Query 033079
Match_columns 128
No_of_seqs 157 out of 1109
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:34:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033079.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033079hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1782 Small Nuclear ribonucl 99.9 3.1E-26 6.8E-31 164.7 4.9 119 8-128 7-129 (129)
2 cd01728 LSm1 The eukaryotic Sm 99.9 9.3E-23 2E-27 136.3 10.0 73 10-82 2-74 (74)
3 cd01729 LSm7 The eukaryotic Sm 99.9 2E-22 4.3E-27 136.6 9.7 73 12-84 4-81 (81)
4 cd01727 LSm8 The eukaryotic Sm 99.9 2.5E-22 5.5E-27 133.6 9.3 72 13-84 2-74 (74)
5 cd01732 LSm5 The eukaryotic Sm 99.9 5.4E-22 1.2E-26 133.2 10.0 74 9-82 2-75 (76)
6 cd01719 Sm_G The eukaryotic Sm 99.9 5.5E-22 1.2E-26 131.7 8.9 69 13-84 3-71 (72)
7 cd01731 archaeal_Sm1 The archa 99.9 1E-21 2.2E-26 128.5 9.0 68 11-81 1-68 (68)
8 cd01717 Sm_B The eukaryotic Sm 99.9 1.7E-21 3.6E-26 131.0 9.0 70 12-81 2-78 (79)
9 cd01730 LSm3 The eukaryotic Sm 99.9 2.2E-21 4.8E-26 131.5 9.2 71 11-81 2-82 (82)
10 PRK00737 small nuclear ribonuc 99.9 3E-21 6.5E-26 127.9 8.9 68 11-81 5-72 (72)
11 cd06168 LSm9 The eukaryotic Sm 99.8 1.7E-20 3.8E-25 125.6 9.3 70 12-81 2-74 (75)
12 cd01726 LSm6 The eukaryotic Sm 99.8 1.7E-20 3.6E-25 122.6 8.6 67 11-80 1-67 (67)
13 KOG1780 Small Nuclear ribonucl 99.8 4.9E-21 1.1E-25 127.2 6.0 73 1-83 1-74 (77)
14 cd01722 Sm_F The eukaryotic Sm 99.8 2.3E-20 5.1E-25 122.3 8.6 67 11-80 2-68 (68)
15 cd01720 Sm_D2 The eukaryotic S 99.8 5.7E-20 1.2E-24 126.3 9.4 72 11-82 3-86 (87)
16 cd01718 Sm_E The eukaryotic Sm 99.8 1.2E-19 2.7E-24 122.7 9.1 70 10-81 6-79 (79)
17 smart00651 Sm snRNP Sm protein 99.8 2.3E-19 5E-24 115.8 8.9 66 14-81 2-67 (67)
18 COG1958 LSM1 Small nuclear rib 99.8 4.2E-19 9.2E-24 119.1 9.9 72 10-81 7-79 (79)
19 PF01423 LSM: LSM domain ; In 99.8 2.4E-19 5.2E-24 115.9 8.3 67 13-81 1-67 (67)
20 cd01721 Sm_D3 The eukaryotic S 99.8 9.2E-19 2E-23 115.5 9.2 70 11-83 1-70 (70)
21 cd01723 LSm4 The eukaryotic Sm 99.8 1.7E-18 3.7E-23 115.8 8.9 73 11-85 2-74 (76)
22 cd00600 Sm_like The eukaryotic 99.8 2.7E-18 5.8E-23 109.3 8.5 63 15-80 1-63 (63)
23 KOG1781 Small Nuclear ribonucl 99.8 7.3E-20 1.6E-24 127.5 0.4 85 11-95 18-107 (108)
24 cd01724 Sm_D1 The eukaryotic S 99.7 2E-17 4.4E-22 114.2 9.4 72 12-86 3-74 (90)
25 PTZ00138 small nuclear ribonuc 99.7 2.3E-17 5.1E-22 113.9 9.3 72 9-82 13-88 (89)
26 cd01733 LSm10 The eukaryotic S 99.7 1E-16 2.2E-21 108.0 9.2 71 9-82 8-78 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.7 1.7E-16 3.7E-21 107.4 8.9 75 12-87 3-77 (81)
28 KOG1784 Small Nuclear ribonucl 99.7 6.9E-18 1.5E-22 116.1 1.1 90 12-102 2-92 (96)
29 KOG3482 Small nuclear ribonucl 99.6 1E-15 2.2E-20 101.6 7.1 71 10-83 8-78 (79)
30 KOG3460 Small nuclear ribonucl 99.6 2.7E-16 5.9E-21 106.8 2.1 74 10-83 5-88 (91)
31 KOG1783 Small nuclear ribonucl 99.5 2.2E-15 4.8E-20 100.0 1.3 72 9-83 5-76 (77)
32 KOG1775 U6 snRNA-associated Sm 99.5 1.2E-14 2.6E-19 97.3 4.5 79 5-83 2-80 (84)
33 KOG3168 U1 snRNP component [Tr 99.4 2E-14 4.3E-19 108.7 0.2 76 11-86 5-87 (177)
34 KOG1774 Small nuclear ribonucl 99.2 2E-11 4.3E-16 82.8 3.7 73 9-83 11-87 (88)
35 KOG3293 Small nuclear ribonucl 99.1 1.7E-10 3.8E-15 83.5 6.4 77 9-87 1-77 (134)
36 KOG3448 Predicted snRNP core p 99.0 9.9E-10 2.1E-14 75.6 7.0 72 13-86 5-77 (96)
37 KOG3172 Small nuclear ribonucl 98.7 5E-08 1.1E-12 69.4 6.8 74 11-87 6-79 (119)
38 KOG3428 Small nuclear ribonucl 98.6 2.1E-07 4.5E-12 66.2 7.7 70 13-86 5-74 (109)
39 KOG3459 Small nuclear ribonucl 98.3 6.6E-08 1.4E-12 68.9 -0.8 69 13-81 27-107 (114)
40 cd01739 LSm11_C The eukaryotic 98.0 5.6E-06 1.2E-10 54.2 2.8 37 21-57 9-49 (66)
41 PF14438 SM-ATX: Ataxin 2 SM d 97.8 5.8E-05 1.3E-09 49.9 5.7 64 14-77 6-76 (77)
42 PF02237 BPL_C: Biotin protein 96.9 0.0081 1.8E-07 36.4 6.7 34 18-52 1-34 (48)
43 PF12701 LSM14: Scd6-like Sm d 96.4 0.019 4.2E-07 40.1 7.0 71 16-86 4-81 (96)
44 PF06372 Gemin6: Gemin6 protei 95.7 0.034 7.3E-07 42.5 5.9 64 13-86 10-74 (166)
45 PF11095 Gemin7: Gem-associate 95.4 0.14 3E-06 34.8 7.3 61 13-81 17-78 (80)
46 cd01716 Hfq Hfq, an abundant, 95.1 0.048 1E-06 35.2 4.3 32 20-51 11-42 (61)
47 cd01736 LSm14_N LSm14 (also kn 95.1 0.13 2.9E-06 34.4 6.5 63 16-78 2-72 (74)
48 TIGR02383 Hfq RNA chaperone Hf 94.9 0.059 1.3E-06 34.9 4.2 32 20-51 15-46 (61)
49 cd01735 LSm12_N LSm12 belongs 94.9 0.081 1.8E-06 34.2 4.8 34 18-51 4-37 (61)
50 PRK14638 hypothetical protein; 94.4 0.11 2.4E-06 38.7 5.4 40 9-49 89-128 (150)
51 PRK00395 hfq RNA-binding prote 94.3 0.091 2E-06 35.6 4.2 39 13-51 10-50 (79)
52 PRK14639 hypothetical protein; 93.7 0.23 5E-06 36.6 5.9 39 9-48 77-115 (140)
53 PRK02001 hypothetical protein; 93.6 0.21 4.4E-06 37.6 5.5 39 9-48 79-117 (152)
54 PRK14644 hypothetical protein; 93.0 0.41 9E-06 35.2 6.2 37 12-49 77-117 (136)
55 cd01734 YlxS_C YxlS is a Bacil 91.9 0.82 1.8E-05 30.5 6.1 39 9-48 14-56 (83)
56 PRK14640 hypothetical protein; 91.8 0.67 1.5E-05 34.5 6.1 40 9-49 86-129 (152)
57 COG1923 Hfq Uncharacterized ho 91.4 0.37 8.1E-06 32.5 3.9 29 20-48 19-47 (77)
58 PRK14636 hypothetical protein; 90.5 0.99 2.1E-05 34.6 6.1 39 9-48 87-129 (176)
59 PRK14633 hypothetical protein; 90.2 0.88 1.9E-05 33.9 5.5 39 9-48 83-125 (150)
60 COG0779 Uncharacterized protei 90.1 1 2.2E-05 34.0 5.7 39 9-48 88-130 (153)
61 PRK14645 hypothetical protein; 89.6 0.92 2E-05 34.0 5.1 38 9-48 91-128 (154)
62 PF02576 DUF150: Uncharacteris 89.0 0.91 2E-05 33.0 4.7 38 10-48 77-118 (141)
63 PRK14643 hypothetical protein; 88.3 1.7 3.8E-05 32.9 5.9 36 9-44 93-132 (164)
64 PRK14647 hypothetical protein; 88.2 1.9 4.2E-05 32.3 6.0 39 9-48 88-135 (159)
65 PRK14642 hypothetical protein; 88.0 1.2 2.7E-05 34.9 5.0 39 9-48 89-140 (197)
66 PRK14632 hypothetical protein; 87.9 1.5 3.2E-05 33.4 5.4 40 9-49 87-133 (172)
67 PRK14634 hypothetical protein; 87.8 1.5 3.3E-05 32.8 5.3 39 9-48 89-131 (155)
68 PRK00092 ribosome maturation p 87.6 1.7 3.6E-05 32.3 5.3 34 10-43 88-125 (154)
69 PRK14091 RNA-binding protein H 87.2 1.1 2.4E-05 34.3 4.2 39 13-51 95-135 (165)
70 PRK14646 hypothetical protein; 87.1 1.8 4E-05 32.4 5.4 39 9-48 89-131 (155)
71 PRK14091 RNA-binding protein H 86.4 1.3 2.7E-05 34.0 4.2 41 11-51 13-55 (165)
72 PRK06955 biotin--protein ligas 85.4 3 6.5E-05 34.0 6.3 34 17-50 246-279 (300)
73 PRK14641 hypothetical protein; 84.4 2.5 5.4E-05 32.4 5.0 33 9-41 93-129 (173)
74 PF10842 DUF2642: Protein of u 84.0 2.6 5.6E-05 27.6 4.3 53 12-80 13-65 (66)
75 PRK14631 hypothetical protein; 83.9 2.5 5.3E-05 32.4 4.8 39 9-48 106-150 (174)
76 PF03614 Flag1_repress: Repres 82.3 2.1 4.5E-05 32.6 3.7 35 18-52 27-61 (165)
77 PRK14637 hypothetical protein; 81.7 3.6 7.9E-05 30.7 4.9 40 9-49 87-127 (151)
78 PRK11886 bifunctional biotin-- 81.1 6.6 0.00014 31.9 6.6 32 17-49 269-300 (319)
79 KOG1073 Uncharacterized mRNA-a 78.7 5.6 0.00012 34.0 5.6 69 16-84 5-81 (361)
80 PRK13325 bifunctional biotin-- 77.7 7.2 0.00016 35.0 6.3 34 17-50 275-308 (592)
81 TIGR00121 birA_ligase birA, bi 77.3 9.7 0.00021 29.7 6.3 33 16-49 189-221 (237)
82 PF11607 DUF3247: Protein of u 76.9 4.4 9.5E-05 28.5 3.7 38 1-38 1-46 (101)
83 PRK08330 biotin--protein ligas 76.4 11 0.00024 29.4 6.4 33 17-50 185-218 (236)
84 COG0340 BirA Biotin-(acetyl-Co 73.9 13 0.00028 29.6 6.3 37 15-51 185-221 (238)
85 PTZ00275 biotin-acetyl-CoA-car 73.5 7.5 0.00016 31.6 4.9 32 18-50 235-266 (285)
86 PRK14630 hypothetical protein; 72.7 9.9 0.00022 28.1 5.0 38 9-48 86-123 (143)
87 PRK14635 hypothetical protein; 69.0 17 0.00037 27.3 5.6 39 9-48 88-131 (162)
88 PF03614 Flag1_repress: Repres 67.2 6.1 0.00013 30.0 2.9 24 19-42 119-142 (165)
89 KOG3382 NADH:ubiquinone oxidor 64.9 3.5 7.7E-05 30.8 1.2 24 28-51 40-63 (151)
90 PF14563 DUF4444: Domain of un 62.9 11 0.00023 22.7 2.7 22 33-54 10-31 (42)
91 PRK10898 serine endoprotease; 62.7 16 0.00034 30.5 4.8 31 21-51 102-132 (353)
92 TIGR02038 protease_degS peripl 61.2 17 0.00037 30.2 4.8 31 21-51 102-132 (351)
93 PF05071 NDUFA12: NADH ubiquin 58.2 5.8 0.00013 27.7 1.3 17 35-51 1-17 (105)
94 PRK09618 flgD flagellar basal 57.7 35 0.00076 25.4 5.4 28 14-41 86-113 (142)
95 PRK10942 serine endoprotease; 56.4 22 0.00047 31.0 4.8 30 21-50 136-165 (473)
96 PRK10139 serine endoprotease; 55.6 24 0.00051 30.6 4.8 31 21-51 115-145 (455)
97 PRK08477 biotin--protein ligas 52.1 31 0.00068 26.9 4.6 35 16-51 171-205 (211)
98 cd04479 RPA3 RPA3: A subfamily 50.8 40 0.00086 23.1 4.5 28 8-43 3-30 (101)
99 PF08661 Rep_fac-A_3: Replicat 50.1 19 0.00042 24.8 2.9 31 1-41 1-31 (109)
100 PF06257 DUF1021: Protein of u 48.8 48 0.001 22.2 4.5 28 13-40 10-41 (76)
101 TIGR02037 degP_htrA_DO peripla 47.7 37 0.0008 28.7 4.7 31 21-51 82-112 (428)
102 TIGR02603 CxxCH_TIGR02603 puta 43.2 37 0.00081 24.2 3.6 29 21-50 58-86 (133)
103 PF07073 ROF: Modulator of Rho 39.0 30 0.00066 23.2 2.3 60 15-84 12-71 (80)
104 PRK06630 hypothetical protein; 38.9 17 0.00037 25.6 1.1 19 33-51 11-29 (99)
105 PLN02732 Probable NADH dehydro 36.8 27 0.00059 26.6 2.0 18 34-51 48-65 (159)
106 KOG3493 Ubiquitin-like protein 36.3 28 0.0006 23.0 1.7 19 14-32 5-23 (73)
107 PF01887 SAM_adeno_trans: S-ad 35.7 53 0.0012 26.5 3.7 19 32-50 169-187 (258)
108 PRK11625 Rho-binding antitermi 34.0 1.5E+02 0.0033 20.1 6.5 53 18-81 21-73 (84)
109 PLN03095 NADH:ubiquinone oxido 33.7 24 0.00051 25.5 1.2 18 34-51 9-26 (115)
110 TIGR03170 flgA_cterm flagella 33.5 56 0.0012 22.5 3.1 24 16-39 92-116 (122)
111 PRK11911 flgD flagellar basal 33.2 77 0.0017 23.6 3.9 27 16-42 89-115 (140)
112 PF03122 Herpes_MCP: Herpes vi 32.6 15 0.00032 36.4 0.0 58 21-79 248-305 (1354)
113 COG4466 Veg Uncharacterized pr 31.4 52 0.0011 22.3 2.5 20 13-32 12-31 (80)
114 smart00333 TUDOR Tudor domain. 30.2 1.2E+02 0.0026 17.7 4.2 25 19-43 5-29 (57)
115 PF07830 PP2C_C: Protein serin 29.3 71 0.0015 21.6 2.9 31 91-121 8-38 (81)
116 PF00789 UBX: UBX domain; Int 28.6 69 0.0015 20.4 2.7 22 21-42 7-28 (82)
117 PF09465 LBR_tudor: Lamin-B re 28.2 1.3E+02 0.0027 19.1 3.7 27 18-44 7-34 (55)
118 COG5316 Uncharacterized conser 28.0 1.6E+02 0.0035 25.7 5.5 45 10-55 72-116 (421)
119 PTZ00276 biotin/lipoate protei 27.9 83 0.0018 24.8 3.6 31 20-50 198-231 (245)
120 smart00166 UBX Domain present 27.7 57 0.0012 21.0 2.2 22 21-42 5-26 (80)
121 COG0265 DegQ Trypsin-like seri 26.8 1.2E+02 0.0026 24.7 4.5 32 20-51 95-126 (347)
122 PRK07018 flgA flagellar basal 25.9 80 0.0017 24.8 3.1 24 16-39 203-227 (235)
123 PF07202 Tcp10_C: T-complex pr 25.3 79 0.0017 24.3 2.9 36 15-50 139-178 (179)
124 PRK08183 NADH dehydrogenase; V 25.3 39 0.00084 24.9 1.1 18 34-51 25-42 (133)
125 cd01767 UBX UBX (ubiquitin reg 24.6 76 0.0016 20.2 2.3 22 21-42 3-24 (77)
126 PRK06792 flgD flagellar basal 23.4 1.2E+02 0.0027 23.7 3.7 27 15-41 113-139 (190)
127 cd01772 SAKS1_UBX SAKS1-like U 23.3 65 0.0014 20.9 1.8 24 18-41 2-25 (79)
128 PF14485 DUF4431: Domain of un 23.1 81 0.0017 19.1 2.1 16 11-26 10-25 (48)
129 PF11743 DUF3301: Protein of u 22.8 1.1E+02 0.0023 21.0 2.9 20 63-82 76-95 (97)
130 PF08149 BING4CT: BING4CT (NUC 21.7 67 0.0014 21.8 1.6 24 103-126 56-79 (80)
131 PRK04337 50S ribosomal protein 21.2 2.4E+02 0.0052 19.4 4.3 39 9-47 29-67 (87)
132 PF14153 Spore_coat_CotO: Spor 20.8 1.3E+02 0.0028 23.3 3.3 50 20-82 134-183 (185)
133 PF07407 Seadorna_VP6: Seadorn 20.4 1.5E+02 0.0033 25.5 3.9 42 82-125 17-58 (420)
134 COG3466 ISA1214 Putative trans 20.2 89 0.0019 19.5 1.8 15 15-29 37-51 (52)
135 KOG4401 Uncharacterized conser 20.1 1.4E+02 0.0031 23.3 3.3 36 17-52 8-43 (184)
No 1
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.92 E-value=3.1e-26 Score=164.67 Aligned_cols=119 Identities=61% Similarity=0.996 Sum_probs=106.4
Q ss_pred CCchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCcccc
Q 033079 8 DVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (128)
Q Consensus 8 ~~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~e 87 (128)
.++.+.+|.+++++++.|.|+|||.+.|.|++||||.|++|.+|+|+++.++.|.++..|.++|||.||++++.+|.++|
T Consensus 7 ~~~~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE 86 (129)
T KOG1782|consen 7 DLPFTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE 86 (129)
T ss_pred CCCchhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence 46777789999999999999999999999999999999999999999998988999999999999999999999999999
Q ss_pred cCCCCCCccCHHHHH----HHHHHHHHHhhhhhhhhhhcccccCC
Q 033079 88 ELPPHLTHVSVAEIK----RAQKAEREASDLKGSMRKRMEFLDLD 128 (128)
Q Consensus 88 ~~~~~~~~v~~~~i~----~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (128)
..++.|+|.++++ ..|++++++...++.|+++++|+|.+
T Consensus 87 --~~~l~~i~~~e~~~~~~~~q~~k~e~~~lkg~m~~rg~~~D~~ 129 (129)
T KOG1782|consen 87 --EEPLEQISFEEALNEIKREQEAKKEEERLKGTMAERGEFLDFD 129 (129)
T ss_pred --hccceeCCHHHHHHHHHHHHHHhhhHHHHHHHHHHhcccccCC
Confidence 4789999988875 35555555556666899999999975
No 2
>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=99.89 E-value=9.3e-23 Score=136.31 Aligned_cols=73 Identities=63% Similarity=0.983 Sum_probs=65.8
Q ss_pred chhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEecc
Q 033079 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~ 82 (128)
++...|.++++++|.|.++|||+|.|+|.|||+|||++|+||.|+...++.+..+.+|.++|||++|++|+.+
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 PGTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred CchHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 4677899999999999999999999999999999999999999998655444568899999999999999853
No 3
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.88 E-value=2e-22 Score=136.60 Aligned_cols=73 Identities=38% Similarity=0.506 Sum_probs=63.8
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCce-----eceeecceEEEecCcEEEEeccCc
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL-----YCDIPLGLYVIRGENVVLIGELDL 84 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~-----~~~r~lG~v~IRG~nIv~I~~~d~ 84 (128)
...|.++++++|+|+|+|||+|+|+|+|||+||||+|++|+|++..++. ...+.+|.++|||+||++|++.+.
T Consensus 4 ~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~~ 81 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVDG 81 (81)
T ss_pred hhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCCC
Confidence 3569999999999999999999999999999999999999999764321 135789999999999999998763
No 4
>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=99.88 E-value=2.5e-22 Score=133.62 Aligned_cols=72 Identities=42% Similarity=0.736 Sum_probs=63.9
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeC-ceeceeecceEEEecCcEEEEeccCc
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG-DLYCDIPLGLYVIRGENVVLIGELDL 84 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~-~~~~~r~lG~v~IRG~nIv~I~~~d~ 84 (128)
+.|.+|++++|+|+++|||.|.|+|+|||+|||++|++|.|+.... +....+.+|.+++||++|++|+++|+
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 5699999999999999999999999999999999999999987533 22345789999999999999998874
No 5
>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=99.88 E-value=5.4e-22 Score=133.17 Aligned_cols=74 Identities=19% Similarity=0.347 Sum_probs=65.1
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEecc
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~ 82 (128)
+.|...|.++++++|+|.+++||+|.|+|+|||+|||++|+||.|++...+....+.+|.++|||+||++|++.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 46789999999999999999999999999999999999999999997433322357899999999999999853
No 6
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=5.5e-22 Score=131.74 Aligned_cols=69 Identities=39% Similarity=0.614 Sum_probs=62.5
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCc
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 84 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~ 84 (128)
+.|+++++++|+|.|++||+|.|+|.|||+||||+|++|.|+.. ++ ..+.+|.++|||++|++|+++|.
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-~~--~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-GG--EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc-CC--ceeEeceEEECCCEEEEEEcccc
Confidence 56999999999999999999999999999999999999999863 22 25789999999999999998864
No 7
>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=99.87 E-value=1e-21 Score=128.52 Aligned_cols=68 Identities=38% Similarity=0.421 Sum_probs=61.4
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
|.+.|+++++++|+|.|++|+.|.|+|.|||+||||+|++|+|++..+ ..+.+|.++|||++|++|++
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 457899999999999999999999999999999999999999986433 35789999999999999974
No 8
>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=99.86 E-value=1.7e-21 Score=131.04 Aligned_cols=70 Identities=33% Similarity=0.478 Sum_probs=61.3
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCc-------eeceeecceEEEecCcEEEEec
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-------LYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~-------~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
++.|.+|++++|+|+|+|||.|.|+|.|||+||||||+||.|++.... ....+.+|+++|||++|++|+.
T Consensus 2 ~~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 2 SSKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred cchhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 357999999999999999999999999999999999999999875321 1245789999999999999973
No 9
>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=99.86 E-value=2.2e-21 Score=131.46 Aligned_cols=71 Identities=25% Similarity=0.405 Sum_probs=61.9
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCc----------eeceeecceEEEecCcEEEEe
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD----------LYCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~----------~~~~r~lG~v~IRG~nIv~I~ 80 (128)
|...|+.+++++|.|+|+|||.|.|+|+|||+||||+|+||.|++.... ....+.+|.++|||++|++|+
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 4577899999999999999999999999999999999999999975321 123578999999999999987
Q ss_pred c
Q 033079 81 E 81 (128)
Q Consensus 81 ~ 81 (128)
+
T Consensus 82 ~ 82 (82)
T cd01730 82 P 82 (82)
T ss_pred C
Confidence 3
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=3e-21 Score=127.91 Aligned_cols=68 Identities=37% Similarity=0.487 Sum_probs=61.0
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
|...|.++++++|.|+|+||+.|.|+|.|||+|||++|+||.|... ++ ..+.+|.++|||++|++|++
T Consensus 5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-GE--VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-CC--eEeEcCcEEEeCCEEEEEcC
Confidence 5688999999999999999999999999999999999999999752 32 25789999999999999863
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=99.84 E-value=1.7e-20 Score=125.63 Aligned_cols=70 Identities=30% Similarity=0.353 Sum_probs=62.2
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCc---eeceeecceEEEecCcEEEEec
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD---LYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~---~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
.+.|++|++++|+|+|+|||.|.|+|.|||++|||+|++|.|+..... ....+.+|+++|||++|++|+.
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 467999999999999999999999999999999999999999985422 2346899999999999999973
No 12
>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=99.84 E-value=1.7e-20 Score=122.63 Aligned_cols=67 Identities=31% Similarity=0.413 Sum_probs=59.4
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEe
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~ 80 (128)
|...|++++|++|+|+|++|++|.|+|.|||+||||+|+||.|... +. ..+.+|.++|||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-~~--~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-GQ--LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-Cc--eeeEeCCEEEECCEEEEEC
Confidence 4578999999999999999999999999999999999999988642 32 2567999999999999985
No 13
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.84 E-value=4.9e-21 Score=127.19 Aligned_cols=73 Identities=40% Similarity=0.689 Sum_probs=65.4
Q ss_pred CCCC-CCCCCchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEE
Q 033079 1 MSWA-GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLI 79 (128)
Q Consensus 1 ms~~-~~~~~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I 79 (128)
||++ +|+ |++|++|++.++|.+||.+.|+|+|||.|||+||++|+|....++ ...+|.++|||++|+++
T Consensus 1 Msksg~Pe-------LkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~ 70 (77)
T KOG1780|consen 1 MSKSGHPE-------LKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMV 70 (77)
T ss_pred CCcccCch-------HHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEE
Confidence 8887 553 999999999999999999999999999999999999999864443 46789999999999999
Q ss_pred eccC
Q 033079 80 GELD 83 (128)
Q Consensus 80 ~~~d 83 (128)
.+.+
T Consensus 71 eaL~ 74 (77)
T KOG1780|consen 71 EALE 74 (77)
T ss_pred eecc
Confidence 8775
No 14
>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=99.83 E-value=2.3e-20 Score=122.33 Aligned_cols=67 Identities=31% Similarity=0.358 Sum_probs=59.8
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEe
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~ 80 (128)
|.+.|++++|++|+|.|++|++|.|+|.|||+||||+|+||.|+.. +. ....+|.++|||++|.+|+
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 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-GK--STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-Cc--cccCcCcEEEECCEEEEEC
Confidence 5678999999999999999999999999999999999999998753 32 2467899999999999984
No 15
>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=99.82 E-value=5.7e-20 Score=126.33 Aligned_cols=72 Identities=25% Similarity=0.343 Sum_probs=61.8
Q ss_pred hhHHHhhcc--CCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCc----------eeceeecceEEEecCcEEE
Q 033079 11 LSTSLASYL--DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD----------LYCDIPLGLYVIRGENVVL 78 (128)
Q Consensus 11 ~~~~L~~~l--~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~----------~~~~r~lG~v~IRG~nIv~ 78 (128)
|.+.|...+ +++|+|+|++||.|.|+|.|||+||||+|+||.|.+.... ....+.+|.+||||++|++
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 567788887 8999999999999999999999999999999999875422 1235678999999999999
Q ss_pred Eecc
Q 033079 79 IGEL 82 (128)
Q Consensus 79 I~~~ 82 (128)
|+..
T Consensus 83 Is~~ 86 (87)
T cd01720 83 VLRN 86 (87)
T ss_pred EecC
Confidence 9853
No 16
>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=99.81 E-value=1.2e-19 Score=122.71 Aligned_cols=70 Identities=24% Similarity=0.451 Sum_probs=60.6
Q ss_pred chhHHHhhccCC--eEEEEEc--CCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 10 YLSTSLASYLDK--KLLVLLR--DGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 10 ~~~~~L~~~l~k--~V~V~Lk--dGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
.|...+.+|+++ +|.|.++ +||+|+|+|.|||+||||+|+||+|++..++ ..+.+|.++|||+||++|++
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 478899999999 6777776 9999999999999999999999999874332 35779999999999999974
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.81 E-value=2.3e-19 Score=115.85 Aligned_cols=66 Identities=45% Similarity=0.610 Sum_probs=59.6
Q ss_pred HHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 14 ~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
+|++++|++|+|.|+||+.+.|+|.|||+|||++|+||.|+...+. ..+.+|.++|||++|++|++
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 5899999999999999999999999999999999999999875422 36789999999999999873
No 18
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.80 E-value=4.2e-19 Score=119.14 Aligned_cols=72 Identities=38% Similarity=0.537 Sum_probs=60.7
Q ss_pred chhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEe-eCceeceeecceEEEecCcEEEEec
Q 033079 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVI-VGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~-~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
.|.+.|+++++++|.|.|++|++|.|+|+|||+|||++|+||.|+.. ++.....+..|.++|||++|.+|..
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 47899999999999999999999999999999999999999999874 2221112334599999999999863
No 19
>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=99.80 E-value=2.4e-19 Score=115.89 Aligned_cols=67 Identities=40% Similarity=0.569 Sum_probs=60.2
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
..|++++|++|+|.|+||++|+|+|.+||+|||++|++|.|....+. ..+++|.++|||++|.+|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence 36899999999999999999999999999999999999999864331 36789999999999999974
No 20
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=9.2e-19 Score=115.48 Aligned_cols=70 Identities=20% Similarity=0.127 Sum_probs=61.9
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccC
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
|...|.+..|++|.|.|++|.+|.|+|.++|+|||++|+||.+...+++ ...+|.++|||+||.+|..+|
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence 3578999999999999999999999999999999999999987644443 356899999999999999876
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=99.78 E-value=1.7e-18 Score=115.79 Aligned_cols=73 Identities=22% Similarity=0.215 Sum_probs=63.5
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCcc
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLE 85 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~ 85 (128)
|...|+++.|++|.|.|++|++|.|+|.+||+|||++|+||.+....++. ...++.++|||++|.+|..+|..
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCHHH
Confidence 67889999999999999999999999999999999999999986444432 24578999999999999977653
No 22
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=2.7e-18 Score=109.32 Aligned_cols=63 Identities=41% Similarity=0.629 Sum_probs=56.8
Q ss_pred HhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEe
Q 033079 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 15 L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~ 80 (128)
|++++|++|+|.|+||+.|.|+|.+||+|||++|++|.+....+ ..+.+|.++|||++|.+|.
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 46789999999999999999999999999999999999986542 3578999999999999874
No 23
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.76 E-value=7.3e-20 Score=127.51 Aligned_cols=85 Identities=34% Similarity=0.424 Sum_probs=76.1
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCce-----eceeecceEEEecCcEEEEeccCcc
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL-----YCDIPLGLYVIRGENVVLIGELDLE 85 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~-----~~~r~lG~v~IRG~nIv~I~~~d~~ 85 (128)
+.-.|.+|++++|+|++.+||+.+|+|.|||+.||+||++|+|+..+++. ...|.+|++++||..+++|++.|..
T Consensus 18 silDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~ 97 (108)
T KOG1781|consen 18 SILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS 97 (108)
T ss_pred HHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence 45569999999999999999999999999999999999999999865431 2359999999999999999999999
Q ss_pred cccCCCCCCc
Q 033079 86 RDELPPHLTH 95 (128)
Q Consensus 86 ~e~~~~~~~~ 95 (128)
.++.+|+++|
T Consensus 98 e~I~npf~~~ 107 (108)
T KOG1781|consen 98 EEIANPFVQQ 107 (108)
T ss_pred hhhccchhcC
Confidence 9988888775
No 24
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.73 E-value=2e-17 Score=114.17 Aligned_cols=72 Identities=21% Similarity=0.248 Sum_probs=63.9
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCccc
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 86 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~ 86 (128)
..+|+++.|++|+|.|++|.+|.|+|.++|.|||++|+||.+....+. ...+|.++|||++|.+|..+|.-.
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~---~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN---PVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc---eeEcceEEEeCCEEEEEEcCCcCC
Confidence 467899999999999999999999999999999999999988754332 467899999999999999988764
No 25
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.73 E-value=2.3e-17 Score=113.85 Aligned_cols=72 Identities=22% Similarity=0.402 Sum_probs=60.0
Q ss_pred CchhHHHhhccCC--eEEEEEcC--CcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEecc
Q 033079 9 VYLSTSLASYLDK--KLLVLLRD--GRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 9 ~~~~~~L~~~l~k--~V~V~Lkd--Gr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~ 82 (128)
.+|...+.+++.. +|.|.+.+ +|+|.|+|+|||+||||+|+||+|++..++ ..+.+|.++||||||++|++.
T Consensus 13 ~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 13 TQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred cCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEcC
Confidence 3578889999985 47777767 489999999999999999999999864332 357899999999999999864
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.70 E-value=1e-16 Score=107.97 Aligned_cols=71 Identities=21% Similarity=0.223 Sum_probs=61.1
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEecc
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~ 82 (128)
.+...+|+.+.|++|.|.|++|.+|.|+|.++|.|||++|+||.+....+. ...+|.++|||++|.+|..+
T Consensus 8 ~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~---~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 8 NTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGK---QVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred chHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCc---eeECCcEEEECCEEEEEEcC
Confidence 345678999999999999999999999999999999999999987642222 34689999999999999864
No 27
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=1.7e-16 Score=107.45 Aligned_cols=75 Identities=23% Similarity=0.171 Sum_probs=62.9
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCcccc
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~e 87 (128)
-.+|+++.|++|.|.|++|.+|.|+|.++|.|||++|+||.+....+. .....++.++|||++|.+|..+|...+
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~-~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY-PHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc-ccccccCeEEEECCEEEEEEeChhHcC
Confidence 467899999999999999999999999999999999999976532211 112456899999999999999887665
No 28
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.68 E-value=6.9e-18 Score=116.14 Aligned_cols=90 Identities=37% Similarity=0.654 Sum_probs=76.4
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCc-eeceeecceEEEecCcEEEEeccCcccccCC
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-LYCDIPLGLYVIRGENVVLIGELDLERDELP 90 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~-~~~~r~lG~v~IRG~nIv~I~~~d~~~e~~~ 90 (128)
++.|+.|++++|.|.+.|||.+.|.|.|||+..||+|+++-|+++... ..+...+|+.+|||+||.+|+.+|+..+. .
T Consensus 2 ts~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~-~ 80 (96)
T KOG1784|consen 2 TSTLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDS-R 80 (96)
T ss_pred chhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhh-h
Confidence 356999999999999999999999999999999999999999986432 24567899999999999999999999884 5
Q ss_pred CCCCccCHHHHH
Q 033079 91 PHLTHVSVAEIK 102 (128)
Q Consensus 91 ~~~~~v~~~~i~ 102 (128)
-+|.++..+.+.
T Consensus 81 ld~tkir~epl~ 92 (96)
T KOG1784|consen 81 LDLTKIRAEPLH 92 (96)
T ss_pred hhhhhcccCCCC
Confidence 666666555543
No 29
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.63 E-value=1e-15 Score=101.61 Aligned_cols=71 Identities=32% Similarity=0.349 Sum_probs=64.0
Q ss_pred chhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccC
Q 033079 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
-|-++|+.+.|++|.|+|+.|.+|.|+|.+.|.|||+.|.+|.|++. +. ....+|.++||.+||.+|..++
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id-G~--~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID-GV--STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc-cc--ccccceeEEEEeccEEEEecCC
Confidence 47789999999999999999999999999999999999999999873 33 3567999999999999998665
No 30
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.60 E-value=2.7e-16 Score=106.77 Aligned_cols=74 Identities=30% Similarity=0.382 Sum_probs=63.9
Q ss_pred chhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEee--Cc--e------eceeecceEEEecCcEEEE
Q 033079 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIV--GD--L------YCDIPLGLYVIRGENVVLI 79 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~--~~--~------~~~r~lG~v~IRG~nIv~I 79 (128)
.|...|+-+++.+|.|+++++|++.|+|.+||+|.|++|.|+.|.+.. .+ . ...|.+..+||||++|++|
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv 84 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV 84 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence 367789999999999999999999999999999999999999998753 11 1 2357788999999999999
Q ss_pred eccC
Q 033079 80 GELD 83 (128)
Q Consensus 80 ~~~d 83 (128)
+++-
T Consensus 85 spp~ 88 (91)
T KOG3460|consen 85 SPPL 88 (91)
T ss_pred cCcc
Confidence 9764
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.53 E-value=2.2e-15 Score=100.01 Aligned_cols=72 Identities=29% Similarity=0.389 Sum_probs=64.4
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccC
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
..|+++|+..+|++|.|+|.+|-.|.|+|.|.|.||||-|+.+.|+. +++ ..+++|.+||||++|.+|+...
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngq--l~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQ--LKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCc--ccccccceeeccccEEEEEecc
Confidence 45789999999999999999999999999999999999999999986 343 3578899999999999998653
No 32
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.52 E-value=1.2e-14 Score=97.32 Aligned_cols=79 Identities=22% Similarity=0.388 Sum_probs=69.4
Q ss_pred CCCCCchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccC
Q 033079 5 GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 5 ~~~~~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
+|++..|.+.+-+.+|.++.|.+++.|+|.|+|.|||.|.|++|+|++|+-...+.....+++.+++.|++|.+..+..
T Consensus 2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 5778899999999999999999999999999999999999999999999865444323457899999999999987654
No 33
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.43 E-value=2e-14 Score=108.69 Aligned_cols=76 Identities=29% Similarity=0.382 Sum_probs=64.3
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeC-------ceeceeecceEEEecCcEEEEeccC
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG-------DLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~-------~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
.++.|..++|.+++|.++|||+|.|+|.+||+|||++|.+|.|..... +..+.|-+|+|++||.||++.+..+
T Consensus 5 ~sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVeg 84 (177)
T KOG3168|consen 5 KSSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEG 84 (177)
T ss_pred chhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccC
Confidence 346799999999999999999999999999999999999999875421 2245688999999999999998655
Q ss_pred ccc
Q 033079 84 LER 86 (128)
Q Consensus 84 ~~~ 86 (128)
...
T Consensus 85 ppp 87 (177)
T KOG3168|consen 85 PPP 87 (177)
T ss_pred CCC
Confidence 443
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.18 E-value=2e-11 Score=82.79 Aligned_cols=73 Identities=25% Similarity=0.428 Sum_probs=58.5
Q ss_pred CchhHHHhhccCC--eEEEEEcC--CcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccC
Q 033079 9 VYLSTSLASYLDK--KLLVLLRD--GRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (128)
Q Consensus 9 ~~~~~~L~~~l~k--~V~V~Lkd--Gr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d 83 (128)
.+|...+.+|+.. +|.|.|.+ |-.+.|.++|||.|||+||++|+|.....+ ..+.+|.+++.||||.+|...+
T Consensus 11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~--~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK--SRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc--CCCccccEEEcCCcEEEEeecC
Confidence 4577888888875 46666655 778999999999999999999999754333 1348999999999999997653
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=99.11 E-value=1.7e-10 Score=83.52 Aligned_cols=77 Identities=22% Similarity=0.220 Sum_probs=68.4
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCcccc
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~e 87 (128)
+.|.+.|+..-+++|.|.|++|.+|.|.|...|.+|||.|.+++++..++++ -..+..+.|||++|-++-.+|+..+
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdk--f~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDK--FFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCc--eeecceeEEecceeEEEeccHHHHH
Confidence 3577889999999999999999999999999999999999999998776664 2456789999999999998887776
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.03 E-value=9.9e-10 Score=75.59 Aligned_cols=72 Identities=25% Similarity=0.276 Sum_probs=58.9
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceece-eecceEEEecCcEEEEeccCccc
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCD-IPLGLYVIRGENVVLIGELDLER 86 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~-r~lG~v~IRG~nIv~I~~~d~~~ 86 (128)
++.+.++|++|.|.|+++-.+.|+|.|.|+|.|+-|.|..-. +.++++. ..+..++|||+.|.+|..+....
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~v 77 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLPKDAV 77 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeChhHH
Confidence 578899999999999999999999999999999999997543 3333322 45678999999999998655444
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.71 E-value=5e-08 Score=69.37 Aligned_cols=74 Identities=18% Similarity=0.135 Sum_probs=64.7
Q ss_pred hhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCcccc
Q 033079 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~e 87 (128)
|...|++.-|.-|.+.+..|..|.|.|.-.+.+||+.|.|.+-...++. ...+..++|||+.|.++..+|..+.
T Consensus 6 piKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLKn 79 (119)
T KOG3172|consen 6 PIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLKN 79 (119)
T ss_pred ceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhhc
Confidence 4567888999999999999999999999999999999999877654442 3567899999999999999998875
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.62 E-value=2.1e-07 Score=66.20 Aligned_cols=70 Identities=26% Similarity=0.298 Sum_probs=60.3
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCccc
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 86 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~ 86 (128)
.+|+.+.+.+|.|.|++|....|++.+.|.+||..|.++.-... ++ ...+..+.|||++|.++..+|.--
T Consensus 5 r~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-~~---pv~l~~lsirgnniRy~~lpD~l~ 74 (109)
T KOG3428|consen 5 RFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-GE---PVRLDTLSIRGNNIRYYILPDSLN 74 (109)
T ss_pred HHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-CC---ceeEEEEEeecceEEEEEccCCcC
Confidence 46899999999999999999999999999999999999866542 22 346789999999999999887544
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.34 E-value=6.6e-08 Score=68.87 Aligned_cols=69 Identities=26% Similarity=0.365 Sum_probs=55.3
Q ss_pred HHHhhcc--CCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeC----c--e----eceeecceEEEecCcEEEEe
Q 033079 13 TSLASYL--DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG----D--L----YCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 13 ~~L~~~l--~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~----~--~----~~~r~lG~v~IRG~nIv~I~ 80 (128)
+.+...+ ..+|.|.++|++.+.|...|||.|.|++|+++.|.+..- + . ...|++|.++||||+|+.+.
T Consensus 27 s~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 27 SVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred hhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 3444444 367999999999999999999999999999998876531 1 1 13688999999999999887
Q ss_pred c
Q 033079 81 E 81 (128)
Q Consensus 81 ~ 81 (128)
.
T Consensus 107 r 107 (114)
T KOG3459|consen 107 R 107 (114)
T ss_pred e
Confidence 3
No 40
>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=97.98 E-value=5.6e-06 Score=54.16 Aligned_cols=37 Identities=30% Similarity=0.278 Sum_probs=30.8
Q ss_pred CeEEEEEcCC---c-EEEEEEEEecCCcceEecceEEEEee
Q 033079 21 KKLLVLLRDG---R-KLMGTLCSFDQFANAVLEGACERVIV 57 (128)
Q Consensus 21 k~V~V~LkdG---r-~~~G~L~~fD~~mNlVL~da~E~~~~ 57 (128)
.+|+|.++.- | .++|.|.+||+|+||+|.|+.|.+..
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 6788887643 2 78999999999999999999998643
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.83 E-value=5.8e-05 Score=49.91 Aligned_cols=64 Identities=17% Similarity=0.134 Sum_probs=40.0
Q ss_pred HHhhccCCeEEEEEcCCcEEEEEEEEecC---CcceEecceEEEEeeC---ce-eceeecceEEEecCcEE
Q 033079 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQ---FANAVLEGACERVIVG---DL-YCDIPLGLYVIRGENVV 77 (128)
Q Consensus 14 ~L~~~l~k~V~V~LkdGr~~~G~L~~fD~---~mNlVL~da~E~~~~~---~~-~~~r~lG~v~IRG~nIv 77 (128)
.+..++|++|.|+++||..|.|.|.+++. -+.++|.-|....... .. ........++|+++.|+
T Consensus 6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 46789999999999999999999999998 8899998875532211 11 12234567888887765
No 42
>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=96.85 E-value=0.0081 Score=36.42 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=29.9
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEecCCcceEecceE
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGAC 52 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~ 52 (128)
.+|++|+|.+ ++..++|+..++|.++.|++....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence 4799999999 677779999999999999997653
No 43
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.42 E-value=0.019 Score=40.09 Aligned_cols=71 Identities=17% Similarity=0.211 Sum_probs=53.9
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEecC-CcceEecceEEEEeeCc----e--eceeecceEEEecCcEEEEeccCccc
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQ-FANAVLEGACERVIVGD----L--YCDIPLGLYVIRGENVVLIGELDLER 86 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD~-~mNlVL~da~E~~~~~~----~--~~~r~lG~v~IRG~nIv~I~~~d~~~ 86 (128)
..|+|++|.+..+.+-.|.|+|...|. ...|.|.++..+-..+. . -.......++.||..|.-+...+...
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 469999999999999999999999995 78999999865432221 0 01234679999999999888766555
No 44
>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=95.71 E-value=0.034 Score=42.50 Aligned_cols=64 Identities=27% Similarity=0.265 Sum_probs=44.7
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEec-CCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCccc
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 86 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD-~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~~ 86 (128)
..+..|++|.|+|.+.| +++.|.+.++| -..||||-+-.| + .....-+|-|..|-.|..+++..
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~----~~~sv~~I~ghaVk~vevl~~~~ 74 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----D----GKRSVKVIMGHAVKSVEVLSEGD 74 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----T----S-EEEEEE-GGGEEEEEEEE---
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----C----CceeEEEEEccceEEEEEccCCc
Confidence 45889999999999999 99999999999 566999975332 1 11245789999999999887643
No 45
>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=95.36 E-value=0.14 Score=34.83 Aligned_cols=61 Identities=15% Similarity=0.092 Sum_probs=44.3
Q ss_pred HHHhhccCCeEEEEEcCCcEEEEEEEEecC-CcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQ-FANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~-~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
..|....|++|.+.|.++.++.|+|.|+|. ..|+..++- + . +-......++|+..|++++.
T Consensus 17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L-~---T----PlGv~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNL-Q---T----PLGVQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE-E---T----TTTEEEEEEEEGGGEEEEEE
T ss_pred HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhc-C---C----CcccChhheeecCCEEEEEe
Confidence 347778899999999999999999999994 457766553 1 1 11224578999999999874
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=95.09 E-value=0.048 Score=35.24 Aligned_cols=32 Identities=25% Similarity=0.410 Sum_probs=27.6
Q ss_pred CCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 20 ~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+|.|.|.+|-.+.|.+.|||+|+=++-.+.
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~g 42 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESDG 42 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEECC
Confidence 46799999999999999999999987766553
No 47
>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=95.06 E-value=0.13 Score=34.41 Aligned_cols=63 Identities=16% Similarity=0.241 Sum_probs=46.1
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEec-CCcceEecceEEEEeeCce-----e--ceeecceEEEecCcEEE
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGDL-----Y--CDIPLGLYVIRGENVVL 78 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD-~~mNlVL~da~E~~~~~~~-----~--~~r~lG~v~IRG~nIv~ 78 (128)
..|+|+++.+..+.+-.|+|+|.++| +..-|-|.++..+-.++.. . ....+..++.||+.|--
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 36899999999999999999999999 4556779987655333211 0 12345778889987743
No 48
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=94.88 E-value=0.059 Score=34.85 Aligned_cols=32 Identities=28% Similarity=0.415 Sum_probs=27.5
Q ss_pred CCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 20 ~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+|.|-|.+|-.+.|.+.|||+|+=++-.+.
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~g 46 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQG 46 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEECC
Confidence 46799999999999999999999987766543
No 49
>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=94.86 E-value=0.081 Score=34.15 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=29.8
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
.+|..|.+++..|.+|.|.+.+||.-.++++-.|
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 5789999999999999999999998887775544
No 50
>PRK14638 hypothetical protein; Provisional
Probab=94.42 E-value=0.11 Score=38.72 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=33.4
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEec
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~ 49 (128)
......+..++|++|.|++.+++.|+|+|.++|.. ++.|.
T Consensus 89 L~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 89 LRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 44566799999999999999999999999999863 45553
No 51
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.28 E-value=0.091 Score=35.64 Aligned_cols=39 Identities=26% Similarity=0.344 Sum_probs=31.2
Q ss_pred HHHhhcc--CCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 13 TSLASYL--DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 13 ~~L~~~l--~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
.+|+.+- ..+|.|-|.+|-.+.|.+.|||+|+=++-.+.
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 4455444 46799999999999999999999997776554
No 52
>PRK14639 hypothetical protein; Provisional
Probab=93.70 E-value=0.23 Score=36.62 Aligned_cols=39 Identities=18% Similarity=0.228 Sum_probs=33.2
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL 48 (128)
.........++|+.|.|++.+++.|.|+|.++|.. ++.|
T Consensus 77 L~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 77 LSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred CCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 44566799999999999999999999999999884 5555
No 53
>PRK02001 hypothetical protein; Validated
Probab=93.60 E-value=0.21 Score=37.55 Aligned_cols=39 Identities=26% Similarity=0.418 Sum_probs=33.2
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL 48 (128)
.........++|+.|.|++.+++.|.|+|.++|.. ++.|
T Consensus 79 L~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 79 LKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 44566799999999999999999999999999975 4555
No 54
>PRK14644 hypothetical protein; Provisional
Probab=93.01 E-value=0.41 Score=35.22 Aligned_cols=37 Identities=16% Similarity=0.201 Sum_probs=31.4
Q ss_pred hHHHhhccCCeEEEEEcCC----cEEEEEEEEecCCcceEec
Q 033079 12 STSLASYLDKKLLVLLRDG----RKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdG----r~~~G~L~~fD~~mNlVL~ 49 (128)
...+..++|+.|.|+|++. +.|.|+|.++|. .++.|.
T Consensus 77 ~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~ 117 (136)
T PRK14644 77 TDELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK 117 (136)
T ss_pred HHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence 4689999999999999877 899999999997 356663
No 55
>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=91.87 E-value=0.82 Score=30.48 Aligned_cols=39 Identities=26% Similarity=0.325 Sum_probs=31.5
Q ss_pred CchhHHHhhccCCeEEEEEc---CC-cEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR---DG-RKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk---dG-r~~~G~L~~fD~~mNlVL 48 (128)
.........++|+.|.|.++ +| +.+.|.|.++|.. +++|
T Consensus 14 L~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 14 LKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred CCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 44566799999999999997 56 5899999999984 4444
No 56
>PRK14640 hypothetical protein; Provisional
Probab=91.77 E-value=0.67 Score=34.54 Aligned_cols=40 Identities=18% Similarity=0.309 Sum_probs=32.3
Q ss_pred CchhHHHhhccCCeEEEEE----cCCcEEEEEEEEecCCcceEec
Q 033079 9 VYLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~L----kdGr~~~G~L~~fD~~mNlVL~ 49 (128)
......+..++|+.|.|++ .+++.|+|+|.++|.. ++.|.
T Consensus 86 L~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 86 LFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred CCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 4556779999999999999 4668999999999874 45553
No 57
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.36 E-value=0.37 Score=32.49 Aligned_cols=29 Identities=31% Similarity=0.467 Sum_probs=25.1
Q ss_pred CCeEEEEEcCCcEEEEEEEEecCCcceEe
Q 033079 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 20 ~k~V~V~LkdGr~~~G~L~~fD~~mNlVL 48 (128)
..+|.|-|.+|-.+.|.+.|||+|.=+.=
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~VlL~ 47 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFVVLLK 47 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEEEEEE
Confidence 46799999999999999999999974443
No 58
>PRK14636 hypothetical protein; Provisional
Probab=90.51 E-value=0.99 Score=34.60 Aligned_cols=39 Identities=18% Similarity=0.328 Sum_probs=31.2
Q ss_pred CchhHHHhhccCCeEEEEEc---CC-cEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR---DG-RKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk---dG-r~~~G~L~~fD~~mNlVL 48 (128)
......+..++|+.|.|+|+ +| +.|+|+|.++|.. ++.|
T Consensus 87 L~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 87 LTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred CCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 34456799999999999997 56 6999999999873 4544
No 59
>PRK14633 hypothetical protein; Provisional
Probab=90.22 E-value=0.88 Score=33.88 Aligned_cols=39 Identities=13% Similarity=0.176 Sum_probs=31.6
Q ss_pred CchhHHHhhccCCeEEEEEc----CCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk----dGr~~~G~L~~fD~~mNlVL 48 (128)
......+..++|++|.|+++ +++.|+|+|.+++.. ++.|
T Consensus 83 L~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 83 IFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred CCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 44567799999999999994 668999999999874 5555
No 60
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.07 E-value=1 Score=33.98 Aligned_cols=39 Identities=21% Similarity=0.355 Sum_probs=34.0
Q ss_pred CchhHHHhhccCCeEEEEE----cCCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~L----kdGr~~~G~L~~fD~~mNlVL 48 (128)
..+......++|+.|.|.| .+++.+.|+|.++|..+ +++
T Consensus 88 L~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 88 LKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred cCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 5567789999999999999 78899999999999887 444
No 61
>PRK14645 hypothetical protein; Provisional
Probab=89.56 E-value=0.92 Score=34.04 Aligned_cols=38 Identities=11% Similarity=0.183 Sum_probs=30.9
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL 48 (128)
......+..++|++|.|++ +++.|.|+|.++|.. .+.|
T Consensus 91 L~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 91 LFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred CCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 4456679999999999986 889999999999874 3444
No 62
>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=89.05 E-value=0.91 Score=33.01 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=28.5
Q ss_pred chhHHHhhccCCeEEEEEc----CCcEEEEEEEEecCCcceEe
Q 033079 10 YLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~Lk----dGr~~~G~L~~fD~~mNlVL 48 (128)
.....+..++|+.|.|+++ +.+.|.|+|.++|. -.++|
T Consensus 77 ~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 77 KSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred CCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 3457899999999999994 45799999999998 44555
No 63
>PRK14643 hypothetical protein; Provisional
Probab=88.28 E-value=1.7 Score=32.89 Aligned_cols=36 Identities=14% Similarity=0.241 Sum_probs=29.9
Q ss_pred CchhHHHhhccCCeEEEEEcC----CcEEEEEEEEecCCc
Q 033079 9 VYLSTSLASYLDKKLLVLLRD----GRKLMGTLCSFDQFA 44 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lkd----Gr~~~G~L~~fD~~m 44 (128)
......+..++|++|.|+|+. .+.|.|+|.++|...
T Consensus 93 L~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~ 132 (164)
T PRK14643 93 IRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT 132 (164)
T ss_pred CCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCc
Confidence 345677999999999999965 589999999998653
No 64
>PRK14647 hypothetical protein; Provisional
Probab=88.17 E-value=1.9 Score=32.29 Aligned_cols=39 Identities=10% Similarity=0.183 Sum_probs=30.7
Q ss_pred CchhHHHhhccCCeEEEEEc---------CCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR---------DGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk---------dGr~~~G~L~~fD~~mNlVL 48 (128)
......+..++|+.|.|+++ +.+.|.|+|.++|. ..+.|
T Consensus 88 L~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l 135 (159)
T PRK14647 88 LKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI 135 (159)
T ss_pred CCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence 44567799999999999995 34799999999986 33444
No 65
>PRK14642 hypothetical protein; Provisional
Probab=88.00 E-value=1.2 Score=34.86 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=32.3
Q ss_pred CchhHHHhhccCCeEEEEEc-------------CCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR-------------DGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk-------------dGr~~~G~L~~fD~~mNlVL 48 (128)
+........++|+.|.|+|+ +.+.|.|+|.++|.. ++.|
T Consensus 89 Lk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 89 LRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 44567799999999999998 678999999999974 4444
No 66
>PRK14632 hypothetical protein; Provisional
Probab=87.92 E-value=1.5 Score=33.45 Aligned_cols=40 Identities=23% Similarity=0.471 Sum_probs=32.0
Q ss_pred CchhHHHhhccCCeEEEEEcC-------CcEEEEEEEEecCCcceEec
Q 033079 9 VYLSTSLASYLDKKLLVLLRD-------GRKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lkd-------Gr~~~G~L~~fD~~mNlVL~ 49 (128)
.........++|+.|.|+|.+ .+.|.|+|.++|. .++.|.
T Consensus 87 L~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~ 133 (172)
T PRK14632 87 FFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR 133 (172)
T ss_pred CCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence 445667999999999999976 5799999999985 355553
No 67
>PRK14634 hypothetical protein; Provisional
Probab=87.76 E-value=1.5 Score=32.79 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=31.1
Q ss_pred CchhHHHhhccCCeEEEEEcC---C-cEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRD---G-RKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lkd---G-r~~~G~L~~fD~~mNlVL 48 (128)
.........++|+.|.|++.+ | +.|.|+|.++|.. ++.|
T Consensus 89 L~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 89 LSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 455677999999999999963 3 6999999999874 4555
No 68
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=87.56 E-value=1.7 Score=32.27 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=29.1
Q ss_pred chhHHHhhccCCeEEEEE----cCCcEEEEEEEEecCC
Q 033079 10 YLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQF 43 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~L----kdGr~~~G~L~~fD~~ 43 (128)
.....+..++|+.|.|++ .+++.|.|+|..+|..
T Consensus 88 ~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 88 KKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred CCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 345779999999999997 5778999999999873
No 69
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=87.16 E-value=1.1 Score=34.28 Aligned_cols=39 Identities=23% Similarity=0.386 Sum_probs=31.0
Q ss_pred HHHhhccC--CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 13 TSLASYLD--KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 13 ~~L~~~l~--k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
.+|+.+-. .+|.|-|.+|-.+.|.+.|||+|.=|.-.+.
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 34555443 5699999999999999999999987776564
No 70
>PRK14646 hypothetical protein; Provisional
Probab=87.08 E-value=1.8 Score=32.36 Aligned_cols=39 Identities=13% Similarity=0.077 Sum_probs=31.1
Q ss_pred CchhHHHhhccCCeEEEEEcC---C-cEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRD---G-RKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lkd---G-r~~~G~L~~fD~~mNlVL 48 (128)
.........++|++|.|+|++ | +.|.|+|.++|.. ++.|
T Consensus 89 L~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 89 LTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 445677999999999999964 3 6889999999984 5555
No 71
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=86.44 E-value=1.3 Score=33.96 Aligned_cols=41 Identities=24% Similarity=0.316 Sum_probs=32.1
Q ss_pred hhHHHhhccC--CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 11 LSTSLASYLD--KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 11 ~~~~L~~~l~--k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
.-.+|+.+-. .+|.|-|.+|-.+.|.+.+||+|.=|+-.+.
T Consensus 13 QD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 13 QDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 3445665554 5688899999999999999999987776554
No 72
>PRK06955 biotin--protein ligase; Provisional
Probab=85.43 E-value=3 Score=34.02 Aligned_cols=34 Identities=15% Similarity=0.306 Sum_probs=29.6
Q ss_pred hccCCeEEEEEcCCcEEEEEEEEecCCcceEecc
Q 033079 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 17 ~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
-++|++|+|...+++.+.|++.|+|..+.|+|..
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 4678999997767788999999999999999953
No 73
>PRK14641 hypothetical protein; Provisional
Probab=84.37 E-value=2.5 Score=32.39 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=27.8
Q ss_pred CchhHHHhhccCCeEEEEEcC----CcEEEEEEEEec
Q 033079 9 VYLSTSLASYLDKKLLVLLRD----GRKLMGTLCSFD 41 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lkd----Gr~~~G~L~~fD 41 (128)
.........++|+.|.|+|.+ .+.|+|+|.++|
T Consensus 93 L~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 93 IILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 445667999999999999975 468999999995
No 74
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=84.02 E-value=2.6 Score=27.59 Aligned_cols=53 Identities=23% Similarity=0.276 Sum_probs=39.1
Q ss_pred hHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEe
Q 033079 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (128)
Q Consensus 12 ~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~ 80 (128)
-+.|++++|++|.|.+..|.. .|+|.+.-.. .++|+.+ -..++||=..|++|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~--------------~~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN--------------GTPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--------------CcEEEEEeeeEEEEc
Confidence 356999999999999987776 9999988532 3444321 246788888888875
No 75
>PRK14631 hypothetical protein; Provisional
Probab=83.93 E-value=2.5 Score=32.38 Aligned_cols=39 Identities=18% Similarity=0.356 Sum_probs=31.3
Q ss_pred CchhHHHhhccCCeEEEEEc----CCcEEEEEEEEec--CCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFD--QFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk----dGr~~~G~L~~fD--~~mNlVL 48 (128)
+.....+..++|+.|.|+|. +.+.|+|+|.++| . .++.|
T Consensus 106 L~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 106 FFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred CCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 45567799999999999996 4589999999998 4 34444
No 76
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=82.26 E-value=2.1 Score=32.57 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=31.2
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEecCCcceEecceE
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGAC 52 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~ 52 (128)
+-+-+|+|++.||..|.|.+.||+.--|.+|..+.
T Consensus 27 ~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 27 FNDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred hcCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 34678999999999999999999999999997753
No 77
>PRK14637 hypothetical protein; Provisional
Probab=81.70 E-value=3.6 Score=30.69 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=30.4
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEE-EEEEEEecCCcceEec
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKL-MGTLCSFDQFANAVLE 49 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~-~G~L~~fD~~mNlVL~ 49 (128)
......+..++|+.|.|++.+.+.+ +|+|.++|.. ++.|.
T Consensus 87 L~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 87 IKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred CCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 4456779999999999999444455 7999999875 45553
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=81.12 E-value=6.6 Score=31.95 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=27.7
Q ss_pred hccCCeEEEEEcCCcEEEEEEEEecCCcceEec
Q 033079 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 17 ~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~ 49 (128)
-++|++|.+.. ++..+.|++.|+|..+.|+|.
T Consensus 269 ~~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 269 LFLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred cccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 36789999987 446799999999999999995
No 79
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=78.70 E-value=5.6 Score=33.96 Aligned_cols=69 Identities=14% Similarity=0.145 Sum_probs=52.1
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEec-CCcceEecceEEEEeeCc----e---eceeecceEEEecCcEEEEeccCc
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGD----L---YCDIPLGLYVIRGENVVLIGELDL 84 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD-~~mNlVL~da~E~~~~~~----~---~~~r~lG~v~IRG~nIv~I~~~d~ 84 (128)
..|||++|.+.-+..-.|+|+|.-.| +..=|=|.++..+-+++. . .....+..|+.||+.|-.+...+.
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~ 81 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQET 81 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccC
Confidence 46899999999999999999999999 777888988643322221 1 112256789999999997776653
No 80
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=77.69 E-value=7.2 Score=35.05 Aligned_cols=34 Identities=24% Similarity=0.157 Sum_probs=29.7
Q ss_pred hccCCeEEEEEcCCcEEEEEEEEecCCcceEecc
Q 033079 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 17 ~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
-++|++|.+...+++.+.|+..|+|..+.|+|..
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 3679999997777788999999999999999963
No 81
>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=77.34 E-value=9.7 Score=29.71 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=28.1
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEecCCcceEec
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~ 49 (128)
..++|++|.|...+ ..+.|++.|+|..+.|+|.
T Consensus 189 ~~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 189 SAHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred hhccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 34679999998754 5799999999999999996
No 82
>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=76.94 E-value=4.4 Score=28.49 Aligned_cols=38 Identities=29% Similarity=0.347 Sum_probs=19.6
Q ss_pred CCCCCCCCCchhHH---Hhhc---c--CCeEEEEEcCCcEEEEEEE
Q 033079 1 MSWAGPDDVYLSTS---LASY---L--DKKLLVLLRDGRKLMGTLC 38 (128)
Q Consensus 1 ms~~~~~~~~~~~~---L~~~---l--~k~V~V~LkdGr~~~G~L~ 38 (128)
||++-|--|+--+. |+.+ + +.+|.+.|+||+.+.||+.
T Consensus 1 M~k~AprV~Td~~qIa~LE~lv~~L~ge~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 1 MSKYAPRVYTDPAQIARLEHLVSELDGEERVELELDDGSMLRGTVA 46 (101)
T ss_dssp ---B-S--B--HHHHHHHHHHHHCTTTT-EEEEEETTS-EEEEEEC
T ss_pred CCcccccccCCHHHHHHHHHHHhhcCCcceEEEEEcCCCeeeeeec
Confidence 67776644443333 3333 3 3789999999999999874
No 83
>PRK08330 biotin--protein ligase; Provisional
Probab=76.44 E-value=11 Score=29.41 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=27.6
Q ss_pred hccCCeEEEEEcCCcEE-EEEEEEecCCcceEecc
Q 033079 17 SYLDKKLLVLLRDGRKL-MGTLCSFDQFANAVLEG 50 (128)
Q Consensus 17 ~~l~k~V~V~LkdGr~~-~G~L~~fD~~mNlVL~d 50 (128)
.++|++|.+.. ++..+ .|++.|+|..+.|++..
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 46899999975 66665 69999999999999964
No 84
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=73.87 E-value=13 Score=29.60 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=33.2
Q ss_pred HhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 15 L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
....+|++|++...++..+.|+..++|..+.|+|...
T Consensus 185 ~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 185 RSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred HhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 3456899999999999999999999999999999776
No 85
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=73.54 E-value=7.5 Score=31.59 Aligned_cols=32 Identities=28% Similarity=0.330 Sum_probs=27.8
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEecCCcceEecc
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
++|++|.|.. ++..+.|++.|+|..+.|+|..
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 4799999875 6789999999999999999964
No 86
>PRK14630 hypothetical protein; Provisional
Probab=72.69 E-value=9.9 Score=28.06 Aligned_cols=38 Identities=11% Similarity=0.161 Sum_probs=29.6
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL 48 (128)
.........++|++|.|++.. ....|+|.++|. .++.|
T Consensus 86 L~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 86 IKSDREFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIF 123 (143)
T ss_pred CCCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEE
Confidence 455677999999999999955 446999999987 34444
No 87
>PRK14635 hypothetical protein; Provisional
Probab=68.97 E-value=17 Score=27.26 Aligned_cols=39 Identities=18% Similarity=0.226 Sum_probs=30.3
Q ss_pred CchhHHHhhccCCeEEEEEc--CCcEEEE---EEEEecCCcceEe
Q 033079 9 VYLSTSLASYLDKKLLVLLR--DGRKLMG---TLCSFDQFANAVL 48 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~Lk--dGr~~~G---~L~~fD~~mNlVL 48 (128)
......+..++|+.|.|++. ++..+.| +|.++|.. ++.|
T Consensus 88 L~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 88 LRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred CCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 34556799999999999886 4678887 99999874 4555
No 88
>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=67.22 E-value=6.1 Score=30.05 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=21.5
Q ss_pred cCCeEEEEEcCCcEEEEEEEEecC
Q 033079 19 LDKKLLVLLRDGRKLMGTLCSFDQ 42 (128)
Q Consensus 19 l~k~V~V~LkdGr~~~G~L~~fD~ 42 (128)
-|+-|+|-+.|||+++|.-.|.|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 368899999999999999999874
No 89
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=64.92 E-value=3.5 Score=30.75 Aligned_cols=24 Identities=33% Similarity=0.540 Sum_probs=19.4
Q ss_pred cCCcEEEEEEEEecCCcceEecce
Q 033079 28 RDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 28 kdGr~~~G~L~~fD~~mNlVL~da 51 (128)
+....=+|||+|.|+|+|=.-+|-
T Consensus 40 rtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 40 RTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred hcccccceeeeeecccccchhccc
Confidence 445556799999999999888775
No 90
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=62.89 E-value=11 Score=22.69 Aligned_cols=22 Identities=23% Similarity=0.233 Sum_probs=14.7
Q ss_pred EEEEEEEecCCcceEecceEEE
Q 033079 33 LMGTLCSFDQFANAVLEGACER 54 (128)
Q Consensus 33 ~~G~L~~fD~~mNlVL~da~E~ 54 (128)
.+|++.|.|....+.|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999886543
No 91
>PRK10898 serine endoprotease; Provisional
Probab=62.67 E-value=16 Score=30.49 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=27.3
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+.|.+.||+.|.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999999866444
No 92
>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=61.20 E-value=17 Score=30.18 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=27.3
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+.|.+.||+.+.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999999887544
No 93
>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=58.21 E-value=5.8 Score=27.73 Aligned_cols=17 Identities=41% Similarity=0.624 Sum_probs=15.3
Q ss_pred EEEEEecCCcceEecce
Q 033079 35 GTLCSFDQFANAVLEGA 51 (128)
Q Consensus 35 G~L~~fD~~mNlVL~da 51 (128)
|+|+|.|.|+|..-+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999998765
No 94
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=57.67 E-value=35 Score=25.44 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=25.1
Q ss_pred HHhhccCCeEEEEEcCCcEEEEEEEEec
Q 033079 14 SLASYLDKKLLVLLRDGRKLMGTLCSFD 41 (128)
Q Consensus 14 ~L~~~l~k~V~V~LkdGr~~~G~L~~fD 41 (128)
....++||.|.+...+|..++|+..+.-
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 3568999999999999999999999985
No 95
>PRK10942 serine endoprotease; Provisional
Probab=56.39 E-value=22 Score=30.97 Aligned_cols=30 Identities=30% Similarity=0.351 Sum_probs=26.9
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecc
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
..+.|++.||+.|.+++.++|...+|-|=.
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 579999999999999999999999987654
No 96
>PRK10139 serine endoprotease; Provisional
Probab=55.61 E-value=24 Score=30.60 Aligned_cols=31 Identities=26% Similarity=0.362 Sum_probs=27.5
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+.|++.||+.|.+++.++|....|-+=..
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5799999999999999999999999877544
No 97
>PRK08477 biotin--protein ligase; Provisional
Probab=52.13 E-value=31 Score=26.95 Aligned_cols=35 Identities=11% Similarity=0.041 Sum_probs=29.6
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
.-.+++.|+|. .+++.++|+..+.|..+-|+++.-
T Consensus 171 ~~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~ 205 (211)
T PRK08477 171 EFEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGK 205 (211)
T ss_pred HHHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCE
Confidence 34678999986 578999999999999999998764
No 98
>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=50.75 E-value=40 Score=23.11 Aligned_cols=28 Identities=14% Similarity=0.218 Sum_probs=20.1
Q ss_pred CCchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCC
Q 033079 8 DVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQF 43 (128)
Q Consensus 8 ~~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~ 43 (128)
.....+.|.+|+|++|++. |++.++|..
T Consensus 3 prVn~~~L~~f~gk~V~iv--------GkV~~~~~~ 30 (101)
T cd04479 3 PRINGAMLSQFVGKTVRIV--------GKVEKVDGD 30 (101)
T ss_pred ceeCHHHHHhhCCCEEEEE--------EEEEEecCC
Confidence 3556788999999999876 555555543
No 99
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=50.09 E-value=19 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=21.2
Q ss_pred CCCCCCCCCchhHHHhhccCCeEEEEEcCCcEEEEEEEEec
Q 033079 1 MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFD 41 (128)
Q Consensus 1 ms~~~~~~~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD 41 (128)
|+ .|......+.|.+|.|+.|++. |++.++|
T Consensus 1 M~--~~~pRVn~~~L~~~~gk~Vriv--------Gkv~~~~ 31 (109)
T PF08661_consen 1 MD--APTPRVNGSMLSQFVGKTVRIV--------GKVESVD 31 (109)
T ss_dssp GG--S--EEE-GGGGGGGTTSEEEEE--------EEEEEE-
T ss_pred CC--CCcceECHHHHHhhCCCeEEEE--------EEEeeEc
Confidence 55 4444677888999999999875 6777777
No 100
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=48.78 E-value=48 Score=22.16 Aligned_cols=28 Identities=25% Similarity=0.299 Sum_probs=21.4
Q ss_pred HHHhhccCCeEEEEEcCCc----EEEEEEEEe
Q 033079 13 TSLASYLDKKLLVLLRDGR----KLMGTLCSF 40 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr----~~~G~L~~f 40 (128)
..|..++|++|.++.+.|| +-.|+|...
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 4689999999999999998 577888754
No 101
>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=47.72 E-value=37 Score=28.73 Aligned_cols=31 Identities=23% Similarity=0.314 Sum_probs=27.5
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..+.|.+.||+.|.+++.++|...+|-|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999999877554
No 102
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=43.20 E-value=37 Score=24.18 Aligned_cols=29 Identities=28% Similarity=0.322 Sum_probs=21.1
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecc
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
....|.++||+.+.|.+..=| ...+.|.+
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~-~~~~~l~~ 86 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET-ADGVTVKM 86 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC-CCeEEEEc
Confidence 348999999999999988844 33444443
No 103
>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=38.97 E-value=30 Score=23.21 Aligned_cols=60 Identities=22% Similarity=0.279 Sum_probs=28.7
Q ss_pred HhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEeccCc
Q 033079 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 84 (128)
Q Consensus 15 L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~ 84 (128)
+.-.-+.+|+++|+||..+.|+- .|-..|- +-.|+..- ...-+...||=+.|..+++...
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~A--~dt~~~~---~k~E~L~l-----~~~~~~~~i~Ld~I~~~~al~~ 71 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGKA--LDTRTNA---KKEECLVL-----EQDGGEQEIRLDQIASMSALTD 71 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEESS---EEE------SSS-EEEE-----EETTEEEEESTT--SEEE----
T ss_pred HHHhcCCeEEEEEeCCCEEEEEE--EEEEEec---CceEEEEE-----ecCCcEEEEEhhheeeeeecCC
Confidence 44455789999999999999972 2222221 22333321 1123677889999998886554
No 104
>PRK06630 hypothetical protein; Provisional
Probab=38.93 E-value=17 Score=25.62 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=16.7
Q ss_pred EEEEEEEecCCcceEecce
Q 033079 33 LMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 33 ~~G~L~~fD~~mNlVL~da 51 (128)
..|+|+|-|+|+|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999998874
No 105
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=36.77 E-value=27 Score=26.58 Aligned_cols=18 Identities=28% Similarity=0.361 Sum_probs=16.0
Q ss_pred EEEEEEecCCcceEecce
Q 033079 34 MGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 34 ~G~L~~fD~~mNlVL~da 51 (128)
.|+|+|-|.|+|-.-++.
T Consensus 48 ~G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKL 65 (159)
T ss_pred CcEEEEecCCCCeeeecC
Confidence 399999999999998775
No 106
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.33 E-value=28 Score=23.05 Aligned_cols=19 Identities=26% Similarity=0.204 Sum_probs=15.2
Q ss_pred HHhhccCCeEEEEEcCCcE
Q 033079 14 SLASYLDKKLLVLLRDGRK 32 (128)
Q Consensus 14 ~L~~~l~k~V~V~LkdGr~ 32 (128)
.+++.+||+|+|++....+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 4788999999999876543
No 107
>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=35.71 E-value=53 Score=26.47 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=17.5
Q ss_pred EEEEEEEEecCCcceEecc
Q 033079 32 KLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 32 ~~~G~L~~fD~~mNlVL~d 50 (128)
.+.|...-+|.|+|+++.=
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 8999999999999999854
No 108
>PRK11625 Rho-binding antiterminator; Provisional
Probab=34.04 E-value=1.5e+02 Score=20.08 Aligned_cols=53 Identities=17% Similarity=0.146 Sum_probs=36.1
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEec
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~ 81 (128)
.-+.+|.+.++||..+.|+-. |=+ ..+-+|+..-.. .=+.-.||=+.|+.++.
T Consensus 21 ~~~~~l~l~l~dGe~~~g~A~--D~~----~~~k~EyL~l~~-----~g~~~~iRLD~I~s~~~ 73 (84)
T PRK11625 21 QHHLMLTLELKDGEVLQAKAS--DLV----SRKNVEYLVVEA-----AGETRELRLDKIASFSH 73 (84)
T ss_pred hcCCeEEEEECCCCEEEEEEE--eee----cCCceEEEEEEc-----CCCEEEEEeeeEeeccC
Confidence 357889999999999999873 333 335566654221 12466788888888873
No 109
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=33.68 E-value=24 Score=25.50 Aligned_cols=18 Identities=33% Similarity=0.495 Sum_probs=16.0
Q ss_pred EEEEEEecCCcceEecce
Q 033079 34 MGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 34 ~G~L~~fD~~mNlVL~da 51 (128)
.|+|+|.|.|+|-.-++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 699999999999998764
No 110
>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=33.53 E-value=56 Score=22.53 Aligned_cols=24 Identities=17% Similarity=0.338 Sum_probs=20.1
Q ss_pred hhccCCeEEEE-EcCCcEEEEEEEE
Q 033079 16 ASYLDKKLLVL-LRDGRKLMGTLCS 39 (128)
Q Consensus 16 ~~~l~k~V~V~-LkdGr~~~G~L~~ 39 (128)
.-.+|..|+|. +..|+.+.|+..+
T Consensus 92 ~g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 92 DGAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred ccCCCCEEEEEECCCCCEEEEEEeC
Confidence 45688999999 7899999998875
No 111
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=33.23 E-value=77 Score=23.57 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=23.4
Q ss_pred hhccCCeEEEEEcCCcEEEEEEEEecC
Q 033079 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQ 42 (128)
Q Consensus 16 ~~~l~k~V~V~LkdGr~~~G~L~~fD~ 42 (128)
..++||.|.....+|..+.|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 478999999888999999999987753
No 112
>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=32.56 E-value=15 Score=36.37 Aligned_cols=58 Identities=21% Similarity=0.269 Sum_probs=0.0
Q ss_pred CeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEE
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLI 79 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I 79 (128)
-+.+=+..+|+.+.|.|++.|.-++.+|+---+ +....-.....+|.++|+|+|.|--
T Consensus 248 ~~~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~v~~PatYg~~Vi~geNlVTA 305 (1354)
T PF03122_consen 248 NRSTYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTSVSVPATYGEFVISGENLVTA 305 (1354)
T ss_dssp -----------------------------------------------------------
T ss_pred CcceeecCCCCEeceEEeccHHHHHHHHHHHhh-hccceeecchhheeeeecCccHHHH
Confidence 344555689999999999999998887765443 2221112345689999999997643
No 113
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.40 E-value=52 Score=22.31 Aligned_cols=20 Identities=25% Similarity=0.424 Sum_probs=17.7
Q ss_pred HHHhhccCCeEEEEEcCCcE
Q 033079 13 TSLASYLDKKLLVLLRDGRK 32 (128)
Q Consensus 13 ~~L~~~l~k~V~V~LkdGr~ 32 (128)
+.+...+|++|.++..+||.
T Consensus 12 ~~i~ah~G~~v~lk~ngGRK 31 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRK 31 (80)
T ss_pred HHHHhccCcEEEEEecCCce
Confidence 46888999999999999985
No 114
>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=30.18 E-value=1.2e+02 Score=17.71 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=21.0
Q ss_pred cCCeEEEEEcCCcEEEEEEEEecCC
Q 033079 19 LDKKLLVLLRDGRKLMGTLCSFDQF 43 (128)
Q Consensus 19 l~k~V~V~LkdGr~~~G~L~~fD~~ 43 (128)
.|..+.+...+|..|.|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4667777778999999999999964
No 115
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=29.31 E-value=71 Score=21.58 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=20.3
Q ss_pred CCCCccCHHHHHHHHHHHHHHhhhhhhhhhh
Q 033079 91 PHLTHVSVAEIKRAQKAEREASDLKGSMRKR 121 (128)
Q Consensus 91 ~~~~~v~~~~i~~~~~~~~~~~~~~~~~~~~ 121 (128)
|++++++.+.+++.++=++.+..+-+++-++
T Consensus 8 PgAPkvs~EAv~~E~eLd~~l~~rv~ei~~~ 38 (81)
T PF07830_consen 8 PGAPKVSEEAVKKEAELDKYLEQRVEEIIEK 38 (81)
T ss_dssp TTS----HHHHHHHHHHHHHHHHHHHHHT--
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778999999998888888887777776655
No 116
>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=28.56 E-value=69 Score=20.42 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=18.7
Q ss_pred CeEEEEEcCCcEEEEEEEEecC
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQ 42 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~ 42 (128)
.+|.|.+.||..++.+|..-|.
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 117
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=28.16 E-value=1.3e+02 Score=19.06 Aligned_cols=27 Identities=15% Similarity=0.219 Sum_probs=19.1
Q ss_pred ccCCeEEEEEcCCcE-EEEEEEEecCCc
Q 033079 18 YLDKKLLVLLRDGRK-LMGTLCSFDQFA 44 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~-~~G~L~~fD~~m 44 (128)
-.|..|.+.-.++.. |.|.+.+||.-.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKS 34 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccC
Confidence 468899999988765 599999999643
No 118
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=27.99 E-value=1.6e+02 Score=25.73 Aligned_cols=45 Identities=20% Similarity=0.086 Sum_probs=37.4
Q ss_pred chhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEE
Q 033079 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERV 55 (128)
Q Consensus 10 ~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~ 55 (128)
.+-..+++++||.|+- =+||++.+++|.+-|.-.=+-+.+-+|..
T Consensus 72 s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~ 116 (421)
T COG5316 72 SPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVL 116 (421)
T ss_pred CchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEE
Confidence 3446688999999998 89999999999999988777777776654
No 119
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=27.88 E-value=83 Score=24.83 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=23.7
Q ss_pred CCeEEE---EEcCCcEEEEEEEEecCCcceEecc
Q 033079 20 DKKLLV---LLRDGRKLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 20 ~k~V~V---~LkdGr~~~G~L~~fD~~mNlVL~d 50 (128)
++.+.+ ...++..+.|++.|+|..+.|++..
T Consensus 198 ~~~~~~~~~~~~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 198 DKSLKLHKRTPTGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred hhhhccCeEEEcCCcEEEEEEEEECCCCeEEEEE
Confidence 555443 2246778999999999999999964
No 120
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=27.73 E-value=57 Score=20.99 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=18.9
Q ss_pred CeEEEEEcCCcEEEEEEEEecC
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQ 42 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~ 42 (128)
.+|.|.+-||..+.++|..-|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~t 26 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDT 26 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCc
Confidence 5799999999999999987653
No 121
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.78 E-value=1.2e+02 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=26.8
Q ss_pred CCeEEEEEcCCcEEEEEEEEecCCcceEecce
Q 033079 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 20 ~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da 51 (128)
..++.|.+.||+.+.+.+.|+|...-+-+-..
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki 126 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKI 126 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEe
Confidence 57788999999999999999998877665443
No 122
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.85 E-value=80 Score=24.78 Aligned_cols=24 Identities=13% Similarity=0.304 Sum_probs=20.7
Q ss_pred hhccCCeEEEE-EcCCcEEEEEEEE
Q 033079 16 ASYLDKKLLVL-LRDGRKLMGTLCS 39 (128)
Q Consensus 16 ~~~l~k~V~V~-LkdGr~~~G~L~~ 39 (128)
.-.+|..|+|. +..|+.+.|+..+
T Consensus 203 ~G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 203 DGAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCCeEEEEECCCCCEEEEEEeC
Confidence 45688999999 9999999999875
No 123
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=25.31 E-value=79 Score=24.30 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=29.5
Q ss_pred HhhccCCeEEEEEcCCc----EEEEEEEEecCCcceEecc
Q 033079 15 LASYLDKKLLVLLRDGR----KLMGTLCSFDQFANAVLEG 50 (128)
Q Consensus 15 L~~~l~k~V~V~LkdGr----~~~G~L~~fD~~mNlVL~d 50 (128)
-..|.+-.|.+...||+ .-.|.++.=|..+||+|+.
T Consensus 139 rreyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d~ 178 (179)
T PF07202_consen 139 RREYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMDT 178 (179)
T ss_pred EEEcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEecC
Confidence 35677888999999995 4569999999999999863
No 124
>PRK08183 NADH dehydrogenase; Validated
Probab=25.26 E-value=39 Score=24.94 Aligned_cols=18 Identities=22% Similarity=0.279 Sum_probs=15.8
Q ss_pred EEEEEEecCCcceEecce
Q 033079 34 MGTLCSFDQFANAVLEGA 51 (128)
Q Consensus 34 ~G~L~~fD~~mNlVL~da 51 (128)
.|+|+|-|.++|-.-++.
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 699999999999988664
No 125
>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=24.62 E-value=76 Score=20.20 Aligned_cols=22 Identities=27% Similarity=0.427 Sum_probs=18.2
Q ss_pred CeEEEEEcCCcEEEEEEEEecC
Q 033079 21 KKLLVLLRDGRKLMGTLCSFDQ 42 (128)
Q Consensus 21 k~V~V~LkdGr~~~G~L~~fD~ 42 (128)
.+|.|.+-||..++++|..-|.
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~t 24 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHK 24 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCC
Confidence 4789999999999999875543
No 126
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=23.41 E-value=1.2e+02 Score=23.67 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=23.4
Q ss_pred HhhccCCeEEEEEcCCcEEEEEEEEec
Q 033079 15 LASYLDKKLLVLLRDGRKLMGTLCSFD 41 (128)
Q Consensus 15 L~~~l~k~V~V~LkdGr~~~G~L~~fD 41 (128)
-..++||.|.+.-.+|..+.|++.+..
T Consensus 113 a~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 113 GMKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 357899999998899999999998774
No 127
>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=23.31 E-value=65 Score=20.93 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=19.6
Q ss_pred ccCCeEEEEEcCCcEEEEEEEEec
Q 033079 18 YLDKKLLVLLRDGRKLMGTLCSFD 41 (128)
Q Consensus 18 ~l~k~V~V~LkdGr~~~G~L~~fD 41 (128)
|-..+|.|.|-||..+.++|..-|
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCC
Confidence 345689999999999999987654
No 128
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=23.14 E-value=81 Score=19.06 Aligned_cols=16 Identities=31% Similarity=0.237 Sum_probs=13.3
Q ss_pred hhHHHhhccCCeEEEE
Q 033079 11 LSTSLASYLDKKLLVL 26 (128)
Q Consensus 11 ~~~~L~~~l~k~V~V~ 26 (128)
..+.++.++||+|+|.
T Consensus 10 ~~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 10 DYSYLKSLLGKRVSVT 25 (48)
T ss_pred hhHHHHHhcCCeEEEE
Confidence 4566888999999997
No 129
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=22.84 E-value=1.1e+02 Score=21.01 Aligned_cols=20 Identities=20% Similarity=0.208 Sum_probs=17.5
Q ss_pred eeecceEEEecCcEEEEecc
Q 033079 63 DIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 63 ~r~lG~v~IRG~nIv~I~~~ 82 (128)
.+.-|.+++.|..+..+..+
T Consensus 76 ~ry~G~l~m~G~~l~~v~lp 95 (97)
T PF11743_consen 76 DRYQGELVMLGRRLISVELP 95 (97)
T ss_pred hcceEEEEEECCeeeEEEcC
Confidence 57889999999999988865
No 130
>PF08149 BING4CT: BING4CT (NUC141) domain; InterPro: IPR012952 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This C-terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [].
Probab=21.69 E-value=67 Score=21.81 Aligned_cols=24 Identities=33% Similarity=0.409 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhhhhhhhhccccc
Q 033079 103 RAQKAEREASDLKGSMRKRMEFLD 126 (128)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~ 126 (128)
+-|++|++-|...+|+..+|--||
T Consensus 56 ~kqRrE~EV~~LLeKippd~I~Ld 79 (80)
T PF08149_consen 56 KKQRREREVRSLLEKIPPDMITLD 79 (80)
T ss_pred hhHHhHHHHHHHHHhCCccceecC
Confidence 349999999999999999887665
No 131
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=21.22 E-value=2.4e+02 Score=19.38 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=29.1
Q ss_pred CchhHHHhhccCCeEEEEEcCCcEEEEEEEEecCCcceE
Q 033079 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAV 47 (128)
Q Consensus 9 ~~~~~~L~~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlV 47 (128)
......-.-|+||+|.-.-+.|+.+-|.+.---.....|
T Consensus 29 v~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 29 VDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred cCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 345566788999999999999999999887554433333
No 132
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=20.82 E-value=1.3e+02 Score=23.25 Aligned_cols=50 Identities=10% Similarity=0.017 Sum_probs=29.4
Q ss_pred CCeEEEEEcCCcEEEEEEEEecCCcceEecceEEEEeeCceeceeecceEEEecCcEEEEecc
Q 033079 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (128)
Q Consensus 20 ~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~E~~~~~~~~~~r~lG~v~IRG~nIv~I~~~ 82 (128)
-.--+-...++..|+|++.+||.-- |.|... + ....+.|.=+.|+.|..+
T Consensus 134 p~i~C~i~t~~~~Y~G~I~~~~~~~-v~i~~~------~------~~~~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 134 PPIKCEIETKDKSYRGIILSYDEGE-VSIMPF------N------QGEEIEIPIDDITSIKMI 183 (185)
T ss_pred CCCceEEEeCCceEEEEEEeccCCE-EEEecc------C------CCcceEeehhheeeeeec
Confidence 3444445568899999999998651 222111 1 124556666666666543
No 133
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=20.45 E-value=1.5e+02 Score=25.50 Aligned_cols=42 Identities=14% Similarity=0.139 Sum_probs=30.7
Q ss_pred cCcccccCCCCCCccCHHHHHHHHHHHHHHhhhhhhhhhhcccc
Q 033079 82 LDLERDELPPHLTHVSVAEIKRAQKAEREASDLKGSMRKRMEFL 125 (128)
Q Consensus 82 ~d~~~e~~~~~~~~v~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 125 (128)
+++..+ +-.+..|+.++.-.+|+++-.+|++.++.|.+.+-|
T Consensus 17 ~~~~~~--~~~~~~~~~~e~~aLr~EN~~LKkEN~~Lk~eVerL 58 (420)
T PF07407_consen 17 VEETVE--NHELEGVSIDENFALRMENHSLKKENNDLKIEVERL 58 (420)
T ss_pred eecccc--cccccccchhhhhhHHHHhHHHHHHHHHHHHHHHHH
Confidence 344444 566778888888888888888888888887776543
No 134
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=20.22 E-value=89 Score=19.51 Aligned_cols=15 Identities=20% Similarity=0.507 Sum_probs=12.0
Q ss_pred HhhccCCeEEEEEcC
Q 033079 15 LASYLDKKLLVLLRD 29 (128)
Q Consensus 15 L~~~l~k~V~V~Lkd 29 (128)
-++|+|++|+|...+
T Consensus 37 PK~yiG~rv~viI~k 51 (52)
T COG3466 37 PKRYIGKRVYVIILK 51 (52)
T ss_pred chHHcCcEEEEEEeC
Confidence 478999999998643
No 135
>KOG4401 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.10 E-value=1.4e+02 Score=23.28 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=31.4
Q ss_pred hccCCeEEEEEcCCcEEEEEEEEecCCcceEecceE
Q 033079 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGAC 52 (128)
Q Consensus 17 ~~l~k~V~V~LkdGr~~~G~L~~fD~~mNlVL~da~ 52 (128)
-.+|..|.|..-+|...+|.+.+||--.+...-+|.
T Consensus 8 vavg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 8 VAVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred eEEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 356788999999999999999999988888777776
Done!