Query psy488
Match_columns 86
No_of_seqs 45 out of 47
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 20:10:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/488hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11095 Gemin7: Gem-associate 100.0 5.8E-45 1.3E-49 239.9 8.3 78 8-86 1-78 (80)
2 cd01725 LSm2 The eukaryotic Sm 97.3 0.0017 3.8E-08 41.9 7.1 62 22-85 2-70 (81)
3 cd00600 Sm_like The eukaryotic 96.8 0.0058 1.3E-07 36.2 5.4 57 27-85 2-63 (63)
4 PF14438 SM-ATX: Ataxin 2 SM d 96.7 0.0038 8.3E-08 39.2 4.4 36 20-55 1-36 (77)
5 cd01722 Sm_F The eukaryotic Sm 96.5 0.029 6.2E-07 34.8 7.2 60 23-84 3-67 (68)
6 cd01726 LSm6 The eukaryotic Sm 96.4 0.022 4.8E-07 35.2 6.4 60 23-84 2-66 (67)
7 PF01423 LSM: LSM domain ; In 96.3 0.019 4.1E-07 34.6 5.7 60 25-85 2-66 (67)
8 cd01724 Sm_D1 The eukaryotic S 96.1 0.036 7.7E-07 36.7 6.7 63 22-86 2-69 (90)
9 cd01719 Sm_G The eukaryotic Sm 96.1 0.039 8.5E-07 34.9 6.4 59 25-85 4-67 (72)
10 cd01723 LSm4 The eukaryotic Sm 96.0 0.057 1.2E-06 34.2 6.9 62 23-86 3-70 (76)
11 cd01721 Sm_D3 The eukaryotic S 96.0 0.055 1.2E-06 33.9 6.7 62 23-86 2-68 (70)
12 smart00651 Sm snRNP Sm protein 95.9 0.056 1.2E-06 32.4 6.3 59 25-85 2-66 (67)
13 cd01731 archaeal_Sm1 The archa 95.8 0.061 1.3E-06 33.1 6.4 61 23-85 2-67 (68)
14 cd01733 LSm10 The eukaryotic S 95.7 0.08 1.7E-06 34.1 6.9 62 23-86 11-77 (78)
15 cd01717 Sm_B The eukaryotic Sm 95.5 0.049 1.1E-06 34.6 5.2 60 25-86 4-78 (79)
16 PRK00737 small nuclear ribonuc 95.2 0.17 3.6E-06 31.8 7.0 61 22-84 5-70 (72)
17 cd06168 LSm9 The eukaryotic Sm 94.1 0.29 6.2E-06 31.4 6.2 60 25-86 4-74 (75)
18 cd01732 LSm5 The eukaryotic Sm 93.7 0.57 1.2E-05 30.0 6.9 61 23-85 5-73 (76)
19 KOG3482|consensus 93.5 0.33 7.1E-06 32.3 5.7 58 25-84 12-74 (79)
20 cd01727 LSm8 The eukaryotic Sm 92.6 0.57 1.2E-05 29.4 5.6 58 25-84 3-69 (74)
21 COG1958 LSM1 Small nuclear rib 91.6 1.1 2.5E-05 28.2 6.2 64 21-85 7-78 (79)
22 cd01730 LSm3 The eukaryotic Sm 89.7 1.9 4.2E-05 27.5 6.0 60 23-84 3-80 (82)
23 cd01728 LSm1 The eukaryotic Sm 89.6 2.5 5.3E-05 27.0 6.4 60 23-84 4-71 (74)
24 cd01729 LSm7 The eukaryotic Sm 89.3 2 4.2E-05 27.7 5.9 58 26-85 7-77 (81)
25 cd01720 Sm_D2 The eukaryotic S 87.2 3.3 7.1E-05 27.3 6.0 60 24-85 5-84 (87)
26 PF02237 BPL_C: Biotin protein 78.9 5.6 0.00012 22.9 4.1 28 30-58 2-29 (48)
27 PTZ00138 small nuclear ribonuc 77.2 19 0.00041 24.0 6.8 51 33-85 28-86 (89)
28 PF10842 DUF2642: Protein of u 75.0 19 0.00041 23.0 6.4 54 22-85 12-65 (66)
29 KOG3428|consensus 67.3 10 0.00023 26.6 3.8 38 22-59 3-40 (109)
30 PRK06955 biotin--protein ligas 66.0 25 0.00054 27.1 6.0 38 27-68 245-282 (300)
31 KOG3448|consensus 65.6 12 0.00027 25.7 3.9 33 22-54 3-35 (96)
32 PRK02001 hypothetical protein; 65.4 16 0.00035 26.3 4.6 38 24-61 83-120 (152)
33 PRK11886 bifunctional biotin-- 65.3 22 0.00048 27.1 5.6 40 18-59 260-299 (319)
34 PRK14638 hypothetical protein; 62.2 22 0.00047 25.3 4.8 52 24-76 93-146 (150)
35 PRK14639 hypothetical protein; 60.7 20 0.00044 25.2 4.4 52 24-76 81-136 (140)
36 cd01734 YlxS_C YxlS is a Bacil 59.1 32 0.00068 21.7 4.7 52 24-76 18-79 (83)
37 cd01718 Sm_E The eukaryotic Sm 53.9 59 0.0013 21.1 6.7 50 33-84 20-77 (79)
38 PRK14632 hypothetical protein; 51.8 40 0.00087 24.5 4.8 37 24-60 91-134 (172)
39 COG0340 BirA Biotin-(acetyl-Co 48.3 71 0.0015 24.2 5.8 34 29-62 188-221 (238)
40 TIGR00121 birA_ligase birA, bi 47.3 79 0.0017 23.2 5.8 31 27-58 189-219 (237)
41 TIGR02383 Hfq RNA chaperone Hf 47.3 71 0.0015 20.1 5.4 53 19-75 4-56 (61)
42 PRK14636 hypothetical protein; 46.4 51 0.0011 24.1 4.7 56 24-80 91-153 (176)
43 PRK08330 biotin--protein ligas 46.1 97 0.0021 22.8 6.1 31 28-58 185-215 (236)
44 PRK14647 hypothetical protein; 42.9 81 0.0018 22.4 5.2 52 24-76 92-155 (159)
45 PRK14631 hypothetical protein; 42.7 72 0.0016 23.4 5.0 54 24-78 110-172 (174)
46 PRK14643 hypothetical protein; 42.6 59 0.0013 23.6 4.4 51 25-76 98-160 (164)
47 PTZ00275 biotin-acetyl-CoA-car 41.8 1.1E+02 0.0023 23.6 6.0 29 29-58 235-263 (285)
48 PRK00395 hfq RNA-binding prote 41.5 57 0.0012 21.6 3.9 54 18-75 7-60 (79)
49 PF06372 Gemin6: Gemin6 protei 38.7 71 0.0015 23.6 4.4 41 25-66 11-51 (166)
50 PF05979 DUF896: Bacterial pro 37.9 29 0.00064 22.1 2.0 20 9-28 21-40 (65)
51 PF08863 YolD: YolD-like prote 37.1 1E+02 0.0022 18.9 5.4 49 30-84 41-92 (92)
52 PF12701 LSM14: Scd6-like Sm d 36.0 1.3E+02 0.0029 20.1 5.7 57 28-85 5-75 (96)
53 PRK13325 bifunctional biotin-- 33.7 1.3E+02 0.0028 25.8 5.8 31 29-59 276-306 (592)
54 KOG1783|consensus 33.1 32 0.0007 22.9 1.7 55 25-84 10-72 (77)
55 PF00058 Ldl_recept_b: Low-den 32.8 43 0.00092 18.6 2.0 24 46-69 12-38 (42)
56 PF10907 DUF2749: Protein of u 32.8 44 0.00095 21.6 2.2 17 5-24 32-48 (66)
57 cd01716 Hfq Hfq, an abundant, 32.4 98 0.0021 19.4 3.7 32 30-61 10-41 (61)
58 PHA02947 S-S bond formation pa 30.7 39 0.00083 26.2 2.0 46 19-67 15-63 (215)
59 PF07073 ROF: Modulator of Rho 30.4 79 0.0017 20.6 3.2 53 27-85 13-67 (80)
60 TIGR01080 rplX_A_E ribosomal p 29.6 1.1E+02 0.0024 21.2 4.0 67 17-84 30-99 (114)
61 PRK14640 hypothetical protein; 29.6 1.5E+02 0.0032 21.0 4.7 52 24-76 90-147 (152)
62 PF04921 XAP5: XAP5, circadian 29.5 56 0.0012 25.5 2.7 43 5-47 70-114 (239)
63 PRK02539 hypothetical protein; 29.3 71 0.0015 21.5 2.9 22 8-29 22-43 (85)
64 PRK01631 hypothetical protein; 29.2 73 0.0016 21.0 2.9 21 8-28 21-41 (76)
65 PF15538 Toxin_61: Putative to 28.9 2.1E+02 0.0047 21.2 5.6 73 9-82 23-105 (157)
66 COG1931 Uncharacterized protei 28.7 55 0.0012 23.9 2.4 56 11-80 60-115 (140)
67 PF08348 PAS_6: YheO-like PAS 28.6 67 0.0015 21.9 2.7 22 21-42 7-28 (118)
68 PRK01546 hypothetical protein; 28.0 79 0.0017 20.9 2.9 21 9-29 24-44 (79)
69 COG1117 PstB ABC-type phosphat 27.3 37 0.0008 26.9 1.4 44 21-70 48-93 (253)
70 PRK14633 hypothetical protein; 26.1 2.1E+02 0.0046 20.2 5.0 52 24-76 87-145 (150)
71 PHA03222 single-stranded bindi 25.5 58 0.0013 26.8 2.2 15 15-29 172-186 (337)
72 TIGR00760 araD L-ribulose-5-ph 25.0 1E+02 0.0022 22.9 3.3 57 18-86 5-61 (231)
73 PRK01885 greB transcription el 24.5 1.7E+02 0.0036 20.8 4.3 71 9-84 52-140 (157)
74 PF12793 SgrR_N: Sugar transpo 24.3 56 0.0012 22.2 1.7 23 18-40 2-24 (115)
75 KOG1780|consensus 24.2 1E+02 0.0022 20.5 2.8 58 26-84 9-70 (77)
76 PHA02662 ORF131 putative membr 24.1 59 0.0013 25.4 2.0 47 18-67 27-76 (226)
77 PRK14646 hypothetical protein; 23.3 2.1E+02 0.0045 20.4 4.6 53 24-77 93-151 (155)
78 KOG1486|consensus 23.3 1.3E+02 0.0028 24.9 3.8 58 26-84 79-145 (364)
79 TIGR02447 yiiD_Cterm thioester 22.5 2.6E+02 0.0055 18.9 4.9 33 19-51 99-133 (138)
80 PRK09618 flgD flagellar basal 22.0 2.8E+02 0.0062 19.9 5.0 29 25-53 86-114 (142)
81 PRK07490 hypothetical protein; 21.7 1.6E+02 0.0034 22.1 3.8 25 55-85 43-67 (245)
82 PF07217 Het-C: Heterokaryon i 20.7 45 0.00098 29.4 0.8 24 30-53 254-280 (606)
83 PRK14630 hypothetical protein; 20.6 2.5E+02 0.0055 19.7 4.5 36 24-60 90-125 (143)
84 PF11335 DUF3137: Protein of u 20.2 2.6E+02 0.0057 18.8 4.4 41 8-48 59-102 (142)
No 1
>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=100.00 E-value=5.8e-45 Score=239.94 Aligned_cols=78 Identities=36% Similarity=0.667 Sum_probs=73.2
Q ss_pred CcHHHHHHHHHHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEEeC
Q psy488 8 SRSDEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 8 ~~~eQ~aRa~LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~~ 86 (86)
+++||+||++||||||++|++|+||||+|+|||||+|+|+|+|||+|++||+||||+||||++|+ |+|||+|||+|+|
T Consensus 1 ~~~eQ~aR~~LRerfLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~TPlGv~~e-AlLR~~DVi~~~f 78 (80)
T PF11095_consen 1 ESEEQEARAFLRERFLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQTPLGVQPE-ALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEETTTTEEEE-EEEEGGGEEEEEE
T ss_pred ChHHHHHHHHHHHHHHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCCCcccChh-heeecCCEEEEEe
Confidence 47899999999999999999999999999999999999999999999999999999999999999 9999999999975
No 2
>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=97.32 E-value=0.0017 Score=41.91 Aligned_cols=62 Identities=13% Similarity=0.322 Sum_probs=50.2
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC--CC-----cCccccceeeecCceeEEe
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK--TP-----IGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TP-----iGv~~e~AlLR~~DIi~~~ 85 (86)
||.+|.++.|++|.+.|..+.++.|+..++|..- |+..+|-+ .| .+..++ ..+|++-|..+.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Ni~L~n~~~~~~~~~~~~~~~~~-v~IRG~~I~~I~ 70 (81)
T cd01725 2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYL-NIKLTNISVTDPEKYPHMLSVKN-CFIRGSVVRYVQ 70 (81)
T ss_pred hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCc-ccEEEEEEEEcCCCcccccccCe-EEEECCEEEEEE
Confidence 7889999999999999999999999999999764 77777664 12 233456 899999887664
No 3
>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=96.77 E-value=0.0058 Score=36.16 Aligned_cols=57 Identities=11% Similarity=0.225 Sum_probs=44.9
Q ss_pred HhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-----CCcCccccceeeecCceeEEe
Q psy488 27 SSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-----TPIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 27 ~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-----TPiGv~~e~AlLR~~DIi~~~ 85 (86)
.++.|++|.+.+.++....|++.++|... |+..++-. ..-...+. .++|.+.|..++
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~-Ni~L~~~~~~~~~~~~~~~~~-~~irG~~I~~I~ 63 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDKYM-NLVLDDVEETIKEGKKRVLGL-VLIRGDNVRLVT 63 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECCCC-CEEECCEEEEecCCcEEECCe-EEEECCEEEEEC
Confidence 46689999999999999999999999766 77766653 22334556 899999998763
No 4
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=96.69 E-value=0.0038 Score=39.16 Aligned_cols=36 Identities=14% Similarity=0.331 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCc
Q psy488 20 EKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDL 55 (86)
Q Consensus 20 erfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~ 55 (86)
+|++..+..+.|++|++++.++..-+|.|.+++.+.
T Consensus 1 dRl~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~ 36 (77)
T PF14438_consen 1 DRLVYLLTNLVGQTVEVTTKNGSVYEGIFHSASPES 36 (77)
T ss_dssp ---HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T--
T ss_pred ChHHHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcc
Confidence 589999999999999999999999999999999964
No 5
>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=96.46 E-value=0.029 Score=34.84 Aligned_cols=60 Identities=15% Similarity=0.274 Sum_probs=47.7
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CCcC----ccccceeeecCceeEE
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TPIG----TFHEHALLRVDDIVDI 84 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPiG----v~~e~AlLR~~DIi~~ 84 (86)
+..|.++.|++|.+.|.++.++.|+..++| +..|+..++-. +.-| ..+. .++|.+-|+.|
T Consensus 3 ~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D-~~mNi~L~~~~e~~~~~~~~~lg~-~~IRG~~I~~i 67 (68)
T cd01722 3 KPFLNDLTGKPVIVKLKWGMEYKGTLVSVD-SYMNLQLANTEEYIDGKSTGNLGE-VLIRCNNVLYI 67 (68)
T ss_pred HHHHHHcCCCEEEEEECCCcEEEEEEEEEC-CCEEEEEeeEEEEeCCccccCcCc-EEEECCEEEEE
Confidence 456778899999999999999999999999 67777777763 2222 3355 89999998765
No 6
>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=96.38 E-value=0.022 Score=35.18 Aligned_cols=60 Identities=10% Similarity=0.247 Sum_probs=47.5
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-CcC----ccccceeeecCceeEE
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-PIG----TFHEHALLRVDDIVDI 84 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-PiG----v~~e~AlLR~~DIi~~ 84 (86)
|.+|.++.|++|.+.|..+..+.|+..++| +..|+..++-.. .-| ..+. .++|++-|+.+
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D-~~mNlvL~~~~~~~~~~~~~~~~~-v~IRG~~I~~I 66 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLD-GYMNIALEQTEEYVNGQLKNKYGD-AFIRGNNVLYI 66 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEc-cceeeEEeeEEEEeCCceeeEeCC-EEEECCEEEEE
Confidence 456778899999999999999999999999 677888887642 222 2345 88999888765
No 7
>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=96.32 E-value=0.019 Score=34.56 Aligned_cols=60 Identities=10% Similarity=0.076 Sum_probs=44.4
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCc-----cccceeeecCceeEEe
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT-----FHEHALLRVDDIVDIE 85 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv-----~~e~AlLR~~DIi~~~ 85 (86)
+|.++.|++|.+.|.++..+.|++.++|....-.+-.--++.-+. .+. .++|.+-|+.+.
T Consensus 2 ~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~-~~irG~~I~~I~ 66 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGL-VFIRGSNIRYIS 66 (67)
T ss_dssp HHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEE-EEEEGGGEEEEE
T ss_pred hhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcE-EEEECCEEEEEE
Confidence 467788999999999999999999999975444443333443332 345 788998888764
No 8
>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=96.12 E-value=0.036 Score=36.66 Aligned_cols=63 Identities=16% Similarity=0.271 Sum_probs=49.2
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEeC
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~~ 86 (86)
++++|.++.|++|.+.|..++++.|+..++|..- |+..+|- .| .....++ ..||.+-|..+.+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Nl~L~~a~~~~~~~~~~~~~~-v~IRG~nI~yi~l 69 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSM-NTHLKNVKLTLKGRNPVPLDT-LSIRGNNIRYFIL 69 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCce-eEEEEEEEEEcCCCceeEcce-EEEeCCEEEEEEc
Confidence 5788899999999999999999999999999765 6666653 11 1223455 8999999987764
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=96.06 E-value=0.039 Score=34.92 Aligned_cols=59 Identities=10% Similarity=0.216 Sum_probs=45.7
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEe
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~ 85 (86)
.|..+.||+|.+.|.++..+.|++.|+| ...|+..++- ++ .-..... .++|.+.|+++.
T Consensus 4 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~~~~E~~~~~~~~~lg~-v~IRG~~I~~i~ 67 (72)
T cd01719 4 ELKKYMDKKLSLKLNGNRKVSGILRGFD-PFMNLVLDDAVEVNSGGEKNNIGM-VVIRGNSIVMLE 67 (72)
T ss_pred hhHHhCCCeEEEEECCCeEEEEEEEEEc-ccccEEeccEEEEccCCceeEece-EEECCCEEEEEE
Confidence 4667799999999999999999999999 6677766554 11 1223345 899999998874
No 10
>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=95.99 E-value=0.057 Score=34.22 Aligned_cols=62 Identities=11% Similarity=0.239 Sum_probs=48.7
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc--CCCcCc----cccceeeecCceeEEeC
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL--KTPIGT----FHEHALLRVDDIVDIEI 86 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L--~TPiGv----~~e~AlLR~~DIi~~~~ 86 (86)
|.+|.++.|++|.+.|..+.++.|+..++|.. .|+..+|- .+|=|. .++ ..+|.+-|..+.+
T Consensus 3 l~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~-mNi~L~~~~~~~~~g~~~~~~~~-v~IRG~~I~~i~~ 70 (76)
T cd01723 3 LSLLKTAQNHPMLVELKNGETYNGHLVNCDNW-MNIHLREVICTSKDGDKFWKMPE-CYIRGNTIKYLRV 70 (76)
T ss_pred hHHHHhcCCCEEEEEECCCCEEEEEEEEEcCC-CceEEEeEEEECCCCcEeeeCCc-EEEeCCEEEEEEc
Confidence 56788899999999999999999999999974 56666665 234442 245 8899999987753
No 11
>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=95.95 E-value=0.055 Score=33.85 Aligned_cols=62 Identities=11% Similarity=0.198 Sum_probs=48.1
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C-Cc---CccccceeeecCceeEEeC
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T-PI---GTFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T-Pi---Gv~~e~AlLR~~DIi~~~~ 86 (86)
+++|..+.|++|.+.|..++++.|+..++|.. .|+..++-+ + |= ....+ -.+|.+-|..+.+
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~-MNl~L~~~~~~~~~g~~~~~~~-v~IRG~nI~~v~l 68 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDN-MNCQLKDVTVTARDGRVSQLEQ-VYIRGSKIRFFIL 68 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCC-ceeEEEEEEEECCCCcEeEcCc-EEEeCCEEEEEEe
Confidence 56788899999999999999999999999984 477776662 2 22 23345 7899998877654
No 12
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=95.91 E-value=0.056 Score=32.42 Aligned_cols=59 Identities=14% Similarity=0.203 Sum_probs=44.2
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-CC-----cCccccceeeecCceeEEe
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-TP-----IGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TP-----iGv~~e~AlLR~~DIi~~~ 85 (86)
+|..+.|++|.+.|.++..+.|++.++|.. .|+..++-. +. -...+. .++|.+-|..+.
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~-~NlvL~~~~e~~~~~~~~~~~~~-~~IrG~~I~~i~ 66 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQF-MNLVLEDVEETVKDGEKKRKLGL-VFIRGNNIVYII 66 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECcc-ccEEEccEEEEecCCcEEeEeCC-EEEcCCEEEEEe
Confidence 467789999999999999999999999975 555554431 22 123345 789999888775
No 13
>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=95.83 E-value=0.061 Score=33.12 Aligned_cols=61 Identities=11% Similarity=0.314 Sum_probs=45.5
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----CcCccccceeeecCceeEEe
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----PiGv~~e~AlLR~~DIi~~~ 85 (86)
|.+|..+.|++|.+.|.++..+.|++.++|.. .|+..++- ++ .-..... -+||...|+.+.
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~-mNlvL~~~~e~~~~~~~~~lg~-~~iRG~~I~~i~ 67 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQH-MNLVLEDAEEIDDGEPVRKYGR-VVIRGDNVLFIS 67 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCc-ceEEEeeEEEEecCCeEeEcCc-EEEeCCEEEEEc
Confidence 46677889999999999999999999999974 44444443 22 1223345 789999998763
No 14
>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=95.74 E-value=0.08 Score=34.09 Aligned_cols=62 Identities=16% Similarity=0.285 Sum_probs=47.7
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC--CCcC---ccccceeeecCceeEEeC
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK--TPIG---TFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TPiG---v~~e~AlLR~~DIi~~~~ 86 (86)
+.+|..+.|++|.+.|..++.+.|+..++|..- |+..+|-+ .|-| ..++ -.+|++-|..++|
T Consensus 11 ~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~M-Nl~L~~~~~~~~~~~~~~~~~-v~IRG~nI~yI~l 77 (78)
T cd01733 11 IILLQGLQGKVVTVELRNETTVTGRIASVDAFM-NIRLAKVTIIDRNGKQVQVEE-IMVTGRNIRYVHI 77 (78)
T ss_pred HHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCc-eeEEEEEEEEcCCCceeECCc-EEEECCEEEEEEc
Confidence 456688999999999999999999999999765 66665542 2222 2355 8899999988764
No 15
>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=95.49 E-value=0.049 Score=34.62 Aligned_cols=60 Identities=15% Similarity=0.255 Sum_probs=43.4
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-----------Cc----CccccceeeecCceeEEeC
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-----------PI----GTFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-----------Pi----Gv~~e~AlLR~~DIi~~~~ 86 (86)
-|.++.|+++.+.|.++-.+.|+|.|+|... |+..+|-.= |. ..... .++|..-|+++.+
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~-NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~-v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHM-NLVLSDCEEFRKVKKKKSKNSEREEKRTLGL-VLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCcc-CEEcCCEEEEEeccccccccccCcceeEeee-EEEcCCEEEEEEE
Confidence 3667899999999999999999999999653 444333211 01 12234 7999999999864
No 16
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=95.25 E-value=0.17 Score=31.76 Aligned_cols=61 Identities=15% Similarity=0.263 Sum_probs=46.6
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC-C----CcCccccceeeecCceeEE
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK-T----PIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-T----PiGv~~e~AlLR~~DIi~~ 84 (86)
-+..|....|++|.+.|.++..+.|+..++|. ..|+..+|-. + +...... .++|.+-|+.+
T Consensus 5 P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~lg~-v~iRG~~V~~i 70 (72)
T PRK00737 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDI-HMNLVLDNAEEIQDGEVVRKLGK-VVIRGDNVVYV 70 (72)
T ss_pred hHHHHHHhCCCEEEEEECCCCEEEEEEEEEcc-cceeEEeeEEEEcCCCeEeEcCc-EEEeCCEEEEE
Confidence 35677788999999999999999999999997 5666666631 1 2223334 78999999876
No 17
>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=94.13 E-value=0.29 Score=31.38 Aligned_cols=60 Identities=20% Similarity=0.254 Sum_probs=41.8
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecc-cCCCcC----------ccccceeeecCceeEEeC
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRN-LKTPIG----------TFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~-L~TPiG----------v~~e~AlLR~~DIi~~~~ 86 (86)
.|.++.|+++.+.+.++..+.|+|.++|....-+ .++ -++..+ ...- .++|..-|+++++
T Consensus 4 ~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~Niv-L~~~~E~~~~~~~~~~~~~r~lGl-v~IrG~~Iv~i~v 74 (75)
T cd06168 4 KLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNII-LGSAQEYRPPPDSFSPTEPRVLGL-VMIPGHHIVSIEV 74 (75)
T ss_pred HHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEE-ecCcEEEEcccCccCCccEEEeee-EEEeCCeEEEEEE
Confidence 3556689999999999999999999999765433 332 222111 1222 5788988888864
No 18
>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=93.68 E-value=0.57 Score=30.01 Aligned_cols=61 Identities=16% Similarity=0.208 Sum_probs=44.0
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc----CCCc----CccccceeeecCceeEEe
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL----KTPI----GTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L----~TPi----Gv~~e~AlLR~~DIi~~~ 85 (86)
|..|.++.+++|.+.+.++..+.|+..|+|.- .|+..++- .+|= ..... -+||..-|+.+.
T Consensus 5 ~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~-mNlvL~da~E~~~~~~~~~~~~lg~-v~iRG~nV~~i~ 73 (76)
T cd01732 5 LELIDKCIGSRIWIVMKSDKEFVGTLLGFDDY-VNMVLEDVTEYEITPEGRKITKLDQ-ILLNGNNICMLV 73 (76)
T ss_pred HHHHHHhCCCEEEEEECCCeEEEEEEEEeccc-eEEEEccEEEEEEcCCCceeeEcCe-EEEeCCeEEEEE
Confidence 45677788999999999999999999999964 44444441 1222 12334 789999988763
No 19
>KOG3482|consensus
Probab=93.54 E-value=0.33 Score=32.33 Aligned_cols=58 Identities=16% Similarity=0.325 Sum_probs=46.3
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCC-----CcCccccceeeecCceeEE
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKT-----PIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~T-----PiGv~~e~AlLR~~DIi~~ 84 (86)
+|++|.||+|-+.|.=+..-+|+..++|.. -|++..+-+- .-|...| -++||+.|..+
T Consensus 12 FL~~l~gk~V~vkLKwg~eYkG~LvsvD~Y-mNlqL~~~eE~idG~~~g~lGE-ilIRCNNvlyi 74 (79)
T KOG3482|consen 12 FLNGLTGKPVLVKLKWGQEYKGTLVSVDNY-MNLQLANAEEYIDGVSTGNLGE-ILIRCNNVLYI 74 (79)
T ss_pred HHhhccCCeEEEEEecCcEEEEEEEEecch-hheehhhhhhhhccccccccee-EEEEeccEEEE
Confidence 678899999999999999999999999964 4555544332 3467778 99999999765
No 20
>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=92.59 E-value=0.57 Score=29.40 Aligned_cols=58 Identities=12% Similarity=0.307 Sum_probs=41.2
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc-----Cc----cccceeeecCceeEE
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI-----GT----FHEHALLRVDDIVDI 84 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi-----Gv----~~e~AlLR~~DIi~~ 84 (86)
.|....++++.+.|.++-.+.|+|++.|.. .|+..++=.-++ |. ..- .++|..-|+.+
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~-~NlvL~~~~E~~~~~~~~~~~~~lG~-~~iRG~~I~~i 69 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQA-TNLILDDSHERVYSSDEGVEQVVLGL-YIIRGDNIAVV 69 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccc-cCEEccceEEEEecCCCCceeeEece-EEECCCEEEEE
Confidence 366778999999999999999999999985 444444421111 11 222 68888888765
No 21
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=91.60 E-value=1.1 Score=28.15 Aligned_cols=64 Identities=16% Similarity=0.059 Sum_probs=46.4
Q ss_pred HHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCC--------cCccccceeeecCceeEEe
Q psy488 21 KFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP--------IGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 21 rfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP--------iGv~~e~AlLR~~DIi~~~ 85 (86)
..+.+|..+.|++|.+.|.++.++.|+-.|+|....-++-..-++. .....+ -+||...|+.|.
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~-~~IRG~~I~~I~ 78 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGE-VLIRGDNIVLIS 78 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccE-EEEECCcEEEEe
Confidence 4567788888899999999999999999999975544332222221 122235 899999998774
No 22
>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=89.68 E-value=1.9 Score=27.52 Aligned_cols=60 Identities=7% Similarity=0.154 Sum_probs=42.0
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCC------------------cCccccceeeecCceeEE
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP------------------IGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP------------------iGv~~e~AlLR~~DIi~~ 84 (86)
|..|....+++|.+.|.++..+.|+..|+|.-- |+..++-+-- ...... .+||..-|+++
T Consensus 3 l~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~m-NlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~-~~iRGd~Vv~i 80 (82)
T cd01730 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHL-NMILGDVEETITTVEIDEETYEEIVKTTKRNIPM-LFVRGDSVILV 80 (82)
T ss_pred hHHHHHhCCCEEEEEECCCCEEEEEEEEEccce-EEeccceEEEeecccccccccccccceeEEEcCe-EEEeCCEEEEE
Confidence 345566689999999999999999999999754 5554433111 111223 68888888776
No 23
>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=89.58 E-value=2.5 Score=26.98 Aligned_cols=60 Identities=3% Similarity=0.015 Sum_probs=42.4
Q ss_pred HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CCCcCc-------cccceeeecCceeEE
Q psy488 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KTPIGT-------FHEHALLRVDDIVDI 84 (86)
Q Consensus 23 Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~TPiGv-------~~e~AlLR~~DIi~~ 84 (86)
+..|.+..++++.+.+.++..+.|+++++|.- .|+..++- ++-... ... .++|..-|+.+
T Consensus 4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~-~NlvL~d~~E~~~~~~~~~~~~lG~-~viRG~~V~~i 71 (74)
T cd01728 4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQF-ANLVLQDTVERIYVGDKYGDIPRGI-FIIRGENVVLL 71 (74)
T ss_pred hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCc-ccEEecceEEEEecCCccceeEeeE-EEEECCEEEEE
Confidence 34567789999999999999999999999954 45555443 221111 113 58898888765
No 24
>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=89.34 E-value=2 Score=27.67 Aligned_cols=58 Identities=14% Similarity=0.147 Sum_probs=40.7
Q ss_pred HHhcCCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC------------CcCccccceeeecCceeEEe
Q psy488 26 MSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT------------PIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 26 l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T------------PiGv~~e~AlLR~~DIi~~~ 85 (86)
|.++.|+++.+.|.++..+.|++.+.|..- |+..++= +. .-..... .++|+.-|+++.
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~m-NlvL~~~~E~~~~~~~~~~~~~~~~~lG~-v~iRG~nV~~i~ 77 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLL-NLVLDDTVEYLRDPDDPYKLTDKTRQLGL-VVCRGTSVVLIS 77 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCcc-cEEecCEEEEEccCCcccccccceeEccE-EEEcCCEEEEEe
Confidence 677899999999999999999999999743 2222221 11 1111234 799999998763
No 25
>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=87.18 E-value=3.3 Score=27.30 Aligned_cols=60 Identities=12% Similarity=0.213 Sum_probs=40.6
Q ss_pred HHHHhc--CCCceEEEeecCcEEEEEEeeecCCcceeeeccc-CC----Cc------------C-ccccceeeecCceeE
Q psy488 24 KAMSSL--SGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNL-KT----PI------------G-TFHEHALLRVDDIVD 83 (86)
Q Consensus 24 r~l~~~--~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L-~T----Pi------------G-v~~e~AlLR~~DIi~ 83 (86)
..|... .|++|.+.|..+..+.|++.|+|.- .|+..++- ++ |- . .... .+||..-||+
T Consensus 5 ~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~h-mNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~-v~iRGd~Vv~ 82 (87)
T cd01720 5 SLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRH-CNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISK-MFLRGDSVIL 82 (87)
T ss_pred HHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCc-cEEEEcceEEEeeccccccccccccceeeeeEccc-EEEeCCEEEE
Confidence 344444 4899999999999999999999974 34443332 11 11 1 1244 7899988887
Q ss_pred Ee
Q psy488 84 IE 85 (86)
Q Consensus 84 ~~ 85 (86)
+.
T Consensus 83 Is 84 (87)
T cd01720 83 VL 84 (87)
T ss_pred Ee
Confidence 63
No 26
>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=78.89 E-value=5.6 Score=22.90 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=24.4
Q ss_pred CCCceEEEeecCcEEEEEEeeecCCccee
Q psy488 30 SGQPCTINMFERTVVTAEFQGTNSDLTEF 58 (86)
Q Consensus 30 ~gk~v~f~m~E~t~V~a~F~a~d~d~~~f 58 (86)
.|++|.+.+ .+-.+.|.+.+.|.++.-+
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEE
Confidence 489999999 7777899999999998765
No 27
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=77.17 E-value=19 Score=24.01 Aligned_cols=51 Identities=14% Similarity=0.240 Sum_probs=35.2
Q ss_pred ceEEEeecC--cEEEEEEeeecCCcceeeecccC-C-----CcCccccceeeecCceeEEe
Q psy488 33 PCTINMFER--TVVTAEFQGTNSDLTEFYVRNLK-T-----PIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 33 ~v~f~m~E~--t~V~a~F~a~d~d~~~f~Vs~L~-T-----PiGv~~e~AlLR~~DIi~~~ 85 (86)
+|.+.+.++ ..+.|+..|+|.-- |+..+|-+ . .-..... .+||++-|+.+.
T Consensus 28 ~V~i~l~~~~~r~~~G~L~gfD~~m-NlVL~d~~E~~~~~~~~~~lG~-ilIRGnnV~~I~ 86 (89)
T PTZ00138 28 RVQIWLYDHPNLRIEGKILGFDEYM-NMVLDDAEEVYTKKNTRKDLGR-ILLKGDNITLIM 86 (89)
T ss_pred EEEEEEEeCCCcEEEEEEEEEcccc-eEEEccEEEEecCCceeeEcCe-EEEcCCEEEEEE
Confidence 677777675 88999999999754 66655531 1 1122345 899999998874
No 28
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=75.01 E-value=19 Score=22.95 Aligned_cols=54 Identities=19% Similarity=0.249 Sum_probs=40.0
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEEe
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~ 85 (86)
+...|+++.|+.|.+.. .+-.+.|+..++.+|-- .++.=. .. -.+|.+-|+++.
T Consensus 12 vyq~lq~liG~~vvV~T-~~g~v~G~L~~V~pDhI--vl~~~~------~~-~~IR~~~IV~v~ 65 (66)
T PF10842_consen 12 VYQTLQSLIGQRVVVQT-TRGSVRGILVDVKPDHI--VLEENG------TP-FFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHHhcCCEEEEEE-cCCcEEEEEEeecCCEE--EEEeCC------cE-EEEEeeeEEEEc
Confidence 45789999999999999 55567999988888844 443222 22 788888888874
No 29
>KOG3428|consensus
Probab=67.30 E-value=10 Score=26.59 Aligned_cols=38 Identities=13% Similarity=0.297 Sum_probs=32.3
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceee
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFY 59 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~ 59 (86)
-+++|.++.+..++|.|.+.+.|.|+..++|..-.-..
T Consensus 3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l 40 (109)
T KOG3428|consen 3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHL 40 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEE
Confidence 46888999999999999999999999999997544333
No 30
>PRK06955 biotin--protein ligase; Provisional
Probab=65.96 E-value=25 Score=27.13 Aligned_cols=38 Identities=13% Similarity=0.195 Sum_probs=29.2
Q ss_pred HhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcC
Q psy488 27 SSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68 (86)
Q Consensus 27 ~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiG 68 (86)
....|++|.+...++..+.|++.+.|.++.-. | +++=|
T Consensus 245 ~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-v---~~~~g 282 (300)
T PRK06955 245 HAYAGREVVLLEDGAELARGVAHGIDETGQLL-L---DTPAG 282 (300)
T ss_pred hhcCCCeEEEEECCCcEEEEEEeeECCCceEE-E---EeCCC
Confidence 34579999997666777999999999988764 3 46655
No 31
>KOG3448|consensus
Probab=65.62 E-value=12 Score=25.67 Aligned_cols=33 Identities=12% Similarity=0.277 Sum_probs=29.2
Q ss_pred HHHHHHhcCCCceEEEeecCcEEEEEEeeecCC
Q psy488 22 FLKAMSSLSGQPCTINMFERTVVTAEFQGTNSD 54 (86)
Q Consensus 22 fLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d 54 (86)
|-.+...+.|+.|.+.|.....+.|+.+++|..
T Consensus 3 FysfFkslvg~~V~VeLKnd~~i~GtL~svDqy 35 (96)
T KOG3448|consen 3 FYSFFKSLVGKEVVVELKNDLSICGTLHSVDQY 35 (96)
T ss_pred hHHHHHHhcCCeEEEEEcCCcEEEEEecccchh
Confidence 556677889999999999999999999999864
No 32
>PRK02001 hypothetical protein; Validated
Probab=65.42 E-value=16 Score=26.26 Aligned_cols=38 Identities=8% Similarity=0.135 Sum_probs=31.4
Q ss_pred HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeec
Q psy488 24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVR 61 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs 61 (86)
+-+....|++|.+.++++..+.|+..+.+-+.-.+.++
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~ 120 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADENDITLEVK 120 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEc
Confidence 34556789999999999999999999999776666655
No 33
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=65.28 E-value=22 Score=27.15 Aligned_cols=40 Identities=10% Similarity=0.137 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceee
Q psy488 18 MREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFY 59 (86)
Q Consensus 18 LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~ 59 (86)
++++|.+... ..|++|.|...+ ..++|+|.+.|.++.-..
T Consensus 260 ~~~~~~~~~~-~~g~~v~~~~~~-~~~~G~~~gi~~~G~L~i 299 (319)
T PRK11886 260 FLERWKKLDL-FLGREVKLIIGD-KEISGIARGIDEQGALLL 299 (319)
T ss_pred HHHHHHHhcc-ccCCeEEEEeCC-cEEEEEEEEECCCceEEE
Confidence 4455544433 359999998754 569999999998886643
No 34
>PRK14638 hypothetical protein; Provisional
Probab=62.21 E-value=22 Score=25.30 Aligned_cols=52 Identities=12% Similarity=0.095 Sum_probs=35.9
Q ss_pred HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeec--ccCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVR--NLKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs--~L~TPiGv~~e~AlL 76 (86)
+-+....|+.|.++++++..++|+..+.|-+.-.+.+. ..+=|+..++. |.|
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~~~~~~~i~~~~I~~-a~l 146 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDGTITISDEKEKYEINIDDVKR-ANL 146 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEECCcEEEEEhHHcce-EEE
Confidence 34556789999999999999999999988654333321 22236666655 554
No 35
>PRK14639 hypothetical protein; Provisional
Probab=60.71 E-value=20 Score=25.16 Aligned_cols=52 Identities=8% Similarity=0.084 Sum_probs=37.7
Q ss_pred HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeee-c---ccCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYV-R---NLKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~V-s---~L~TPiGv~~e~AlL 76 (86)
+-+....|++|.+.+.++-.++|+..+.|-+.-.+.. . ..+-|+..++. |-|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k-a~l 136 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK-AKT 136 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee-EEE
Confidence 4456678999999999999999999998776555522 2 24556666665 554
No 36
>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=59.10 E-value=32 Score=21.73 Aligned_cols=52 Identities=13% Similarity=0.322 Sum_probs=35.5
Q ss_pred HHHHhcCCCceEEEee---cC-cEEEEEEeeecCCcceeeec------ccCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMF---ER-TVVTAEFQGTNSDLTEFYVR------NLKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~---E~-t~V~a~F~a~d~d~~~f~Vs------~L~TPiGv~~e~AlL 76 (86)
+-+....|+.|.+.++ ++ .++.|...+.|-+.--+.+. .+.-|+.-++. |-|
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k-a~l 79 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK-ARL 79 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE-EEE
Confidence 3455678999999998 33 46899999998877666654 33345555544 443
No 37
>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=53.90 E-value=59 Score=21.09 Aligned_cols=50 Identities=14% Similarity=0.214 Sum_probs=34.6
Q ss_pred ceEEEee--cCcEEEEEEeeecCCcceeeeccc-CC-----CcCccccceeeecCceeEE
Q psy488 33 PCTINMF--ERTVVTAEFQGTNSDLTEFYVRNL-KT-----PIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 33 ~v~f~m~--E~t~V~a~F~a~d~d~~~f~Vs~L-~T-----PiGv~~e~AlLR~~DIi~~ 84 (86)
+|.+.+. .+..+.|+..|+|.-- |+..+|= ++ ..+.... .++|+.-|+.+
T Consensus 20 ~V~V~l~~~~g~~~~G~L~gfD~~m-NlvL~d~~E~~~~~~~~~~lG~-iliRGnnV~~I 77 (79)
T cd01718 20 RVQIWLYEQTDLRIEGVIIGFDEYM-NLVLDDAEEVHLKTKTRKPLGR-ILLKGDNITLI 77 (79)
T ss_pred EEEEEEEeCCCcEEEEEEEEEccce-eEEEcCEEEEecCCceEeEcCc-EEEeCCEEEEE
Confidence 6777766 7888999999999755 6665552 11 1123334 79999998875
No 38
>PRK14632 hypothetical protein; Provisional
Probab=51.76 E-value=40 Score=24.51 Aligned_cols=37 Identities=16% Similarity=0.293 Sum_probs=28.4
Q ss_pred HHHHhcCCCceEEEeec-------CcEEEEEEeeecCCcceeee
Q psy488 24 KAMSSLSGQPCTINMFE-------RTVVTAEFQGTNSDLTEFYV 60 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E-------~t~V~a~F~a~d~d~~~f~V 60 (86)
+-+....|+.|.+.+++ +.++.|+....+-+.--+.+
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~ 134 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRP 134 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEE
Confidence 34556789999999998 56899999998766554444
No 39
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=48.26 E-value=71 Score=24.24 Aligned_cols=34 Identities=9% Similarity=0.100 Sum_probs=29.5
Q ss_pred cCCCceEEEeecCcEEEEEEeeecCCcceeeecc
Q psy488 29 LSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRN 62 (86)
Q Consensus 29 ~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~ 62 (86)
..|++|.+....+....|.+.+.|-++.-..-.+
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4899999999999999999999999998765544
No 40
>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=47.26 E-value=79 Score=23.19 Aligned_cols=31 Identities=13% Similarity=0.130 Sum_probs=24.4
Q ss_pred HhcCCCceEEEeecCcEEEEEEeeecCCccee
Q psy488 27 SSLSGQPCTINMFERTVVTAEFQGTNSDLTEF 58 (86)
Q Consensus 27 ~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f 58 (86)
....|++|.|.-. +..+.|++.+.|.++.-.
T Consensus 189 ~~~~g~~V~v~~~-~~~~~G~~~gI~~~G~L~ 219 (237)
T TIGR00121 189 SAHIGREVSLTTG-NGEIEGIARGIDKDGALL 219 (237)
T ss_pred hhccCCeEEEEeC-CcEEEEEEEeECCCceEE
Confidence 3457999999864 456899999999998654
No 41
>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=47.26 E-value=71 Score=20.10 Aligned_cols=53 Identities=9% Similarity=0.176 Sum_probs=36.3
Q ss_pred HHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCcccccee
Q psy488 19 REKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75 (86)
Q Consensus 19 RerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~Al 75 (86)
-+.||..+ .-.+.||++.|-.+..+.|...++|...--.-+.. .+--++|. |+
T Consensus 4 Qd~fln~~-r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~g--~qqLIYKh-AI 56 (61)
T TIGR02383 4 QDQFLNTL-RKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQG--KQQLIYKH-AI 56 (61)
T ss_pred HHHHHHHH-HHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEECC--cEEEEEEE-EE
Confidence 34555543 33678999999999999999999997765555443 23344444 54
No 42
>PRK14636 hypothetical protein; Provisional
Probab=46.44 E-value=51 Score=24.13 Aligned_cols=56 Identities=20% Similarity=0.328 Sum_probs=37.7
Q ss_pred HHHHhcCCCceEEEee----cCcEEEEEEeeecCCcceeeec---ccCCCcCccccceeeecCc
Q psy488 24 KAMSSLSGQPCTINMF----ERTVVTAEFQGTNSDLTEFYVR---NLKTPIGTFHEHALLRVDD 80 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~----E~t~V~a~F~a~d~d~~~f~Vs---~L~TPiGv~~e~AlLR~~D 80 (86)
+-+....|++|.++++ .+.+++|+..+.+-+.--+.+. ...=|+.-++. |-|-..|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~~~~~~i~~~~I~k-A~l~~~~ 153 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNKAGEVILPFAAIES-AKLILTD 153 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcCCcEEEEEhHHcce-EEEeccH
Confidence 4556678999999998 3467999999887765555442 33346666666 6554443
No 43
>PRK08330 biotin--protein ligase; Provisional
Probab=46.06 E-value=97 Score=22.77 Aligned_cols=31 Identities=10% Similarity=-0.074 Sum_probs=23.6
Q ss_pred hcCCCceEEEeecCcEEEEEEeeecCCccee
Q psy488 28 SLSGQPCTINMFERTVVTAEFQGTNSDLTEF 58 (86)
Q Consensus 28 ~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f 58 (86)
...|++|.+....+....|+|.+.|.++.-.
T Consensus 185 ~~~g~~v~~~~~~~~~~~G~~~gI~~~G~L~ 215 (236)
T PRK08330 185 MILGKRVKIIGDGEILVEGIAEDIDEFGALI 215 (236)
T ss_pred HhcCCeEEEEECCcEEEEEEEEEECCCCEEE
Confidence 4579999998644443479999999988664
No 44
>PRK14647 hypothetical protein; Provisional
Probab=42.89 E-value=81 Score=22.44 Aligned_cols=52 Identities=17% Similarity=0.378 Sum_probs=36.0
Q ss_pred HHHHhcCCCceEEEeec---------CcEEEEEEeeecCCcceeeecc---cCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMFE---------RTVVTAEFQGTNSDLTEFYVRN---LKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E---------~t~V~a~F~a~d~d~~~f~Vs~---L~TPiGv~~e~AlL 76 (86)
+-+....|++|.+++++ +..++|+....+-+.-.+.+.+ ++=|+.-+.. |.|
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~i~~~~I~k-a~l 155 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKEGQQARIPLDKIAK-ANL 155 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcCCcEEEEEHHHCCE-EEE
Confidence 45667789999999975 5779999999886655554432 3336666655 554
No 45
>PRK14631 hypothetical protein; Provisional
Probab=42.74 E-value=72 Score=23.35 Aligned_cols=54 Identities=17% Similarity=0.238 Sum_probs=36.7
Q ss_pred HHHHhcCCCceEEEeec----CcEEEEEEeeecCCcceeeec--c---cCCCcCccccceeeec
Q psy488 24 KAMSSLSGQPCTINMFE----RTVVTAEFQGTNSDLTEFYVR--N---LKTPIGTFHEHALLRV 78 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E----~t~V~a~F~a~d~d~~~f~Vs--~---L~TPiGv~~e~AlLR~ 78 (86)
+-+....|+.|.+.+++ +..++|+..+.|.+...+.+. + +.-|+.-++. |-|=.
T Consensus 110 ~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~~~~~i~~~~I~k-a~L~~ 172 (174)
T PRK14631 110 EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGKHVLDIDSNNIDK-ANLIY 172 (174)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCCcEEEEEhHHcce-EEEee
Confidence 44556789999999984 477999999998444454432 2 4447776666 65533
No 46
>PRK14643 hypothetical protein; Provisional
Probab=42.58 E-value=59 Score=23.56 Aligned_cols=51 Identities=8% Similarity=0.024 Sum_probs=35.6
Q ss_pred HHHhcCCCceEEEeec----CcEEEEEEeeecCCcceee----e----cccCCCcCccccceee
Q psy488 25 AMSSLSGQPCTINMFE----RTVVTAEFQGTNSDLTEFY----V----RNLKTPIGTFHEHALL 76 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E----~t~V~a~F~a~d~d~~~f~----V----s~L~TPiGv~~e~AlL 76 (86)
-+....|++|.+.+++ +...+|...++|-+...+. + ..++-|+.-++. |-|
T Consensus 98 df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~k-arl 160 (164)
T PRK14643 98 ELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKF-IRY 160 (164)
T ss_pred HHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhh-eEe
Confidence 3455679999999998 5778999999887655543 2 245557766665 544
No 47
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=41.83 E-value=1.1e+02 Score=23.64 Aligned_cols=29 Identities=14% Similarity=0.213 Sum_probs=24.0
Q ss_pred cCCCceEEEeecCcEEEEEEeeecCCccee
Q psy488 29 LSGQPCTINMFERTVVTAEFQGTNSDLTEF 58 (86)
Q Consensus 29 ~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f 58 (86)
..|++|.+.. ++..+.|.|.+.|.|+.-+
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~ 263 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLL 263 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEE
Confidence 4799999975 5678999999999998654
No 48
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=41.46 E-value=57 Score=21.60 Aligned_cols=54 Identities=13% Similarity=0.238 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCcccccee
Q psy488 18 MREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75 (86)
Q Consensus 18 LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~Al 75 (86)
|-+.||-.+ .-.+.+|++.|-.+..+.|...++|-..--.-+.. .+--++|. ||
T Consensus 7 lQd~fLn~l-r~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g--kqqLIYKH-AI 60 (79)
T PRK00395 7 LQDPFLNAL-RKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG--KSQLVYKH-AI 60 (79)
T ss_pred hHHHHHHHH-HHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC--cEEEEEEe-ee
Confidence 445666544 34678999999999999999999998766555554 22245554 54
No 49
>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=38.73 E-value=71 Score=23.56 Aligned_cols=41 Identities=5% Similarity=0.063 Sum_probs=30.9
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCC
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP 66 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TP 66 (86)
.|+...||+|.+++.| .+..|---.+|+-..++-.-+.++.
T Consensus 11 ~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e~ 51 (166)
T PF06372_consen 11 EWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQED 51 (166)
T ss_dssp HHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-TT
T ss_pred HHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEcccC
Confidence 4677899999999999 9999999999998888877766664
No 50
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=37.86 E-value=29 Score=22.09 Aligned_cols=20 Identities=20% Similarity=0.503 Sum_probs=15.9
Q ss_pred cHHHHHHHHHHHHHHHHHHh
Q psy488 9 RSDEEIAAEMREKFLKAMSS 28 (86)
Q Consensus 9 ~~eQ~aRa~LRerfLr~l~~ 28 (86)
.+|..=|+.||..||..+-+
T Consensus 21 ~eE~~Eq~~LR~eYl~~fR~ 40 (65)
T PF05979_consen 21 EEEKAEQAELRQEYLQNFRG 40 (65)
T ss_dssp HHHHHHHHHHHHHHHHTTHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 46677789999999987654
No 51
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=37.13 E-value=1e+02 Score=18.92 Aligned_cols=49 Identities=27% Similarity=0.394 Sum_probs=37.6
Q ss_pred CCCceEEEeecCc---EEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEE
Q psy488 30 SGQPCTINMFERT---VVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 30 ~gk~v~f~m~E~t---~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~ 84 (86)
.+.+|+|+.+++- +++|.....|.....+.+.+ +-|-. --+...||+++
T Consensus 41 ~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~---~~~~~---~~I~~~~I~~I 92 (92)
T PF08863_consen 41 ENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKD---EDGET---EKIPFDDIIDI 92 (92)
T ss_pred CCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEe---CCCCE---EEEEhhhEEEC
Confidence 6889999999875 49999999999999999988 11332 34666777653
No 52
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=36.02 E-value=1.3e+02 Score=20.08 Aligned_cols=57 Identities=14% Similarity=0.240 Sum_probs=46.6
Q ss_pred hcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCc--------------cccceeeecCceeEEe
Q psy488 28 SLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGT--------------FHEHALLRVDDIVDIE 85 (86)
Q Consensus 28 ~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv--------------~~e~AlLR~~DIi~~~ 85 (86)
...|+.+.+.-..+..-.|..-..|...+.+...|... +|+ .-+.-++|.+||=.+.
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~-~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~ 75 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRS-FGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLK 75 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEE-TTETTSS-SS---C-CSSSSEEEEETTTEEEEE
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeee-cCcCCCCcCcccCCCCceeeEEEEEccccceEE
Confidence 45799999999999999999999999999998888653 455 3344889999996664
No 53
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=33.65 E-value=1.3e+02 Score=25.84 Aligned_cols=31 Identities=13% Similarity=0.075 Sum_probs=25.8
Q ss_pred cCCCceEEEeecCcEEEEEEeeecCCcceee
Q psy488 29 LSGQPCTINMFERTVVTAEFQGTNSDLTEFY 59 (86)
Q Consensus 29 ~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~ 59 (86)
..|++|.+...++..+.|++.+.|.++.-..
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l 306 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHL 306 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEE
Confidence 5799999976677789999999999886543
No 54
>KOG1783|consensus
Probab=33.14 E-value=32 Score=22.85 Aligned_cols=55 Identities=11% Similarity=0.218 Sum_probs=39.2
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeec--------ccCCCcCccccceeeecCceeEE
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVR--------NLKTPIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs--------~L~TPiGv~~e~AlLR~~DIi~~ 84 (86)
+|.++.||||.+.+...+.-.|+..+.|-- .|+..+ +|+--. .. |-||.+-|..|
T Consensus 10 fl~~iiGr~V~VKl~sgvdyrG~l~~lDgy-mNiaLe~tee~~ngql~n~y---gd-aFirGnnVlyI 72 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNSGVDYRGTLVCLDGY-MNIALESTEEYVNGQLKNKY---GD-AFIRGNNVLYI 72 (77)
T ss_pred HHHHHhCCeEEEEecCCccccceehhhhhH-HHHHHHHHHHHhcCcccccc---cc-eeeccccEEEE
Confidence 577889999999999999999999888742 233322 233333 35 88888877554
No 55
>PF00058 Ldl_recept_b: Low-density lipoprotein receptor repeat class B; InterPro: IPR000033 The low-density lipoprotein receptor (LDLR) is the major cholesterol-carrying lipoprotein of plasma, acting to regulate cholesterol homeostasis in mammalian cells. The LDL receptor binds LDL and transports it into cells by acidic endocytosis. In order to be internalized, the receptor-ligand complex must first cluster into clathrin-coated pits. Once inside the cell, the LDLR separates from its ligand, which is degraded in the lysosomes, while the receptor returns to the cell surface []. The internal dissociation of the LDLR with its ligand is mediated by proton pumps within the walls of the endosome that lower the pH. The LDLR is a multi-domain protein, containing: The ligand-binding domain contains seven or eight 40-amino acid LDLR class A (cysteine-rich) repeats, each of which contains a coordinated calcium ion and six cysteine residues involved in disulphide bond formation []. Similar domains have been found in other extracellular and membrane proteins []. The second conserved region contains two EGF repeats, followed by six LDLR class B (YWTD) repeats, and another EGF repeat. The LDLR class B repeats each contain a conserved YWTD motif, and is predicted to form a beta-propeller structure []. This region is critical for ligand release and recycling of the receptor []. The third domain is rich in serine and threonine residues and contains clustered O-linked carbohydrate chains. The fourth domain is the hydrophobic transmembrane region. The fifth domain is the cytoplasmic tail that directs the receptor to clathrin-coated pits. LDLR is closely related in structure to several other receptors, including LRP1, LRP1b, megalin/LRP2, VLDL receptor, lipoprotein receptor, MEGF7/LRP4, and LRP8/apolipoprotein E receptor2); these proteins participate in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins []. This entry represents the LDLR classB (YWTD) repeat, the structure of which has been solved []. The six YWTD repeats together fold into a six-bladed beta-propeller. Each blade of the propeller consists of four antiparallel beta-strands; the innermost strand of each blade is labeled 1 and the outermost strand, 4. The sequence repeats are offset with respect to the blades of the propeller, such that any given 40-residue YWTD repeat spans strands 24 of one propeller blade and strand 1 of the subsequent blade. This offset ensures circularization of the propeller because the last strand of the final sequence repeat acts as an innermost strand 1 of the blade that harbors strands 24 from the first sequence repeat. The repeat is found in a variety of proteins that include, vitellogenin receptor from Drosophila melanogaster, low-density lipoprotein (LDL) receptor [], preproepidermal growth factor, and nidogen (entactin).; PDB: 3S2K_A 3S8Z_A 3S8V_B 4A0P_A 3SOB_B 3S94_B 4DG6_A 3SOV_A 3SOQ_A 1NPE_A ....
Probab=32.84 E-value=43 Score=18.60 Aligned_cols=24 Identities=21% Similarity=0.329 Sum_probs=16.6
Q ss_pred EEEeeecCCcce---eeecccCCCcCc
Q psy488 46 AEFQGTNSDLTE---FYVRNLKTPIGT 69 (86)
Q Consensus 46 a~F~a~d~d~~~---f~Vs~L~TPiGv 69 (86)
+....++.|+++ +.-++|+.|-|+
T Consensus 12 ~~I~~a~~dGs~~~~vi~~~l~~P~gi 38 (42)
T PF00058_consen 12 PSIERANLDGSNRRTVISDDLQHPEGI 38 (42)
T ss_dssp EEEEEEETTSTSEEEEEESSTSSEEEE
T ss_pred cEEEEEECCCCCeEEEEECCCCCcCEE
Confidence 455666666666 566788888775
No 56
>PF10907 DUF2749: Protein of unknown function (DUF2749); InterPro: IPR024475 This bacterial family of proteins represent the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon [].
Probab=32.79 E-value=44 Score=21.64 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=11.9
Q ss_pred cCCCcHHHHHHHHHHHHHHH
Q psy488 5 RTSSRSDEEIAAEMREKFLK 24 (86)
Q Consensus 5 ~~~~~~eQ~aRa~LRerfLr 24 (86)
...+++||+++ ||+|+-
T Consensus 32 ~p~s~eeQr~~---re~ff~ 48 (66)
T PF10907_consen 32 NPASSEEQRAH---REKFFG 48 (66)
T ss_pred CCCChHHHHHH---HHHHcC
Confidence 45567788765 888864
No 57
>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=32.44 E-value=98 Score=19.40 Aligned_cols=32 Identities=9% Similarity=0.093 Sum_probs=26.9
Q ss_pred CCCceEEEeecCcEEEEEEeeecCCcceeeec
Q psy488 30 SGQPCTINMFERTVVTAEFQGTNSDLTEFYVR 61 (86)
Q Consensus 30 ~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs 61 (86)
...||++.|-.+..+.|...++|...--.-+.
T Consensus 10 ~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 10 EKIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred cCCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 67799999999999999999999766555444
No 58
>PHA02947 S-S bond formation pathway protein; Provisional
Probab=30.72 E-value=39 Score=26.21 Aligned_cols=46 Identities=17% Similarity=0.380 Sum_probs=34.4
Q ss_pred HHHHHHHHHhc---CCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc
Q psy488 19 REKFLKAMSSL---SGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI 67 (86)
Q Consensus 19 RerfLr~l~~~---~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi 67 (86)
=||||+-|+.- +.-.|.++.-+ +.|++++|...+.|...+|=+.-+
T Consensus 15 ~~ryL~kL~~~s~~~n~~C~I~IG~---I~g~~k~C~v~V~N~C~sna~~sf 63 (215)
T PHA02947 15 IERYLQNLSLYSVPTNTTCGIHIGE---IKGQFKRCKLRIINKCLNNKRLSF 63 (215)
T ss_pred HHHHHHHHHhccCcccccccEEEee---eeeecCCceEEEEEhhcCCHHHHH
Confidence 48999988876 44466666654 459999999999999888755443
No 59
>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=30.38 E-value=79 Score=20.55 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=28.2
Q ss_pred HhcCCCceEEEeecCcEEEEEEeeecCC--cceeeecccCCCcCccccceeeecCceeEEe
Q psy488 27 SSLSGQPCTINMFERTVVTAEFQGTNSD--LTEFYVRNLKTPIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 27 ~~~~gk~v~f~m~E~t~V~a~F~a~d~d--~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~ 85 (86)
.-|.+-|+.++|.++..+.|++.-+-.+ -.++++ |++ ..+.-.||...|++++
T Consensus 13 AC~~~~~v~L~l~dG~~~~g~A~dt~~~~~k~E~L~--l~~----~~~~~~i~Ld~I~~~~ 67 (80)
T PF07073_consen 13 ACMYRYPVKLTLKDGEQIEGKALDTRTNAKKEECLV--LEQ----DGGEQEIRLDQIASMS 67 (80)
T ss_dssp HHTTTT-EEEE-TTT--EEESS-EEE---SSS-EEE--EEE----TTEEEEESTT--SEEE
T ss_pred HHhcCCeEEEEEeCCCEEEEEEEEEEEecCceEEEE--Eec----CCcEEEEEhhheeeee
Confidence 4577889999999999999976654433 444544 222 1222468888888775
No 60
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=29.62 E-value=1.1e+02 Score=21.21 Aligned_cols=67 Identities=16% Similarity=0.177 Sum_probs=50.2
Q ss_pred HHHHHH-HHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccC--CCcCccccceeeecCceeEE
Q psy488 17 EMREKF-LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLK--TPIGTFHEHALLRVDDIVDI 84 (86)
Q Consensus 17 ~LRerf-Lr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~--TPiGv~~e~AlLR~~DIi~~ 84 (86)
.||+.| -++|.-..|..|.+.--..--..|++..++.....+.|+.+- +|=|+..| |=|..+-|..+
T Consensus 30 elr~~y~~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~~e-~pIh~SnV~l~ 99 (114)
T TIGR01080 30 ELREKYGKRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTEVP-VPIHPSNVMIT 99 (114)
T ss_pred HHHHHcCcccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeEEE-eeechHHeEEE
Confidence 577877 777766688888887777777889999999888889998765 66676666 66666665443
No 61
>PRK14640 hypothetical protein; Provisional
Probab=29.59 E-value=1.5e+02 Score=21.00 Aligned_cols=52 Identities=12% Similarity=0.211 Sum_probs=33.5
Q ss_pred HHHHhcCCCceEEEee----cCcEEEEEEeeecCCcceeeec--ccCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMF----ERTVVTAEFQGTNSDLTEFYVR--NLKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~----E~t~V~a~F~a~d~d~~~f~Vs--~L~TPiGv~~e~AlL 76 (86)
+-+....|++|.+.++ .+..++|+..++|-+.--+.+. ...=|+.-++. |-|
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~~~~~~i~~~~I~k-a~l 147 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQK-ANI 147 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEECCeEEEEEhHHeee-EEE
Confidence 4456678999999996 4578999999886544333332 22235555555 544
No 62
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=29.48 E-value=56 Score=25.49 Aligned_cols=43 Identities=7% Similarity=0.233 Sum_probs=33.1
Q ss_pred cCCCcHHHHHHHHHHHHHHHHHHhcCCCc--eEEEeecCcEEEEE
Q psy488 5 RTSSRSDEEIAAEMREKFLKAMSSLSGQP--CTINMFERTVVTAE 47 (86)
Q Consensus 5 ~~~~~~eQ~aRa~LRerfLr~l~~~~gk~--v~f~m~E~t~V~a~ 47 (86)
.+-..+|++.|..||+-||..--++.+.+ +.|.-++++...+.
T Consensus 70 k~Re~~E~~~Re~LRkE~~~~Qe~vK~eeI~I~fsywDGs~hrr~ 114 (239)
T PF04921_consen 70 KEREEEEAQEREELRKEWLAKQEAVKAEEIEIPFSYWDGSGHRRT 114 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCeeEEEEEEECCCCCcce
Confidence 34456778889999999999999998885 55667887776653
No 63
>PRK02539 hypothetical protein; Provisional
Probab=29.25 E-value=71 Score=21.47 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=16.8
Q ss_pred CcHHHHHHHHHHHHHHHHHHhc
Q psy488 8 SRSDEEIAAEMREKFLKAMSSL 29 (86)
Q Consensus 8 ~~~eQ~aRa~LRerfLr~l~~~ 29 (86)
..+|.+=|..||..||..+-+-
T Consensus 22 T~eEk~Eq~~LR~eYl~~fR~~ 43 (85)
T PRK02539 22 TGEEKVEQAKLREEYIEGYRRS 43 (85)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH
Confidence 3466777889999999887653
No 64
>PRK01631 hypothetical protein; Provisional
Probab=29.24 E-value=73 Score=20.98 Aligned_cols=21 Identities=5% Similarity=0.291 Sum_probs=16.1
Q ss_pred CcHHHHHHHHHHHHHHHHHHh
Q psy488 8 SRSDEEIAAEMREKFLKAMSS 28 (86)
Q Consensus 8 ~~~eQ~aRa~LRerfLr~l~~ 28 (86)
..+|..=|..||+.||...-+
T Consensus 21 T~eE~~Eq~~LR~eYl~~fR~ 41 (76)
T PRK01631 21 TVDEKQEQQMLRQNYTQTFRG 41 (76)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 346677788999999987654
No 65
>PF15538 Toxin_61: Putative toxin 61
Probab=28.94 E-value=2.1e+02 Score=21.22 Aligned_cols=73 Identities=16% Similarity=0.175 Sum_probs=56.4
Q ss_pred cHHHHHHHHH------HHHHHHHHHhc-CCCceEEEeecCcEEEEEEeeecCCcceee---ecccCCCcCccccceeeec
Q psy488 9 RSDEEIAAEM------REKFLKAMSSL-SGQPCTINMFERTVVTAEFQGTNSDLTEFY---VRNLKTPIGTFHEHALLRV 78 (86)
Q Consensus 9 ~~eQ~aRa~L------RerfLr~l~~~-~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~---Vs~L~TPiGv~~e~AlLR~ 78 (86)
...+.|+.|. +++++..|.+| -.+||.+..-.+-+.-..|.+.+.-.-|+. ++---|-||+-|+ .-+|-
T Consensus 23 gn~e~a~~F~~s~G~~~~~~~~~m~GIDf~~PV~VetIn~Gk~~yQ~q~pg~~qGnwys~~~~~~pt~LGINP~-g~~~~ 101 (157)
T PF15538_consen 23 GNREIASDFFKSQGLTEADMESYMNGIDFSKPVKVETINRGKNLYQNQRPGGWQGNWYSPDENAPPTELGINPE-GRIRG 101 (157)
T ss_pred cchHHHHHHHHHcCCCHHHHHHHhccCCcCCceEEEEeCCCCEEEEEEcCCCcCceeeccCCCCCcccceeCcc-ccccc
Confidence 3445566665 45688888888 788999999999999999999987776665 3344577999999 98888
Q ss_pred Ccee
Q psy488 79 DDIV 82 (86)
Q Consensus 79 ~DIi 82 (86)
.|++
T Consensus 102 t~~~ 105 (157)
T PF15538_consen 102 TDII 105 (157)
T ss_pred ccce
Confidence 8875
No 66
>COG1931 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.69 E-value=55 Score=23.90 Aligned_cols=56 Identities=18% Similarity=0.369 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCc
Q psy488 11 DEEIAAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDD 80 (86)
Q Consensus 11 eQ~aRa~LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~D 80 (86)
.|++.-..|+-+ ..++.|..+.|++|-++--. ..-||..++ +.|+|-+. --+|+.+
T Consensus 60 ~qrIlDtAR~~l---~kG~~~~~v~f~lnKQAA~v--------G~vnF~~e~-espLG~I~--v~I~~~~ 115 (140)
T COG1931 60 KQRILDTARMVL---EKGLTGNEVTFYLNKQAAYV--------GRVNFVEED-ESPLGPIT--VTIRTDE 115 (140)
T ss_pred HhHHHHHHHHHH---HccccCCeEEEEEehhhhhc--------CccccccCC-CCCCCCEE--EEEEcCC
Confidence 344444444332 33567899999999875433 346788888 99999773 3455544
No 67
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=28.64 E-value=67 Score=21.86 Aligned_cols=22 Identities=9% Similarity=0.387 Sum_probs=18.8
Q ss_pred HHHHHHHhcCCCceEEEeecCc
Q psy488 21 KFLKAMSSLSGQPCTINMFERT 42 (86)
Q Consensus 21 rfLr~l~~~~gk~v~f~m~E~t 42 (86)
.+..+|.++-|..||+.+||=.
T Consensus 7 ~l~~~l~~~lG~~~EVVLHDl~ 28 (118)
T PF08348_consen 7 PLVDFLAATLGPNCEVVLHDLS 28 (118)
T ss_pred HHHHHHHHHhCCCeEEEEEECC
Confidence 4567888889999999999866
No 68
>PRK01546 hypothetical protein; Provisional
Probab=27.99 E-value=79 Score=20.93 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=16.3
Q ss_pred cHHHHHHHHHHHHHHHHHHhc
Q psy488 9 RSDEEIAAEMREKFLKAMSSL 29 (86)
Q Consensus 9 ~~eQ~aRa~LRerfLr~l~~~ 29 (86)
.+|..=|..||+.||..+-+-
T Consensus 24 ~eEk~Eq~~LR~eYl~~fR~~ 44 (79)
T PRK01546 24 EEEQRERQSLREQYLKGFRQN 44 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456677889999999887553
No 69
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=27.30 E-value=37 Score=26.94 Aligned_cols=44 Identities=16% Similarity=0.313 Sum_probs=36.3
Q ss_pred HHHHHHHhcCCCceEEEeecCcEEEE--EEeeecCCcceeeecccCCCcCcc
Q psy488 21 KFLKAMSSLSGQPCTINMFERTVVTA--EFQGTNSDLTEFYVRNLKTPIGTF 70 (86)
Q Consensus 21 rfLr~l~~~~gk~v~f~m~E~t~V~a--~F~a~d~d~~~f~Vs~L~TPiGv~ 70 (86)
-|||+++.|. .+.++++|+| .|.+-|+....+-|-.|..-+|+.
T Consensus 48 T~LR~lNRmn------dl~~~~r~~G~v~~~g~ni~~~~~d~~~lRr~vGMV 93 (253)
T COG1117 48 TLLRCLNRMN------DLIPGARVEGEVLLDGKNIYDPKVDVVELRRRVGMV 93 (253)
T ss_pred HHHHHHHhhc------ccCcCceEEEEEEECCeeccCCCCCHHHHHHHheee
Confidence 4899999996 4788889998 678888888888888998888864
No 70
>PRK14633 hypothetical protein; Provisional
Probab=26.14 E-value=2.1e+02 Score=20.19 Aligned_cols=52 Identities=6% Similarity=0.084 Sum_probs=33.6
Q ss_pred HHHHhcCCCceEEEeec----CcEEEEEEeeecCCcceeeecc---cCCCcCccccceee
Q psy488 24 KAMSSLSGQPCTINMFE----RTVVTAEFQGTNSDLTEFYVRN---LKTPIGTFHEHALL 76 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E----~t~V~a~F~a~d~d~~~f~Vs~---L~TPiGv~~e~AlL 76 (86)
+-+....|++|.+.+++ +..++|+..+.+-+.-.+.+.+ ..=|+--++. |-|
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~~~~~~i~~~~I~k-a~l 145 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLEDGKEISFDFDELKK-LRV 145 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcCCcEEEEEhHHeee-EEE
Confidence 44566789999999964 5678898888876655554432 2225555554 544
No 71
>PHA03222 single-stranded binding protein UL29; Provisional
Probab=25.47 E-value=58 Score=26.84 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHhc
Q psy488 15 AAEMREKFLKAMSSL 29 (86)
Q Consensus 15 Ra~LRerfLr~l~~~ 29 (86)
|..+|+|||++|+..
T Consensus 172 ~~s~R~rYl~sl~~f 186 (337)
T PHA03222 172 RISARERYLHSLLCF 186 (337)
T ss_pred hHHHHHHHHHHHHHH
Confidence 457999999999863
No 72
>TIGR00760 araD L-ribulose-5-phosphate 4-epimerase. The homolog to this family from Mycobacterium smegmatis is flanked by putative araB and araA genes, consistent with it also being araD.
Probab=24.99 E-value=1e+02 Score=22.90 Aligned_cols=57 Identities=14% Similarity=0.269 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCccccceeeecCceeEEeC
Q psy488 18 MREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIVDIEI 86 (86)
Q Consensus 18 LRerfLr~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~~ 86 (86)
+|+.+++.-..|..+........|..+ + +.+...|.+ ||-|+... -|...|++.+++
T Consensus 5 ~~~ei~~~~~~l~~~gl~~~~~GNiS~--R----~~~~~~~lI----TPsG~~~~--~l~~~div~vdl 61 (231)
T TIGR00760 5 LKKEVLEANLALPKHQLVTFTWGNVSA--I----DRERGLVVI----KPSGVEYD--VMTADDMVVVDL 61 (231)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCeEEE--E----ecCCCEEEE----eCCCCChh--hCCHHHEEEEcC
Confidence 566666655555444433333333332 1 223334554 89998865 568889887753
No 73
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=24.54 E-value=1.7e+02 Score=20.83 Aligned_cols=71 Identities=20% Similarity=0.164 Sum_probs=39.8
Q ss_pred cHHHHHHHHHHHHHHHHHHhc---------------CCCceEEEeecCcEEEEEE-eeecCCcceeeecccCCCcCcccc
Q psy488 9 RSDEEIAAEMREKFLKAMSSL---------------SGQPCTINMFERTVVTAEF-QGTNSDLTEFYVRNLKTPIGTFHE 72 (86)
Q Consensus 9 ~~eQ~aRa~LRerfLr~l~~~---------------~gk~v~f~m~E~t~V~a~F-~a~d~d~~~f~Vs~L~TPiGv~~e 72 (86)
..++.++-.-|-++|...++- .|..|++.-.++....-+| +.++.|..+=.||. .+|||-
T Consensus 52 Ak~~~~~~e~rI~~L~~~L~~A~iid~~~~~~~~V~~Gs~V~l~d~~~~~~~~~iVgp~e~d~~~~~IS~-~SPlG~--- 127 (157)
T PRK01885 52 GKKRLREIDRRVRFLTKRLENLKVVDYSPQQEGKVFFGAWVEIENEDGEEKRFRIVGPDEIDGRKGYISI-DSPMAR--- 127 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHccCEEECCCCCCCCEEEeCCEEEEEECCCCEEEEEEEChHHhCcCCCeEec-cCHHHH---
Confidence 455666667777888877763 2233444333333333334 44455555556666 899983
Q ss_pred ceee--ecCceeEE
Q psy488 73 HALL--RVDDIVDI 84 (86)
Q Consensus 73 ~AlL--R~~DIi~~ 84 (86)
||| +.+|.+.+
T Consensus 128 -ALlGk~vGd~v~v 140 (157)
T PRK01885 128 -ALLKKEVGDEVTV 140 (157)
T ss_pred -HHhCCCCCCEEEE
Confidence 443 45555544
No 74
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=24.33 E-value=56 Score=22.22 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhcCCCceEEEeec
Q psy488 18 MREKFLKAMSSLSGQPCTINMFE 40 (86)
Q Consensus 18 LRerfLr~l~~~~gk~v~f~m~E 40 (86)
|.++|++.+....|.++.+++-|
T Consensus 2 l~~~y~~L~~~~~~~~~~vtl~e 24 (115)
T PF12793_consen 2 LLEQYQRLWQHYGGQPVEVTLDE 24 (115)
T ss_pred HHHHHHHHHHHcCCCCcceeHHH
Confidence 56899999999999999988765
No 75
>KOG1780|consensus
Probab=24.20 E-value=1e+02 Score=20.54 Aligned_cols=58 Identities=14% Similarity=0.194 Sum_probs=39.3
Q ss_pred HHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCcCcccc----ceeeecCceeEE
Q psy488 26 MSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHE----HALLRVDDIVDI 84 (86)
Q Consensus 26 l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPiGv~~e----~AlLR~~DIi~~ 84 (86)
|.+.-+|++.+.+..+-+|+|..+|.|+. .|+-+++---|=|.-+. .-.+|-+-||..
T Consensus 9 LkkymdKki~lklnG~r~v~GiLrGyD~F-mNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~ 70 (77)
T KOG1780|consen 9 LKKYMDKKIVLKLNGGRKVTGILRGYDPF-MNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMV 70 (77)
T ss_pred HHHhhhheEEEEeCCCcEEEEEEeccchH-HhhhhhhceeecCcCCcceeeeEEEeccEEEEE
Confidence 34556899999999999999999999984 45555554444444322 135566666654
No 76
>PHA02662 ORF131 putative membrane protein; Provisional
Probab=24.09 E-value=59 Score=25.41 Aligned_cols=47 Identities=9% Similarity=0.244 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhcC---CCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc
Q psy488 18 MREKFLKAMSSLS---GQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI 67 (86)
Q Consensus 18 LRerfLr~l~~~~---gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi 67 (86)
.=||||+-|+.-+ .-.|.|+.-+ +.+++++|..-+.|...+|=++-+
T Consensus 27 f~~ryL~kLs~~s~~a~a~C~IhIG~---I~g~~k~C~v~V~N~C~sna~~sf 76 (226)
T PHA02662 27 FLARFLRRLAARAAPASAACAVRVGA---VRGRLRNCELVVLNRCHTDAADAL 76 (226)
T ss_pred HHHHHHHHHHhccCccccccceEEee---EeeecCCceEEEEecccCCHHHHH
Confidence 3489999988763 3466666654 458999999999999988865544
No 77
>PRK14646 hypothetical protein; Provisional
Probab=23.31 E-value=2.1e+02 Score=20.37 Aligned_cols=53 Identities=11% Similarity=0.268 Sum_probs=34.3
Q ss_pred HHHHhcCCCceEEEeecC----cEEEEEEeeecCCcceeeec--ccCCCcCccccceeee
Q psy488 24 KAMSSLSGQPCTINMFER----TVVTAEFQGTNSDLTEFYVR--NLKTPIGTFHEHALLR 77 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E~----t~V~a~F~a~d~d~~~f~Vs--~L~TPiGv~~e~AlLR 77 (86)
+-+....|++|.+.+++. ..+.|...+.|-+.-.+.+. ..+=|+.-++. |-|-
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~~g~~~~i~~~~I~k-a~L~ 151 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINIKGKIKKIPFNEVLK-ISLC 151 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEECCEEEEEEHHHeee-EEeC
Confidence 445667899999999875 45777777777765555443 23336666655 5553
No 78
>KOG1486|consensus
Probab=23.25 E-value=1.3e+02 Score=24.85 Aligned_cols=58 Identities=17% Similarity=0.155 Sum_probs=44.2
Q ss_pred HHhcCCCceEEEeecCcEEEEEEeeecCCcceeeecccCCCc---------CccccceeeecCceeEE
Q psy488 26 MSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPI---------GTFHEHALLRVDDIVDI 84 (86)
Q Consensus 26 l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~TPi---------Gv~~e~AlLR~~DIi~~ 84 (86)
|+.|.+-.-+..=||=|++++.=+-...+..|+++-+|---| |-|-= |+-|++|.|.+
T Consensus 79 Ls~iT~T~SeaA~yeFTTLtcIpGvi~y~ga~IQllDLPGIieGAsqgkGRGRQvi-avArtaDlilM 145 (364)
T KOG1486|consen 79 LSKITSTHSEAASYEFTTLTCIPGVIHYNGANIQLLDLPGIIEGASQGKGRGRQVI-AVARTADLILM 145 (364)
T ss_pred HHHhhcchhhhhceeeeEEEeecceEEecCceEEEecCcccccccccCCCCCceEE-EEeecccEEEE
Confidence 445555555666788899999989999999999999985433 45555 78899999865
No 79
>TIGR02447 yiiD_Cterm thioesterase domain, putative. This family consists of a broadly distributed uncharacterized domain found often as a standalone protein. The member from Shewanella oneidensis, PDB|1T82_A (Forouhar, et al., unpublished) is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an Acetyltransf_1 domain (PFAM model pfam00583). The function of this protein is unknown.
Probab=22.50 E-value=2.6e+02 Score=18.93 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.6
Q ss_pred HHHHHHHHHhcCCC--ceEEEeecCcEEEEEEeee
Q psy488 19 REKFLKAMSSLSGQ--PCTINMFERTVVTAEFQGT 51 (86)
Q Consensus 19 RerfLr~l~~~~gk--~v~f~m~E~t~V~a~F~a~ 51 (86)
.++|++.+..-.-. .+++.++|+-++-|+|.|.
T Consensus 99 ~~~~~~~l~~~gr~~~~~~~~v~~~~~lvA~~~g~ 133 (138)
T TIGR02447 99 WEAFLATLQRGGKARVKLEAQISSDGKLAATFSGE 133 (138)
T ss_pred HHHHHHHHHhCCceEEEEEEEEEECCEEEEEEEEE
Confidence 45666666554332 3677888888988888864
No 80
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=21.96 E-value=2.8e+02 Score=19.94 Aligned_cols=29 Identities=14% Similarity=0.171 Sum_probs=24.7
Q ss_pred HHHhcCCCceEEEeecCcEEEEEEeeecC
Q psy488 25 AMSSLSGQPCTINMFERTVVTAEFQGTNS 53 (86)
Q Consensus 25 ~l~~~~gk~v~f~m~E~t~V~a~F~a~d~ 53 (86)
....+.||.|.+..-+...++|+..++..
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~~ 114 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVKQ 114 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEEE
Confidence 45678999999988888899999998874
No 81
>PRK07490 hypothetical protein; Provisional
Probab=21.70 E-value=1.6e+02 Score=22.11 Aligned_cols=25 Identities=16% Similarity=0.335 Sum_probs=17.5
Q ss_pred cceeeecccCCCcCccccceeeecCceeEEe
Q psy488 55 LTEFYVRNLKTPIGTFHEHALLRVDDIVDIE 85 (86)
Q Consensus 55 ~~~f~Vs~L~TPiGv~~e~AlLR~~DIi~~~ 85 (86)
..+|+| ||.|+.++ -|+..|++.++
T Consensus 43 ~~~~lI----tpsG~~~~--~l~~~div~vd 67 (245)
T PRK07490 43 GKQFLL----NPKWKHFS--RIRASDLLLLD 67 (245)
T ss_pred CCeEEE----cCCCCChh--hCcHHHeEEEc
Confidence 345655 78888865 56888887765
No 82
>PF07217 Het-C: Heterokaryon incompatibility protein Het-C; InterPro: IPR010816 In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci [].
Probab=20.68 E-value=45 Score=29.40 Aligned_cols=24 Identities=33% Similarity=0.497 Sum_probs=19.6
Q ss_pred CCCceEEEeecCcE---EEEEEeeecC
Q psy488 30 SGQPCTINMFERTV---VTAEFQGTNS 53 (86)
Q Consensus 30 ~gk~v~f~m~E~t~---V~a~F~a~d~ 53 (86)
+|..+.+.+..+-. |+|+|+++|.
T Consensus 254 vG~~t~i~~~g~~V~PlVTGTFG~vDF 280 (606)
T PF07217_consen 254 VGRNTRINLPGKRVYPLVTGTFGGVDF 280 (606)
T ss_pred cccceEEecCCcccCceeeccCcchHH
Confidence 78888888866554 9999999984
No 83
>PRK14630 hypothetical protein; Provisional
Probab=20.64 E-value=2.5e+02 Score=19.74 Aligned_cols=36 Identities=8% Similarity=0.066 Sum_probs=26.3
Q ss_pred HHHHhcCCCceEEEeecCcEEEEEEeeecCCcceeee
Q psy488 24 KAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYV 60 (86)
Q Consensus 24 r~l~~~~gk~v~f~m~E~t~V~a~F~a~d~d~~~f~V 60 (86)
+-+....|++|.+.+++... +|+..+.|-+.--+.+
T Consensus 90 ~df~r~~G~~v~V~l~~~~~-~G~L~~~~d~~i~l~~ 125 (143)
T PRK14630 90 REFKIFEGKKIKLMLDNDFE-EGFILEAKADSFIFKT 125 (143)
T ss_pred HHHHHhCCCEEEEEEcCcce-EEEEEEEeCCEEEEEE
Confidence 44566789999999988764 8888877665544444
No 84
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=20.19 E-value=2.6e+02 Score=18.81 Aligned_cols=41 Identities=17% Similarity=0.193 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHHHhc---CCCceEEEeecCcEEEEEE
Q psy488 8 SRSDEEIAAEMREKFLKAMSSL---SGQPCTINMFERTVVTAEF 48 (86)
Q Consensus 8 ~~~eQ~aRa~LRerfLr~l~~~---~gk~v~f~m~E~t~V~a~F 48 (86)
++.+++||-.|--.++..|..+ .|+++.+...++.-.=|.-
T Consensus 59 s~D~~~AryiLtP~~mE~L~~l~~~~~~~i~~~f~~~~lyiai~ 102 (142)
T PF11335_consen 59 STDQVEARYILTPSFMERLLELRERFGGPISLSFDGNKLYIAIP 102 (142)
T ss_pred eCCHHHHHHhCCHHHHHHHHHHHHhcCCCEEEEEeCCEEEEEEe
Confidence 4678999999999997766665 5679999999877655443
Done!