Query 045257
Match_columns 107
No_of_seqs 107 out of 1090
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 11:25:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045257.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045257hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1782 Small Nuclear ribonucl 99.9 4.6E-25 9.9E-30 155.0 3.2 105 1-107 21-129 (129)
2 cd01728 LSm1 The eukaryotic Sm 99.8 1.3E-20 2.9E-25 122.6 8.4 61 1-61 14-74 (74)
3 cd01729 LSm7 The eukaryotic Sm 99.8 1.4E-20 3.1E-25 124.0 8.3 62 1-62 14-80 (81)
4 cd01732 LSm5 The eukaryotic Sm 99.8 2.9E-20 6.3E-25 121.5 8.4 61 1-61 15-75 (76)
5 cd01727 LSm8 The eukaryotic Sm 99.8 3.8E-20 8.3E-25 119.7 8.2 63 1-63 11-74 (74)
6 cd01730 LSm3 The eukaryotic Sm 99.8 5.9E-20 1.3E-24 121.0 7.7 60 1-60 13-82 (82)
7 cd01719 Sm_G The eukaryotic Sm 99.8 9.1E-20 2E-24 117.8 8.1 60 1-63 12-71 (72)
8 cd01731 archaeal_Sm1 The archa 99.8 3.4E-19 7.3E-24 113.3 7.6 57 1-60 12-68 (68)
9 cd01717 Sm_B The eukaryotic Sm 99.8 3.7E-19 8E-24 116.3 7.9 59 1-59 12-77 (79)
10 cd01720 Sm_D2 The eukaryotic S 99.8 8.5E-19 1.8E-23 117.3 8.3 61 1-61 16-86 (87)
11 PRK00737 small nuclear ribonuc 99.8 8.7E-19 1.9E-23 112.9 7.5 57 1-60 16-72 (72)
12 cd01718 Sm_E The eukaryotic Sm 99.8 1.7E-18 3.7E-23 114.1 8.0 58 1-60 20-79 (79)
13 cd06168 LSm9 The eukaryotic Sm 99.7 1E-17 2.2E-22 109.2 8.1 59 1-59 12-73 (75)
14 cd01726 LSm6 The eukaryotic Sm 99.7 7.9E-18 1.7E-22 106.9 7.4 56 1-59 12-67 (67)
15 PTZ00138 small nuclear ribonuc 99.7 2E-17 4.4E-22 111.2 8.3 59 1-61 28-88 (89)
16 cd01722 Sm_F The eukaryotic Sm 99.7 1.4E-17 3.1E-22 106.1 7.1 56 1-59 13-68 (68)
17 smart00651 Sm snRNP Sm protein 99.7 2.6E-17 5.6E-22 103.1 8.0 58 1-60 10-67 (67)
18 PF01423 LSM: LSM domain ; In 99.7 3.3E-17 7.1E-22 102.8 7.5 58 1-60 10-67 (67)
19 COG1958 LSM1 Small nuclear rib 99.7 4.4E-17 9.6E-22 106.2 7.8 60 1-60 19-79 (79)
20 cd00600 Sm_like The eukaryotic 99.7 4.4E-16 9.6E-21 96.1 8.0 56 1-59 8-63 (63)
21 cd01721 Sm_D3 The eukaryotic S 99.6 8.7E-16 1.9E-20 98.5 7.9 59 1-62 12-70 (70)
22 KOG1780 Small Nuclear ribonucl 99.6 2.3E-16 5E-21 102.7 5.2 60 1-63 16-75 (77)
23 cd01723 LSm4 The eukaryotic Sm 99.6 8.9E-16 1.9E-20 99.8 7.3 61 1-63 13-73 (76)
24 KOG1784 Small Nuclear ribonucl 99.6 2.3E-16 5E-21 106.2 2.2 79 1-80 12-91 (96)
25 KOG1781 Small Nuclear ribonucl 99.6 6.3E-17 1.4E-21 110.4 -1.0 72 1-73 29-105 (108)
26 cd01724 Sm_D1 The eukaryotic S 99.6 6E-15 1.3E-19 99.1 8.0 61 1-64 13-73 (90)
27 cd01733 LSm10 The eukaryotic S 99.5 2.6E-14 5.6E-19 93.7 7.6 57 1-60 21-77 (78)
28 cd01725 LSm2 The eukaryotic Sm 99.5 3.4E-14 7.3E-19 93.6 7.3 65 1-66 13-77 (81)
29 KOG3460 Small nuclear ribonucl 99.5 1.2E-14 2.7E-19 96.6 0.8 61 1-61 17-87 (91)
30 KOG3482 Small nuclear ribonucl 99.4 4.6E-13 1E-17 87.1 5.2 59 1-62 20-78 (79)
31 KOG1775 U6 snRNA-associated Sm 99.3 1.4E-12 3E-17 85.7 3.1 63 1-63 19-81 (84)
32 KOG3168 U1 snRNP component [Tr 99.3 2.7E-13 5.8E-18 100.1 -0.4 65 1-65 16-87 (177)
33 KOG1774 Small nuclear ribonucl 99.1 3.9E-11 8.6E-16 79.6 3.8 53 8-62 35-87 (88)
34 KOG1783 Small nuclear ribonucl 99.1 1.2E-11 2.6E-16 80.5 -0.3 58 1-61 18-75 (77)
35 KOG3293 Small nuclear ribonucl 98.9 3.9E-09 8.3E-14 74.8 4.7 63 2-66 15-77 (134)
36 KOG3448 Predicted snRNP core p 98.6 1.9E-07 4.1E-12 63.0 6.1 61 1-63 14-75 (96)
37 KOG3459 Small nuclear ribonucl 98.3 5.2E-08 1.1E-12 67.8 -1.3 60 1-60 38-107 (114)
38 KOG3172 Small nuclear ribonucl 97.9 7.6E-05 1.6E-09 52.1 6.8 61 2-65 18-78 (119)
39 cd01739 LSm11_C The eukaryotic 97.8 1.3E-05 2.8E-10 51.3 2.0 36 1-36 10-49 (66)
40 KOG3428 Small nuclear ribonucl 97.7 0.00022 4.9E-09 49.6 7.0 60 1-64 14-73 (109)
41 PF14438 SM-ATX: Ataxin 2 SM d 96.8 0.0029 6.3E-08 40.5 4.4 56 1-56 14-76 (77)
42 cd01716 Hfq Hfq, an abundant, 95.1 0.056 1.2E-06 34.1 4.4 27 1-27 13-39 (61)
43 TIGR02383 Hfq RNA chaperone Hf 94.8 0.072 1.6E-06 33.6 4.4 27 1-27 17-43 (61)
44 PRK00395 hfq RNA-binding prote 94.2 0.11 2.4E-06 34.3 4.4 27 1-27 21-47 (79)
45 PF02237 BPL_C: Biotin protein 93.5 0.48 1E-05 27.7 5.9 28 2-30 6-33 (48)
46 COG1923 Hfq Uncharacterized ho 93.2 0.19 4.1E-06 33.1 4.1 27 1-28 21-47 (77)
47 PF12701 LSM14: Scd6-like Sm d 91.6 0.94 2E-05 30.7 6.2 65 1-65 10-81 (96)
48 cd01735 LSm12_N LSm12 belongs 90.2 0.64 1.4E-05 29.2 4.0 30 1-30 8-37 (61)
49 PRK14091 RNA-binding protein H 88.1 0.99 2.1E-05 33.6 4.3 29 1-29 106-134 (165)
50 PRK14091 RNA-binding protein H 87.1 1.2 2.6E-05 33.1 4.3 27 1-27 26-52 (165)
51 PF11095 Gemin7: Gem-associate 83.3 7.5 0.00016 25.7 6.3 50 2-59 27-77 (80)
52 cd01736 LSm14_N LSm14 (also kn 82.9 6.8 0.00015 25.6 5.9 56 1-56 8-71 (74)
53 PF06372 Gemin6: Gemin6 protei 82.3 1.7 3.8E-05 32.2 3.3 55 1-65 19-74 (166)
54 PF03614 Flag1_repress: Repres 78.3 3.5 7.5E-05 30.6 3.7 30 2-31 32-61 (165)
55 PRK14638 hypothetical protein; 74.8 4.4 9.5E-05 29.3 3.5 26 1-27 102-127 (150)
56 PRK02001 hypothetical protein; 67.6 8 0.00017 28.1 3.5 26 1-27 92-117 (152)
57 PRK14639 hypothetical protein; 65.8 9.3 0.0002 27.3 3.5 26 1-27 90-115 (140)
58 PRK10898 serine endoprotease; 64.3 12 0.00026 30.2 4.2 30 1-30 103-132 (353)
59 TIGR02038 protease_degS peripl 62.3 13 0.00029 29.8 4.2 29 2-30 104-132 (351)
60 PRK10942 serine endoprotease; 57.5 17 0.00037 30.6 4.2 29 1-29 137-165 (473)
61 PF05071 NDUFA12: NADH ubiquin 55.6 5 0.00011 27.3 0.5 17 14-30 1-17 (105)
62 PRK10139 serine endoprotease; 54.7 21 0.00045 29.9 4.2 30 1-30 116-145 (455)
63 KOG3382 NADH:ubiquinone oxidor 54.6 6.7 0.00014 28.6 1.1 22 9-30 42-63 (151)
64 PRK14644 hypothetical protein; 51.5 31 0.00066 24.6 4.1 27 1-28 87-117 (136)
65 PF11607 DUF3247: Protein of u 51.2 17 0.00037 25.0 2.6 17 1-17 30-46 (101)
66 TIGR02037 degP_htrA_DO peripla 50.7 27 0.0006 28.5 4.2 30 1-30 83-112 (428)
67 PRK06955 biotin--protein ligas 50.5 28 0.00061 27.4 4.2 27 2-28 252-278 (300)
68 PF03614 Flag1_repress: Repres 50.0 16 0.00035 27.1 2.5 21 2-22 123-143 (165)
69 cd01734 YlxS_C YxlS is a Bacil 49.2 29 0.00063 22.2 3.4 25 2-27 28-56 (83)
70 PRK14640 hypothetical protein; 49.1 35 0.00075 24.6 4.1 25 2-27 100-128 (152)
71 TIGR02603 CxxCH_TIGR02603 puta 48.8 25 0.00054 24.3 3.3 20 2-21 60-79 (133)
72 PRK14642 hypothetical protein; 45.7 30 0.00065 26.4 3.5 25 2-27 103-140 (197)
73 PRK11886 bifunctional biotin-- 45.0 76 0.0016 24.9 5.8 26 2-28 275-300 (319)
74 PRK14645 hypothetical protein; 43.6 30 0.00065 25.1 3.1 24 2-27 105-128 (154)
75 PRK14633 hypothetical protein; 41.8 39 0.00084 24.3 3.4 25 2-27 97-125 (150)
76 TIGR00121 birA_ligase birA, bi 40.8 96 0.0021 23.3 5.6 26 2-28 196-221 (237)
77 PF14563 DUF4444: Domain of un 40.6 39 0.00086 19.8 2.7 21 12-32 10-30 (42)
78 PRK13325 bifunctional biotin-- 40.5 71 0.0015 27.9 5.4 28 2-29 281-308 (592)
79 PRK14636 hypothetical protein; 36.8 48 0.001 24.6 3.3 26 1-27 100-129 (176)
80 PRK14643 hypothetical protein; 35.0 55 0.0012 24.0 3.4 21 2-22 107-131 (164)
81 PF02576 DUF150: Uncharacteris 34.9 77 0.0017 22.1 4.0 25 2-27 90-118 (141)
82 PRK14632 hypothetical protein; 32.8 62 0.0013 23.8 3.4 25 2-27 101-132 (172)
83 PRK14634 hypothetical protein; 32.2 67 0.0015 23.2 3.4 25 2-27 103-131 (155)
84 COG0340 BirA Biotin-(acetyl-Co 32.1 1.3E+02 0.0027 23.3 5.1 29 2-30 193-221 (238)
85 COG0779 Uncharacterized protei 31.5 1E+02 0.0022 22.5 4.2 25 2-27 102-130 (153)
86 PTZ00275 biotin-acetyl-CoA-car 31.1 1E+02 0.0022 24.2 4.5 23 7-29 244-266 (285)
87 PRK14646 hypothetical protein; 30.9 71 0.0015 23.1 3.4 25 2-27 103-131 (155)
88 PRK00092 ribosome maturation p 30.0 78 0.0017 22.5 3.4 20 2-21 101-124 (154)
89 PF03122 Herpes_MCP: Herpes vi 29.7 18 0.00038 34.8 0.0 52 5-57 253-304 (1354)
90 PF01887 SAM_adeno_trans: S-ad 29.5 78 0.0017 24.7 3.6 19 11-29 169-187 (258)
91 PRK06630 hypothetical protein; 28.8 30 0.00065 23.8 1.0 19 12-30 11-29 (99)
92 PRK14647 hypothetical protein; 28.6 82 0.0018 22.8 3.3 20 2-21 102-130 (159)
93 PLN02732 Probable NADH dehydro 28.5 43 0.00093 24.8 1.9 17 14-30 49-65 (159)
94 PRK08330 biotin--protein ligas 26.3 1.3E+02 0.0027 22.7 4.1 28 2-30 191-219 (236)
95 PLN03095 NADH:ubiquinone oxido 26.3 37 0.00079 23.9 1.1 18 13-30 9-26 (115)
96 PF07073 ROF: Modulator of Rho 25.6 60 0.0013 21.2 2.0 53 1-63 19-71 (80)
97 COG0265 DegQ Trypsin-like seri 25.5 1.2E+02 0.0026 23.9 4.1 27 1-27 97-123 (347)
98 KOG1073 Uncharacterized mRNA-a 23.2 2.2E+02 0.0047 23.8 5.2 64 2-65 12-83 (361)
99 PRK14631 hypothetical protein; 22.4 1.2E+02 0.0026 22.5 3.3 19 2-20 120-142 (174)
100 PRK14641 hypothetical protein; 22.2 1.1E+02 0.0024 22.7 3.0 19 2-20 107-129 (173)
101 PRK14637 hypothetical protein; 21.7 1.3E+02 0.0027 21.8 3.2 25 2-27 101-126 (151)
102 TIGR00741 yfiA ribosomal subun 21.0 2.3E+02 0.0049 17.8 4.8 19 82-100 77-95 (95)
103 PF00789 UBX: UBX domain; Int 20.9 1.3E+02 0.0028 18.5 2.9 22 1-22 8-29 (82)
104 PRK08183 NADH dehydrogenase; V 20.4 53 0.0011 23.6 1.0 18 13-30 25-42 (133)
No 1
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.90 E-value=4.6e-25 Score=155.04 Aligned_cols=105 Identities=62% Similarity=1.016 Sum_probs=93.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCccccccCCCCccccHHHH
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLEKEELPAHMTCVSTAEI 80 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~~e~~~~~~~~v~~~~i 80 (107)
++.|.|+|||.+.|.|+|||||-|++|+.|+|+++-++.|..+..|.++|||+||++++.+|.++| ..++.++|.+++
T Consensus 21 KllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE--~~~l~~i~~~e~ 98 (129)
T KOG1782|consen 21 KLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE--EEPLEQISFEEA 98 (129)
T ss_pred eEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh--hccceeCCHHHH
Confidence 578999999999999999999999999999999998888889999999999999999999999998 589999999888
Q ss_pred HHHHHHHH----HHHHhhhhhhhhcccccCC
Q 045257 81 KRAQKAEK----DATVLKGSMRKRMEFLDFD 107 (107)
Q Consensus 81 ~~~~~~e~----~~~~~~~~~~~~~~~~~~~ 107 (107)
...++.++ ....+|+.|++||+|+||+
T Consensus 99 ~~~~~~~q~~k~e~~~lkg~m~~rg~~~D~~ 129 (129)
T KOG1782|consen 99 LNEIKREQEAKKEEERLKGTMAERGEFLDFD 129 (129)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHhcccccCC
Confidence 65555444 4456777899999999996
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=99.84 E-value=1.3e-20 Score=122.56 Aligned_cols=61 Identities=70% Similarity=1.204 Sum_probs=54.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
+|.|+|+|||.|.|+|+|||+||||+|+||.|+...++.+.++.+|+++|||++|++|+.+
T Consensus 14 ~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 14 KVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred EEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 5899999999999999999999999999999987665445568899999999999999863
No 3
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=1.4e-20 Score=124.03 Aligned_cols=62 Identities=40% Similarity=0.598 Sum_probs=54.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc-----eeeeeecceEEEecCcEEEEEecC
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD-----LYCDIPLGLYVIRGENVVLIGELD 62 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~-----~~~~~~lG~vlIRG~nIv~I~~~d 62 (107)
+|.|+|+|||.|.|+|+|||+||||+|++|+|+...++ ....+.+|+++|||+||++|++.+
T Consensus 14 ~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 14 KIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred eEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 58999999999999999999999999999999875432 124578999999999999999765
No 4
>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=99.83 E-value=2.9e-20 Score=121.47 Aligned_cols=61 Identities=23% Similarity=0.410 Sum_probs=53.6
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
+|+|++++||.+.|+|.|||+||||+|+||.|++..++....+.+|.++|||+||++|+++
T Consensus 15 ~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 15 RIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred EEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 5899999999999999999999999999999987543322457899999999999999975
No 5
>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=99.82 E-value=3.8e-20 Score=119.70 Aligned_cols=63 Identities=38% Similarity=0.741 Sum_probs=55.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcC-ceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVG-DLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~-~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
||+|+|+|||.|.|+|+|||+||||+|++|.|+.... +...++.+|++++||++|++|+++|+
T Consensus 11 ~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 11 TVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred EEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 6899999999999999999999999999999986533 22346789999999999999998874
No 6
>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=99.82 E-value=5.9e-20 Score=121.00 Aligned_cols=60 Identities=28% Similarity=0.492 Sum_probs=52.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc----------eeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD----------LYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~----------~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|.|+|+|||.+.|+|.|||+||||+|+||.|++.... ....+.+|.++|||++|++|++
T Consensus 13 ~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i~~ 82 (82)
T cd01730 13 RVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILVSP 82 (82)
T ss_pred EEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEECC
Confidence 58999999999999999999999999999999875421 1236799999999999999874
No 7
>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=99.81 E-value=9.1e-20 Score=117.83 Aligned_cols=60 Identities=38% Similarity=0.623 Sum_probs=53.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
+|+|+|++||.+.|+|.|||+||||+|++|.|++... ..+.+|.++|||++|++|+++|+
T Consensus 12 ~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~---~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 12 KLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGG---EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred eEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCC---ceeEeceEEECCCEEEEEEcccc
Confidence 5899999999999999999999999999999985322 35789999999999999998864
No 8
>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=99.79 E-value=3.4e-19 Score=113.31 Aligned_cols=57 Identities=40% Similarity=0.503 Sum_probs=51.3
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|.|.|++||.|.|+|.|||+||||+|++|.|.+..+ ..+.+|.++|||++|++|++
T Consensus 12 ~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 12 PVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE---PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred EEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC---eEeEcCcEEEeCCEEEEEcC
Confidence 5899999999999999999999999999999976443 35789999999999999974
No 9
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=3.7e-19 Score=116.26 Aligned_cols=59 Identities=36% Similarity=0.526 Sum_probs=51.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc-------eeeeeecceEEEecCcEEEEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD-------LYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~-------~~~~~~lG~vlIRG~nIv~I~ 59 (107)
+|.|+|+|||.|.|+|.|||+||||+|+||.|++.... ..+.+.+|+++|||++|++|+
T Consensus 12 ~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 12 RLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred EEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 58999999999999999999999999999999875321 134688999999999999997
No 10
>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=8.5e-19 Score=117.33 Aligned_cols=61 Identities=30% Similarity=0.444 Sum_probs=52.4
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc----------eeeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD----------LYCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~----------~~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
+|.|+|++||.+.|+|.|||+||||+|+||.|.+...+ ....+.+|.++|||++|++|++.
T Consensus 16 ~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~Is~~ 86 (87)
T cd01720 16 QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVILVLRN 86 (87)
T ss_pred EEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEEEecC
Confidence 58999999999999999999999999999999765421 12356799999999999999864
No 11
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.78 E-value=8.7e-19 Score=112.92 Aligned_cols=57 Identities=40% Similarity=0.593 Sum_probs=50.3
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|.|.|+||+.|.|+|.|||+|||++|+||.|.+ .++ ..+.+|.++|||++|++|++
T Consensus 16 ~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~--~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 16 PVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGE--VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred EEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCC--eEeEcCcEEEeCCEEEEEcC
Confidence 5899999999999999999999999999999964 232 35789999999999999873
No 12
>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=99.77 E-value=1.7e-18 Score=114.13 Aligned_cols=58 Identities=28% Similarity=0.548 Sum_probs=49.7
Q ss_pred CEEEEEc--CCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLR--DGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~--dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|.|.++ +||.+.|+|.|||+||||+|+||+|+...++ ..+.+|.++|||+||++|++
T Consensus 20 ~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 20 RVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred EEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 4677776 9999999999999999999999999864332 35789999999999999874
No 13
>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=99.74 E-value=1e-17 Score=109.22 Aligned_cols=59 Identities=31% Similarity=0.385 Sum_probs=52.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc---eeeeeecceEEEecCcEEEEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD---LYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~---~~~~~~lG~vlIRG~nIv~I~ 59 (107)
+|+|+|+|||.|.|+|.|||+||||+|++|.|+..... ..+.+.+|+++|||++|++|+
T Consensus 12 ~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 12 TMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred eEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 58999999999999999999999999999999875422 235789999999999999987
No 14
>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=99.74 E-value=7.9e-18 Score=106.91 Aligned_cols=56 Identities=32% Similarity=0.497 Sum_probs=49.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~ 59 (107)
+|.|.|++|++|.|+|.|||+||||+|++|.|.. .+. ..+.+|.++|||++|.+|+
T Consensus 12 ~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~--~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 12 PVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQ--LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred eEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCc--eeeEeCCEEEECCEEEEEC
Confidence 5899999999999999999999999999998853 232 3568999999999999985
No 15
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.73 E-value=2e-17 Score=111.22 Aligned_cols=59 Identities=27% Similarity=0.472 Sum_probs=50.3
Q ss_pred CEEEEEcC--CcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRD--GRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~d--Gr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
+|.|.+.+ +|++.|+|.|||+||||+|+||.|.+..++ ..+.+|.++||||||++|++.
T Consensus 28 ~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 28 RVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred EEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEcC
Confidence 57788877 599999999999999999999999754332 357899999999999999864
No 16
>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=99.73 E-value=1.4e-17 Score=106.09 Aligned_cols=56 Identities=34% Similarity=0.417 Sum_probs=49.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~ 59 (107)
+|+|.|+||++|.|+|.|||+||||+|++|.|.. .+. ....+|.++|||++|.+|+
T Consensus 13 ~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~--~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 13 PVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGK--STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred EEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCc--cccCcCcEEEECCEEEEEC
Confidence 5899999999999999999999999999999874 332 2468999999999999884
No 17
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.73 E-value=2.6e-17 Score=103.11 Aligned_cols=58 Identities=45% Similarity=0.683 Sum_probs=51.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|+|.|+||+.+.|+|.|||+||||+|++|.|....+. ..+.+|.++|||++|++|++
T Consensus 10 ~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~--~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 10 RVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE--KKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred EEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCc--EEeEeCCEEEcCCEEEEEeC
Confidence 58999999999999999999999999999999865422 35799999999999999873
No 18
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.72 E-value=3.3e-17 Score=102.78 Aligned_cols=58 Identities=43% Similarity=0.607 Sum_probs=51.6
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|+|.|+||++++|+|.+||+||||+|++|.+....+. +.+.+|.++|||++|.+|++
T Consensus 10 ~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 10 RVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp EEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred EEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence 58999999999999999999999999999999754331 46789999999999999974
No 19
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.71 E-value=4.4e-17 Score=106.21 Aligned_cols=60 Identities=40% Similarity=0.597 Sum_probs=49.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEE-cCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERII-VGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~-~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
+|.|.|++|++|.|+|+|||+||||+|+||.|... ++.....+..|.++|||++|.+|.+
T Consensus 19 ~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 19 RVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred EEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 58999999999999999999999999999999864 2221112344599999999999863
No 20
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.67 E-value=4.4e-16 Score=96.13 Aligned_cols=56 Identities=45% Similarity=0.678 Sum_probs=50.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~ 59 (107)
+|+|.|+||+.|.|+|.+||+|||++|++|.+....+ ..+.+|.++|||++|.+|.
T Consensus 8 ~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~---~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 8 TVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEG---KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred EEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCC---cEEECCeEEEECCEEEEEC
Confidence 5899999999999999999999999999999976543 3578999999999999873
No 21
>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=99.65 E-value=8.7e-16 Score=98.49 Aligned_cols=59 Identities=22% Similarity=0.167 Sum_probs=50.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecC
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELD 62 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d 62 (107)
+|.|.|++|.+|.|+|.++|+|||++|++|.+...+++ ...+|.++|||+||.++...|
T Consensus 12 ~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 12 IVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred EEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence 48999999999999999999999999999987543443 357899999999999998654
No 22
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.65 E-value=2.3e-16 Score=102.67 Aligned_cols=60 Identities=40% Similarity=0.709 Sum_probs=52.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
|+.++|.+||.+.|+|+|||.|||+||++|+|...+++ +..+|.++|||++|+++++++.
T Consensus 16 ki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 16 KIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred eEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEEeeccc
Confidence 57899999999999999999999999999999744432 4689999999999999998764
No 23
>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=99.64 E-value=8.9e-16 Score=99.78 Aligned_cols=61 Identities=25% Similarity=0.268 Sum_probs=51.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
+|.|.|++|+++.|+|.+||+|||++|++|.+...+++. ...+|.++|||++|.+|...+.
T Consensus 13 ~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~~ 73 (76)
T cd01723 13 PMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPDE 73 (76)
T ss_pred EEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCHH
Confidence 589999999999999999999999999999886444432 2457899999999999986543
No 24
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.61 E-value=2.3e-16 Score=106.23 Aligned_cols=79 Identities=38% Similarity=0.644 Sum_probs=68.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc-eeeeeecceEEEecCcEEEEEecCccccccCCCCccccHHH
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD-LYCDIPLGLYVIRGENVVLIGELDLEKEELPAHMTCVSTAE 79 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~-~~~~~~lG~vlIRG~nIv~I~~~d~~~e~~~~~~~~v~~~~ 79 (107)
+|.|.+.|||.+.|.|+|||+-.||+|+++.|++++.. ..++..+|+.+|||+||.+|+++|+..+ ...+|.++..++
T Consensus 12 ~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d-~~ld~tkir~ep 90 (96)
T KOG1784|consen 12 RVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD-SRLDLTKIRAEP 90 (96)
T ss_pred eEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh-hhhhhhhcccCC
Confidence 58899999999999999999999999999999987643 3456889999999999999999999888 357777777665
Q ss_pred H
Q 045257 80 I 80 (107)
Q Consensus 80 i 80 (107)
+
T Consensus 91 l 91 (96)
T KOG1784|consen 91 L 91 (96)
T ss_pred C
Confidence 5
No 25
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=99.60 E-value=6.3e-17 Score=110.38 Aligned_cols=72 Identities=35% Similarity=0.474 Sum_probs=61.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCc-e----eeeeecceEEEecCcEEEEEecCccccccCCCCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGD-L----YCDIPLGLYVIRGENVVLIGELDLEKEELPAHMT 73 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~-~----~~~~~lG~vlIRG~nIv~I~~~d~~~e~~~~~~~ 73 (107)
+|+|++.+||+.+|+|+|||+.|||||++|+|+..+++ + .+.|.+|++++||..+++|++.|...+ ...||-
T Consensus 29 ~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e~-I~npf~ 105 (108)
T KOG1781|consen 29 KIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSEE-IANPFV 105 (108)
T ss_pred ceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchhh-hccchh
Confidence 58999999999999999999999999999999876543 1 245899999999999999999998776 355553
No 26
>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=99.59 E-value=6e-15 Score=99.07 Aligned_cols=61 Identities=21% Similarity=0.270 Sum_probs=53.3
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCcc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLE 64 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~ 64 (107)
+|+|.|++|.+|.|+|.++|.|||++|+||.+...++. ...+|.++|||++|.+|...|.-
T Consensus 13 ~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~---~~~~~~v~IRG~nI~yi~lPd~l 73 (90)
T cd01724 13 TVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN---PVPLDTLSIRGNNIRYFILPDSL 73 (90)
T ss_pred EEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc---eeEcceEEEeCCEEEEEEcCCcC
Confidence 48999999999999999999999999999988643332 46789999999999999988664
No 27
>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=99.55 E-value=2.6e-14 Score=93.70 Aligned_cols=57 Identities=21% Similarity=0.286 Sum_probs=48.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~ 60 (107)
.|.|.|++|.+|.|+|.++|+|||++|+||.+...++. ...+|.++|||++|.+|..
T Consensus 21 ~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~---~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 21 VVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGK---QVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred EEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCc---eeECCcEEEECCEEEEEEc
Confidence 48999999999999999999999999999987532222 3478999999999999874
No 28
>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=99.53 E-value=3.4e-14 Score=93.56 Aligned_cols=65 Identities=22% Similarity=0.177 Sum_probs=52.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCcccc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLEKE 66 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~~e 66 (107)
+|+|.|++|.+|.|+|.++|+|||++|+||.+...++. .....+|.++|||++|.+|...|...+
T Consensus 13 ~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~-~~~~~~~~v~IRG~~I~~I~lp~~~i~ 77 (81)
T cd01725 13 EVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKY-PHMLSVKNCFIRGSVVRYVQLPADEVD 77 (81)
T ss_pred EEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCc-ccccccCeEEEECCEEEEEEeChhHcC
Confidence 48999999999999999999999999999976522221 113456899999999999998776554
No 29
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.46 E-value=1.2e-14 Score=96.59 Aligned_cols=61 Identities=31% Similarity=0.495 Sum_probs=52.6
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc--Cc--e------eeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIV--GD--L------YCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~--~~--~------~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
||+|+++++|++.|+|.+||+|.|++|.++.|.+.. .+ . ..++.+..+++||++|++|++.
T Consensus 17 rVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilvspp 87 (91)
T KOG3460|consen 17 RVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILVSPP 87 (91)
T ss_pred eEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEEcCc
Confidence 699999999999999999999999999999997653 11 1 2467889999999999999964
No 30
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.40 E-value=4.6e-13 Score=87.12 Aligned_cols=59 Identities=36% Similarity=0.419 Sum_probs=52.0
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecC
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELD 62 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d 62 (107)
.|.|+|+.|.+|.|+|.+.|.||||.|.+|+|++ ++. ....+|.++||.+||.+|..++
T Consensus 20 ~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i-dG~--~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 20 PVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI-DGV--STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred eEEEEEecCcEEEEEEEEecchhheehhhhhhhh-ccc--ccccceeEEEEeccEEEEecCC
Confidence 4899999999999999999999999999999975 332 3468999999999999998764
No 31
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.31 E-value=1.4e-12 Score=85.65 Aligned_cols=63 Identities=25% Similarity=0.409 Sum_probs=54.6
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
+|+|.+++.|++.|+|.|||.|.|++|+|++|+...++...-.+++.+++.|+||.++.++-+
T Consensus 19 ki~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGGe 81 (84)
T KOG1775|consen 19 KIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGGE 81 (84)
T ss_pred eEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCCC
Confidence 689999999999999999999999999999998655443334688999999999999988753
No 32
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=99.30 E-value=2.7e-13 Score=100.10 Aligned_cols=65 Identities=32% Similarity=0.460 Sum_probs=55.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc-------CceeeeeecceEEEecCcEEEEEecCccc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIV-------GDLYCDIPLGLYVIRGENVVLIGELDLEK 65 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~-------~~~~~~~~lG~vlIRG~nIv~I~~~d~~~ 65 (107)
+++|.++|||.|.|.+.+||.||||+|.+|+|...- .+..+++.+|++++||.+|++.+..+...
T Consensus 16 r~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp 87 (177)
T KOG3168|consen 16 RMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPP 87 (177)
T ss_pred eEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCC
Confidence 578999999999999999999999999999885321 12357899999999999999998766554
No 33
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.14 E-value=3.9e-11 Score=79.58 Aligned_cols=53 Identities=28% Similarity=0.458 Sum_probs=43.6
Q ss_pred CCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecC
Q 045257 8 DGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELD 62 (107)
Q Consensus 8 dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d 62 (107)
-|-.++|.+.|||+|||+||++|+|.....+ ..+.+|.+++.||||.+|...+
T Consensus 35 ~~~rieG~IvGFDEyMNvVlD~aeev~~k~~--~rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 35 VGLRIEGRIVGFDEYMNLVLDDAEEVHSKTK--SRKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred cCcEEeEEEechHHhhhhhhcchhhcccccc--CCCccccEEEcCCcEEEEeecC
Confidence 4788999999999999999999999632222 2358999999999999997653
No 34
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.09 E-value=1.2e-11 Score=80.50 Aligned_cols=58 Identities=31% Similarity=0.451 Sum_probs=51.4
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEec
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGEL 61 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~ 61 (107)
.|.|+|.+|-.|.|+|.+.|.||||-|+.+.|+. +++ .++.+|..+|||++|.+|+..
T Consensus 18 ~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngq--l~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 18 TVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQ--LKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred eEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCc--ccccccceeeccccEEEEEec
Confidence 4889999999999999999999999999998874 333 467899999999999999864
No 35
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=98.85 E-value=3.9e-09 Score=74.83 Aligned_cols=63 Identities=24% Similarity=0.246 Sum_probs=55.8
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCcccc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLEKE 66 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~~e 66 (107)
+.|.|++|.+|.|.|...|.+|||.|.++++...+++. -..+..+.|||++|-++...|+..+
T Consensus 15 mlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdk--f~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 15 MLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDK--FFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred EEEEecCCCEecceeecchhhhhcchheeEEeccCCCc--eeecceeEEecceeEEEeccHHHHH
Confidence 68999999999999999999999999999998766654 2567899999999999998877766
No 36
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=98.57 E-value=1.9e-07 Score=62.98 Aligned_cols=61 Identities=25% Similarity=0.286 Sum_probs=49.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceee-eeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYC-DIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~-~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
+|.|.|+++-.+.|+|.|.|||.|+-|.|.--. +++++. --.+..++|||+.|-+|.....
T Consensus 14 ~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~--d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd 75 (96)
T KOG3448|consen 14 EVVVELKNDLSICGTLHSVDQYLNLKLTDISVT--DPDKYPHMLSVKNCFIRGSVVRYVQLPKD 75 (96)
T ss_pred eEEEEEcCCcEEEEEecccchhheeEEeeeEee--CcccCCCeeeeeeEEEeccEEEEEEeChh
Confidence 589999999999999999999999999998543 444332 2355689999999999986533
No 37
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=98.33 E-value=5.2e-08 Score=67.81 Aligned_cols=60 Identities=32% Similarity=0.466 Sum_probs=50.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEc----Cce------eeeeecceEEEecCcEEEEEe
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIV----GDL------YCDIPLGLYVIRGENVVLIGE 60 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~----~~~------~~~~~lG~vlIRG~nIv~I~~ 60 (107)
.|.|.++|++.+.|...|||.|.|++|+++.|.|+. ++. ...|.+|.++||||+|+.+..
T Consensus 38 ~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~r 107 (114)
T KOG3459|consen 38 QVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVLR 107 (114)
T ss_pred eeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEEe
Confidence 478999999999999999999999999999987753 111 125789999999999998873
No 38
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=97.86 E-value=7.6e-05 Score=52.07 Aligned_cols=61 Identities=21% Similarity=0.175 Sum_probs=51.2
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCccc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLEK 65 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~~ 65 (107)
|++.+..|..|.|.|.--+.+||+.|+|.+-...++. ..++..++|||+.|-++-..|--+
T Consensus 18 Vt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLK 78 (119)
T KOG3172|consen 18 VTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLK 78 (119)
T ss_pred EEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhh
Confidence 6889999999999999999999999999977544443 346778999999999988776544
No 39
>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=97.79 E-value=1.3e-05 Score=51.29 Aligned_cols=36 Identities=33% Similarity=0.469 Sum_probs=27.8
Q ss_pred CEEEEEc--CC-c-EEEEEEEEeccccceEEcceEEEEEc
Q 045257 1 KILVLLR--DG-R-KLLGLLRSFDQFANVVLEGACERIIV 36 (107)
Q Consensus 1 rV~V~L~--dG-r-~i~G~L~gfD~~mNLvL~d~~E~~~~ 36 (107)
||.|.++ +| | .++|.|.+||+|+||+|.|+.|.+..
T Consensus 10 RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 10 RVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred EEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 3455554 44 3 78899999999999999999997543
No 40
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=97.69 E-value=0.00022 Score=49.58 Aligned_cols=60 Identities=23% Similarity=0.263 Sum_probs=49.6
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCcc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLE 64 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~ 64 (107)
+|+|.|++|....|++.+.|-+||..|.++.-... + +...+-.+.+||+||-++-..|.-
T Consensus 14 ~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-~---~pv~l~~lsirgnniRy~~lpD~l 73 (109)
T KOG3428|consen 14 RVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-G---EPVRLDTLSIRGNNIRYYILPDSL 73 (109)
T ss_pred eEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-C---CceeEEEEEeecceEEEEEccCCc
Confidence 58999999999999999999999999998864322 2 234677899999999999877553
No 41
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.77 E-value=0.0029 Score=40.49 Aligned_cols=56 Identities=20% Similarity=0.162 Sum_probs=32.0
Q ss_pred CEEEEEcCCcEEEEEEEEecc---ccceEEcceEEEEEcC---ce-eeeeecceEEEecCcEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQ---FANVVLEGACERIIVG---DL-YCDIPLGLYVIRGENVV 56 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~---~mNLvL~d~~E~~~~~---~~-~~~~~lG~vlIRG~nIv 56 (107)
+|.|.++||..|+|+|.+++. -+.++|.-|....... .. ........++|.++.|+
T Consensus 14 ~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 14 TVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp EEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred EEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 478999999999999999998 7889998886532111 11 12234557777777665
No 42
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.08 E-value=0.056 Score=34.08 Aligned_cols=27 Identities=30% Similarity=0.562 Sum_probs=23.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|+|.|.+|-.+.|.+.|||+|+=|+-
T Consensus 13 ~Vtv~L~NG~~l~G~I~~fD~ftVll~ 39 (61)
T cd01716 13 PVTIYLVNGVQLKGQIESFDNFTVLLE 39 (61)
T ss_pred cEEEEEeCCcEEEEEEEEEcceEEEEE
Confidence 488999999999999999999995543
No 43
>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=94.79 E-value=0.072 Score=33.61 Aligned_cols=27 Identities=33% Similarity=0.632 Sum_probs=23.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|+|.|.+|-.+.|.+.|||+|+=|+-
T Consensus 17 ~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 17 PVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred cEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 488999999999999999999995543
No 44
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.19 E-value=0.11 Score=34.33 Aligned_cols=27 Identities=33% Similarity=0.586 Sum_probs=23.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|+|-|.+|-.+.|.+.|||+|+=|+-
T Consensus 21 ~VtifL~NG~~l~G~I~~fD~ftVll~ 47 (79)
T PRK00395 21 PVTIYLVNGIKLQGQIESFDNFVVLLR 47 (79)
T ss_pred CEEEEEeCCcEEEEEEEEEccEEEEEE
Confidence 488999999999999999999995553
No 45
>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=93.48 E-value=0.48 Score=27.73 Aligned_cols=28 Identities=11% Similarity=0.200 Sum_probs=23.8
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
|++.+ ++..++|+..|+|....|++...
T Consensus 6 V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 6 VRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp EEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred EEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 66666 67888999999999999998655
No 46
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.16 E-value=0.19 Score=33.13 Aligned_cols=27 Identities=41% Similarity=0.726 Sum_probs=23.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLE 28 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~ 28 (107)
.|.|-|.+|-.+.|...|||+|. +.|+
T Consensus 21 ~VtIfLvNG~~L~G~V~sfD~f~-VlL~ 47 (77)
T COG1923 21 PVTIFLVNGFKLQGQVESFDNFV-VLLK 47 (77)
T ss_pred eEEEEEEcCEEEEEEEEeeeeEE-EEEE
Confidence 37899999999999999999998 4443
No 47
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=91.64 E-value=0.94 Score=30.73 Aligned_cols=65 Identities=18% Similarity=0.205 Sum_probs=47.1
Q ss_pred CEEEEEcCCcEEEEEEEEecc-ccceEEcceEEEEEcCce------eeeeecceEEEecCcEEEEEecCccc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQ-FANVVLEGACERIIVGDL------YCDIPLGLYVIRGENVVLIGELDLEK 65 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~-~mNLvL~d~~E~~~~~~~------~~~~~lG~vlIRG~nIv~I~~~d~~~ 65 (107)
+|.+..+++-.|+|+|...|. -..|.|.++...=..+.. .....+..++.||+.|--+...+.+.
T Consensus 10 ~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 10 KISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp EEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred EEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 467888999999999999996 678999998653111110 11235689999999999998876655
No 48
>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=90.25 E-value=0.64 Score=29.22 Aligned_cols=30 Identities=13% Similarity=0.154 Sum_probs=24.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
+|.+++..|..|+|.+.+||.-.++++=.|
T Consensus 8 ~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 8 QVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred EEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 478999999999999999998876664443
No 49
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.12 E-value=0.99 Score=33.64 Aligned_cols=29 Identities=24% Similarity=0.442 Sum_probs=24.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEG 29 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d 29 (107)
.|+|-|.+|-.+.|.+.|||+|.=|+-.+
T Consensus 106 ~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 106 PVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred cEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 48899999999999999999998554333
No 50
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=87.15 E-value=1.2 Score=33.15 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=23.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|.|-|.+|-.+.|.+.|||+|.=|+-
T Consensus 26 ~VtvfL~nG~rl~G~I~~fD~ftVlL~ 52 (165)
T PRK14091 26 PVTMFLVKGVKLQGIITWFDNFSILLR 52 (165)
T ss_pred cEEEEEecCcEEEEEEEEEcceEEEEE
Confidence 378999999999999999999985543
No 51
>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=83.25 E-value=7.5 Score=25.68 Aligned_cols=50 Identities=12% Similarity=0.036 Sum_probs=35.1
Q ss_pred EEEEEcCCcEEEEEEEEeccc-cceEEcceEEEEEcCceeeeeecceEEEecCcEEEEE
Q 045257 2 ILVLLRDGRKLLGLLRSFDQF-ANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIG 59 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~-mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~ 59 (107)
|.+.|.++.+..|++.++|.. .|+..++-. .+- ..+...++|++.|++++
T Consensus 27 v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TPl----Gv~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 27 VEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TPL----GVQPEALLRCSDVISIS 77 (80)
T ss_dssp EEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TTT----TEEEEEEEEGGGEEEEE
T ss_pred eEEEEeCCeEEEEEEEEecCchheEEhhhcC----CCc----ccChhheeecCCEEEEE
Confidence 678899999999999999954 677665441 121 13458899999999876
No 52
>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=82.89 E-value=6.8 Score=25.57 Aligned_cols=56 Identities=18% Similarity=0.235 Sum_probs=38.2
Q ss_pred CEEEEEcCCcEEEEEEEEeccc-cceEEcceEEEEEcCce-------eeeeecceEEEecCcEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQF-ANVVLEGACERIIVGDL-------YCDIPLGLYVIRGENVV 56 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~-mNLvL~d~~E~~~~~~~-------~~~~~lG~vlIRG~nIv 56 (107)
++.+..+.+-.|+|+|.++|.. .-+.|.|+...=.++.. .....+..++.||+.|-
T Consensus 8 ~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 8 KISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred eEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 3567778889999999999955 56889998653222110 12234567888888774
No 53
>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=82.26 E-value=1.7 Score=32.24 Aligned_cols=55 Identities=27% Similarity=0.326 Sum_probs=37.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccc-cceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCccc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQF-ANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDLEK 65 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~-mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~~~ 65 (107)
.|.|.+.| +++.|.|.++|+- .||||-+..| ++ ....-+|-|.+|-.+..++...
T Consensus 19 ~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~------~~sv~~I~ghaVk~vevl~~~~ 74 (166)
T PF06372_consen 19 EVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DG------KRSVKVIMGHAVKSVEVLSEGD 74 (166)
T ss_dssp EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS-------EEEEEE-GGGEEEEEEEE---
T ss_pred EEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CC------ceeEEEEEccceEEEEEccCCc
Confidence 38899999 9999999999965 6899875543 12 1235789999999999887543
No 54
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=78.34 E-value=3.5 Score=30.62 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=27.7
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcceE
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGAC 31 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~~ 31 (107)
|+|++.||+.|.|-..||++--|.+|..+-
T Consensus 32 Vrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 32 VRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred eEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 789999999999999999999999997763
No 55
>PRK14638 hypothetical protein; Provisional
Probab=74.85 E-value=4.4 Score=29.28 Aligned_cols=26 Identities=19% Similarity=0.465 Sum_probs=21.4
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
+|.|++.+++.++|+|.++|.- ++.|
T Consensus 102 ~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 102 LAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred EEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4789999999999999999863 3544
No 56
>PRK02001 hypothetical protein; Validated
Probab=67.57 E-value=8 Score=28.14 Aligned_cols=26 Identities=35% Similarity=0.612 Sum_probs=21.3
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|.|++.+++.|.|.|.++|.- ++.|
T Consensus 92 ~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 92 ELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred EEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 3788999999999999999864 3444
No 57
>PRK14639 hypothetical protein; Provisional
Probab=65.80 E-value=9.3 Score=27.28 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=21.4
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
.|.|++.+++.+.|+|.++|.- ++.|
T Consensus 90 ~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 90 LVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred EEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 3788899999999999999873 4554
No 58
>PRK10898 serine endoprotease; Provisional
Probab=64.32 E-value=12 Score=30.24 Aligned_cols=30 Identities=30% Similarity=0.471 Sum_probs=25.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
++.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 103 ~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 103 QIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred EEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 378999999999999999999988865444
No 59
>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=62.25 E-value=13 Score=29.84 Aligned_cols=29 Identities=31% Similarity=0.432 Sum_probs=25.3
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
+.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 104 i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 104 IVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred EEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 67899999999999999999988876444
No 60
>PRK10942 serine endoprotease; Provisional
Probab=57.49 E-value=17 Score=30.62 Aligned_cols=29 Identities=34% Similarity=0.361 Sum_probs=25.3
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEG 29 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d 29 (107)
++.|++.||+.+.+.+.++|...+|-|=.
T Consensus 137 ~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 137 KIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred EEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 37899999999999999999998886643
No 61
>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=55.64 E-value=5 Score=27.28 Aligned_cols=17 Identities=35% Similarity=0.485 Sum_probs=15.1
Q ss_pred EEEEEeccccceEEcce
Q 045257 14 GLLRSFDQFANVVLEGA 30 (107)
Q Consensus 14 G~L~gfD~~mNLvL~d~ 30 (107)
|+|+|.|.|+|..-+.-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 88999999999987666
No 62
>PRK10139 serine endoprotease; Provisional
Probab=54.70 E-value=21 Score=29.95 Aligned_cols=30 Identities=30% Similarity=0.364 Sum_probs=25.7
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
++.|++.||+.+.+.+.|+|....|-+=..
T Consensus 116 ~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 116 KISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred EEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 478999999999999999999988866443
No 63
>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion]
Probab=54.60 E-value=6.7 Score=28.61 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=17.3
Q ss_pred CcEEEEEEEEeccccceEEcce
Q 045257 9 GRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 9 Gr~i~G~L~gfD~~mNLvL~d~ 30 (107)
.-.=.|+|+|.|+|+|=.-+|-
T Consensus 42 d~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 42 DDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred ccccceeeeeecccccchhccc
Confidence 3344699999999999876665
No 64
>PRK14644 hypothetical protein; Provisional
Probab=51.52 E-value=31 Score=24.57 Aligned_cols=27 Identities=22% Similarity=0.134 Sum_probs=21.0
Q ss_pred CEEEEEcCC----cEEEEEEEEeccccceEEc
Q 045257 1 KILVLLRDG----RKLLGLLRSFDQFANVVLE 28 (107)
Q Consensus 1 rV~V~L~dG----r~i~G~L~gfD~~mNLvL~ 28 (107)
.|.|+|++. +.++|.|.++|.. ++.|.
T Consensus 87 ~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 87 IIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred eEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 377888876 9999999999873 45553
No 65
>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=51.15 E-value=17 Score=24.97 Aligned_cols=17 Identities=29% Similarity=0.466 Sum_probs=13.9
Q ss_pred CEEEEEcCCcEEEEEEE
Q 045257 1 KILVLLRDGRKLLGLLR 17 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~ 17 (107)
+|.+.|+||+.+.|++.
T Consensus 30 ~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 30 RVELELDDGSMLRGTVA 46 (101)
T ss_dssp EEEEEETTS-EEEEEEC
T ss_pred eEEEEEcCCCeeeeeec
Confidence 58899999999999863
No 66
>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=50.67 E-value=27 Score=28.54 Aligned_cols=30 Identities=27% Similarity=0.321 Sum_probs=25.9
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
++.|.+.||+.+.+.+.++|...+|-|=..
T Consensus 83 ~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 83 EITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred eEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 367899999999999999999998876544
No 67
>PRK06955 biotin--protein ligase; Provisional
Probab=50.55 E-value=28 Score=27.44 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=21.9
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLE 28 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~ 28 (107)
|.|...+++.+.|+..|+|..+.|++.
T Consensus 252 V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 252 VVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred EEEEECCCcEEEEEEeeECCCceEEEE
Confidence 445444667899999999999999985
No 68
>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=49.96 E-value=16 Score=27.12 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=18.9
Q ss_pred EEEEEcCCcEEEEEEEEeccc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQF 22 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~ 22 (107)
|+|-+.|||+++|.=.|.|..
T Consensus 123 IrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 123 IRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred EEEEEcCCcEEEeeecccceE
Confidence 789999999999999998854
No 69
>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=49.23 E-value=29 Score=22.18 Aligned_cols=25 Identities=36% Similarity=0.477 Sum_probs=18.5
Q ss_pred EEEEEc---CC-cEEEEEEEEeccccceEE
Q 045257 2 ILVLLR---DG-RKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~---dG-r~i~G~L~gfD~~mNLvL 27 (107)
|.|+++ +| +.+.|.|.++|.- ++.|
T Consensus 28 v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 28 VHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred EEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 667776 55 6999999999873 3444
No 70
>PRK14640 hypothetical protein; Provisional
Probab=49.09 E-value=35 Score=24.57 Aligned_cols=25 Identities=24% Similarity=0.385 Sum_probs=19.4
Q ss_pred EEEEE----cCCcEEEEEEEEeccccceEE
Q 045257 2 ILVLL----RDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L----~dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|+| .+++.++|.|.++|.- ++.|
T Consensus 100 v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 100 AAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred EEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 67777 5679999999999874 3544
No 71
>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=48.80 E-value=25 Score=24.34 Aligned_cols=20 Identities=40% Similarity=0.507 Sum_probs=17.0
Q ss_pred EEEEEcCCcEEEEEEEEecc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQ 21 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~ 21 (107)
..|.++||+.++|.+..=|.
T Consensus 60 ~~v~~~dG~~~~G~~~~e~~ 79 (133)
T TIGR02603 60 YRVTLKDGRILSGIVASETA 79 (133)
T ss_pred EEEEECCCCEEEEEEEecCC
Confidence 57899999999999988553
No 72
>PRK14642 hypothetical protein; Provisional
Probab=45.71 E-value=30 Score=26.37 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=19.7
Q ss_pred EEEEEc-------------CCcEEEEEEEEeccccceEE
Q 045257 2 ILVLLR-------------DGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~-------------dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|+|+ +.+.|+|+|.++|.. ++.|
T Consensus 103 V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 103 IDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred EEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 678887 679999999999874 3444
No 73
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=44.97 E-value=76 Score=24.88 Aligned_cols=26 Identities=19% Similarity=0.548 Sum_probs=21.1
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLE 28 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~ 28 (107)
|.+.. ++..++|++.|+|..+.|++.
T Consensus 275 v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 275 VKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred EEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 44443 556799999999999999995
No 74
>PRK14645 hypothetical protein; Provisional
Probab=43.60 E-value=30 Score=25.12 Aligned_cols=24 Identities=17% Similarity=0.195 Sum_probs=17.5
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEE
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|++ +++.++|+|.++|.- .+.|
T Consensus 105 v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 105 AKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred EEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 45554 789999999999874 3444
No 75
>PRK14633 hypothetical protein; Provisional
Probab=41.78 E-value=39 Score=24.29 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=19.0
Q ss_pred EEEEE----cCCcEEEEEEEEeccccceEE
Q 045257 2 ILVLL----RDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L----~dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|++ .+++.|+|+|.+++.- ++.|
T Consensus 97 v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 97 VKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred EEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 56766 4679999999999874 4555
No 76
>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=40.76 E-value=96 Score=23.31 Aligned_cols=26 Identities=19% Similarity=0.364 Sum_probs=20.9
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLE 28 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~ 28 (107)
|.+.. ++..+.|+..|+|..+.|+|+
T Consensus 196 V~v~~-~~~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 196 VSLTT-GNGEIEGIARGIDKDGALLLE 221 (237)
T ss_pred EEEEe-CCcEEEEEEEeECCCceEEEE
Confidence 44443 456799999999999999996
No 77
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=40.57 E-value=39 Score=19.78 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=13.7
Q ss_pred EEEEEEEeccccceEEcceEE
Q 045257 12 LLGLLRSFDQFANVVLEGACE 32 (107)
Q Consensus 12 i~G~L~gfD~~mNLvL~d~~E 32 (107)
.+|++.|.|+...+.|.+...
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 589999999988898877643
No 78
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=40.54 E-value=71 Score=27.91 Aligned_cols=28 Identities=21% Similarity=0.275 Sum_probs=22.1
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcc
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEG 29 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d 29 (107)
|.+...+++.+.|+..|+|..+.|+|+.
T Consensus 281 V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 281 VLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred EEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 4444356677999999999999999963
No 79
>PRK14636 hypothetical protein; Provisional
Probab=36.77 E-value=48 Score=24.58 Aligned_cols=26 Identities=27% Similarity=0.475 Sum_probs=19.3
Q ss_pred CEEEEEc---CC-cEEEEEEEEeccccceEE
Q 045257 1 KILVLLR---DG-RKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~---dG-r~i~G~L~gfD~~mNLvL 27 (107)
.|.|+|. +| +.|+|.|.++|.- ++.|
T Consensus 100 ~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 100 EARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred eEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 3778886 55 7999999999873 3444
No 80
>PRK14643 hypothetical protein; Provisional
Probab=34.95 E-value=55 Score=23.98 Aligned_cols=21 Identities=14% Similarity=0.354 Sum_probs=16.7
Q ss_pred EEEEEcC----CcEEEEEEEEeccc
Q 045257 2 ILVLLRD----GRKLLGLLRSFDQF 22 (107)
Q Consensus 2 V~V~L~d----Gr~i~G~L~gfD~~ 22 (107)
|.|+|.. .+.|+|+|.++|.-
T Consensus 107 V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 107 VYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred EEEEEecccCCceEEEEEEEEEeCC
Confidence 6677754 69999999999854
No 81
>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=34.86 E-value=77 Score=22.07 Aligned_cols=25 Identities=24% Similarity=0.395 Sum_probs=17.4
Q ss_pred EEEEE----cCCcEEEEEEEEeccccceEE
Q 045257 2 ILVLL----RDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L----~dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|.+ .+.+.+.|+|.++|. -.++|
T Consensus 90 v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 90 VKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp EEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred EEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 67777 355899999999998 34554
No 82
>PRK14632 hypothetical protein; Provisional
Probab=32.83 E-value=62 Score=23.83 Aligned_cols=25 Identities=40% Similarity=0.401 Sum_probs=19.1
Q ss_pred EEEEEcC-------CcEEEEEEEEeccccceEE
Q 045257 2 ILVLLRD-------GRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~d-------Gr~i~G~L~gfD~~mNLvL 27 (107)
|.|+|.+ .+.|.|+|.++|.- ++.|
T Consensus 101 V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 101 IELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred EEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 6787765 68999999999863 4554
No 83
>PRK14634 hypothetical protein; Provisional
Probab=32.20 E-value=67 Score=23.21 Aligned_cols=25 Identities=28% Similarity=0.359 Sum_probs=18.3
Q ss_pred EEEEEcC----CcEEEEEEEEeccccceEE
Q 045257 2 ILVLLRD----GRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~d----Gr~i~G~L~gfD~~mNLvL 27 (107)
|.|+|.+ .+.|+|+|.++|.- ++.|
T Consensus 103 V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 103 VEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred EEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 6777763 28999999999864 3444
No 84
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=32.13 E-value=1.3e+02 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=24.1
Q ss_pred EEEEEcCCcEEEEEEEEeccccceEEcce
Q 045257 2 ILVLLRDGRKLLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD~~mNLvL~d~ 30 (107)
|++...++..+.|+..|+|..+.|+|+..
T Consensus 193 V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 193 VRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred EEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 66666677777789999999999999766
No 85
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.54 E-value=1e+02 Score=22.53 Aligned_cols=25 Identities=28% Similarity=0.337 Sum_probs=19.8
Q ss_pred EEEEE----cCCcEEEEEEEEeccccceEE
Q 045257 2 ILVLL----RDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L----~dGr~i~G~L~gfD~~mNLvL 27 (107)
|.|.| .+++.++|+|.++|.-+ +++
T Consensus 102 Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 102 VKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred EEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 56667 78899999999999876 444
No 86
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=31.11 E-value=1e+02 Score=24.24 Aligned_cols=23 Identities=17% Similarity=0.319 Sum_probs=20.2
Q ss_pred cCCcEEEEEEEEeccccceEEcc
Q 045257 7 RDGRKLLGLLRSFDQFANVVLEG 29 (107)
Q Consensus 7 ~dGr~i~G~L~gfD~~mNLvL~d 29 (107)
.++..+.|++.|+|..+.|+|..
T Consensus 244 ~~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 244 QDNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred eCCCEEEEEEEEECCCCeEEEEe
Confidence 46789999999999999999863
No 87
>PRK14646 hypothetical protein; Provisional
Probab=30.90 E-value=71 Score=23.08 Aligned_cols=25 Identities=24% Similarity=0.211 Sum_probs=18.1
Q ss_pred EEEEEcCC----cEEEEEEEEeccccceEE
Q 045257 2 ILVLLRDG----RKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~dG----r~i~G~L~gfD~~mNLvL 27 (107)
|.|+|.+. +.+.|+|.++|.- ++.|
T Consensus 103 v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 103 VNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred EEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 67777532 7889999999874 4555
No 88
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=30.03 E-value=78 Score=22.54 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=16.8
Q ss_pred EEEEE----cCCcEEEEEEEEecc
Q 045257 2 ILVLL----RDGRKLLGLLRSFDQ 21 (107)
Q Consensus 2 V~V~L----~dGr~i~G~L~gfD~ 21 (107)
|.|++ .+++.++|.|.++|.
T Consensus 101 v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 101 VKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred EEEEEEcccCCceEEEEEEEEeeC
Confidence 67776 577999999999987
No 89
>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=29.71 E-value=18 Score=34.85 Aligned_cols=52 Identities=25% Similarity=0.301 Sum_probs=0.0
Q ss_pred EEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEE
Q 045257 5 LLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVL 57 (107)
Q Consensus 5 ~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~ 57 (107)
...+|+.+.|+|.+=|.-|+.+|.---+ +.+..-.....+|.++|+|+|.|-
T Consensus 253 tt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 253 TTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTSVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp -----------------------------------------------------
T ss_pred ecCCCCEeceEEeccHHHHHHHHHHHhh-hccceeecchhheeeeecCccHHH
Confidence 4578999999999999888776654433 222111224578999999999764
No 90
>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=29.55 E-value=78 Score=24.73 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=17.0
Q ss_pred EEEEEEEEeccccceEEcc
Q 045257 11 KLLGLLRSFDQFANVVLEG 29 (107)
Q Consensus 11 ~i~G~L~gfD~~mNLvL~d 29 (107)
.+.|...-.|.|+|+++.=
T Consensus 169 ~i~g~Vi~iD~FGNlitnI 187 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNI 187 (258)
T ss_dssp EEEEEEEEEETTSEEEEEE
T ss_pred eEEEEEEEECccCCeeeCC
Confidence 8999999999999999743
No 91
>PRK06630 hypothetical protein; Provisional
Probab=28.83 E-value=30 Score=23.81 Aligned_cols=19 Identities=21% Similarity=0.172 Sum_probs=16.4
Q ss_pred EEEEEEEeccccceEEcce
Q 045257 12 LLGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 12 i~G~L~gfD~~mNLvL~d~ 30 (107)
..|.|+|-|+|+|-.-++.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4699999999999987764
No 92
>PRK14647 hypothetical protein; Provisional
Probab=28.62 E-value=82 Score=22.75 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=16.2
Q ss_pred EEEEEc---------CCcEEEEEEEEecc
Q 045257 2 ILVLLR---------DGRKLLGLLRSFDQ 21 (107)
Q Consensus 2 V~V~L~---------dGr~i~G~L~gfD~ 21 (107)
|.|+|. +.+.|+|+|.++|.
T Consensus 102 v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 102 VKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred EEEEEeccccccccCCceEEEEEEEeecC
Confidence 677774 35999999999986
No 93
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=28.46 E-value=43 Score=24.80 Aligned_cols=17 Identities=24% Similarity=0.311 Sum_probs=15.3
Q ss_pred EEEEEeccccceEEcce
Q 045257 14 GLLRSFDQFANVVLEGA 30 (107)
Q Consensus 14 G~L~gfD~~mNLvL~d~ 30 (107)
|+|+|-|.|+|-.-++.
T Consensus 49 G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 49 ATLVGVDKFGNKYYQKL 65 (159)
T ss_pred cEEEEecCCCCeeeecC
Confidence 99999999999987765
No 94
>PRK08330 biotin--protein ligase; Provisional
Probab=26.33 E-value=1.3e+02 Score=22.70 Aligned_cols=28 Identities=25% Similarity=0.536 Sum_probs=21.1
Q ss_pred EEEEEcCCcEE-EEEEEEeccccceEEcce
Q 045257 2 ILVLLRDGRKL-LGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 2 V~V~L~dGr~i-~G~L~gfD~~mNLvL~d~ 30 (107)
|.+. .++..+ .|+..|.|..+.|++...
T Consensus 191 v~~~-~~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 191 VKII-GDGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred EEEE-ECCcEEEEEEEEEECCCCEEEEEEC
Confidence 4443 466665 699999999999998643
No 95
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=26.32 E-value=37 Score=23.87 Aligned_cols=18 Identities=33% Similarity=0.388 Sum_probs=15.8
Q ss_pred EEEEEEeccccceEEcce
Q 045257 13 LGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 13 ~G~L~gfD~~mNLvL~d~ 30 (107)
.|.|+|-|.|+|-.-++.
T Consensus 9 ~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENP 26 (115)
T ss_pred cceEeEEcCCCCeeeEcC
Confidence 689999999999987764
No 96
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [].; PDB: 1SG5_A.
Probab=25.60 E-value=60 Score=21.20 Aligned_cols=53 Identities=21% Similarity=0.295 Sum_probs=23.1
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEEcceEEEEEcCceeeeeecceEEEecCcEEEEEecCc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVLEGACERIIVGDLYCDIPLGLYVIRGENVVLIGELDL 63 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL~d~~E~~~~~~~~~~~~lG~vlIRG~nIv~I~~~d~ 63 (107)
.|.+.|+||..++|+ +.|-..|- +-.|...- ...-|...||=+.|..+++...
T Consensus 19 ~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l-----~~~~~~~~i~Ld~I~~~~al~~ 71 (80)
T PF07073_consen 19 PVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVL-----EQDGGEQEIRLDQIASMSALTD 71 (80)
T ss_dssp -EEEE-TTT--EEES--S-EEE------SSS-EEEE-----EETTEEEEESTT--SEEE----
T ss_pred eEEEEEeCCCEEEEE--EEEEEEec---CceEEEEE-----ecCCcEEEEEhhheeeeeecCC
Confidence 478999999999997 33322221 11121110 1123577888888888887644
No 97
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.51 E-value=1.2e+02 Score=23.89 Aligned_cols=27 Identities=30% Similarity=0.447 Sum_probs=22.5
Q ss_pred CEEEEEcCCcEEEEEEEEeccccceEE
Q 045257 1 KILVLLRDGRKLLGLLRSFDQFANVVL 27 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~mNLvL 27 (107)
++.|.+.||+.+.+.+.|+|...-+-+
T Consensus 97 ~i~v~l~dg~~~~a~~vg~d~~~dlav 123 (347)
T COG0265 97 EITVTLADGREVPAKLVGKDPISDLAV 123 (347)
T ss_pred eEEEEeCCCCEEEEEEEecCCccCEEE
Confidence 367888999999999999998765544
No 98
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.25 E-value=2.2e+02 Score=23.79 Aligned_cols=64 Identities=14% Similarity=0.122 Sum_probs=44.4
Q ss_pred EEEEEcCCcEEEEEEEEec-cccceEEcceEEEEEcC----ce---eeeeecceEEEecCcEEEEEecCccc
Q 045257 2 ILVLLRDGRKLLGLLRSFD-QFANVVLEGACERIIVG----DL---YCDIPLGLYVIRGENVVLIGELDLEK 65 (107)
Q Consensus 2 V~V~L~dGr~i~G~L~gfD-~~mNLvL~d~~E~~~~~----~~---~~~~~lG~vlIRG~nIv~I~~~d~~~ 65 (107)
|.++-+..-.|+|+|.-.| +-.-|=|.++-..=+++ .. .....+.-|+.||+.|-.+...+.+.
T Consensus 12 ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p~ 83 (361)
T KOG1073|consen 12 ISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETPA 83 (361)
T ss_pred eEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCcc
Confidence 5667778889999999999 55678888872211111 11 11226678999999999888776555
No 99
>PRK14631 hypothetical protein; Provisional
Probab=22.37 E-value=1.2e+02 Score=22.46 Aligned_cols=19 Identities=26% Similarity=0.329 Sum_probs=15.8
Q ss_pred EEEEEc----CCcEEEEEEEEec
Q 045257 2 ILVLLR----DGRKLLGLLRSFD 20 (107)
Q Consensus 2 V~V~L~----dGr~i~G~L~gfD 20 (107)
|.|+|. +.+.|+|+|.++|
T Consensus 120 V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 120 VALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred EEEEEecccCCceEEEEEEEEee
Confidence 677775 5599999999998
No 100
>PRK14641 hypothetical protein; Provisional
Probab=22.24 E-value=1.1e+02 Score=22.70 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=15.2
Q ss_pred EEEEEcC----CcEEEEEEEEec
Q 045257 2 ILVLLRD----GRKLLGLLRSFD 20 (107)
Q Consensus 2 V~V~L~d----Gr~i~G~L~gfD 20 (107)
|.|+|.+ .+.|+|+|.+++
T Consensus 107 V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 107 LRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred EEEEEecccCCeEEEEEEEEeee
Confidence 6777765 578999999995
No 101
>PRK14637 hypothetical protein; Provisional
Probab=21.75 E-value=1.3e+02 Score=21.76 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=17.2
Q ss_pred EEEEEcCCcEE-EEEEEEeccccceEE
Q 045257 2 ILVLLRDGRKL-LGLLRSFDQFANVVL 27 (107)
Q Consensus 2 V~V~L~dGr~i-~G~L~gfD~~mNLvL 27 (107)
|.|++.+.+.+ +|+|.++|.- ++.|
T Consensus 101 V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 101 VKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred EEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 67877444455 7999999874 3444
No 102
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=21.02 E-value=2.3e+02 Score=17.78 Aligned_cols=19 Identities=21% Similarity=0.263 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHhhhhhhhh
Q 045257 82 RAQKAEKDATVLKGSMRKR 100 (107)
Q Consensus 82 ~~~~~e~~~~~~~~~~~~~ 100 (107)
...+-|+|++.+|++++.|
T Consensus 77 a~~klerql~k~k~k~~~~ 95 (95)
T TIGR00741 77 AIDKLERQLRKLKEKRKEH 95 (95)
T ss_pred HHHHHHHHHHHHHhhhhcC
Confidence 5688999999999998765
No 103
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=20.95 E-value=1.3e+02 Score=18.48 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=17.8
Q ss_pred CEEEEEcCCcEEEEEEEEeccc
Q 045257 1 KILVLLRDGRKLLGLLRSFDQF 22 (107)
Q Consensus 1 rV~V~L~dGr~i~G~L~gfD~~ 22 (107)
+|.|+|-||..++..+..-|..
T Consensus 8 ~I~vRlpdG~~l~~~F~~~~tl 29 (82)
T PF00789_consen 8 RIQVRLPDGSRLQRRFPKSDTL 29 (82)
T ss_dssp EEEEEETTSTEEEEEEETTSBH
T ss_pred EEEEECCCCCEEEEEECCcchH
Confidence 4789999999999998865543
No 104
>PRK08183 NADH dehydrogenase; Validated
Probab=20.37 E-value=53 Score=23.58 Aligned_cols=18 Identities=28% Similarity=0.241 Sum_probs=15.5
Q ss_pred EEEEEEeccccceEEcce
Q 045257 13 LGLLRSFDQFANVVLEGA 30 (107)
Q Consensus 13 ~G~L~gfD~~mNLvL~d~ 30 (107)
.|.|+|-|.++|-.-++.
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 599999999999887654
Done!