61.0
Q ss_pred hhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDHKE 98 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~~~ 98 (105)
...|+++.+.+|+|.|++|....|++.+.|.+||..|.++.-..+. + ...+..+.|||++|.++..+|.-.
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~----pv~l~~lsirgnniRy~~lpD~l~ 74 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-E----PVRLDTLSIRGNNIRYYILPDSLN 74 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-C----ceeEEEEEeecceEEEEEccCCcC
Confidence 4578899999999999999999999999999999999987765442 2 456788999999999999887643
No 39
>KOG3459|consensus
Probab=98.34 E-value=4.8e-08 Score=66.74 Aligned_cols=72 Identities=19% Similarity=0.176 Sum_probs=56.9
Q ss_pred cchhhHHhhc--CCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecC----c--e---eeeeeEEeeEEEcCCcEE
Q psy17123 21 ESILDLSKFL--DKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT----Y--Q---SVQVRSWCSIVRRQESRR 89 (105)
Q Consensus 21 ~~~~~L~~~i--~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~----~--~---~~~~~~lg~vlIRG~~I~ 89 (105)
.+...|.... ..+|.|.++|++.+.|++.+||.|.|++|+++.|.+..- + . ....|.+|.++|||++|+
T Consensus 24 Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI 103 (114)
T KOG3459|consen 24 GPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVI 103 (114)
T ss_pred CchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEE
Confidence 4444454554 468999999999999999999999999999999877531 1 1 123688999999999998
Q ss_pred EEE
Q psy17123 90 NVH 92 (105)
Q Consensus 90 ~i~ 92 (105)
.+-
T Consensus 104 ~v~ 106 (114)
T KOG3459|consen 104 LVL 106 (114)
T ss_pred EEE
Confidence 875
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.14 E-value=7.8e-06 Score=51.91 Aligned_cols=69 Identities=12% Similarity=0.201 Sum_probs=42.2
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC---ccCeEecceEEEEecC---ceeeeeeEEeeEEEcCCcEE
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP---LLNLVLDNTTEYLRVT---YQSVQVRSWCSIVRRQESRR 89 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~---~mNlvL~da~E~~~~~---~~~~~~~~lg~vlIRG~~I~ 89 (105)
+....+..++|++|.|+++||..|+|+|.+++. -+.++|..+....... ...........++|+++.|+
T Consensus 2 Rl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 2 RLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp --HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred hHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 345667889999999999999999999999998 8999998887653321 11122344556777776654
No 41
>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=97.94 E-value=7.8e-06 Score=51.36 Aligned_cols=38 Identities=34% Similarity=0.541 Sum_probs=31.4
Q ss_pred CCEEEEEEcC--C--eEEEEEEEEecCccCeEecceEEEEec
Q psy17123 31 DKVIRVKFAG--G--RECSGILKGFDPLLNLVLDNTTEYLRV 68 (105)
Q Consensus 31 ~k~V~V~Lkd--G--r~i~G~L~~fD~~mNlvL~da~E~~~~ 68 (105)
.++|+|.++. | -.++|.|.+||+|+|++|.|+.|.+..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3678887764 3 278999999999999999999998764
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.29 E-value=0.001 Score=44.56 Aligned_cols=72 Identities=14% Similarity=0.134 Sum_probs=55.0
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCce-----eeeeeEEeeEEEcCCcEEEEEecCCcc
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQ-----SVQVRSWCSIVRRQESRRNVHRRDHKE 98 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~-----~~~~~~lg~vlIRG~~I~~i~~~d~~~ 98 (105)
.+|+|++|.+..+.+-.|+|+|...|. --.|.|.++..+-.++.. ......+..|..||+.|..+...+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 368999999999999999999999995 789999998876432210 112335678999999999998766544
No 43
>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=96.80 E-value=0.0036 Score=45.79 Aligned_cols=65 Identities=23% Similarity=0.302 Sum_probs=45.8
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
-.+....+|++|.|.|.+.| +++.|.+..+|+ .-||||-+..| ++. + ..-+|-|..|..|...+.
T Consensus 7 ~~p~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~-----~--sv~~I~ghaVk~vevl~~ 72 (166)
T PF06372_consen 7 KSPLEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK-----R--SVKVIMGHAVKSVEVLSE 72 (166)
T ss_dssp S-HHHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS------E--EEEEE-GGGEEEEEEEE-
T ss_pred CCHHHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc-----e--eEEEEEccceEEEEEccC
Confidence 35778899999999999999 999999999995 56999975443 221 2 357899999999987664
No 44
>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=96.74 E-value=0.0062 Score=35.41 Aligned_cols=33 Identities=30% Similarity=0.418 Sum_probs=29.0
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
.+||+|+|.+ ++..++|+..++|+...|+|...
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 4799999999 77777999999999999999653
No 45
>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=96.64 E-value=0.011 Score=38.04 Aligned_cols=65 Identities=14% Similarity=0.147 Sum_probs=49.5
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce------eeeeeEEeeEEEcCCcEEEE
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ------SVQVRSWCSIVRRQESRRNV 91 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~------~~~~~~lg~vlIRG~~I~~i 91 (105)
.+++|++|.+..+.+..|+|+|..+| +---|.|.|+..+-.++-. +.....+..++.||+.|.-+
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence 36899999999999999999999999 4556789998876443221 12345567899999988643
No 46
>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=96.42 E-value=0.0066 Score=37.66 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=27.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d 61 (105)
-..+|+|.|.||-.++|.+.+||+|+=++-.+
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 35689999999999999999999998766544
No 47
>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=96.29 E-value=0.0084 Score=37.19 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=27.8
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d 61 (105)
-..+|+|.|.+|-.+.|.+.+||+|+=|+-.+
T Consensus 14 ~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 14 ERIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 46799999999999999999999998766544
No 48
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.89 E-value=0.016 Score=37.72 Aligned_cols=34 Identities=15% Similarity=0.269 Sum_probs=29.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
--...|+|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus 17 ~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 17 KERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 3467999999999999999999999987776553
No 49
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=95.64 E-value=0.075 Score=34.62 Aligned_cols=63 Identities=11% Similarity=0.090 Sum_probs=46.6
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecC-ccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDP-LLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~-~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
+....|....||+|.+.|.++....|++.++|. ..|+..++-. .+ .......++|..-|++++
T Consensus 14 rfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TP-----lGv~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 14 RFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TP-----LGVQPEALLRCSDVISIS 77 (80)
T ss_dssp HHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TT-----TTEEEEEEEEGGGEEEEE
T ss_pred HHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----CC-----cccChhheeecCCEEEEE
Confidence 445567788899999999999999999999995 4566665522 22 344678999999999886
No 50
>PRK14638 hypothetical protein; Provisional
Probab=95.35 E-value=0.046 Score=39.06 Aligned_cols=45 Identities=18% Similarity=0.286 Sum_probs=35.0
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL 59 (105)
|--|.|-+. +.++.+++|++|.|++++++.++|+|.++|.- ++.|
T Consensus 83 PGldRpL~~-~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 83 PGLDRPLRG-PKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred CCCCCCCCC-HHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 334444444 56788999999999999999999999999963 4545
No 51
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.12 E-value=0.036 Score=35.84 Aligned_cols=29 Identities=17% Similarity=0.330 Sum_probs=25.3
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeE
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLV 58 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlv 58 (105)
-..+|.|.|.||-.+.|.+.|||+|.=|.
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL 46 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFVVLL 46 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEEEEE
Confidence 45799999999999999999999997443
No 52
>PRK14639 hypothetical protein; Provisional
Probab=94.79 E-value=0.085 Score=37.30 Aligned_cols=45 Identities=18% Similarity=0.302 Sum_probs=35.6
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL 59 (105)
|--+.|.+. +.+..+++|+.|.|++.+++.+.|+|.++|. .++.|
T Consensus 71 PGl~RpL~~-~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 71 PGLERKLSK-IEHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred CCCCCcCCC-HHHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence 344444444 6778899999999999999999999999998 35544
No 53
>PRK02001 hypothetical protein; Validated
Probab=94.72 E-value=0.091 Score=37.77 Aligned_cols=45 Identities=20% Similarity=0.197 Sum_probs=35.0
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL 59 (105)
|--+.|.+. +.+..+++|+.|+|++.+++.|+|+|.++|.- ++.|
T Consensus 73 PGldRpL~~-~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 73 AGLTSPLKV-PRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CCCCCcCCC-HHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 333444443 56788999999999999999999999999974 4555
No 54
>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=94.51 E-value=0.12 Score=31.93 Aligned_cols=35 Identities=9% Similarity=0.093 Sum_probs=29.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~ 63 (105)
.+|..|++++-.|..|+|.+.+||.-.++++-.|.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~ 38 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCP 38 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECc
Confidence 47899999999999999999999988877654433
No 55
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=94.15 E-value=0.59 Score=29.33 Aligned_cols=56 Identities=20% Similarity=0.221 Sum_probs=40.9
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
-....|++++|++|.|.+..|.. .|+|.+.-.- .|+|+.. + ...+||=.+|++|.|
T Consensus 11 yvyq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~------~---------~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 11 YVYQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN------G---------TPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC------C---------cEEEEEeeeEEEEcC
Confidence 34667999999999999988776 9999997632 1233221 1 258899999998864
No 56
>PRK14644 hypothetical protein; Provisional
Probab=93.68 E-value=0.23 Score=35.04 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=36.6
Q ss_pred CCCccccccccchhhHHhhcCCEEEEEEcCC----eEEEEEEEEecCccCeEec
Q psy17123 11 GAETKDRKRKESILDLSKFLDKVIRVKFAGG----RECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 11 ~~~~~~~~~~~~~~~L~~~i~k~V~V~LkdG----r~i~G~L~~fD~~mNlvL~ 60 (105)
..|--++|.+. .++.+++|+.|.|+|++. +.++|.|.++|. -++.|.
T Consensus 67 SSPGldRpL~~--~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~ 117 (136)
T PRK14644 67 SSPGFDMDYET--DELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK 117 (136)
T ss_pred ECCCCCCCCCH--HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence 34555666664 389999999999999876 899999999997 345553
No 57
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.19 E-value=0.19 Score=36.76 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=28.4
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
-..+|+|.|.+|-.++|.+.+||+|.=|.-.+.
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 457999999999999999999999987665553
No 58
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.11 E-value=0.23 Score=36.37 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=28.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
-..+|+|.|.+|-.++|.+.+||+|.=|+-.+.
T Consensus 23 ~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 23 TKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 356899999999999999999999986666554
No 59
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=93.01 E-value=0.38 Score=30.73 Aligned_cols=43 Identities=30% Similarity=0.461 Sum_probs=32.6
Q ss_pred cccccccchhhHHhhcCCEEEEEEc---CC-eEEEEEEEEecCccCeEe
Q psy17123 15 KDRKRKESILDLSKFLDKVIRVKFA---GG-RECSGILKGFDPLLNLVL 59 (105)
Q Consensus 15 ~~~~~~~~~~~L~~~i~k~V~V~Lk---dG-r~i~G~L~~fD~~mNlvL 59 (105)
-+.|... +.++.+++|+.|.|+++ +| +.+.|.|.++|.- ++.|
T Consensus 10 l~RpL~~-~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 10 AERPLKK-EADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CCCcCCC-HHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 3434443 67788999999999997 56 5999999999983 4444
No 60
>PRK14640 hypothetical protein; Provisional
Probab=92.85 E-value=0.43 Score=34.06 Aligned_cols=45 Identities=18% Similarity=0.303 Sum_probs=33.5
Q ss_pred ccccccccchhhHHhhcCCEEEEEE----cCCeEEEEEEEEecCccCeEec
Q psy17123 14 TKDRKRKESILDLSKFLDKVIRVKF----AGGRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 14 ~~~~~~~~~~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~~mNlvL~ 60 (105)
--+.|-+. +.+..+++|+.|.|++ .+++.++|+|.++|.. ++.|.
T Consensus 81 Gl~RpL~~-~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 81 GLDRPLFK-VAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CCCCcCCC-HHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 33434433 5678899999999999 5678999999999873 45553
No 61
>PRK14633 hypothetical protein; Provisional
Probab=92.28 E-value=0.45 Score=33.95 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=32.9
Q ss_pred cccccccchhhHHhhcCCEEEEEEc----CCeEEEEEEEEecCccCeEec
Q psy17123 15 KDRKRKESILDLSKFLDKVIRVKFA----GGRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 15 ~~~~~~~~~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD~~mNlvL~ 60 (105)
-|.|-+. ..++.+++|++|.|+++ +++.|+|+|.+++.- ++.|.
T Consensus 79 ldRpL~~-~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 79 MNRQIFN-IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCCCCCC-HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 3434433 56778999999999993 668999999999874 55553
No 62
>KOG1073|consensus
Probab=91.95 E-value=0.57 Score=38.18 Aligned_cols=71 Identities=13% Similarity=0.149 Sum_probs=54.4
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEec-CccCeEecceEEEEecCce------eeeeeEEeeEEEcCCcEEEEEecCCc
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFD-PLLNLVLDNTTEYLRVTYQ------SVQVRSWCSIVRRQESRRNVHRRDHK 97 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD-~~mNlvL~da~E~~~~~~~------~~~~~~lg~vlIRG~~I~~i~~~d~~ 97 (105)
..|||++|.++-|....|+|+|.-.| +--=|-|.++..+-.++.. ..-...+..|+.||+.|+-+...+..
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 47899999999999999999999999 7778899997554332211 01112678899999999988766644
No 63
>PRK14645 hypothetical protein; Provisional
Probab=91.51 E-value=0.53 Score=33.84 Aligned_cols=42 Identities=14% Similarity=0.183 Sum_probs=31.7
Q ss_pred cccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123 15 KDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 15 ~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL 59 (105)
-|.|-+. ..++.+++|++|.|++ +++.++|+|.++|.- .+.|
T Consensus 87 ldRpL~~-~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 87 PKRPLFT-ARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred CCCCCCC-HHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 3434433 5667889999999985 889999999999974 3444
No 64
>PRK14642 hypothetical protein; Provisional
Probab=91.32 E-value=0.57 Score=35.13 Aligned_cols=42 Identities=19% Similarity=0.350 Sum_probs=32.8
Q ss_pred ccccccchhhHHhhcCCEEEEEEc-------------CCeEEEEEEEEecCccCeEe
Q psy17123 16 DRKRKESILDLSKFLDKVIRVKFA-------------GGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 16 ~~~~~~~~~~L~~~i~k~V~V~Lk-------------dGr~i~G~L~~fD~~mNlvL 59 (105)
|.|.+. ..+..+++|+.|.|+|+ +.+.|+|+|.++|.. ++.|
T Consensus 86 dRPLk~-~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 86 DRPLRH-EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCCCCC-HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 334433 56788899999999998 679999999999974 4444
No 65
>PRK14636 hypothetical protein; Provisional
Probab=91.09 E-value=0.62 Score=34.18 Aligned_cols=45 Identities=22% Similarity=0.378 Sum_probs=33.9
Q ss_pred CccccccccchhhHHhhcCCEEEEEEc---CC-eEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFA---GG-RECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk---dG-r~i~G~L~~fD~~mNlvL 59 (105)
|--+.|... ..+..+++|++|.|+|+ +| +.|+|+|.++|.- ++.|
T Consensus 81 PGldRpL~~-~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 81 PGIDRPLTR-PKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CCCCCCCCC-HHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 444445544 56788999999999997 55 6999999999873 4544
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=91.02 E-value=0.51 Score=32.84 Aligned_cols=36 Identities=28% Similarity=0.506 Sum_probs=27.2
Q ss_pred hhhHHhhcCCEEEEEEc----CCeEEEEEEEEecCccCeEe
Q psy17123 23 ILDLSKFLDKVIRVKFA----GGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD~~mNlvL 59 (105)
..++.+++|+.|.|+++ +.+.+.|+|.++|. -.++|
T Consensus 79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 56789999999999994 45799999999998 44444
No 67
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=90.83 E-value=0.75 Score=32.65 Aligned_cols=31 Identities=29% Similarity=0.604 Sum_probs=27.8
Q ss_pred hhhHHhhcCCEEEEEE----cCCeEEEEEEEEecC
Q psy17123 23 ILDLSKFLDKVIRVKF----AGGRECSGILKGFDP 53 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~ 53 (105)
..++.+++|+.|.|++ .+++.++|+|.++|.
T Consensus 90 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 90 ARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 5678899999999997 567899999999997
No 68
>PRK14632 hypothetical protein; Provisional
Probab=90.54 E-value=0.79 Score=33.44 Aligned_cols=44 Identities=18% Similarity=0.251 Sum_probs=32.9
Q ss_pred cccccccchhhHHhhcCCEEEEEEcC-------CeEEEEEEEEecCccCeEec
Q psy17123 15 KDRKRKESILDLSKFLDKVIRVKFAG-------GRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 15 ~~~~~~~~~~~L~~~i~k~V~V~Lkd-------Gr~i~G~L~~fD~~mNlvL~ 60 (105)
-|.|-+. ..+..+++|+.|.|+|++ .+.|+|+|.++|. -++.|.
T Consensus 83 ldRpL~~-~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~ 133 (172)
T PRK14632 83 LERPFFR-AEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR 133 (172)
T ss_pred CCCcCCC-HHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence 3434433 567889999999999976 5799999999986 355553
No 69
>PRK14634 hypothetical protein; Provisional
Probab=90.49 E-value=0.8 Score=32.83 Aligned_cols=45 Identities=13% Similarity=0.107 Sum_probs=33.2
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD~~mNlvL 59 (105)
|--|.|.+. ..+..+++|+.|.|++.+ .+.|+|+|.++|.- ++.|
T Consensus 83 PGldRpL~~-~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 83 PGIGDQLSS-DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CCCCCcCCC-HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 334444444 667889999999999963 27999999999973 4555
No 70
>PRK14643 hypothetical protein; Provisional
Probab=90.47 E-value=0.84 Score=33.13 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=31.3
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEecCc
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFDPL 54 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD~~ 54 (105)
|--++|.+. ..++.+++|++|.|+|+. .+.|+|+|.++|.-
T Consensus 87 PGleRpL~~-~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 87 SGIEKQIRS-QEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred CCCCCCCCC-HHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 333434433 567889999999999965 58999999999964
No 71
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.15 E-value=1.3 Score=32.00 Aligned_cols=42 Identities=24% Similarity=0.445 Sum_probs=33.3
Q ss_pred ccccccchhhHHhhcCCEEEEEE----cCCeEEEEEEEEecCccCeEe
Q psy17123 16 DRKRKESILDLSKFLDKVIRVKF----AGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 16 ~~~~~~~~~~L~~~i~k~V~V~L----kdGr~i~G~L~~fD~~mNlvL 59 (105)
|.|... ..+..+++|+.|.|.| .+++.++|+|.++|.-. +++
T Consensus 85 dRpL~~-~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 85 DRPLKT-AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCcCC-HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 434333 4567889999999999 78899999999999876 444
No 72
>PRK14647 hypothetical protein; Provisional
Probab=89.82 E-value=1 Score=32.29 Aligned_cols=40 Identities=20% Similarity=0.345 Sum_probs=30.9
Q ss_pred CccccccccchhhHHhhcCCEEEEEEc---------CCeEEEEEEEEecC
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFA---------GGRECSGILKGFDP 53 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk---------dGr~i~G~L~~fD~ 53 (105)
|--+.|.+. ..++.+++|+.|.|+++ +.+.|+|+|.++|.
T Consensus 82 PG~~RpL~~-~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 82 PGLDRPLKK-EADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CCCCCcCCC-HHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 333444444 66788999999999995 35899999999996
No 73
>PRK14646 hypothetical protein; Provisional
Probab=89.32 E-value=1.2 Score=31.93 Aligned_cols=45 Identities=13% Similarity=0.111 Sum_probs=33.0
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcC---C-eEEEEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAG---G-RECSGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lkd---G-r~i~G~L~~fD~~mNlvL 59 (105)
|--+.|-+. ..+..+++|+.|.|+|++ | +.++|+|.++|.- ++.|
T Consensus 83 PGldRpL~~-~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 83 QGVSDELTS-ERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCCCCcCCC-HHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 333444443 567889999999999964 3 6889999999984 5555
No 74
>PRK14631 hypothetical protein; Provisional
Probab=88.49 E-value=1.4 Score=32.35 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=30.7
Q ss_pred CccccccccchhhHHhhcCCEEEEEEc----CCeEEEEEEEEec
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFA----GGRECSGILKGFD 52 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk----dGr~i~G~L~~fD 52 (105)
|--+.|-+. ..++.+++|+.|.|+|. +.+.|+|+|.++|
T Consensus 100 PGldRpL~~-~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 100 PGWDRPFFQ-LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CCCCCcCCC-HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 334444444 66788999999999995 4589999999998
No 75
>PRK06955 biotin--protein ligase; Provisional
Probab=87.69 E-value=2.5 Score=32.93 Aligned_cols=32 Identities=22% Similarity=0.385 Sum_probs=28.4
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~ 60 (105)
+++++|+|...+++.++|++.|+|+...|+|.
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 47899999766778899999999999999985
No 76
>PRK14637 hypothetical protein; Provisional
Probab=87.44 E-value=1.6 Score=31.16 Aligned_cols=45 Identities=24% Similarity=0.318 Sum_probs=32.0
Q ss_pred CccccccccchhhHHhhcCCEEEEEEcCCeEE-EEEEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFAGGREC-SGILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~LkdGr~i-~G~L~~fD~~mNlvL 59 (105)
|--|.|-+. ..+..+++|+.|.|++.+.+.+ +|+|.++|.- ++.|
T Consensus 81 PGldRpL~~-~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 81 PGIERVIKN-AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred CCCCCCCCC-HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 334444444 6678899999999999544455 7999999874 4444
No 77
>PRK14641 hypothetical protein; Provisional
Probab=87.35 E-value=1.6 Score=32.07 Aligned_cols=36 Identities=14% Similarity=0.264 Sum_probs=28.6
Q ss_pred ccccccchhhHHhhcCCEEEEEEcC----CeEEEEEEEEec
Q psy17123 16 DRKRKESILDLSKFLDKVIRVKFAG----GRECSGILKGFD 52 (105)
Q Consensus 16 ~~~~~~~~~~L~~~i~k~V~V~Lkd----Gr~i~G~L~~fD 52 (105)
+.|.+. ..+..+++|+.|.|+|.+ .+.|+|+|.++|
T Consensus 90 dRpL~~-~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 90 GEPIIL-PRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCcCCC-HHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 344443 567888999999999975 569999999995
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=84.28 E-value=5.4 Score=31.02 Aligned_cols=49 Identities=27% Similarity=0.347 Sum_probs=34.9
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCC
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQE 86 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~ 86 (105)
++|++|++.. ++..++|++.++|+...|+|.. ++. .+.-..|.|.+|+.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~------~g~--~~~~~~gev~~~~~ 318 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLED------DGV--EKPFNGGEISLRSW 318 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEe------CCc--EEEEEEeEEEEecC
Confidence 4799999986 4567999999999999999951 121 12334566766653
No 79
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=82.09 E-value=5.8 Score=34.10 Aligned_cols=32 Identities=25% Similarity=0.195 Sum_probs=28.5
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~ 60 (105)
++|++|++...+++.+.|+..|+|+...|+|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 47999999767778899999999999999995
No 80
>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=81.92 E-value=9.3 Score=28.50 Aligned_cols=32 Identities=22% Similarity=0.376 Sum_probs=27.3
Q ss_pred hhcCCEEEEEEcCCeEEEEEEEEecCccCeEec
Q psy17123 28 KFLDKVIRVKFAGGRECSGILKGFDPLLNLVLD 60 (105)
Q Consensus 28 ~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~ 60 (105)
-++|++|+|...+ ..+.|++.|+|+...|+|.
T Consensus 190 ~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 190 AHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 3479999998644 5699999999999999995
No 81
>PRK14635 hypothetical protein; Provisional
Probab=78.97 E-value=6.4 Score=28.31 Aligned_cols=45 Identities=22% Similarity=0.217 Sum_probs=32.6
Q ss_pred CccccccccchhhHHhhcCCEEEEEEc--CCeEEEE---EEEEecCccCeEe
Q psy17123 13 ETKDRKRKESILDLSKFLDKVIRVKFA--GGRECSG---ILKGFDPLLNLVL 59 (105)
Q Consensus 13 ~~~~~~~~~~~~~L~~~i~k~V~V~Lk--dGr~i~G---~L~~fD~~mNlvL 59 (105)
|--+.|.+. +.++.+++|+.|.|++. ++..+.| +|.++|.- ++.|
T Consensus 82 PGldRpL~~-~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 82 AGAERKLRL-PEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CCCCCcCCC-HHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 333444444 66788999999999886 4678888 99999864 4555
No 82
>PRK08330 biotin--protein ligase; Provisional
Probab=78.29 E-value=9.7 Score=28.44 Aligned_cols=33 Identities=24% Similarity=0.311 Sum_probs=27.1
Q ss_pred hhcCCEEEEEEcCCeEE-EEEEEEecCccCeEecc
Q psy17123 28 KFLDKVIRVKFAGGREC-SGILKGFDPLLNLVLDN 61 (105)
Q Consensus 28 ~~i~k~V~V~LkdGr~i-~G~L~~fD~~mNlvL~d 61 (105)
-+++++|++.. +++.+ .|++.|+|+...|+|..
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 35799999975 56665 79999999999999964
No 83
>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=78.25 E-value=3.6 Score=29.99 Aligned_cols=34 Identities=24% Similarity=0.216 Sum_probs=30.7
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~ 63 (105)
-+-.|+|.+.||..|.|.+.+|++--|.+|..+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 4569999999999999999999999999997654
No 84
>PRK14630 hypothetical protein; Provisional
Probab=75.54 E-value=8.1 Score=27.32 Aligned_cols=41 Identities=17% Similarity=0.215 Sum_probs=29.7
Q ss_pred ccccccchhhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEe
Q psy17123 16 DRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVL 59 (105)
Q Consensus 16 ~~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL 59 (105)
+.|-+. ..+..+++|++|.|++... ..+|+|.++|. -++.|
T Consensus 83 dRpL~~-~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 83 NRKIKS-DREFKIFEGKKIKLMLDND-FEEGFILEAKA-DSFIF 123 (143)
T ss_pred CCcCCC-HHHHHHhCCCEEEEEEcCc-ceEEEEEEEeC-CEEEE
Confidence 334433 5667889999999999654 45999999987 44444
No 85
>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=74.88 E-value=5.2 Score=29.18 Aligned_cols=24 Identities=42% Similarity=0.563 Sum_probs=22.1
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecC
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
.++-|+|-|.|||+++|.=.|.|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 689999999999999999999874
No 86
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=73.35 E-value=8.5 Score=29.90 Aligned_cols=31 Identities=23% Similarity=0.169 Sum_probs=27.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d 61 (105)
+|++|.|.. ++..+.|++.|+|+...|+|..
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 799999874 6789999999999999999863
No 87
>PRK10898 serine endoprotease; Provisional
Probab=72.71 E-value=8.4 Score=30.72 Aligned_cols=32 Identities=28% Similarity=0.371 Sum_probs=27.9
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 31 DKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 31 ~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
...+.|++.||+.+.+.+.++|...+|-|=..
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 36899999999999999999999999876543
No 88
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=72.13 E-value=16 Score=27.86 Aligned_cols=36 Identities=36% Similarity=0.480 Sum_probs=32.0
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
...+|++|++...++..+.|+..++|....|+|+..
T Consensus 186 ~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 186 SLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred hccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 334899999999999999999999999999999765
No 89
>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=70.89 E-value=9.6 Score=30.30 Aligned_cols=31 Identities=32% Similarity=0.442 Sum_probs=27.5
Q ss_pred CEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 32 KVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
..+.|.+.||+.+.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4799999999999999999999999987543
No 90
>PRK10942 serine endoprotease; Provisional
Probab=65.44 E-value=13 Score=30.84 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=27.6
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123 31 DKVIRVKFAGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 31 ~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d 61 (105)
...|.|.+.||+.+.+.+.++|...+|-|=.
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 3579999999999999999999999987754
No 91
>PRK10139 serine endoprotease; Provisional
Probab=65.34 E-value=14 Score=30.57 Aligned_cols=32 Identities=25% Similarity=0.354 Sum_probs=28.1
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 31 DKVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 31 ~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
..++.|++.||+.+.+.+.++|....|-|=..
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 36899999999999999999999999877543
No 92
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=65.06 E-value=8.9 Score=24.74 Aligned_cols=61 Identities=11% Similarity=0.127 Sum_probs=27.6
Q ss_pred hHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEecCC
Q psy17123 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRRDH 96 (105)
Q Consensus 25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~d~ 96 (105)
+|.=.-+.+|+++|+||..++|+- .|-..|- +=.|+.. -...-+...||=++|.+++....
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~A--~dt~~~~---~k~E~L~------l~~~~~~~~i~Ld~I~~~~al~~ 71 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGKA--LDTRTNA---KKEECLV------LEQDGGEQEIRLDQIASMSALTD 71 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEESS---EEE------SSS-EEE------EEETTEEEEESTT--SEEE----
T ss_pred HHHHhcCCeEEEEEeCCCEEEEEE--EEEEEec---CceEEEE------EecCCcEEEEEhhheeeeeecCC
Confidence 333445779999999999999982 2222221 1112111 01123567899999999886443
No 93
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=64.14 E-value=10 Score=21.80 Aligned_cols=21 Identities=19% Similarity=0.407 Sum_probs=14.0
Q ss_pred EEEEEEEecCccCeEecceEE
Q psy17123 44 CSGILKGFDPLLNLVLDNTTE 64 (105)
Q Consensus 44 i~G~L~~fD~~mNlvL~da~E 64 (105)
..|++.|.|+.+.+.|.+...
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 689999999999999987543
No 94
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=62.38 E-value=20 Score=22.96 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=22.1
Q ss_pred hhhHHhhcCCEEEEEEcCCe----EEEEEEEEe
Q psy17123 23 ILDLSKFLDKVIRVKFAGGR----ECSGILKGF 51 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~LkdGr----~i~G~L~~f 51 (105)
-..|.+++|++|.++.+.|| +-+|+|...
T Consensus 9 k~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 9 KKELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 34688999999999999998 678988765
No 95
>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=62.34 E-value=12 Score=25.16 Aligned_cols=27 Identities=19% Similarity=0.416 Sum_probs=18.8
Q ss_pred hhhHHhh---c--CCEEEEEEcCCeEEEEEEE
Q psy17123 23 ILDLSKF---L--DKVIRVKFAGGRECSGILK 49 (105)
Q Consensus 23 ~~~L~~~---i--~k~V~V~LkdGr~i~G~L~ 49 (105)
+..|+.+ + +-+|.+.|+||+.+.|++.
T Consensus 15 Ia~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 15 IARLEHLVSELDGEERVELELDDGSMLRGTVA 46 (101)
T ss_dssp HHHHHHHHHCTTTT-EEEEEETTS-EEEEEEC
T ss_pred HHHHHHHHhhcCCcceEEEEEcCCCeeeeeec
Confidence 4445554 3 3699999999999999963
No 96
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=57.07 E-value=6.9 Score=26.17 Aligned_cols=17 Identities=35% Similarity=0.427 Sum_probs=15.3
Q ss_pred EEEEEecCccCeEecce
Q psy17123 46 GILKGFDPLLNLVLDNT 62 (105)
Q Consensus 46 G~L~~fD~~mNlvL~da 62 (105)
|+|+|.|.|.|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999988765
No 97
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=56.83 E-value=24 Score=28.53 Aligned_cols=31 Identities=29% Similarity=0.423 Sum_probs=27.7
Q ss_pred CEEEEEEcCCeEEEEEEEEecCccCeEecce
Q psy17123 32 KVIRVKFAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
..+.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 5889999999999999999999999887544
No 98
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=56.33 E-value=28 Score=24.87 Aligned_cols=28 Identities=18% Similarity=0.270 Sum_probs=24.7
Q ss_pred hHHhhcCCEEEEEEcCCeEEEEEEEEec
Q psy17123 25 DLSKFLDKVIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 25 ~L~~~i~k~V~V~LkdGr~i~G~L~~fD 52 (105)
....++||.|.+...+|..+.|+..+.-
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 4467899999999999999999998875
No 99
>KOG3382|consensus
Probab=53.55 E-value=7.5 Score=27.83 Aligned_cols=25 Identities=24% Similarity=0.312 Sum_probs=19.4
Q ss_pred EcCCeEEEEEEEEecCccCeEecce
Q psy17123 38 FAGGRECSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 38 LkdGr~i~G~L~~fD~~mNlvL~da 62 (105)
++....=.|+|+|.|+|.|=.-+|-
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred Hhcccccceeeeeecccccchhccc
Confidence 3444555799999999999887765
No 100
>PRK08477 biotin--protein ligase; Provisional
Probab=52.24 E-value=55 Score=24.43 Aligned_cols=34 Identities=9% Similarity=-0.049 Sum_probs=29.1
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~ 63 (105)
.+++.|+|. .+++.++|+..+.|+..-|++.--.
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 379999987 5789999999999999999887543
No 101
>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=50.16 E-value=27 Score=23.87 Aligned_cols=20 Identities=35% Similarity=0.453 Sum_probs=17.7
Q ss_pred EEEEEEcCCeEEEEEEEEec
Q psy17123 33 VIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 33 ~V~V~LkdGr~i~G~L~~fD 52 (105)
...|.++||+.+.|.+..=|
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET 78 (133)
T ss_pred cEEEEECCCCEEEEEEEecC
Confidence 58999999999999998844
No 102
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=43.91 E-value=21 Score=20.74 Aligned_cols=18 Identities=28% Similarity=0.327 Sum_probs=14.4
Q ss_pred ccchhhHHhhcCCEEEEE
Q psy17123 20 KESILDLSKFLDKVIRVK 37 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~ 37 (105)
++.+..+++++||+|+|.
T Consensus 8 ~~~~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 8 EEDYSYLKSLLGKRVSVT 25 (48)
T ss_pred hhhhHHHHHhcCCeEEEE
Confidence 345677888999999987
No 103
>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=41.93 E-value=35 Score=22.57 Aligned_cols=22 Identities=36% Similarity=0.662 Sum_probs=17.0
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy17123 29 FLDKVIRVK-FAGGRECSGILKG 50 (105)
Q Consensus 29 ~i~k~V~V~-LkdGr~i~G~L~~ 50 (105)
.+|..|+|+ +..|+.+.|+..+
T Consensus 94 ~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 94 AVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred CCCCEEEEEECCCCCEEEEEEeC
Confidence 367888888 6888888887764
No 104
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=41.09 E-value=42 Score=22.04 Aligned_cols=27 Identities=15% Similarity=-0.092 Sum_probs=21.9
Q ss_pred EEEEecCceeeeeeEEeeEEEcCCcEEEEEe
Q psy17123 63 TEYLRVTYQSVQVRSWCSIVRRQESRRNVHR 93 (105)
Q Consensus 63 ~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~ 93 (105)
.|++.+++ .++-|.++.+|..+..|..
T Consensus 68 FEFS~~G~----~ry~G~l~m~G~~l~~v~l 94 (97)
T PF11743_consen 68 FEFSSDGE----DRYQGELVMLGRRLISVEL 94 (97)
T ss_pred EEEeCCCh----hcceEEEEEECCeeeEEEc
Confidence 46666665 6889999999999998874
No 105
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=39.86 E-value=56 Score=23.28 Aligned_cols=27 Identities=22% Similarity=0.286 Sum_probs=23.1
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEecC
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
..++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 478999999888999999999987753
No 106
>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=39.57 E-value=71 Score=17.91 Aligned_cols=25 Identities=8% Similarity=0.133 Sum_probs=21.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCc
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPL 54 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~ 54 (105)
.|..+.+...+|+.++|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4677777778999999999999964
No 107
>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=38.35 E-value=68 Score=19.40 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=19.5
Q ss_pred cCCEEEEEEcCCe-EEEEEEEEecCcc
Q psy17123 30 LDKVIRVKFAGGR-ECSGILKGFDPLL 55 (105)
Q Consensus 30 i~k~V~V~LkdGr-~i~G~L~~fD~~m 55 (105)
.|.+|.+.--+.. .|+|.+.+||.--
T Consensus 8 ~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 8 IGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred CCCEEEEECCCCCcEEEEEEEEecccC
Confidence 6899999998765 5699999999643
No 108
>PRK06630 hypothetical protein; Provisional
Probab=38.24 E-value=19 Score=24.33 Aligned_cols=19 Identities=21% Similarity=0.116 Sum_probs=16.7
Q ss_pred EEEEEEEecCccCeEecce
Q psy17123 44 CSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 44 i~G~L~~fD~~mNlvL~da 62 (105)
..|+|+|-|+|.|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999988864
No 109
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=36.33 E-value=76 Score=24.78 Aligned_cols=31 Identities=35% Similarity=0.517 Sum_probs=26.5
Q ss_pred CCEEEEEEcCCeEEEEEEEEecCccCeEecc
Q psy17123 31 DKVIRVKFAGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 31 ~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~d 61 (105)
-.++.|.+.||+++.+.+.++|...-+-+-.
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 4688999999999999999999888766544
No 110
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=35.55 E-value=31 Score=25.14 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=16.0
Q ss_pred EEEEEEecCccCeEecce
Q psy17123 45 SGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 45 ~G~L~~fD~~mNlvL~da 62 (105)
.|+|+|-|+|.|-.-++.
T Consensus 48 ~G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKL 65 (159)
T ss_pred CcEEEEecCCCCeeeecC
Confidence 499999999999988765
No 111
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=33.36 E-value=42 Score=20.72 Aligned_cols=22 Identities=9% Similarity=0.190 Sum_probs=19.0
Q ss_pred CEEEEEEcCCeEEEEEEEEecC
Q psy17123 32 KVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
.+|.|+|-||..++++|..-|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCc
Confidence 5899999999999999887654
No 112
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=33.19 E-value=51 Score=24.77 Aligned_cols=22 Identities=41% Similarity=0.702 Sum_probs=18.3
Q ss_pred hcCCEEEEE-EcCCeEEEEEEEE
Q psy17123 29 FLDKVIRVK-FAGGRECSGILKG 50 (105)
Q Consensus 29 ~i~k~V~V~-LkdGr~i~G~L~~ 50 (105)
.+|..|+|+ +..|+.+.|+..+
T Consensus 205 ~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 205 AVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCeEEEEECCCCCEEEEEEeC
Confidence 378889999 8899999998765
No 113
>KOG3493|consensus
Probab=32.91 E-value=37 Score=21.55 Aligned_cols=19 Identities=32% Similarity=0.296 Sum_probs=14.7
Q ss_pred hHHhhcCCEEEEEEcCCeE
Q psy17123 25 DLSKFLDKVIRVKFAGGRE 43 (105)
Q Consensus 25 ~L~~~i~k~V~V~LkdGr~ 43 (105)
.++..+||+|+|+....-+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 4678899999999765433
No 114
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=32.88 E-value=41 Score=24.92 Aligned_cols=51 Identities=10% Similarity=-0.003 Sum_probs=31.2
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEEec
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVHRR 94 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~~~ 94 (105)
+-+.-+-...++..|+|++.++|.- .+- +.... ....+.|.-+.|.+|+++
T Consensus 133 lp~i~C~i~t~~~~Y~G~I~~~~~~-------~v~-i~~~~------~~~~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 133 LPPIKCEIETKDKSYRGIILSYDEG-------EVS-IMPFN------QGEEIEIPIDDITSIKMI 183 (185)
T ss_pred CCCCceEEEeCCceEEEEEEeccCC-------EEE-EeccC------CCcceEeehhheeeeeec
Confidence 4444444446889999999999854 111 11110 124567777888888765
No 115
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.65 E-value=38 Score=22.00 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=19.4
Q ss_pred ccchhhHHhhcCCEEEEEEcCCeE
Q psy17123 20 KESILDLSKFLDKVIRVKFAGGRE 43 (105)
Q Consensus 20 ~~~~~~L~~~i~k~V~V~LkdGr~ 43 (105)
...-..+...+|++|.++..+||.
T Consensus 8 ~~IK~~i~ah~G~~v~lk~ngGRK 31 (80)
T COG4466 8 VDIKESIDAHLGERVTLKANGGRK 31 (80)
T ss_pred HHHHHHHHhccCcEEEEEecCCce
Confidence 334456788899999999999985
No 116
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=32.63 E-value=15 Score=34.84 Aligned_cols=58 Identities=14% Similarity=0.104 Sum_probs=0.0
Q ss_pred CEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEE
Q psy17123 32 KVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNV 91 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i 91 (105)
-+.+=...+|+.+.|.|...|.-|+.+|.--.+. .+.. -.....+|..+|+|+|.|+-
T Consensus 248 ~~~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~i-~~~~-v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 248 NRSTYTTSSGRPVDGVLVTTANVMQKLLNLLGQI-SDTS-VSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp ------------------------------------------------------------
T ss_pred CcceeecCCCCEeceEEeccHHHHHHHHHHHhhh-ccce-eecchhheeeeecCccHHHH
Confidence 3445556899999999999999888877655442 2211 12356799999999998754
No 117
>PRK11625 Rho-binding antiterminator; Provisional
Probab=31.47 E-value=86 Score=20.37 Aligned_cols=55 Identities=15% Similarity=0.088 Sum_probs=33.9
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcCCcEEEEE
Q psy17123 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQESRRNVH 92 (105)
Q Consensus 26 L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG~~I~~i~ 92 (105)
|.=.-+-+|.++++||..+.|+- .|-+.+ +-.|+..-.. .-+.-.||=++|.+++
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A--~D~~~~----~k~EyL~l~~------~g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKA--SDLVSR----KNVEYLVVEA------AGETRELRLDKIASFS 72 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEE--EeeecC----CceEEEEEEc------CCCEEEEEeeeEeecc
Confidence 33335789999999999999986 343322 3344443111 1134567777777776
No 118
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=31.01 E-value=59 Score=19.85 Aligned_cols=22 Identities=18% Similarity=0.224 Sum_probs=18.6
Q ss_pred CEEEEEEcCCeEEEEEEEEecC
Q psy17123 32 KVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
-+|.|++-||..++.++..-|.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~t 28 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDT 28 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSB
T ss_pred EEEEEECCCCCEEEEEECCcch
Confidence 4789999999999999986654
No 119
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=30.44 E-value=72 Score=24.60 Aligned_cols=19 Identities=21% Similarity=0.155 Sum_probs=17.6
Q ss_pred EEEEEEEEecCccCeEecc
Q psy17123 43 ECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 43 ~i~G~L~~fD~~mNlvL~d 61 (105)
.+.|...-+|.|.|++++=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999864
No 120
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=30.05 E-value=58 Score=19.84 Aligned_cols=22 Identities=9% Similarity=0.273 Sum_probs=18.3
Q ss_pred CEEEEEEcCCeEEEEEEEEecC
Q psy17123 32 KVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 32 k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
.+|.|+|-||..++++|..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4789999999999999876554
No 121
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=26.80 E-value=50 Score=22.80 Aligned_cols=19 Identities=32% Similarity=0.301 Sum_probs=16.4
Q ss_pred EEEEEEEecCccCeEecce
Q psy17123 44 CSGILKGFDPLLNLVLDNT 62 (105)
Q Consensus 44 i~G~L~~fD~~mNlvL~da 62 (105)
-.|.|+|.|+|.|-.-++.
T Consensus 8 r~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 8 RAGRLVGEDEFGNKYYENP 26 (115)
T ss_pred ecceEeEEcCCCCeeeEcC
Confidence 3699999999999988764
No 122
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=26.69 E-value=72 Score=21.36 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=27.4
Q ss_pred CCCccc----cccccchhhHHhhcCCEEEEEEcCCeEEEEEEEE
Q psy17123 11 GAETKD----RKRKESILDLSKFLDKVIRVKFAGGRECSGILKG 50 (105)
Q Consensus 11 ~~~~~~----~~~~~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~ 50 (105)
++|+.. +.....+-..++.+-|.++|.|.+|+.+...+=|
T Consensus 11 ~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L~ngk~v~ayIPg 54 (95)
T cd00319 11 GAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPG 54 (95)
T ss_pred CCcccCeEEEEEEeccccCCChhhceEEEEEccCCCEEEEECCC
Confidence 445554 2333444556788999999999999998655544
No 123
>KOG1719|consensus
Probab=26.18 E-value=51 Score=24.43 Aligned_cols=60 Identities=18% Similarity=0.128 Sum_probs=40.4
Q ss_pred ccccCCCCccccccccchhhHHhh--cCCEEEEEEcCCeEEEEEEEEec--CccCeEecceEEE
Q psy17123 6 TTTDAGAETKDRKRKESILDLSKF--LDKVIRVKFAGGRECSGILKGFD--PLLNLVLDNTTEY 65 (105)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~L~~~--i~k~V~V~LkdGr~i~G~L~~fD--~~mNlvL~da~E~ 65 (105)
|+.|-+..|..-........++++ +||.|.|..|-||.=.-++.+.= ++-|..-+.|+|.
T Consensus 82 ~T~D~~~~Ps~~~i~~aVeFi~k~asLGktvYVHCKAGRtRSaTvV~cYLmq~~~wtpe~A~~~ 145 (183)
T KOG1719|consen 82 PTRDYTGAPSLENIQKAVEFIHKNASLGKTVYVHCKAGRTRSATVVACYLMQHKNWTPEAAVEH 145 (183)
T ss_pred ccccccCCCCHHHHHHHHHHHHhccccCCeEEEEecCCCccchhhhhhhhhhhcCCCHHHHHHH
Confidence 566666666655666667777776 89999999999998777665432 4444444444443
No 124
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=25.90 E-value=1e+02 Score=22.64 Aligned_cols=27 Identities=26% Similarity=0.463 Sum_probs=22.5
Q ss_pred HHhhcCCEEEEEEcCCeEEEEEEEEec
Q psy17123 26 LSKFLDKVIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 26 L~~~i~k~V~V~LkdGr~i~G~L~~fD 52 (105)
+..++|++|.|.+...+.+.|.+..++
T Consensus 23 ~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 23 LKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 345899999999998899999998884
No 125
>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=25.71 E-value=98 Score=21.45 Aligned_cols=42 Identities=19% Similarity=0.304 Sum_probs=28.9
Q ss_pred CCCCccc----cccccchhhHHhhcCCEEEEEE-cCCeEEEEEEEEe
Q psy17123 10 AGAETKD----RKRKESILDLSKFLDKVIRVKF-AGGRECSGILKGF 51 (105)
Q Consensus 10 ~~~~~~~----~~~~~~~~~L~~~i~k~V~V~L-kdGr~i~G~L~~f 51 (105)
.++|+.. +.....+-..++.+-|.++|.| ++|+.++..+=|-
T Consensus 17 ~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~ 63 (115)
T cd03367 17 GGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGD 63 (115)
T ss_pred cCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCC
Confidence 3455555 2334445556788999999999 6999987665553
No 126
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.51 E-value=86 Score=23.58 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=17.6
Q ss_pred cCCEEEEE-EcCCeEEEEEEEE
Q psy17123 30 LDKVIRVK-FAGGRECSGILKG 50 (105)
Q Consensus 30 i~k~V~V~-LkdGr~i~G~L~~ 50 (105)
+|..|+|+ +..||.+.|+..+
T Consensus 185 ~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 185 ENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCEEEEEECCCCCEEEEEEeC
Confidence 68899999 6889999998764
No 127
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=24.87 E-value=1.2e+02 Score=22.67 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=22.5
Q ss_pred HhhcCCEEEEEEcCCeEEEEEEEEec
Q psy17123 27 SKFLDKVIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 27 ~~~i~k~V~V~LkdGr~i~G~L~~fD 52 (105)
..++||.|.+.-.+|..+.|+..+..
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 47799999998889999999988765
No 128
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.82 E-value=95 Score=22.17 Aligned_cols=21 Identities=29% Similarity=0.422 Sum_probs=16.2
Q ss_pred cCCEEEEE-EcCCeEEEEEEEE
Q psy17123 30 LDKVIRVK-FAGGRECSGILKG 50 (105)
Q Consensus 30 i~k~V~V~-LkdGr~i~G~L~~ 50 (105)
+|..|+|+ +..|+.+.|+..+
T Consensus 130 ~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 130 AGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCEEEEEECCCCCEEEEEEec
Confidence 67788888 7788888887653
No 129
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=24.82 E-value=1.3e+02 Score=18.56 Aligned_cols=36 Identities=11% Similarity=0.223 Sum_probs=28.4
Q ss_pred hhcCCEEEEEEcCCe-EEEEEEEEecCcc-CeEecceE
Q psy17123 28 KFLDKVIRVKFAGGR-ECSGILKGFDPLL-NLVLDNTT 63 (105)
Q Consensus 28 ~~i~k~V~V~LkdGr-~i~G~L~~fD~~m-NlvL~da~ 63 (105)
.|+|+-|.|...+-. .|.|.+...|+-- -|+|....
T Consensus 3 dWiGs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~~~~ 40 (62)
T cd01737 3 DWLGSIVSINCGETLGVYQGLVSAVDQESQTISLAFPF 40 (62)
T ss_pred cccceEEEEecCCceEEEEEEEEEeCccceEEEEeecc
Confidence 689999999998875 9999999999653 46665544
No 130
>KOG4401|consensus
Probab=24.60 E-value=77 Score=23.67 Aligned_cols=35 Identities=11% Similarity=0.108 Sum_probs=29.8
Q ss_pred hcCCEEEEEEcCCeEEEEEEEEecCccCeEecceE
Q psy17123 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~ 63 (105)
.++.+|.|..-+|...+|.+.+||--.+...-.+.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 46889999999999999999999977776666655
No 131
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=24.45 E-value=1.7e+02 Score=19.07 Aligned_cols=14 Identities=36% Similarity=0.591 Sum_probs=11.7
Q ss_pred hhHHhhcCCEEEEE
Q psy17123 24 LDLSKFLDKVIRVK 37 (105)
Q Consensus 24 ~~L~~~i~k~V~V~ 37 (105)
..|.+|+||.|++.
T Consensus 8 ~~L~~f~gk~V~iv 21 (101)
T cd04479 8 AMLSQFVGKTVRIV 21 (101)
T ss_pred HHHHhhCCCEEEEE
Confidence 46889999999876
No 132
>PRK08183 NADH dehydrogenase; Validated
Probab=24.43 E-value=42 Score=23.69 Aligned_cols=20 Identities=20% Similarity=0.104 Sum_probs=16.5
Q ss_pred EEEEEEEecCccCeEecceE
Q psy17123 44 CSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 44 i~G~L~~fD~~mNlvL~da~ 63 (105)
-.|.|+|.|++.|-.-++-.
T Consensus 24 r~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 24 RKGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred ccCeEeEecCCCCeeeecCC
Confidence 36999999999999886543
No 133
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=23.91 E-value=1.4e+02 Score=24.72 Aligned_cols=29 Identities=31% Similarity=0.653 Sum_probs=24.2
Q ss_pred hhHHhhcCCEEEEEEc--CC--eEEEEEEEEec
Q psy17123 24 LDLSKFLDKVIRVKFA--GG--RECSGILKGFD 52 (105)
Q Consensus 24 ~~L~~~i~k~V~V~Lk--dG--r~i~G~L~~fD 52 (105)
..|.+++|+.+.|.+. +| |.|.|.+..+.
T Consensus 40 l~~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 40 IDLEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred CCHHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 5588899999999995 33 78999999886
No 134
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=23.87 E-value=77 Score=18.97 Aligned_cols=18 Identities=11% Similarity=0.135 Sum_probs=13.9
Q ss_pred hhhHHhhcCCEEEEEEcC
Q psy17123 23 ILDLSKFLDKVIRVKFAG 40 (105)
Q Consensus 23 ~~~L~~~i~k~V~V~Lkd 40 (105)
....++|+|++|.|+..+
T Consensus 34 VdvPK~yiG~rv~viI~k 51 (52)
T COG3466 34 VDVPKRYIGKRVYVIILK 51 (52)
T ss_pred eeCchHHcCcEEEEEEeC
Confidence 344679999999998753
No 135
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.29 E-value=1.2e+02 Score=22.62 Aligned_cols=22 Identities=14% Similarity=0.120 Sum_probs=17.3
Q ss_pred hcCCEEEEEEcCCeEEEEEEEE
Q psy17123 29 FLDKVIRVKFAGGRECSGILKG 50 (105)
Q Consensus 29 ~i~k~V~V~LkdGr~i~G~L~~ 50 (105)
.+|..|+|+...|+.+.|+..+
T Consensus 194 ~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 194 NLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCEEEEEeCCCCEEEEEEec
Confidence 3678888888888888888765
No 136
>PRK10708 hypothetical protein; Provisional
Probab=23.05 E-value=1e+02 Score=18.97 Aligned_cols=26 Identities=19% Similarity=0.418 Sum_probs=22.3
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecCcc
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDPLL 55 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~~m 55 (105)
++-+|+|++.+|..=+|++.....|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 57789999999989999999888764
No 137
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=23.04 E-value=1.7e+02 Score=24.54 Aligned_cols=43 Identities=28% Similarity=0.208 Sum_probs=36.1
Q ss_pred hhHHhhcCCEEEEEEcCCeEEEEEEEEecCccCeEecceEEEEe
Q psy17123 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67 (105)
Q Consensus 24 ~~L~~~i~k~V~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~ 67 (105)
..+++++||.|+- =+||++.+++|.+-|.-.=+.+.+-+|..-
T Consensus 75 ~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 75 KLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred hHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 3467889999998 799999999999999988888888777654
No 138
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=22.89 E-value=65 Score=20.02 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=19.5
Q ss_pred cCCEEEEEEcCCeEEEEEEEEecC
Q psy17123 30 LDKVIRVKFAGGRECSGILKGFDP 53 (105)
Q Consensus 30 i~k~V~V~LkdGr~i~G~L~~fD~ 53 (105)
-..+|.|+|-||..+++++..-|.
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~t 26 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKAREQ 26 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCCh
Confidence 346899999999999999876553
No 139
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=22.84 E-value=97 Score=21.74 Aligned_cols=32 Identities=25% Similarity=0.316 Sum_probs=24.1
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEec
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD 52 (105)
..+-..++.+-|.++|.|++|+++...+=|--
T Consensus 40 ~~pKKPNSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 40 TTPKKPNSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred cCccCCCchhheEEEEEeCCCCEEEEEcCCCC
Confidence 33445678899999999999999876665543
No 140
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=21.93 E-value=1e+02 Score=21.66 Aligned_cols=31 Identities=26% Similarity=0.325 Sum_probs=23.3
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEe
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGF 51 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~f 51 (105)
..+-..++.+-|.++|.|++|+.+...+=|-
T Consensus 40 ~~pKKPNSA~RKvarVrL~ngk~v~AyIPG~ 70 (124)
T TIGR00981 40 TTPKKPNSALRKVARVRLTNGFEVTAYIPGE 70 (124)
T ss_pred ccccCCCchhheeEEEEeCCCCEEEEEcCCC
Confidence 3344567888999999999999987655543
No 141
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=21.32 E-value=1.3e+02 Score=22.74 Aligned_cols=23 Identities=9% Similarity=0.052 Sum_probs=20.0
Q ss_pred cCCeEEEEEEEEecCccCeEecc
Q psy17123 39 AGGRECSGILKGFDPLLNLVLDN 61 (105)
Q Consensus 39 kdGr~i~G~L~~fD~~mNlvL~d 61 (105)
.++..+.|++.++|+...|++..
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 46678899999999999999964
No 142
>PHA00672 hypothetical protein
Probab=20.99 E-value=3.2e+02 Score=19.54 Aligned_cols=46 Identities=13% Similarity=0.121 Sum_probs=29.0
Q ss_pred EEEEcCCeEEEEEEEEecCccCeEecceEEEEecCceeeeeeEEeeEEEcC
Q psy17123 35 RVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRRQ 85 (105)
Q Consensus 35 ~V~LkdGr~i~G~L~~fD~~mNlvL~da~E~~~~~~~~~~~~~lg~vlIRG 85 (105)
.+.+--|..++|.+.-||.+ |+++--.-...+++ ..+--|..+|.|
T Consensus 51 ei~IPkGt~LtG~~hkf~~~--ii~sG~itV~tdge---~~rl~g~~~i~~ 96 (152)
T PHA00672 51 TIRIPAGVALTGALIKVSTV--LIFSGHATVFIGGE---AVELRGYHVIPA 96 (152)
T ss_pred EEeccCceeeeeeeeEeeEE--EEecccEEEEeCCc---EEEEecceeeec
Confidence 35567899999999999999 77765443333433 233334444443
No 143
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=20.79 E-value=87 Score=20.98 Aligned_cols=21 Identities=24% Similarity=0.445 Sum_probs=8.1
Q ss_pred EEEEEEEEecCccCeEecceE
Q psy17123 43 ECSGILKGFDPLLNLVLDNTT 63 (105)
Q Consensus 43 ~i~G~L~~fD~~mNlvL~da~ 63 (105)
++.|++.|||-..++.|++|.
T Consensus 124 ti~G~~~g~~~~~~v~l~~c~ 144 (144)
T PF12869_consen 124 TIKGICTGYSLMGVVMLDDCQ 144 (144)
T ss_dssp EEEEE-----SSS-EEEE---
T ss_pred EEEEEEEeeecCCcEEeeccC
Confidence 456888888855577777763
No 144
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=20.78 E-value=1.3e+02 Score=21.72 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=27.8
Q ss_pred CCCCccc----cccccchhhHHhhcCCEEEEEE-cCCeEEEEEEEE
Q psy17123 10 AGAETKD----RKRKESILDLSKFLDKVIRVKF-AGGRECSGILKG 50 (105)
Q Consensus 10 ~~~~~~~----~~~~~~~~~L~~~i~k~V~V~L-kdGr~i~G~L~~ 50 (105)
.++|+.. ++....+-..++.+-|.++|.| ++|+.++..+=|
T Consensus 43 ~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg 88 (145)
T PRK04211 43 EGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPG 88 (145)
T ss_pred cCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCC
Confidence 3455555 2333445556788999999999 799998654443
No 145
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=20.46 E-value=1.4e+02 Score=21.35 Aligned_cols=41 Identities=20% Similarity=0.291 Sum_probs=28.3
Q ss_pred CCCCccc----cccccchhhHHhhcCCEEEEEE-cCCeEEEEEEEE
Q psy17123 10 AGAETKD----RKRKESILDLSKFLDKVIRVKF-AGGRECSGILKG 50 (105)
Q Consensus 10 ~~~~~~~----~~~~~~~~~L~~~i~k~V~V~L-kdGr~i~G~L~~ 50 (105)
.++|+.. ++....+-..++.+-|.++|.| ++|+.++..+=|
T Consensus 37 ~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiPg 82 (139)
T TIGR00982 37 EGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPG 82 (139)
T ss_pred cCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeCC
Confidence 3455555 2333445556788999999999 799998766554
No 146
>CHL00051 rps12 ribosomal protein S12
Probab=20.11 E-value=1.1e+02 Score=21.48 Aligned_cols=32 Identities=25% Similarity=0.328 Sum_probs=24.5
Q ss_pred cchhhHHhhcCCEEEEEEcCCeEEEEEEEEec
Q psy17123 21 ESILDLSKFLDKVIRVKFAGGRECSGILKGFD 52 (105)
Q Consensus 21 ~~~~~L~~~i~k~V~V~LkdGr~i~G~L~~fD 52 (105)
..+-..++.+-|.++|.|++|+++...+=|.-
T Consensus 40 ~~pKKPNSA~RKvarVrLsngk~v~AyIPGeG 71 (123)
T CHL00051 40 ITPKKPNSALRKVARVRLTSGFEITAYIPGIG 71 (123)
T ss_pred ccccCCChhheeEEEEEccCCCEEEEEcCCCC
Confidence 33445678899999999999999887665544
Done!