Query 032108
Match_columns 147
No_of_seqs 211 out of 1114
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:42:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032108.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032108hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1782 Small Nuclear ribonucl 100.0 3.9E-32 8.4E-37 202.5 5.2 122 8-132 7-128 (129)
2 cd01728 LSm1 The eukaryotic Sm 99.9 1.5E-22 3.1E-27 140.1 9.9 73 10-82 2-74 (74)
3 cd01727 LSm8 The eukaryotic Sm 99.9 7.5E-22 1.6E-26 135.7 9.1 72 13-84 2-74 (74)
4 cd01729 LSm7 The eukaryotic Sm 99.9 1.5E-21 3.3E-26 136.7 9.5 71 13-83 5-80 (81)
5 cd01719 Sm_G The eukaryotic Sm 99.9 3.9E-21 8.4E-26 132.0 8.8 69 13-84 3-71 (72)
6 cd01732 LSm5 The eukaryotic Sm 99.8 1E-20 2.2E-25 131.4 10.1 73 9-81 2-74 (76)
7 cd01731 archaeal_Sm1 The archa 99.8 1.3E-20 2.8E-25 127.4 8.9 68 11-81 1-68 (68)
8 cd01717 Sm_B The eukaryotic Sm 99.8 2.2E-20 4.8E-25 129.8 8.7 69 12-80 2-77 (79)
9 cd01730 LSm3 The eukaryotic Sm 99.8 3.3E-20 7.1E-25 129.9 9.0 70 11-80 2-81 (82)
10 PRK00737 small nuclear ribonuc 99.8 5.8E-20 1.3E-24 125.8 9.1 67 11-80 5-71 (72)
11 cd06168 LSm9 The eukaryotic Sm 99.8 5.6E-19 1.2E-23 122.4 9.2 69 12-80 2-73 (75)
12 cd01726 LSm6 The eukaryotic Sm 99.8 4.6E-19 1E-23 119.6 8.5 67 11-80 1-67 (67)
13 cd01722 Sm_F The eukaryotic Sm 99.8 5.7E-19 1.2E-23 119.6 8.4 67 11-80 2-68 (68)
14 cd01720 Sm_D2 The eukaryotic S 99.8 1.5E-18 3.2E-23 123.5 9.4 71 11-81 3-85 (87)
15 cd01718 Sm_E The eukaryotic Sm 99.8 1.4E-18 3E-23 121.8 9.1 71 9-81 5-79 (79)
16 COG1958 LSM1 Small nuclear rib 99.8 2.2E-18 4.8E-23 119.5 9.8 73 9-81 6-79 (79)
17 smart00651 Sm snRNP Sm protein 99.8 1.9E-18 4.1E-23 115.1 8.7 66 14-81 2-67 (67)
18 KOG1780 Small Nuclear ribonucl 99.8 5.4E-19 1.2E-23 121.9 5.9 74 1-84 1-75 (77)
19 PF01423 LSM: LSM domain ; In 99.8 2.9E-18 6.4E-23 114.3 8.7 67 13-81 1-67 (67)
20 cd01721 Sm_D3 The eukaryotic S 99.7 2.7E-17 5.9E-22 112.1 9.1 70 11-83 1-70 (70)
21 cd00600 Sm_like The eukaryotic 99.7 2.7E-17 5.9E-22 107.9 8.3 63 15-80 1-63 (63)
22 cd01723 LSm4 The eukaryotic Sm 99.7 6E-17 1.3E-21 111.9 8.9 72 11-84 2-73 (76)
23 PTZ00138 small nuclear ribonuc 99.7 7.3E-17 1.6E-21 115.4 9.6 72 9-82 13-88 (89)
24 KOG1784 Small Nuclear ribonucl 99.7 1.7E-17 3.7E-22 118.5 2.7 85 12-97 2-87 (96)
25 cd01724 Sm_D1 The eukaryotic S 99.7 3.7E-16 8.1E-21 111.6 9.3 72 12-86 3-74 (90)
26 cd01733 LSm10 The eukaryotic S 99.6 1.9E-15 4.1E-20 105.3 9.1 70 10-82 9-78 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.6 1.7E-15 3.7E-20 106.1 8.5 75 12-87 3-77 (81)
28 KOG3482 Small nuclear ribonucl 99.6 1.7E-15 3.6E-20 104.5 7.1 72 9-83 7-78 (79)
29 KOG1781 Small Nuclear ribonucl 99.6 7.2E-17 1.6E-21 116.9 -0.1 80 14-93 21-105 (108)
30 KOG3460 Small nuclear ribonucl 99.4 3.8E-14 8.2E-19 100.0 1.9 73 11-83 6-88 (91)
31 KOG1783 Small nuclear ribonucl 99.4 7.3E-14 1.6E-18 96.3 1.5 71 10-83 6-76 (77)
32 KOG3168 U1 snRNP component [Tr 99.3 2.1E-13 4.6E-18 107.0 1.0 76 11-86 5-87 (177)
33 KOG1775 U6 snRNA-associated Sm 99.3 2.8E-12 6E-17 89.3 4.7 79 5-83 2-80 (84)
34 KOG1774 Small nuclear ribonucl 99.2 2.3E-11 4.9E-16 85.7 4.0 75 7-83 9-87 (88)
35 KOG3293 Small nuclear ribonucl 99.0 1.4E-09 3.1E-14 81.8 6.0 76 10-87 2-77 (134)
36 KOG3448 Predicted snRNP core p 98.9 6.7E-09 1.5E-13 74.3 6.8 70 13-84 5-75 (96)
37 KOG3172 Small nuclear ribonucl 98.6 9.3E-08 2E-12 70.6 6.6 79 12-95 7-85 (119)
38 KOG3428 Small nuclear ribonucl 98.1 1.5E-05 3.2E-10 59.0 7.6 70 12-85 4-73 (109)
39 KOG3459 Small nuclear ribonucl 97.9 2.3E-06 5.1E-11 63.3 -0.7 62 21-82 37-108 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 97.7 0.00012 2.5E-09 50.1 5.9 64 14-77 6-76 (77)
41 cd01739 LSm11_C The eukaryotic 97.7 4.2E-05 9.2E-10 52.0 3.2 38 20-57 8-49 (66)
42 PF02237 BPL_C: Biotin protein 96.3 0.028 6.2E-07 35.2 6.8 35 18-53 1-35 (48)
43 PF12701 LSM14: Scd6-like Sm d 95.7 0.064 1.4E-06 38.8 7.1 71 16-86 4-81 (96)
44 cd01716 Hfq Hfq, an abundant, 94.8 0.063 1.4E-06 36.0 4.3 31 20-50 11-41 (61)
45 PF06372 Gemin6: Gemin6 protei 94.7 0.091 2E-06 41.6 5.7 63 13-85 10-73 (166)
46 TIGR02383 Hfq RNA chaperone Hf 94.5 0.08 1.7E-06 35.6 4.3 31 20-50 15-45 (61)
47 PRK00395 hfq RNA-binding prote 93.7 0.13 2.8E-06 36.2 4.3 32 20-51 19-50 (79)
48 PF11095 Gemin7: Gem-associate 93.5 0.59 1.3E-05 33.0 7.4 60 13-80 17-77 (80)
49 cd01736 LSm14_N LSm14 (also kn 93.1 0.48 1E-05 33.0 6.2 62 17-78 3-72 (74)
50 PRK14638 hypothetical protein; 93.0 0.4 8.6E-06 37.1 6.4 40 9-49 89-128 (150)
51 PRK14639 hypothetical protein; 92.2 0.6 1.3E-05 35.7 6.4 39 9-48 77-115 (140)
52 COG1923 Hfq Uncharacterized ho 91.2 0.41 8.9E-06 33.6 4.1 27 20-46 19-45 (77)
53 PRK02001 hypothetical protein; 90.9 0.72 1.6E-05 35.9 5.7 40 9-49 79-118 (152)
54 cd01734 YlxS_C YxlS is a Bacil 90.4 1.4 3E-05 30.4 6.3 39 9-48 14-56 (83)
55 PRK14644 hypothetical protein; 89.9 1.3 2.9E-05 33.7 6.3 37 12-49 77-117 (136)
56 cd01735 LSm12_N LSm12 belongs 89.7 0.96 2.1E-05 30.3 4.7 34 18-51 4-37 (61)
57 PRK14640 hypothetical protein; 88.5 2 4.3E-05 33.1 6.5 40 9-49 86-129 (152)
58 PF10842 DUF2642: Protein of u 87.8 4.1 8.9E-05 27.7 6.9 53 12-80 13-65 (66)
59 PRK14636 hypothetical protein; 86.1 3 6.6E-05 33.1 6.4 39 9-48 87-129 (176)
60 PRK14091 RNA-binding protein H 85.1 1.5 3.3E-05 34.8 4.3 31 21-51 105-135 (165)
61 PRK14633 hypothetical protein; 85.1 3 6.5E-05 32.1 5.8 40 9-49 83-126 (150)
62 PF02576 DUF150: Uncharacteris 85.0 2 4.3E-05 32.3 4.7 39 9-48 76-118 (141)
63 PRK14645 hypothetical protein; 84.9 2.7 5.9E-05 32.7 5.5 38 9-48 91-128 (154)
64 PRK14091 RNA-binding protein H 84.8 1.6 3.5E-05 34.6 4.2 38 14-51 16-55 (165)
65 PRK14632 hypothetical protein; 83.9 4.4 9.6E-05 32.0 6.4 40 9-49 87-133 (172)
66 COG0779 Uncharacterized protei 83.8 3.6 7.8E-05 32.2 5.8 39 9-48 88-130 (153)
67 PRK14642 hypothetical protein; 83.8 3.2 7E-05 33.7 5.7 39 9-48 89-140 (197)
68 PRK14634 hypothetical protein; 83.5 4.8 0.0001 31.2 6.4 40 9-49 89-132 (155)
69 PRK14647 hypothetical protein; 81.5 6.5 0.00014 30.5 6.4 39 9-48 88-135 (159)
70 PRK00092 ribosome maturation p 81.2 5.1 0.00011 30.7 5.7 34 9-42 87-124 (154)
71 PRK14646 hypothetical protein; 80.2 7.8 0.00017 30.0 6.5 40 9-49 89-132 (155)
72 PRK14643 hypothetical protein; 78.2 8.8 0.00019 30.1 6.3 35 9-43 93-131 (164)
73 PRK06955 biotin--protein ligas 77.8 4.4 9.6E-05 34.2 4.8 34 17-50 246-279 (300)
74 PF03614 Flag1_repress: Repres 76.7 3.6 7.9E-05 32.5 3.6 35 18-52 27-61 (165)
75 PRK11886 bifunctional biotin-- 75.7 12 0.00026 31.4 6.9 32 17-49 269-300 (319)
76 PRK14631 hypothetical protein; 75.1 8.8 0.00019 30.4 5.5 39 9-48 106-150 (174)
77 PRK14641 hypothetical protein; 73.2 9.9 0.00021 30.2 5.4 33 9-41 93-129 (173)
78 PRK14637 hypothetical protein; 73.1 11 0.00023 29.2 5.5 40 9-49 87-127 (151)
79 TIGR00121 birA_ligase birA, bi 70.8 14 0.0003 29.8 5.9 33 16-49 189-221 (237)
80 PTZ00275 biotin-acetyl-CoA-car 70.2 13 0.00028 31.2 5.8 32 18-50 235-266 (285)
81 KOG1073 Uncharacterized mRNA-a 70.2 11 0.00023 33.5 5.4 68 16-83 5-80 (361)
82 PRK13325 bifunctional biotin-- 67.7 15 0.00032 34.3 6.1 34 17-50 275-308 (592)
83 PRK08330 biotin--protein ligas 67.3 24 0.00052 28.5 6.6 34 17-51 185-219 (236)
84 COG0340 BirA Biotin-(acetyl-Co 66.0 21 0.00046 29.4 6.1 37 15-51 185-221 (238)
85 PRK14630 hypothetical protein; 59.7 36 0.00079 26.0 6.0 38 9-48 86-123 (143)
86 KOG3382 NADH:ubiquinone oxidor 58.4 5.3 0.00011 31.0 1.1 25 27-51 39-63 (151)
87 PF03614 Flag1_repress: Repres 55.3 13 0.00028 29.4 2.9 25 19-43 119-143 (165)
88 PRK14635 hypothetical protein; 50.8 51 0.0011 25.6 5.6 40 9-49 88-132 (162)
89 PF05071 NDUFA12: NADH ubiquin 50.0 7.1 0.00015 28.3 0.7 17 35-51 1-17 (105)
90 PRK08477 biotin--protein ligas 48.5 37 0.00081 27.5 4.7 35 16-51 171-205 (211)
91 PRK10898 serine endoprotease; 48.4 34 0.00074 29.5 4.7 31 21-51 102-132 (353)
92 PF07073 ROF: Modulator of Rho 48.1 15 0.00033 25.6 2.1 57 16-83 13-70 (80)
93 PF11607 DUF3247: Protein of u 48.1 26 0.00057 25.6 3.3 23 15-37 21-45 (101)
94 TIGR02038 protease_degS peripl 47.5 36 0.00077 29.3 4.7 31 21-51 102-132 (351)
95 PF14563 DUF4444: Domain of un 45.7 29 0.00063 21.7 2.8 21 33-53 10-30 (42)
96 PRK10942 serine endoprotease; 41.0 49 0.0011 29.8 4.7 31 21-51 136-166 (473)
97 PRK10139 serine endoprotease; 40.6 51 0.0011 29.6 4.7 31 21-51 115-145 (455)
98 PF03122 Herpes_MCP: Herpes vi 40.2 9.4 0.0002 39.0 0.0 55 23-78 250-304 (1354)
99 PRK09618 flgD flagellar basal 36.5 69 0.0015 24.8 4.3 28 14-41 86-113 (142)
100 TIGR02603 CxxCH_TIGR02603 puta 35.3 55 0.0012 24.2 3.5 28 22-50 59-86 (133)
101 TIGR02037 degP_htrA_DO peripla 33.3 78 0.0017 27.7 4.6 31 21-51 82-112 (428)
102 PF01887 SAM_adeno_trans: S-ad 33.3 58 0.0013 27.2 3.7 21 32-52 169-189 (258)
103 PRK06630 hypothetical protein; 33.1 23 0.0005 26.0 1.1 19 33-51 11-29 (99)
104 PLN02732 Probable NADH dehydro 32.9 32 0.00069 27.2 1.9 19 34-52 48-66 (159)
105 PLN03095 NADH:ubiquinone oxido 27.8 33 0.00071 25.7 1.1 19 34-52 9-27 (115)
106 PF07202 Tcp10_C: T-complex pr 23.8 85 0.0018 25.0 2.9 34 16-49 140-177 (179)
107 PRK11911 flgD flagellar basal 23.2 1.4E+02 0.0029 23.1 3.8 27 16-42 89-115 (140)
108 PRK08183 NADH dehydrogenase; V 20.6 52 0.0011 25.2 1.1 19 34-52 25-43 (133)
No 1
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.97 E-value=3.9e-32 Score=202.49 Aligned_cols=122 Identities=49% Similarity=0.738 Sum_probs=114.4
Q ss_pred CCchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCccc
Q 032108 8 DVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (147)
Q Consensus 8 ~~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~e 87 (147)
++|.+.+|.++++|++.|.|+|||++.|+|+|||||+|+||++|+||++.++.|++++.|.++|||+||+++|++|.++|
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 57888889999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCccCHHHHHHHHHHhhhhhhhhhhHhhhhhhhccccccc
Q 032108 88 ELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGR 132 (147)
Q Consensus 88 ~~~~~~~~v~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 132 (147)
..+++++|++|++..++.++++|++.++.|- .|+.|++.++.
T Consensus 87 --~~~l~~i~~~e~~~~~~~~q~~k~e~~~lkg-~m~~rg~~~D~ 128 (129)
T KOG1782|consen 87 --EEPLEQISFEEALNEIKREQEAKKEEERLKG-TMAERGEFLDF 128 (129)
T ss_pred --hccceeCCHHHHHHHHHHHHHHhhhHHHHHH-HHHHhcccccC
Confidence 4799999999999888888888888777777 89999998764
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=1.5e-22 Score=140.05 Aligned_cols=73 Identities=63% Similarity=0.983 Sum_probs=67.2
Q ss_pred chhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEecc
Q 032108 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (147)
Q Consensus 10 ~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~i 82 (147)
++...|.++++|+|.|.|+|||+|.|+|.|||+||||+|+||.|++..++.+.++.+|.++|||+||++|+++
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 5677899999999999999999999999999999999999999998766556678999999999999999974
No 3
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=7.5e-22 Score=135.74 Aligned_cols=72 Identities=42% Similarity=0.736 Sum_probs=64.6
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeC-ceeeeeecceEEEeeccEEEEeccCC
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG-DLYCDIPLGLYVIRGENVVLIGELDL 84 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~-~~~~~~~~G~vlIRG~nVv~I~~iD~ 84 (147)
+.|.+++|++|.|.++|||.|.|+|+|||+|||+||++|.|+.... +....+.+|.+++||+||++|+++|+
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 6799999999999999999999999999999999999999987533 22356789999999999999999884
No 4
>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=99.86 E-value=1.5e-21 Score=136.74 Aligned_cols=71 Identities=39% Similarity=0.557 Sum_probs=62.9
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc-e----eeeeecceEEEeeccEEEEeccC
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-L----YCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~-~----~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
..|.++++|+|.|.|+|||.|.|+|+|||+||||||++|+|++..++ . ...+.+|.++|||+||++|++.|
T Consensus 5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 45999999999999999999999999999999999999999986432 1 13578999999999999999876
No 5
>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=99.85 E-value=3.9e-21 Score=132.02 Aligned_cols=69 Identities=39% Similarity=0.614 Sum_probs=62.5
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCC
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 84 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~ 84 (147)
+.|.++++|+|.|.|+||+.|.|+|.|||+||||+|++|.|++. ++ ..+.+|.++|||+||++|+.+|.
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 57999999999999999999999999999999999999999863 32 25789999999999999998874
No 6
>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=99.85 E-value=1e-20 Score=131.37 Aligned_cols=73 Identities=19% Similarity=0.372 Sum_probs=64.2
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
+.|...|..+++++|.|.++|||++.|+|+|||+|||+||+||.|++...+.-..+.+|.++|||+||++|++
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 4567889999999999999999999999999999999999999999743332235789999999999999985
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=99.84 E-value=1.3e-20 Score=127.37 Aligned_cols=68 Identities=38% Similarity=0.421 Sum_probs=61.2
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEec
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
|.+.|.+++|++|.|.|+||+.|.|+|.|||+||||+|++|+|++..+ ..+.+|.++|||+||++|++
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 356799999999999999999999999999999999999999986543 35789999999999999874
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=99.83 E-value=2.2e-20 Score=129.76 Aligned_cols=69 Identities=33% Similarity=0.494 Sum_probs=60.8
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc-------eeeeeecceEEEeeccEEEEe
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-------LYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~-------~~~~~~~G~vlIRG~nVv~I~ 80 (147)
++.|.++++++|.|.|+|||.|.|+|+|||+||||||+||.|++.... ....+.+|.++|||+||++|+
T Consensus 2 ~~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 2 SSKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred cchhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 356999999999999999999999999999999999999999875321 124578999999999999987
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=99.83 E-value=3.3e-20 Score=129.92 Aligned_cols=70 Identities=26% Similarity=0.414 Sum_probs=61.0
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc----------eeeeeecceEEEeeccEEEEe
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD----------LYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~----------~~~~~~~G~vlIRG~nVv~I~ 80 (147)
|...|...++++|.|.|+|||+|.|+|+|||+||||||+||+|++.... ....+.+|.++|||+||++|+
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 4567888999999999999999999999999999999999999985321 123578999999999999986
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.82 E-value=5.8e-20 Score=125.83 Aligned_cols=67 Identities=37% Similarity=0.501 Sum_probs=60.3
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
|...|.++++++|.|.|+||+.|.|+|.|||+|||++|+||.|.. .++ ..+.+|.++|||+||++|+
T Consensus 5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~--~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGE--VVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCC--eEeEcCcEEEeCCEEEEEc
Confidence 568899999999999999999999999999999999999999974 332 2468999999999999986
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=99.79 E-value=5.6e-19 Score=122.42 Aligned_cols=69 Identities=30% Similarity=0.367 Sum_probs=61.6
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc---eeeeeecceEEEeeccEEEEe
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD---LYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~---~~~~~~~G~vlIRG~nVv~I~ 80 (147)
.+.|.++++++|.|.|+|||.|.|+|.|||++|||||++|.|+..... ....+.+|+++|||++|+++.
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 467999999999999999999999999999999999999999976422 234689999999999999987
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=99.79 E-value=4.6e-19 Score=119.63 Aligned_cols=67 Identities=31% Similarity=0.413 Sum_probs=58.9
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
|...|.+++|++|.|.|++|++|+|+|.|||+||||+|+||.|... ++ ....+|.++|||++|++|+
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 3568999999999999999999999999999999999999988642 32 2467899999999999884
No 13
>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=99.79 E-value=5.7e-19 Score=119.60 Aligned_cols=67 Identities=31% Similarity=0.358 Sum_probs=59.3
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
|...|.++++++|.|.|+||++|.|+|.|||+|||++|+||.|+.. +. ....+|.++|||+||++|.
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 4578999999999999999999999999999999999999999753 32 2467899999999999873
No 14
>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=99.78 E-value=1.5e-18 Score=123.53 Aligned_cols=71 Identities=25% Similarity=0.343 Sum_probs=60.5
Q ss_pred hhHHHhhcc--CCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCce----------eeeeecceEEEeeccEEE
Q 032108 11 LSTSLASYL--DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL----------YCDIPLGLYVIRGENVVL 78 (147)
Q Consensus 11 ~~~~L~~~l--dKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~----------~~~~~~G~vlIRG~nVv~ 78 (147)
|.+.|...+ +++|.|.|++|+.+.|+|.|||+||||||+||+|.+...+. ...+.+|.++|||+||++
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 456778886 89999999999999999999999999999999998754221 235678999999999999
Q ss_pred Eec
Q 032108 79 IGE 81 (147)
Q Consensus 79 I~~ 81 (147)
|+.
T Consensus 83 Is~ 85 (87)
T cd01720 83 VLR 85 (87)
T ss_pred Eec
Confidence 874
No 15
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=1.4e-18 Score=121.79 Aligned_cols=71 Identities=25% Similarity=0.461 Sum_probs=61.1
Q ss_pred CchhHHHhhccCC--eEEEEEc--CCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEec
Q 032108 9 VYLSTSLASYLDK--KLLVLLR--DGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 9 ~~~~~~L~~~ldK--kV~V~L~--dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
..|...+.+++++ +|.|.++ +|+.+.|+|+|||+||||||+||+|++..++ ..+.+|.++|||+||++|++
T Consensus 5 ~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 5 VQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred cCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 4578899999999 5677676 8999999999999999999999999975332 35679999999999999873
No 16
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.77 E-value=2.2e-18 Score=119.47 Aligned_cols=73 Identities=37% Similarity=0.521 Sum_probs=61.5
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEee-eCceeeeeecceEEEeeccEEEEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVI-VGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~-~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
..+...|.++++++|.|.|+||++|.|+|+|||+||||+|+||.|+.. ++.....+..|.++|||+||++|.+
T Consensus 6 ~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 446889999999999999999999999999999999999999999874 2221123344599999999999863
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.77 E-value=1.9e-18 Score=115.07 Aligned_cols=66 Identities=45% Similarity=0.582 Sum_probs=59.6
Q ss_pred HHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEec
Q 032108 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 14 ~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
.|.+++|++|.|.|+||+.+.|+|.|||+|||++|+||.|+...+ ...+.+|.++|||++|++|+.
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~--~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC--cEEeEeCCEEEcCCEEEEEeC
Confidence 588999999999999999999999999999999999999987542 246789999999999999873
No 18
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.77 E-value=5.4e-19 Score=121.94 Aligned_cols=74 Identities=39% Similarity=0.659 Sum_probs=64.9
Q ss_pred CCCC-CCCCCchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEE
Q 032108 1 MSWA-GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLI 79 (147)
Q Consensus 1 Ms~~-~~~~~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I 79 (147)
||++ +| .|++|+||++.+.|..||.+.|+|+|||.|||+||++|+|...+++ ...+|.++|||++|+.+
T Consensus 1 Msksg~P-------eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~ 70 (77)
T KOG1780|consen 1 MSKSGHP-------ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMV 70 (77)
T ss_pred CCcccCc-------hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEE
Confidence 8876 44 3999999999999999999999999999999999999999754443 36789999999999999
Q ss_pred eccCC
Q 032108 80 GELDL 84 (147)
Q Consensus 80 ~~iD~ 84 (147)
...|.
T Consensus 71 eaL~~ 75 (77)
T KOG1780|consen 71 EALER 75 (77)
T ss_pred eeccc
Confidence 87663
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=99.76 E-value=2.9e-18 Score=114.28 Aligned_cols=67 Identities=40% Similarity=0.569 Sum_probs=60.0
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEec
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGE 81 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~ 81 (147)
..|.+++|++|.|.|+||+.|+|+|.+||+|||++|+||.|....+. ..+.+|.++|||++|++|++
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 36899999999999999999999999999999999999999864332 46889999999999999874
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=99.73 E-value=2.7e-17 Score=112.10 Aligned_cols=70 Identities=20% Similarity=0.127 Sum_probs=61.6
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
|...|.+..|++|.|.|+||.+|.|+|.++|+|||++|+||.+....++ ...+|.++|||+||.++..+|
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 3467899999999999999999999999999999999999987544443 356799999999999999876
No 21
>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=99.72 E-value=2.7e-17 Score=107.93 Aligned_cols=63 Identities=41% Similarity=0.629 Sum_probs=56.6
Q ss_pred HhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 15 L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
|.+++|++|.|.|+||+.|.|+|.+||+|||++|++|.|....+ ..+.+|.++|||++|.+|.
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 3578999999999999873
No 22
>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=99.71 E-value=6e-17 Score=111.93 Aligned_cols=72 Identities=22% Similarity=0.231 Sum_probs=62.6
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCC
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDL 84 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~ 84 (147)
|...|+++.|++|.|.|++|+++.|+|.+||+|||++|+||.|.-..|+. ....|.++|||++|.++..+|.
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~~ 73 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPDE 73 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCHH
Confidence 56789999999999999999999999999999999999999986444442 2356899999999999987764
No 23
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.71 E-value=7.3e-17 Score=115.37 Aligned_cols=72 Identities=24% Similarity=0.404 Sum_probs=60.8
Q ss_pred CchhHHHhhccCCe--EEEEEcC--CeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEecc
Q 032108 9 VYLSTSLASYLDKK--LLVLLRD--GRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (147)
Q Consensus 9 ~~~~~~L~~~ldKk--V~V~L~d--GR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~i 82 (147)
.+|...+.+++.++ |.|.+.| |+.+.|+|+|||+||||||+||+|++..++ ..+.+|.++|||+||++|++.
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 67889999999976 5556667 489999999999999999999999864332 357899999999999999864
No 24
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.67 E-value=1.7e-17 Score=118.52 Aligned_cols=85 Identities=39% Similarity=0.680 Sum_probs=72.9
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc-eeeeeecceEEEeeccEEEEeccCCcccCCC
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-LYCDIPLGLYVIRGENVVLIGELDLERDELP 90 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~-~~~~~~~G~vlIRG~nVv~I~~iD~~~e~~~ 90 (147)
++.|.+|++++|.|...|||.+.|.|.||||-.||+|+++.||+++.. ......+|+++|||+||..|+++|++++. .
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 467999999999999999999999999999999999999999987543 24568899999999999999999999873 3
Q ss_pred CCCCccC
Q 032108 91 PHLTHVS 97 (147)
Q Consensus 91 ~~~~~v~ 97 (147)
-.++.+.
T Consensus 81 ld~tkir 87 (96)
T KOG1784|consen 81 LDLTKIR 87 (96)
T ss_pred hhhhhcc
Confidence 4444443
No 25
>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=99.67 E-value=3.7e-16 Score=111.61 Aligned_cols=72 Identities=21% Similarity=0.248 Sum_probs=63.7
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCcc
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER 86 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~ 86 (147)
...|.++.|++|.|.|++|.+|.|+|.++|+|||++|+||.+....+. ...+|.++|||+||.++..+|...
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 357899999999999999999999999999999999999988754332 357899999999999999998754
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=99.63 E-value=1.9e-15 Score=105.32 Aligned_cols=70 Identities=21% Similarity=0.236 Sum_probs=59.9
Q ss_pred chhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEecc
Q 032108 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (147)
Q Consensus 10 ~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~i 82 (147)
+....|.++.|+.|.|.|++|..|.|+|.++|+|||++|+||.+....+. ...+|.++|||+||.+|..+
T Consensus 9 tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~---~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGK---QVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCc---eeECCcEEEECCEEEEEEcC
Confidence 34567899999999999999999999999999999999999987532222 34689999999999999753
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=99.63 E-value=1.7e-15 Score=106.06 Aligned_cols=75 Identities=23% Similarity=0.171 Sum_probs=62.4
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCccc
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~e 87 (147)
-.+|.++.|++|.|.|++|..|.|+|.++|+|||++|+||.+....+. .....+|.++|||++|.+|..+|...+
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 357899999999999999999999999999999999999976532111 112456899999999999998887664
No 28
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.61 E-value=1.7e-15 Score=104.49 Aligned_cols=72 Identities=33% Similarity=0.360 Sum_probs=65.1
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
..|.++|..+.+|+|.|.|+.|.+|.|+|.+.|.||||.|.+|.|++. |. ....+|.++||++||.+|+.++
T Consensus 7 vNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~id-G~--~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 7 VNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYID-GV--STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred CCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhc-cc--ccccceeEEEEeccEEEEecCC
Confidence 468899999999999999999999999999999999999999999863 43 3467999999999999998775
No 29
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.61 E-value=7.2e-17 Score=116.86 Aligned_cols=80 Identities=36% Similarity=0.474 Sum_probs=69.7
Q ss_pred HHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCc-e----eeeeecceEEEeeccEEEEeccCCcccC
Q 032108 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGD-L----YCDIPLGLYVIRGENVVLIGELDLERDE 88 (147)
Q Consensus 14 ~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~-~----~~~~~~G~vlIRG~nVv~I~~iD~~~e~ 88 (147)
.|.+|+||+|+|.+.+||..+|+|.||||.|||||++|+|+..+.+ . ...+.+|++++||..+++|++-|...+.
T Consensus 21 DLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~I 100 (108)
T KOG1781|consen 21 DLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEEI 100 (108)
T ss_pred hHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhhh
Confidence 5899999999999999999999999999999999999999876542 1 1348999999999999999999998885
Q ss_pred CCCCC
Q 032108 89 LPPHL 93 (147)
Q Consensus 89 ~~~~~ 93 (147)
++|..
T Consensus 101 ~npf~ 105 (108)
T KOG1781|consen 101 ANPFV 105 (108)
T ss_pred ccchh
Confidence 44443
No 30
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.43 E-value=3.8e-14 Score=100.04 Aligned_cols=73 Identities=30% Similarity=0.399 Sum_probs=62.7
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeee--Cc--e------eeeeecceEEEeeccEEEEe
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIV--GD--L------YCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~--~~--~------~~~~~~G~vlIRG~nVv~I~ 80 (147)
|-..|+-+++.+|.|.++++|++.|+|.+||+|.|+||.|++|.++. ++ . ...+.+..++|||++|++++
T Consensus 6 PldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvs 85 (91)
T KOG3460|consen 6 PLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVS 85 (91)
T ss_pred cHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEc
Confidence 55678889999999999999999999999999999999999998763 11 1 23567789999999999999
Q ss_pred ccC
Q 032108 81 ELD 83 (147)
Q Consensus 81 ~iD 83 (147)
++-
T Consensus 86 pp~ 88 (91)
T KOG3460|consen 86 PPL 88 (91)
T ss_pred Ccc
Confidence 754
No 31
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.40 E-value=7.3e-14 Score=96.33 Aligned_cols=71 Identities=30% Similarity=0.399 Sum_probs=63.1
Q ss_pred chhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 10 ~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
.++.+|.+.+||+|.|.|.+|-.|+|+|.|+|.||||-|+.|.|+. +|+ ..+..|..+|||+||.+|+..+
T Consensus 6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngq--l~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQ--LKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCc--ccccccceeeccccEEEEEecc
Confidence 4678999999999999999999999999999999999999999975 333 2567899999999999998653
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.34 E-value=2.1e-13 Score=106.98 Aligned_cols=76 Identities=29% Similarity=0.382 Sum_probs=64.3
Q ss_pred hhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeC-------ceeeeeecceEEEeeccEEEEeccC
Q 032108 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG-------DLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 11 ~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~-------~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
.+..|.+++|-++.|.++|||+|+|.|.+||+||||||.||+|..... +..+.+-+|++++||+||++...-+
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 456799999999999999999999999999999999999999964321 1235688999999999999988655
Q ss_pred Ccc
Q 032108 84 LER 86 (147)
Q Consensus 84 ~~~ 86 (147)
...
T Consensus 85 ppp 87 (177)
T KOG3168|consen 85 PPP 87 (177)
T ss_pred CCC
Confidence 444
No 33
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.30 E-value=2.8e-12 Score=89.34 Aligned_cols=79 Identities=22% Similarity=0.388 Sum_probs=67.5
Q ss_pred CCCCCchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108 5 GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 5 ~~~~~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
+|+...|...+-+.++.++.|.+++.|++.|+|.|||.|-|+||+|++|+-...+...-.+++.+++.|+||.++.+--
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 4555778899999999999999999999999999999999999999999865443223467899999999999887544
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.18 E-value=2.3e-11 Score=85.68 Aligned_cols=75 Identities=24% Similarity=0.390 Sum_probs=60.2
Q ss_pred CCCchhHHHhhccCCe--EEEEEcC--CeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEecc
Q 032108 7 DDVYLSTSLASYLDKK--LLVLLRD--GRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 82 (147)
Q Consensus 7 ~~~~~~~~L~~~ldKk--V~V~L~d--GR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~i 82 (147)
...+|...+.+++..+ |.|.|.+ |-.+.|.++|||+|||+||++|+|.....+ ..+++|.++++|+||.+|...
T Consensus 9 vmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~--~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 9 VMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK--SRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred eecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhcccccc--CCCccccEEEcCCcEEEEeec
Confidence 4477889999999876 4445554 789999999999999999999999754332 234899999999999998754
Q ss_pred C
Q 032108 83 D 83 (147)
Q Consensus 83 D 83 (147)
+
T Consensus 87 ~ 87 (88)
T KOG1774|consen 87 G 87 (88)
T ss_pred C
Confidence 3
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.96 E-value=1.4e-09 Score=81.83 Aligned_cols=76 Identities=22% Similarity=0.258 Sum_probs=65.9
Q ss_pred chhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCccc
Q 032108 10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD 87 (147)
Q Consensus 10 ~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~e 87 (147)
.|...|...-++++.|.|++|.+|.|.|..+|.+|||.|.+++++..+++++ ..+..+.|||.+|-++..+|+..+
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf--~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKF--FRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCce--eecceeEEecceeEEEeccHHHHH
Confidence 3567788899999999999999999999999999999999999987777653 456789999999999987765443
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.88 E-value=6.7e-09 Score=74.26 Aligned_cols=70 Identities=26% Similarity=0.275 Sum_probs=57.2
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceee-eeecceEEEeeccEEEEeccCC
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYC-DIPLGLYVIRGENVVLIGELDL 84 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~-~~~~G~vlIRG~nVv~I~~iD~ 84 (147)
++.+.++|++|.|.|++|-.+.|+|.|+|||.|+-|.|..- .+.++|. -..+..++|||+.|-++.....
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v--~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISV--TDPDKYPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEe--eCcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence 56789999999999999999999999999999999999854 3333332 2345679999999999985443
No 37
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=98.64 E-value=9.3e-08 Score=70.63 Aligned_cols=79 Identities=18% Similarity=0.176 Sum_probs=68.2
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCcccCCCC
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPP 91 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~e~~~~ 91 (147)
...|++.-+.-|.+.+..|..|.|.|.-.|.+||++|.|.+-...++. ...+..++|||+.|-++..+|..+. +|
T Consensus 7 iKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLKn--AP 81 (119)
T KOG3172|consen 7 IKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLKN--AP 81 (119)
T ss_pred eeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhhc--Cc
Confidence 466889999999999999999999999999999999999987654443 3467889999999999999999985 66
Q ss_pred CCCc
Q 032108 92 HLTH 95 (147)
Q Consensus 92 ~~~~ 95 (147)
.|..
T Consensus 82 mFkk 85 (119)
T KOG3172|consen 82 MFKK 85 (119)
T ss_pred cccc
Confidence 6663
No 38
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=98.12 E-value=1.5e-05 Score=58.99 Aligned_cols=70 Identities=26% Similarity=0.292 Sum_probs=59.1
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCc
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLE 85 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~ 85 (147)
...|..+.+.+|.|.|++|....|++.+.|-+||..|.++.-... ++ ...+....|||+||-++-.+|.-
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-~~---pv~l~~lsirgnniRy~~lpD~l 73 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-GE---PVRLDTLSIRGNNIRYYILPDSL 73 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-CC---ceeEEEEEeecceEEEEEccCCc
Confidence 357899999999999999999999999999999999999865432 22 24567889999999999988743
No 39
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=97.86 E-value=2.3e-06 Score=63.34 Aligned_cols=62 Identities=27% Similarity=0.347 Sum_probs=52.2
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeC------ce----eeeeecceEEEeeccEEEEecc
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVG------DL----YCDIPLGLYVIRGENVVLIGEL 82 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~------~~----~~~~~~G~vlIRG~nVv~I~~i 82 (147)
..|+|..+|++.+.|...+||.+.|++|+++.|.+..- .. -.++.+|.++||||+|+.+...
T Consensus 37 ~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r~ 108 (114)
T KOG3459|consen 37 TQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLRN 108 (114)
T ss_pred ceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEec
Confidence 67999999999999999999999999999998866531 11 1268899999999999988743
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.71 E-value=0.00012 Score=50.10 Aligned_cols=64 Identities=19% Similarity=0.167 Sum_probs=40.5
Q ss_pred HHhhccCCeEEEEEcCCeEEEEEEEEecC---ccceEecceEEEeee----CceeeeeecceEEEeeccEE
Q 032108 14 SLASYLDKKLLVLLRDGRKLMGTLCSFDQ---FANAVLEGACERVIV----GDLYCDIPLGLYVIRGENVV 77 (147)
Q Consensus 14 ~L~~~ldKkV~V~L~dGR~l~G~L~sfDq---~mNLVL~da~E~i~~----~~~~~~~~~G~vlIRG~nVv 77 (147)
.+..++|++|.|+++||..|.|+|.+++. -+.++|..+...-.. ...........++|+++.|+
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 46788999999999999999999999998 889999888653221 11123455677888887765
No 41
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.67 E-value=4.2e-05 Score=52.00 Aligned_cols=38 Identities=29% Similarity=0.322 Sum_probs=31.4
Q ss_pred CCeEEEEEcC--C--eEEEEEEEEecCccceEecceEEEeee
Q 032108 20 DKKLLVLLRD--G--RKLMGTLCSFDQFANAVLEGACERVIV 57 (147)
Q Consensus 20 dKkV~V~L~d--G--R~l~G~L~sfDq~mNLVL~da~E~i~~ 57 (147)
.++|.|.++. | -.++|.|.+||+|+||+|.|+.|.+..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3678888864 3 388999999999999999999997643
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=96.32 E-value=0.028 Score=35.22 Aligned_cols=35 Identities=11% Similarity=0.071 Sum_probs=30.3
Q ss_pred ccCCeEEEEEcCCeEEEEEEEEecCccceEecceEE
Q 032108 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACE 53 (147)
Q Consensus 18 ~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E 53 (147)
.+|++|.|.+ ++..+.|+..++|..+.|++.....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 3799999999 6777799999999999999977644
No 43
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.69 E-value=0.064 Score=38.84 Aligned_cols=71 Identities=17% Similarity=0.213 Sum_probs=54.0
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEecC-ccceEecceEEEeeeCce------eeeeecceEEEeeccEEEEeccCCcc
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQ-FANAVLEGACERVIVGDL------YCDIPLGLYVIRGENVVLIGELDLER 86 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfDq-~mNLVL~da~E~i~~~~~------~~~~~~G~vlIRG~nVv~I~~iD~~~ 86 (147)
..|+|++|.+..+++-.|+|+|..+|. -..|.|.++.-.-..+.. -.+.....++.||..|.-+..++...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 368999999999999999999999995 789999998654332210 11235678999999999888776555
No 44
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=94.77 E-value=0.063 Score=36.03 Aligned_cols=31 Identities=26% Similarity=0.418 Sum_probs=26.7
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 20 dKkV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
..+|.|.|.+|-.+.|...|||+|+=++-.+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 4679999999999999999999998666544
No 45
>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=94.66 E-value=0.091 Score=41.62 Aligned_cols=63 Identities=27% Similarity=0.295 Sum_probs=44.6
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEec-CccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCc
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLE 85 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfD-q~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~ 85 (147)
..+..|++|+|.|.+.| +++.|.+.++| -..|+||-+-.| ++. ...-+|-|..|..+..+++.
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~------~sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK------RSVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS-------EEEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc------eeEEEEEccceEEEEEccCC
Confidence 35889999999999999 99999999999 567999986543 111 23578889999999988753
No 46
>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=94.49 E-value=0.08 Score=35.55 Aligned_cols=31 Identities=29% Similarity=0.423 Sum_probs=26.6
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 20 dKkV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
..+|.|.|.+|-.+.|.+.|||+|+=|+-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 4669999999999999999999998666544
No 47
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=93.71 E-value=0.13 Score=36.23 Aligned_cols=32 Identities=28% Similarity=0.420 Sum_probs=27.3
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 20 DKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 20 dKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
..+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 46699999999999999999999987665443
No 48
>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=93.54 E-value=0.59 Score=32.95 Aligned_cols=60 Identities=15% Similarity=0.101 Sum_probs=43.0
Q ss_pred HHHhhccCCeEEEEEcCCeEEEEEEEEecC-ccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQ-FANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 13 ~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq-~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
..|....||+|.+.|.++.+..|++.++|. ..|+..++-. .+ -......++|+.-|+++.
T Consensus 17 r~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TP----lGv~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TP----LGVQPEALLRCSDVISIS 77 (80)
T ss_dssp HHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TT----TTEEEEEEEEGGGEEEEE
T ss_pred HHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----CC----cccChhheeecCCEEEEE
Confidence 357788999999999999999999999994 4566665531 11 011346799999999886
No 49
>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=93.06 E-value=0.48 Score=33.01 Aligned_cols=62 Identities=16% Similarity=0.229 Sum_probs=45.1
Q ss_pred hccCCeEEEEEcCCeEEEEEEEEec-CccceEecceEEEeeeCce-------eeeeecceEEEeeccEEE
Q 032108 17 SYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGDL-------YCDIPLGLYVIRGENVVL 78 (147)
Q Consensus 17 ~~ldKkV~V~L~dGR~l~G~L~sfD-q~mNLVL~da~E~i~~~~~-------~~~~~~G~vlIRG~nVv~ 78 (147)
.++|+++.+..+.+-.|+|+|.++| +-.-+-|+|+...-..+.. -.......++.||+.|--
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 5899999999999999999999999 4456778887654333211 022345677888887653
No 50
>PRK14638 hypothetical protein; Provisional
Probab=92.98 E-value=0.4 Score=37.07 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=34.2
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|++.+++.++|+|.++|.- ++.|.
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 56677899999999999999999999999999863 45553
No 51
>PRK14639 hypothetical protein; Provisional
Probab=92.18 E-value=0.6 Score=35.65 Aligned_cols=39 Identities=18% Similarity=0.228 Sum_probs=34.0
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL 48 (147)
+........++|++|.|.+.+++.+.|+|.++|.- ++.|
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 56667899999999999999999999999999983 5555
No 52
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.16 E-value=0.41 Score=33.56 Aligned_cols=27 Identities=33% Similarity=0.506 Sum_probs=24.0
Q ss_pred CCeEEEEEcCCeEEEEEEEEecCccce
Q 032108 20 DKKLLVLLRDGRKLMGTLCSFDQFANA 46 (147)
Q Consensus 20 dKkV~V~L~dGR~l~G~L~sfDq~mNL 46 (147)
..+|.|-|.+|-.+.|...|||+|.=|
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~Vl 45 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFVVL 45 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEEEE
Confidence 567999999999999999999999643
No 53
>PRK02001 hypothetical protein; Validated
Probab=90.95 E-value=0.72 Score=35.88 Aligned_cols=40 Identities=28% Similarity=0.438 Sum_probs=34.4
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|+.|.|.+.+++.|.|+|.++|.- +++|.
T Consensus 79 L~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 79 LKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred CCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 66677899999999999999999999999999964 45553
No 54
>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=90.41 E-value=1.4 Score=30.41 Aligned_cols=39 Identities=26% Similarity=0.325 Sum_probs=32.4
Q ss_pred CchhHHHhhccCCeEEEEEc---CC-eEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR---DG-RKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~---dG-R~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|+.|.|.++ +| +.+.|.|.++|.- +++|
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 66677899999999999997 56 6999999999884 4444
No 55
>PRK14644 hypothetical protein; Provisional
Probab=89.90 E-value=1.3 Score=33.72 Aligned_cols=37 Identities=16% Similarity=0.201 Sum_probs=31.7
Q ss_pred hHHHhhccCCeEEEEEcCC----eEEEEEEEEecCccceEec
Q 032108 12 STSLASYLDKKLLVLLRDG----RKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dG----R~l~G~L~sfDq~mNLVL~ 49 (147)
...+..++|++|.|.|++. +.+.|.|.++|. .++.|.
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 3689999999999999877 899999999987 356664
No 56
>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=89.66 E-value=0.96 Score=30.27 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=29.6
Q ss_pred ccCCeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 18 ~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
.+|..|.+++..|.+++|.+.+||.-.+++.-.|
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 4789999999999999999999998887775544
No 57
>PRK14640 hypothetical protein; Provisional
Probab=88.46 E-value=2 Score=33.15 Aligned_cols=40 Identities=18% Similarity=0.309 Sum_probs=33.1
Q ss_pred CchhHHHhhccCCeEEEEE----cCCeEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L----~dGR~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.+ .+++.+.|+|.++|.. ++.|.
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 5667789999999999999 4669999999999874 55553
No 58
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=87.77 E-value=4.1 Score=27.66 Aligned_cols=53 Identities=23% Similarity=0.276 Sum_probs=39.5
Q ss_pred hHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG 80 (147)
Q Consensus 12 ~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~ 80 (147)
-..|.+++|++|.|.+..|.. .|+|.+.... .++|+.. -..++||=..|+.+-
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 9999998643 3455433 125788888888764
No 59
>PRK14636 hypothetical protein; Provisional
Probab=86.07 E-value=3 Score=33.07 Aligned_cols=39 Identities=18% Similarity=0.328 Sum_probs=31.9
Q ss_pred CchhHHHhhccCCeEEEEEc---CC-eEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR---DG-RKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~---dG-R~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|++|.|.++ +| +.++|+|.++|.- ++.|
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 55667899999999999997 56 6999999999873 4444
No 60
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=85.14 E-value=1.5 Score=34.77 Aligned_cols=31 Identities=23% Similarity=0.433 Sum_probs=26.6
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
.+|.|.|.+|-.+.|.+.|||+|.=|+-.+.
T Consensus 105 ~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 105 EPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred CcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 5689999999999999999999986665554
No 61
>PRK14633 hypothetical protein; Provisional
Probab=85.06 E-value=3 Score=32.13 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=32.7
Q ss_pred CchhHHHhhccCCeEEEEEc----CCeEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~----dGR~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.++ +++.++|+|.++|.- ++.|.
T Consensus 83 L~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 83 IFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 56677899999999999984 568999999999874 55553
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=84.99 E-value=2 Score=32.31 Aligned_cols=39 Identities=18% Similarity=0.381 Sum_probs=29.2
Q ss_pred CchhHHHhhccCCeEEEEEc----CCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~----dGR~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|++|.|.++ +.+.+.|+|.++|. .+++|
T Consensus 76 L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 76 LKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp -SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred CCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 44567899999999999994 44799999999998 45555
No 63
>PRK14645 hypothetical protein; Provisional
Probab=84.88 E-value=2.7 Score=32.67 Aligned_cols=38 Identities=11% Similarity=0.183 Sum_probs=31.5
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|++|.|.+ +++.+.|+|.++|.- ++.|
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 5667789999999999986 789999999999873 4444
No 64
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=84.76 E-value=1.6 Score=34.62 Aligned_cols=38 Identities=26% Similarity=0.356 Sum_probs=29.2
Q ss_pred HHhhccC--CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 14 SLASYLD--KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 14 ~L~~~ld--KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
.|..+-. .+|.|.|.+|-.+.|.+.+||+|.=|+-.+.
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 4444444 4588889999999999999999976665443
No 65
>PRK14632 hypothetical protein; Provisional
Probab=83.94 E-value=4.4 Score=31.96 Aligned_cols=40 Identities=23% Similarity=0.471 Sum_probs=32.8
Q ss_pred CchhHHHhhccCCeEEEEEcC-------CeEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRD-------GRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~d-------GR~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|+.|.|.+.+ .+.+.|+|.++|. .++.|.
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 566678999999999999976 5799999999986 355554
No 66
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.76 E-value=3.6 Score=32.15 Aligned_cols=39 Identities=21% Similarity=0.355 Sum_probs=34.2
Q ss_pred CchhHHHhhccCCeEEEEE----cCCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L----~dGR~l~G~L~sfDq~mNLVL 48 (147)
+.+......++|+.|.|.| .+++.+.|+|.++|.-+ +++
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 6677889999999999999 78899999999999876 444
No 67
>PRK14642 hypothetical protein; Provisional
Probab=83.75 E-value=3.2 Score=33.72 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=33.0
Q ss_pred CchhHHHhhccCCeEEEEEc-------------CCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR-------------DGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~-------------dGR~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|+.|.|+|+ +++.|.|+|.++|.. ++.|
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 56677899999999999998 679999999999874 4444
No 68
>PRK14634 hypothetical protein; Provisional
Probab=83.53 E-value=4.8 Score=31.22 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=32.3
Q ss_pred CchhHHHhhccCCeEEEEEcC---C-eEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRD---G-RKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~d---G-R~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.+.+ | +.|.|+|.++|.- ++.|.
T Consensus 89 L~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14634 89 LSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQIN 132 (155)
T ss_pred CCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEEE
Confidence 566778999999999999963 2 7999999999873 45553
No 69
>PRK14647 hypothetical protein; Provisional
Probab=81.48 E-value=6.5 Score=30.49 Aligned_cols=39 Identities=10% Similarity=0.183 Sum_probs=31.5
Q ss_pred CchhHHHhhccCCeEEEEEc---------CCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR---------DGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~---------dGR~l~G~L~sfDq~mNLVL 48 (147)
+.....+..++|++|.|+++ +.+.+.|+|.++|. .++.|
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 55677899999999999995 34899999999986 34444
No 70
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=81.24 E-value=5.1 Score=30.69 Aligned_cols=34 Identities=18% Similarity=0.356 Sum_probs=29.7
Q ss_pred CchhHHHhhccCCeEEEEE----cCCeEEEEEEEEecC
Q 032108 9 VYLSTSLASYLDKKLLVLL----RDGRKLMGTLCSFDQ 42 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L----~dGR~l~G~L~sfDq 42 (147)
+.....+..++|+.|.|.+ .+++.+.|+|.++|.
T Consensus 87 L~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 87 LKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred CCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 4556789999999999997 567899999999987
No 71
>PRK14646 hypothetical protein; Provisional
Probab=80.20 E-value=7.8 Score=30.04 Aligned_cols=40 Identities=13% Similarity=0.083 Sum_probs=32.4
Q ss_pred CchhHHHhhccCCeEEEEEcC---C-eEEEEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRD---G-RKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~d---G-R~l~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.|++ | +.+.|+|.++|.- ++.|.
T Consensus 89 L~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 89 LTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred CCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 556678999999999999964 3 6889999999984 55553
No 72
>PRK14643 hypothetical protein; Provisional
Probab=78.17 E-value=8.8 Score=30.10 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=30.1
Q ss_pred CchhHHHhhccCCeEEEEEcC----CeEEEEEEEEecCc
Q 032108 9 VYLSTSLASYLDKKLLVLLRD----GRKLMGTLCSFDQF 43 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~d----GR~l~G~L~sfDq~ 43 (147)
+.....+..++|++|.|.+++ .+.+.|+|.++|.-
T Consensus 93 L~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 93 IRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred CCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 556678999999999999965 58999999999865
No 73
>PRK06955 biotin--protein ligase; Provisional
Probab=77.80 E-value=4.4 Score=34.18 Aligned_cols=34 Identities=15% Similarity=0.306 Sum_probs=29.6
Q ss_pred hccCCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 17 ~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
-++|++|.|...+++.+.|+..|+|..+.|+++.
T Consensus 246 ~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 246 AYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred hcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 4688999997767788999999999999999963
No 74
>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=76.70 E-value=3.6 Score=32.48 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=31.1
Q ss_pred ccCCeEEEEEcCCeEEEEEEEEecCccceEecceE
Q 032108 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGAC 52 (147)
Q Consensus 18 ~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~ 52 (147)
.-+-+|+|++.||..|.|...+|++--|.||.-+.
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 34678999999999999999999999999987653
No 75
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=75.72 E-value=12 Score=31.45 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=27.7
Q ss_pred hccCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 032108 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 17 ~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~ 49 (147)
-++|++|.+.. ++..+.|++.++|..+.|++.
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 446799999999999999996
No 76
>PRK14631 hypothetical protein; Provisional
Probab=75.07 E-value=8.8 Score=30.41 Aligned_cols=39 Identities=18% Similarity=0.356 Sum_probs=32.0
Q ss_pred CchhHHHhhccCCeEEEEEc----CCeEEEEEEEEec--CccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLR----DGRKLMGTLCSFD--QFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~----dGR~l~G~L~sfD--q~mNLVL 48 (147)
+.....+..++|+.|.|.|. +.+.|.|+|.++| . .++.|
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 66677899999999999996 4599999999998 4 34444
No 77
>PRK14641 hypothetical protein; Provisional
Probab=73.21 E-value=9.9 Score=30.17 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=28.3
Q ss_pred CchhHHHhhccCCeEEEEEcC----CeEEEEEEEEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRD----GRKLMGTLCSFD 41 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~d----GR~l~G~L~sfD 41 (147)
+.....+..++|+.|.|.+.+ .+.+.|+|.++|
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 566678999999999999976 468999999985
No 78
>PRK14637 hypothetical protein; Provisional
Probab=73.13 E-value=11 Score=29.20 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=31.0
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEE-EEEEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKL-MGTLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l-~G~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.+.+...+ +|+|.++|.- ++.|.
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 5667789999999999999444455 7999999874 55554
No 79
>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=70.83 E-value=14 Score=29.84 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=28.1
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEecCccceEec
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~ 49 (147)
...+|++|.|...+ ..+.|+..|+|..+.|+++
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 44679999998754 5699999999999999996
No 80
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=70.25 E-value=13 Score=31.24 Aligned_cols=32 Identities=28% Similarity=0.330 Sum_probs=27.8
Q ss_pred ccCCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 18 YLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 18 ~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
++|++|.|.. ++..+.|++.++|..+.|++..
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 4799999874 6789999999999999999964
No 81
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.24 E-value=11 Score=33.50 Aligned_cols=68 Identities=15% Similarity=0.154 Sum_probs=51.2
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEec-CccceEecceEEEeeeCce-------eeeeecceEEEeeccEEEEeccC
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFD-QFANAVLEGACERVIVGDL-------YCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfD-q~mNLVL~da~E~i~~~~~-------~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
..+||++|.+.-+..-.|+|+|.-+| |-.=|=|.++--.-..+.. ..+....-++.||+.|-.+...+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 45899999999999999999999999 7788888886332222211 12335678999999999777655
No 82
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=67.69 E-value=15 Score=34.26 Aligned_cols=34 Identities=24% Similarity=0.157 Sum_probs=29.5
Q ss_pred hccCCeEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 17 SYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 17 ~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
-++|++|.+...++..+.|+.+|+|..+.|+|+.
T Consensus 275 ~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 275 RDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred ccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 3679999987667778999999999999999963
No 83
>PRK08330 biotin--protein ligase; Provisional
Probab=67.34 E-value=24 Score=28.50 Aligned_cols=34 Identities=26% Similarity=0.386 Sum_probs=28.0
Q ss_pred hccCCeEEEEEcCCeEE-EEEEEEecCccceEecce
Q 032108 17 SYLDKKLLVLLRDGRKL-MGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 17 ~~ldKkV~V~L~dGR~l-~G~L~sfDq~mNLVL~da 51 (147)
-+++++|.+.. +|..+ .|+..++|..+.|++...
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 46889999875 66665 699999999999999743
No 84
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=66.02 E-value=21 Score=29.40 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=33.4
Q ss_pred HhhccCCeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 15 LASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 15 L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
....+|++|.+...++....|+..++|..+.|+|+..
T Consensus 185 ~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 185 RSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred HhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4456899999999999999999999999999999877
No 85
>PRK14630 hypothetical protein; Provisional
Probab=59.67 E-value=36 Score=25.98 Aligned_cols=38 Identities=11% Similarity=0.164 Sum_probs=30.2
Q ss_pred CchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEe
Q 032108 9 VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVL 48 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL 48 (147)
+........++|++|.|.+.+. ...|+|.++|. .++.|
T Consensus 86 L~~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 86 IKSDREFKIFEGKKIKLMLDND-FEEGFILEAKA-DSFIF 123 (143)
T ss_pred CCCHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeC-CEEEE
Confidence 5677789999999999999654 45999999987 35545
No 86
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=58.35 E-value=5.3 Score=31.02 Aligned_cols=25 Identities=32% Similarity=0.518 Sum_probs=19.6
Q ss_pred EcCCeEEEEEEEEecCccceEecce
Q 032108 27 LRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 27 L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
++..-.=+|+|+|.|+|+|=.-+|-
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred Hhcccccceeeeeecccccchhccc
Confidence 3445566899999999999877765
No 87
>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=55.28 E-value=13 Score=29.44 Aligned_cols=25 Identities=24% Similarity=0.425 Sum_probs=22.1
Q ss_pred cCCeEEEEEcCCeEEEEEEEEecCc
Q 032108 19 LDKKLLVLLRDGRKLMGTLCSFDQF 43 (147)
Q Consensus 19 ldKkV~V~L~dGR~l~G~L~sfDq~ 43 (147)
-|+-++|.+.|||+++|.=.|.|..
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 5788999999999999999998853
No 88
>PRK14635 hypothetical protein; Provisional
Probab=50.80 E-value=51 Score=25.58 Aligned_cols=40 Identities=20% Similarity=0.251 Sum_probs=31.3
Q ss_pred CchhHHHhhccCCeEEEEEc--CCeEEEE---EEEEecCccceEec
Q 032108 9 VYLSTSLASYLDKKLLVLLR--DGRKLMG---TLCSFDQFANAVLE 49 (147)
Q Consensus 9 ~~~~~~L~~~ldKkV~V~L~--dGR~l~G---~L~sfDq~mNLVL~ 49 (147)
+.....+..++|++|.|.+. ++..+.| .|.++|.- ++.|.
T Consensus 88 L~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 88 LRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred CCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 55667899999999999886 4678887 99999864 55553
No 89
>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=50.00 E-value=7.1 Score=28.28 Aligned_cols=17 Identities=41% Similarity=0.624 Sum_probs=15.5
Q ss_pred EEEEEecCccceEecce
Q 032108 35 GTLCSFDQFANAVLEGA 51 (147)
Q Consensus 35 G~L~sfDq~mNLVL~da 51 (147)
|+|+|.|.|+|..-++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999988776
No 90
>PRK08477 biotin--protein ligase; Provisional
Probab=48.50 E-value=37 Score=27.48 Aligned_cols=35 Identities=11% Similarity=0.041 Sum_probs=29.6
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
.-.+++.|.|. .+++.+.|+.+++|..+.|+++.-
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 578999999999999999988764
No 91
>PRK10898 serine endoprotease; Provisional
Probab=48.45 E-value=34 Score=29.51 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=27.2
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
..+.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999988866544
No 92
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=48.12 E-value=15 Score=25.64 Aligned_cols=57 Identities=18% Similarity=0.230 Sum_probs=27.5
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEecCccceEec-ceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLE-GACERVIVGDLYCDIPLGLYVIRGENVVLIGELD 83 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~-da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD 83 (147)
.-.-.-+|.++|+||..+.|+ ...+... +-.|.+.. +..-|...||=+.|..+...+
T Consensus 13 AC~~~~~v~L~l~dG~~~~g~------A~dt~~~~~k~E~L~l-----~~~~~~~~i~Ld~I~~~~al~ 70 (80)
T PF07073_consen 13 ACMYRYPVKLTLKDGEQIEGK------ALDTRTNAKKEECLVL-----EQDGGEQEIRLDQIASMSALT 70 (80)
T ss_dssp HHTTTT-EEEE-TTT--EEES------S-EEE---SSS-EEEE-----EETTEEEEESTT--SEEE---
T ss_pred HHhcCCeEEEEEeCCCEEEEE------EEEEEEecCceEEEEE-----ecCCcEEEEEhhheeeeeecC
Confidence 344567899999999999998 2222222 23333221 122356788888888888665
No 93
>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=48.11 E-value=26 Score=25.64 Aligned_cols=23 Identities=43% Similarity=0.592 Sum_probs=16.4
Q ss_pred HhhccC--CeEEEEEcCCeEEEEEE
Q 032108 15 LASYLD--KKLLVLLRDGRKLMGTL 37 (147)
Q Consensus 15 L~~~ld--KkV~V~L~dGR~l~G~L 37 (147)
|...++ .+|.+.|+||+.+.|++
T Consensus 21 lv~~L~ge~~V~l~L~DGs~l~Gtv 45 (101)
T PF11607_consen 21 LVSELDGEERVELELDDGSMLRGTV 45 (101)
T ss_dssp HHHCTTTT-EEEEEETTS-EEEEEE
T ss_pred HHhhcCCcceEEEEEcCCCeeeeee
Confidence 444444 56888999999999986
No 94
>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=47.54 E-value=36 Score=29.29 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=27.1
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
..+.|.+.||+.+.+++.++|...+|-|=..
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999988877544
No 95
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=45.69 E-value=29 Score=21.68 Aligned_cols=21 Identities=24% Similarity=0.248 Sum_probs=14.4
Q ss_pred EEEEEEEecCccceEecceEE
Q 032108 33 LMGTLCSFDQFANAVLEGACE 53 (147)
Q Consensus 33 l~G~L~sfDq~mNLVL~da~E 53 (147)
..|++.|.|+...+.|.+...
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~ 30 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDT 30 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-
T ss_pred cceeEEeeccccceEEEeCCc
Confidence 689999999999999988754
No 96
>PRK10942 serine endoprotease; Provisional
Probab=40.97 E-value=49 Score=29.85 Aligned_cols=31 Identities=29% Similarity=0.327 Sum_probs=27.0
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
..+.|.+.||+++.+.+.++|...+|-|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 5789999999999999999999988866543
No 97
>PRK10139 serine endoprotease; Provisional
Probab=40.58 E-value=51 Score=29.56 Aligned_cols=31 Identities=26% Similarity=0.362 Sum_probs=27.4
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
.++.|++.||+.+.+.+.++|....|-+=..
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5799999999999999999999988876544
No 98
>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=40.22 E-value=9.4 Score=39.00 Aligned_cols=55 Identities=22% Similarity=0.267 Sum_probs=0.0
Q ss_pred EEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEE
Q 032108 23 LLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVL 78 (147)
Q Consensus 23 V~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~ 78 (147)
.+=+..+|+.+.|+|.+.|.-++.+|+--.+ +.+..-.....+|.++|+|+|.|-
T Consensus 250 ~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 250 STYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTSVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp --------------------------------------------------------
T ss_pred ceeecCCCCEeceEEeccHHHHHHHHHHHhh-hccceeecchhheeeeecCccHHH
Confidence 3444678999999999999988877765544 222111234568999999999874
No 99
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=36.53 E-value=69 Score=24.76 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=24.7
Q ss_pred HHhhccCCeEEEEEcCCeEEEEEEEEec
Q 032108 14 SLASYLDKKLLVLLRDGRKLMGTLCSFD 41 (147)
Q Consensus 14 ~L~~~ldKkV~V~L~dGR~l~G~L~sfD 41 (147)
....++||.|.+...+|..+.|+..++.
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 4568999999999999999999988875
No 100
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=35.26 E-value=55 Score=24.16 Aligned_cols=28 Identities=29% Similarity=0.344 Sum_probs=20.7
Q ss_pred eEEEEEcCCeEEEEEEEEecCccceEecc
Q 032108 22 KLLVLLRDGRKLMGTLCSFDQFANAVLEG 50 (147)
Q Consensus 22 kV~V~L~dGR~l~G~L~sfDq~mNLVL~d 50 (147)
...|.++||+.+.|.+.+=|. ..+.|.+
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~~-~~~~l~~ 86 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASETA-DGVTVKM 86 (133)
T ss_pred cEEEEECCCCEEEEEEEecCC-CeEEEEc
Confidence 489999999999999887443 3444443
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=33.31 E-value=78 Score=27.71 Aligned_cols=31 Identities=23% Similarity=0.314 Sum_probs=27.4
Q ss_pred CeEEEEEcCCeEEEEEEEEecCccceEecce
Q 032108 21 KKLLVLLRDGRKLMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 21 KkV~V~L~dGR~l~G~L~sfDq~mNLVL~da 51 (147)
..+.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 4788999999999999999999998877554
No 102
>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=33.29 E-value=58 Score=27.22 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=18.5
Q ss_pred EEEEEEEEecCccceEecceE
Q 032108 32 KLMGTLCSFDQFANAVLEGAC 52 (147)
Q Consensus 32 ~l~G~L~sfDq~mNLVL~da~ 52 (147)
.+.|...-+|.|+|++++=..
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~~ 189 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNISR 189 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEEH
T ss_pred eEEEEEEEECccCCeeeCCCH
Confidence 899999999999999986543
No 103
>PRK06630 hypothetical protein; Provisional
Probab=33.12 E-value=23 Score=25.96 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=16.7
Q ss_pred EEEEEEEecCccceEecce
Q 032108 33 LMGTLCSFDQFANAVLEGA 51 (147)
Q Consensus 33 l~G~L~sfDq~mNLVL~da 51 (147)
..|.|+|-|+|+|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 3799999999999988875
No 104
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=32.90 E-value=32 Score=27.20 Aligned_cols=19 Identities=26% Similarity=0.307 Sum_probs=16.3
Q ss_pred EEEEEEecCccceEecceE
Q 032108 34 MGTLCSFDQFANAVLEGAC 52 (147)
Q Consensus 34 ~G~L~sfDq~mNLVL~da~ 52 (147)
.|+|+|-|+|+|-.-++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 3999999999999887763
No 105
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=27.83 E-value=33 Score=25.74 Aligned_cols=19 Identities=32% Similarity=0.471 Sum_probs=16.4
Q ss_pred EEEEEEecCccceEecceE
Q 032108 34 MGTLCSFDQFANAVLEGAC 52 (147)
Q Consensus 34 ~G~L~sfDq~mNLVL~da~ 52 (147)
.|.|+|.|+|+|-.-++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 6899999999999887653
No 106
>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=23.80 E-value=85 Score=25.02 Aligned_cols=34 Identities=24% Similarity=0.357 Sum_probs=27.7
Q ss_pred hhccCCeEEEEEcCC----eEEEEEEEEecCccceEec
Q 032108 16 ASYLDKKLLVLLRDG----RKLMGTLCSFDQFANAVLE 49 (147)
Q Consensus 16 ~~~ldKkV~V~L~dG----R~l~G~L~sfDq~mNLVL~ 49 (147)
..+.|..+.++..|| +.-.|.++.=|+.+||+|+
T Consensus 140 reyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d 177 (179)
T PF07202_consen 140 REYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMD 177 (179)
T ss_pred EEcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEec
Confidence 457788888888888 4456899999999999986
No 107
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=23.20 E-value=1.4e+02 Score=23.12 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=23.3
Q ss_pred hhccCCeEEEEEcCCeEEEEEEEEecC
Q 032108 16 ASYLDKKLLVLLRDGRKLMGTLCSFDQ 42 (147)
Q Consensus 16 ~~~ldKkV~V~L~dGR~l~G~L~sfDq 42 (147)
..++||.|.....+|..+.|+..++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 478999999888999999999887753
No 108
>PRK08183 NADH dehydrogenase; Validated
Probab=20.62 E-value=52 Score=25.19 Aligned_cols=19 Identities=21% Similarity=0.230 Sum_probs=16.2
Q ss_pred EEEEEEecCccceEecceE
Q 032108 34 MGTLCSFDQFANAVLEGAC 52 (147)
Q Consensus 34 ~G~L~sfDq~mNLVL~da~ 52 (147)
.|.|+|-|+|+|-.-++..
T Consensus 25 ~g~lVG~D~~GNkYYE~~~ 43 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTKG 43 (133)
T ss_pred cCeEeEecCCCCeeeecCC
Confidence 6999999999998887653
Done!