Query 031941
Match_columns 150
No_of_seqs 206 out of 1036
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:28:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031941hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3293 Small nuclear ribonucl 100.0 4.3E-34 9.3E-39 215.5 11.3 91 1-91 1-91 (134)
2 cd01723 LSm4 The eukaryotic Sm 99.9 6.1E-27 1.3E-31 163.1 10.1 76 2-77 1-76 (76)
3 cd01724 Sm_D1 The eukaryotic S 99.9 1.6E-26 3.5E-31 166.3 10.8 82 2-84 1-83 (90)
4 cd01721 Sm_D3 The eukaryotic S 99.9 9.6E-26 2.1E-30 155.0 10.0 70 3-73 1-70 (70)
5 cd01725 LSm2 The eukaryotic Sm 99.9 2.3E-25 5E-30 157.2 9.8 77 2-78 1-78 (81)
6 cd01733 LSm10 The eukaryotic S 99.9 4E-24 8.7E-29 150.2 10.1 69 3-72 10-78 (78)
7 cd01726 LSm6 The eukaryotic Sm 99.9 1.1E-22 2.4E-27 138.3 9.2 67 3-70 1-67 (67)
8 KOG3428 Small nuclear ribonucl 99.9 1.8E-22 3.9E-27 149.4 9.4 89 1-91 1-90 (109)
9 cd01722 Sm_F The eukaryotic Sm 99.9 6.1E-22 1.3E-26 135.1 9.3 68 2-70 1-68 (68)
10 PRK00737 small nuclear ribonuc 99.9 2.2E-21 4.7E-26 133.8 10.0 68 2-70 4-71 (72)
11 KOG3172 Small nuclear ribonucl 99.9 2E-21 4.4E-26 144.1 10.1 80 2-82 5-84 (119)
12 cd01732 LSm5 The eukaryotic Sm 99.9 2.6E-21 5.6E-26 135.4 10.1 70 1-70 2-73 (76)
13 cd01731 archaeal_Sm1 The archa 99.9 4.4E-21 9.6E-26 130.5 9.5 67 3-70 1-67 (68)
14 smart00651 Sm snRNP Sm protein 99.8 7.6E-20 1.6E-24 122.5 9.5 67 5-71 1-67 (67)
15 COG1958 LSM1 Small nuclear rib 99.8 8.5E-20 1.8E-24 127.4 9.4 70 2-71 7-79 (79)
16 PF01423 LSM: LSM domain ; In 99.8 7.7E-20 1.7E-24 122.6 8.3 67 5-71 1-67 (67)
17 cd01719 Sm_G The eukaryotic Sm 99.8 1.6E-19 3.5E-24 124.9 9.1 71 3-74 1-71 (72)
18 KOG3448 Predicted snRNP core p 99.8 1.9E-19 4.1E-24 129.5 8.5 89 1-89 1-90 (96)
19 cd00600 Sm_like The eukaryotic 99.8 1.3E-18 2.9E-23 114.8 8.8 63 7-70 1-63 (63)
20 cd01730 LSm3 The eukaryotic Sm 99.8 1.8E-18 3.9E-23 122.0 9.3 69 2-70 1-81 (82)
21 cd01720 Sm_D2 The eukaryotic S 99.8 3.7E-18 8.1E-23 122.4 9.5 70 2-71 2-85 (87)
22 KOG3482 Small nuclear ribonucl 99.7 2E-18 4.3E-23 120.3 6.1 68 2-70 8-75 (79)
23 cd01729 LSm7 The eukaryotic Sm 99.7 1E-17 2.2E-22 118.3 9.7 71 3-73 3-80 (81)
24 cd01718 Sm_E The eukaryotic Sm 99.7 1.4E-17 3.1E-22 117.6 9.4 69 2-70 6-78 (79)
25 cd01717 Sm_B The eukaryotic Sm 99.7 1.6E-16 3.5E-21 111.1 8.7 67 5-71 3-78 (79)
26 cd01728 LSm1 The eukaryotic Sm 99.7 2.4E-16 5.3E-21 109.8 9.5 69 3-71 3-73 (74)
27 cd01727 LSm8 The eukaryotic Sm 99.7 2.6E-16 5.7E-21 108.9 9.0 69 5-73 2-73 (74)
28 KOG1783 Small nuclear ribonucl 99.7 1.8E-17 3.9E-22 115.4 1.0 71 2-73 6-76 (77)
29 PTZ00138 small nuclear ribonuc 99.6 1.7E-15 3.7E-20 109.3 9.6 70 2-71 14-87 (89)
30 cd06168 LSm9 The eukaryotic Sm 99.6 6.2E-15 1.4E-19 103.0 9.0 67 5-71 3-74 (75)
31 KOG1780 Small Nuclear ribonucl 99.5 1.5E-14 3.3E-19 101.0 6.0 67 5-72 7-73 (77)
32 KOG1775 U6 snRNA-associated Sm 99.4 9.7E-14 2.1E-18 97.7 3.5 70 1-70 6-77 (84)
33 KOG3460 Small nuclear ribonucl 99.4 1.8E-13 3.9E-18 97.7 1.9 73 2-74 5-89 (91)
34 KOG1774 Small nuclear ribonucl 99.2 2.8E-11 6.1E-16 86.2 4.6 70 2-71 12-85 (88)
35 KOG1784 Small Nuclear ribonucl 98.9 2.9E-09 6.2E-14 77.3 4.4 82 5-86 3-87 (96)
36 KOG1781 Small Nuclear ribonucl 98.8 5.1E-10 1.1E-14 82.2 -0.7 72 4-75 19-97 (108)
37 KOG3168 U1 snRNP component [Tr 98.7 2.5E-09 5.3E-14 85.1 -0.5 71 5-75 7-86 (177)
38 KOG1782 Small Nuclear ribonucl 98.7 4.1E-09 8.8E-14 80.1 0.2 68 6-73 13-82 (129)
39 PF14438 SM-ATX: Ataxin 2 SM d 98.0 2.7E-05 5.8E-10 53.6 6.4 45 4-48 4-51 (77)
40 KOG3459 Small nuclear ribonucl 97.8 3.6E-06 7.8E-11 63.0 -0.5 68 3-70 25-106 (114)
41 cd01739 LSm11_C The eukaryotic 97.3 0.00019 4E-09 49.4 2.8 38 12-49 8-49 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.2 0.0022 4.8E-08 46.9 7.5 68 8-75 4-80 (96)
43 KOG3262 H/ACA small nucleolar 97.2 0.0012 2.5E-08 54.1 6.4 10 6-15 59-68 (215)
44 PF11095 Gemin7: Gem-associate 96.8 0.0058 1.3E-07 43.5 6.4 64 3-72 15-79 (80)
45 cd01716 Hfq Hfq, an abundant, 96.1 0.014 3.1E-07 39.5 4.9 36 6-41 3-40 (61)
46 TIGR02383 Hfq RNA chaperone Hf 96.0 0.019 4E-07 39.0 4.8 36 6-41 7-44 (61)
47 KOG3262 H/ACA small nucleolar 95.9 0.06 1.3E-06 44.3 8.3 7 69-75 126-132 (215)
48 PTZ00146 fibrillarin; Provisio 95.7 0.028 6.1E-07 48.4 6.2 7 137-143 44-50 (293)
49 PRK00395 hfq RNA-binding prote 95.6 0.028 6.1E-07 40.0 4.9 37 6-42 11-49 (79)
50 cd01736 LSm14_N LSm14 (also kn 95.5 0.068 1.5E-06 37.6 6.3 62 8-69 2-73 (74)
51 PF02237 BPL_C: Biotin protein 95.2 0.092 2E-06 33.2 5.9 31 11-42 2-32 (48)
52 PF06372 Gemin6: Gemin6 protei 94.7 0.075 1.6E-06 42.5 5.3 63 5-75 10-73 (166)
53 KOG1073 Uncharacterized mRNA-a 93.8 0.1 2.2E-06 46.3 4.9 70 6-75 3-82 (361)
54 PF10842 DUF2642: Protein of u 93.6 0.75 1.6E-05 31.6 7.8 53 4-70 13-65 (66)
55 COG1923 Hfq Uncharacterized ho 93.5 0.15 3.3E-06 36.1 4.3 33 5-37 10-44 (77)
56 PRK14091 RNA-binding protein H 91.6 0.38 8.2E-06 38.6 4.9 37 6-42 96-134 (165)
57 cd01735 LSm12_N LSm12 belongs 91.3 1 2.2E-05 30.5 6.0 31 10-40 4-34 (61)
58 PRK14091 RNA-binding protein H 90.8 0.5 1.1E-05 37.9 4.8 37 6-42 16-54 (165)
59 PRK14639 hypothetical protein; 88.7 1 2.3E-05 34.6 5.1 35 5-40 81-115 (140)
60 PRK14638 hypothetical protein; 87.8 1 2.2E-05 35.1 4.5 35 5-40 93-127 (150)
61 PRK02001 hypothetical protein; 87.5 1.4 3.1E-05 34.5 5.1 35 5-40 83-117 (152)
62 PRK14644 hypothetical protein; 83.0 2.8 6E-05 32.2 4.8 35 6-41 79-117 (136)
63 COG0779 Uncharacterized protei 81.8 4.5 9.8E-05 31.9 5.7 33 4-36 91-127 (153)
64 PRK14642 hypothetical protein; 81.3 3.4 7.4E-05 33.9 5.0 69 5-75 93-182 (197)
65 PRK00092 ribosome maturation p 81.2 6.3 0.00014 30.4 6.3 30 5-34 91-124 (154)
66 cd01734 YlxS_C YxlS is a Bacil 80.9 3.4 7.3E-05 28.7 4.2 31 5-35 18-52 (83)
67 PRK14640 hypothetical protein; 80.0 4.2 9.1E-05 31.6 4.9 35 5-40 90-128 (152)
68 PRK14632 hypothetical protein; 76.6 5.7 0.00012 31.6 4.8 35 5-40 91-132 (172)
69 PF02576 DUF150: Uncharacteris 76.2 4.9 0.00011 30.4 4.2 30 5-34 80-113 (141)
70 PRK14636 hypothetical protein; 75.5 5.8 0.00013 31.7 4.6 35 5-40 91-129 (176)
71 PRK11625 Rho-binding antitermi 73.3 24 0.00052 25.2 6.9 55 7-70 18-72 (84)
72 PRK14647 hypothetical protein; 73.3 7.8 0.00017 30.3 4.8 30 5-34 92-130 (159)
73 PRK14633 hypothetical protein; 73.0 6.4 0.00014 30.6 4.2 35 5-40 87-125 (150)
74 PRK14643 hypothetical protein; 71.8 8.2 0.00018 30.5 4.6 36 5-40 97-137 (164)
75 PRK14645 hypothetical protein; 71.8 6.6 0.00014 30.8 4.1 30 5-35 95-124 (154)
76 PF07073 ROF: Modulator of Rho 71.3 4.1 8.9E-05 28.8 2.5 30 6-37 11-40 (80)
77 PTZ00034 40S ribosomal protein 70.5 3.3 7.2E-05 31.8 2.0 13 68-80 80-92 (124)
78 PRK14634 hypothetical protein; 70.2 7.7 0.00017 30.3 4.1 35 5-40 93-131 (155)
79 PRK11634 ATP-dependent RNA hel 70.0 18 0.00039 34.0 7.2 26 55-81 518-543 (629)
80 PRK14637 hypothetical protein; 69.8 11 0.00023 29.4 4.9 35 5-40 91-126 (151)
81 PRK06955 biotin--protein ligas 68.4 18 0.0004 30.7 6.4 32 10-41 247-278 (300)
82 KOG0921 Dosage compensation co 68.4 13 0.00029 37.4 6.1 18 25-42 1074-1092(1282)
83 PRK09618 flgD flagellar basal 68.4 15 0.00032 28.7 5.3 26 8-33 88-113 (142)
84 PRK14646 hypothetical protein; 68.1 9.1 0.0002 29.9 4.1 35 5-40 93-131 (155)
85 PRK14641 hypothetical protein; 61.7 12 0.00026 29.9 3.8 29 5-33 97-129 (173)
86 PRK14631 hypothetical protein; 61.0 14 0.0003 29.6 4.0 30 4-33 109-142 (174)
87 KOG3293 Small nuclear ribonucl 60.2 8.2 0.00018 29.8 2.5 19 55-73 39-58 (134)
88 PRK10590 ATP-dependent RNA hel 60.2 42 0.0009 29.7 7.3 13 61-73 341-353 (456)
89 PRK13325 bifunctional biotin-- 59.9 30 0.00064 32.5 6.6 32 10-41 276-307 (592)
90 PRK11886 bifunctional biotin-- 57.6 35 0.00076 28.8 6.2 31 10-41 270-300 (319)
91 PF10618 Tail_tube: Phage tail 56.4 28 0.0006 26.0 4.8 27 2-28 64-90 (119)
92 PF11607 DUF3247: Protein of u 55.2 26 0.00055 26.0 4.2 19 12-30 28-46 (101)
93 PRK08330 biotin--protein ligas 52.3 54 0.0012 26.6 6.2 33 9-42 185-218 (236)
94 TIGR02603 CxxCH_TIGR02603 puta 50.7 28 0.00062 25.9 4.0 21 13-33 58-78 (133)
95 PRK14635 hypothetical protein; 50.3 39 0.00085 26.4 4.9 35 5-40 92-131 (162)
96 TIGR00121 birA_ligase birA, bi 49.9 50 0.0011 26.8 5.7 31 10-41 191-221 (237)
97 PRK11911 flgD flagellar basal 48.9 67 0.0015 25.0 6.0 26 9-34 90-115 (140)
98 PRK14630 hypothetical protein; 48.0 32 0.00069 26.5 4.0 30 5-35 90-119 (143)
99 PF03614 Flag1_repress: Repres 43.9 35 0.00077 27.3 3.7 34 11-44 28-61 (165)
100 PF07833 Cu_amine_oxidN1: Copp 43.4 64 0.0014 21.4 4.6 23 1-23 6-28 (93)
101 PRK10898 serine endoprotease; 43.4 46 0.00099 28.9 4.7 60 12-74 101-162 (353)
102 TIGR00567 3mg DNA-3-methyladen 41.1 56 0.0012 26.7 4.6 35 3-37 10-44 (192)
103 smart00333 TUDOR Tudor domain. 40.0 89 0.0019 19.1 4.9 25 11-35 5-29 (57)
104 TIGR02038 protease_degS peripl 37.1 65 0.0014 27.9 4.7 58 13-73 102-161 (351)
105 PRK10139 serine endoprotease; 35.8 68 0.0015 29.0 4.8 61 12-74 114-176 (455)
106 PF13437 HlyD_3: HlyD family s 35.6 80 0.0017 21.6 4.2 33 2-34 42-78 (105)
107 TIGR02037 degP_htrA_DO peripla 34.8 71 0.0015 28.1 4.7 32 13-44 82-113 (428)
108 cd01343 PL1_Passenger_AT Perta 34.2 1.3E+02 0.0028 24.9 5.8 52 14-69 74-125 (233)
109 TIGR01080 rplX_A_E ribosomal p 33.6 1.9E+02 0.0042 21.7 6.2 57 12-72 45-102 (114)
110 PF02245 Pur_DNA_glyco: Methyl 33.5 73 0.0016 25.8 4.1 34 3-37 9-42 (184)
111 PRK10942 serine endoprotease; 33.3 76 0.0016 28.8 4.7 32 12-43 135-166 (473)
112 KOG0116 RasGAP SH3 binding pro 33.2 69 0.0015 29.2 4.3 8 56-63 317-324 (419)
113 PTZ00275 biotin-acetyl-CoA-car 33.0 91 0.002 26.4 4.9 31 10-41 235-265 (285)
114 cd04479 RPA3 RPA3: A subfamily 32.5 87 0.0019 22.4 4.0 16 4-19 7-22 (101)
115 PF03614 Flag1_repress: Repres 32.5 50 0.0011 26.4 3.0 25 11-35 119-143 (165)
116 PRK06789 flagellar motor switc 31.5 83 0.0018 21.9 3.7 36 7-42 36-71 (74)
117 COG4568 Rof Transcriptional an 29.7 67 0.0015 23.0 2.9 30 6-37 17-46 (84)
118 COG0340 BirA Biotin-(acetyl-Co 29.1 1.2E+02 0.0026 25.2 4.8 34 10-43 188-221 (238)
119 PF02751 TFIIA_gamma_C: Transc 28.6 1.6E+02 0.0034 19.3 4.4 31 20-50 3-36 (52)
120 PRK06792 flgD flagellar basal 28.3 84 0.0018 25.8 3.7 26 9-34 115-140 (190)
121 PF14563 DUF4444: Domain of un 27.8 54 0.0012 20.8 1.9 22 25-46 10-31 (42)
122 PF05954 Phage_GPD: Phage late 27.7 65 0.0014 25.8 3.0 27 7-33 23-49 (292)
123 TIGR00999 8a0102 Membrane Fusi 27.5 1.4E+02 0.003 23.7 4.9 35 3-37 132-167 (265)
124 PF07752 S-layer: S-layer prot 27.3 2.8E+02 0.006 23.6 6.8 25 11-35 137-162 (259)
125 KOG3199 Nicotinamide mononucle 27.2 21 0.00045 30.1 0.0 68 13-83 156-228 (234)
126 COG5316 Uncharacterized conser 26.6 1.9E+02 0.0042 26.5 5.9 44 2-46 72-115 (421)
127 PRK01191 rpl24p 50S ribosomal 26.5 2.7E+02 0.0059 21.1 6.0 57 12-72 49-106 (120)
128 cd00540 AAG Alkyladenine DNA g 25.3 1.5E+02 0.0032 23.9 4.6 34 3-37 6-39 (179)
129 PF11743 DUF3301: Protein of u 25.0 93 0.002 22.3 3.1 36 37-73 61-96 (97)
130 PF14485 DUF4431: Domain of un 24.8 69 0.0015 20.4 2.1 30 4-41 11-43 (48)
131 PRK07228 N-ethylammeline chlor 22.8 1.4E+02 0.003 26.1 4.3 35 36-70 1-35 (445)
132 PF03287 Pox_C7_F8A: Poxvirus 22.5 1.2E+02 0.0026 24.0 3.4 54 27-82 2-62 (149)
133 PTZ00194 60S ribosomal protein 22.4 2.7E+02 0.0059 21.8 5.4 57 12-72 50-107 (143)
134 PF01052 SpoA: Surface present 21.4 1.5E+02 0.0033 19.5 3.4 34 11-44 41-74 (77)
135 PF14262 DUF4353: Domain of un 21.3 2.9E+02 0.0062 23.6 5.8 58 10-73 4-69 (264)
136 PF05037 DUF669: Protein of un 21.2 62 0.0013 24.4 1.6 25 5-29 96-121 (141)
137 PRK11634 ATP-dependent RNA hel 20.1 3.1E+02 0.0067 25.9 6.3 22 59-80 512-535 (629)
No 1
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=100.00 E-value=4.3e-34 Score=215.54 Aligned_cols=91 Identities=80% Similarity=1.369 Sum_probs=86.7
Q ss_pred CChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchHH
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQ 80 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~lld~~~ 80 (150)
|+||+||+.+++++|.|||||+++|.|+|++||.||||+|++|+++.+|+++|+.+++|||||++|+||.|||++||.++
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid~vk 80 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIIDKVK 80 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhcCCCC
Q 031941 81 EETKSRSDRKP 91 (150)
Q Consensus 81 ~~~~~~~~~~~ 91 (150)
+|..+..+.+.
T Consensus 81 ee~~~~~~~r~ 91 (134)
T KOG3293|consen 81 EECVSNNRNRK 91 (134)
T ss_pred HHHHHhccchh
Confidence 98886655443
No 2
>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=99.94 E-value=6.1e-27 Score=163.06 Aligned_cols=76 Identities=93% Similarity=1.606 Sum_probs=72.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccc
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVID 77 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~lld 77 (150)
+|++||+++++++|+|||||+++|+|+|.+||.|||++|+||+++.++++++.+++++||||++|+||++||++||
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~~~ 76 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEIID 76 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHHCC
Confidence 6999999999999999999999999999999999999999999998888877789999999999999999999875
No 3
>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=99.94 E-value=1.6e-26 Score=166.34 Aligned_cols=82 Identities=29% Similarity=0.475 Sum_probs=75.8
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc-cchHH
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV-IDKVQ 80 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~l-ld~~~ 80 (150)
.|++||++++|++|+||||||++|+|+|.+||.|||++|+||+++..++.. .+++++||||++|+||+|||++ +|.++
T Consensus 1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~-~~~~~v~IRG~nI~yi~lPd~l~~~~~l 79 (90)
T cd01724 1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNP-VPLDTLSIRGNNIRYFILPDSLNLDTLL 79 (90)
T ss_pred CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCce-eEcceEEEeCCEEEEEEcCCcCCcchhh
Confidence 478999999999999999999999999999999999999999999766654 7899999999999999999999 88888
Q ss_pred HHhh
Q 031941 81 EETK 84 (150)
Q Consensus 81 ~~~~ 84 (150)
++++
T Consensus 80 ~~~~ 83 (90)
T cd01724 80 VDST 83 (90)
T ss_pred hhcC
Confidence 7774
No 4
>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=99.93 E-value=9.6e-26 Score=154.97 Aligned_cols=70 Identities=41% Similarity=0.803 Sum_probs=67.1
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd 73 (150)
|+.||+++++++|+||||||++|+|+|.+||.|||++|+||+++.++++. .+++++||||++|+||+|||
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~-~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRV-SQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcE-eEcCcEEEeCCEEEEEEeCC
Confidence 89999999999999999999999999999999999999999998888875 68999999999999999997
No 5
>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=99.93 E-value=2.3e-25 Score=157.17 Aligned_cols=77 Identities=31% Similarity=0.615 Sum_probs=70.5
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCC-eeeecCeEEEecCeEEEEecCccccch
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD-RFWRMPECYIRGNTIKYLRVPDEVIDK 78 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~-~~~~l~~v~IRGnnIryI~lPd~lld~ 78 (150)
+|+.||++++|++|+||||||++|+|+|.+||.|||++|+||+++.+++. .+.+++++||||++|+||++||+++|.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~ 78 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT 78 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence 68999999999999999999999999999999999999999999876553 235689999999999999999999875
No 6
>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=99.91 E-value=4e-24 Score=150.19 Aligned_cols=69 Identities=32% Similarity=0.606 Sum_probs=65.5
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
+++||++++|++|+|||||+.+|+|+|.+||.|||++|+||+++.+++++ .+++++||||++|+||+||
T Consensus 10 l~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~-~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 10 LIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQ-VQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred HHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCce-eECCcEEEECCEEEEEEcC
Confidence 68999999999999999999999999999999999999999999877765 5799999999999999998
No 7
>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=99.89 E-value=1.1e-22 Score=138.31 Aligned_cols=67 Identities=33% Similarity=0.581 Sum_probs=62.2
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|++||+++++++|+|+|||+++|+|+|.+||+||||+|+||+++. +++...+++++||||++|+||+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~-~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe-CCceeeEeCCEEEECCEEEEEC
Confidence 899999999999999999999999999999999999999999975 4445578999999999999984
No 8
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=99.88 E-value=1.8e-22 Score=149.42 Aligned_cols=89 Identities=33% Similarity=0.507 Sum_probs=79.7
Q ss_pred CChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc-cchH
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV-IDKV 79 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~l-ld~~ 79 (150)
|..+.||+++.+.+|+|||||+++++|+|.++|.+||++|.+|+.+.+ +++ .+++.++|||++|+|+++||++ +|++
T Consensus 1 mklvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~-~~p-v~l~~lsirgnniRy~~lpD~l~ld~L 78 (109)
T KOG3428|consen 1 MKLVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVK-GEP-VRLDTLSIRGNNIRYYILPDSLNLDTL 78 (109)
T ss_pred ChHHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecC-CCc-eeEEEEEeecceEEEEEccCCcCccee
Confidence 678899999999999999999999999999999999999999999975 454 6899999999999999999999 9998
Q ss_pred HHHhhhhcCCCC
Q 031941 80 QEETKSRSDRKP 91 (150)
Q Consensus 80 ~~~~~~~~~~~~ 91 (150)
+++++.+.+.++
T Consensus 79 lvd~~~~~~~~~ 90 (109)
T KOG3428|consen 79 LVDDAPRLHLRK 90 (109)
T ss_pred eeehhhhhhhhc
Confidence 877776544433
No 9
>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=99.87 E-value=6.1e-22 Score=135.14 Aligned_cols=68 Identities=35% Similarity=0.582 Sum_probs=62.5
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
.|+.+|+++++++|+|+|+||++|+|+|.+||+||||+|+||+++. ++.++.+++++||||++|+||.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~-~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI-DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe-CCccccCcCcEEEECCEEEEEC
Confidence 4999999999999999999999999999999999999999999985 4544578999999999999984
No 10
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=2.2e-21 Score=133.85 Aligned_cols=68 Identities=32% Similarity=0.581 Sum_probs=63.2
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
.|+.+|+++++++|+|+|+||++|+|+|.+||+||||+|+||+++. +++.+.+++.+||||++|.||.
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~lg~v~iRG~~V~~i~ 71 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ-DGEVVRKLGKVVIRGDNVVYVS 71 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc-CCCeEeEcCcEEEeCCEEEEEc
Confidence 6999999999999999999999999999999999999999999985 4455578999999999999986
No 11
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification]
Probab=99.86 E-value=2e-21 Score=144.06 Aligned_cols=80 Identities=36% Similarity=0.674 Sum_probs=75.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchHHH
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~lld~~~~ 81 (150)
+|+.+|.+++++-|++|+++|++|.|.|..+|++||++|+|++.|..|+.. .+++.|||||+.|+|+.|||.+.+++..
T Consensus 5 vpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~v-s~le~V~IRGS~IRFlvlPdmLKnAPmF 83 (119)
T KOG3172|consen 5 VPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRV-SQLEQVFIRGSKIRFLVLPDMLKNAPMF 83 (119)
T ss_pred cceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcc-eeeeeEEEecCeEEEEECchHhhcCccc
Confidence 699999999999999999999999999999999999999999999999865 8999999999999999999999888776
Q ss_pred H
Q 031941 82 E 82 (150)
Q Consensus 82 ~ 82 (150)
.
T Consensus 84 k 84 (119)
T KOG3172|consen 84 K 84 (119)
T ss_pred c
Confidence 5
No 12
>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=99.86 E-value=2.6e-21 Score=135.43 Aligned_cols=70 Identities=24% Similarity=0.509 Sum_probs=64.6
Q ss_pred CChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEc--cCCCeeeecCeEEEecCeEEEEe
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS--KDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~--~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|+|+.+|+++++++|+|+|+++++|.|+|.+||+||||+|+||+|+. +++++..+++.++|||++|.+|+
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~ 73 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLV 73 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEE
Confidence 89999999999999999999999999999999999999999999985 34444578999999999999997
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=99.85 E-value=4.4e-21 Score=130.50 Aligned_cols=67 Identities=28% Similarity=0.511 Sum_probs=62.5
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|+.+|+++++++|+|+|+||++|+|+|.+||+||||+|+||+++..+.. ...++.+||||++|.||.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~-~~~lg~~~iRG~~I~~i~ 67 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEP-VRKYGRVVIRGDNVLFIS 67 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCe-EeEcCcEEEeCCEEEEEc
Confidence 8999999999999999999999999999999999999999999875543 478999999999999985
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.82 E-value=7.6e-20 Score=122.48 Aligned_cols=67 Identities=42% Similarity=0.677 Sum_probs=61.4
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~l 71 (150)
.+|+++++++|+|+|+|+++|.|+|.+||.||||+|+||+++..+.....+++.+||||++|+||++
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence 3799999999999999999999999999999999999999998663445789999999999999974
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.82 E-value=8.5e-20 Score=127.40 Aligned_cols=70 Identities=40% Similarity=0.601 Sum_probs=61.6
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEcc-CCCe-ee-ecCeEEEecCeEEEEec
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK-DGDR-FW-RMPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~-~g~~-~~-~l~~v~IRGnnIryI~l 71 (150)
.|+++|+++++++|.|+||||++|.|+|.+||.||||+|+||+++.. ++.. .. ..+++||||++|.||.+
T Consensus 7 ~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 68999999999999999999999999999999999999999999863 4433 23 34499999999999863
No 16
>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=99.81 E-value=7.7e-20 Score=122.64 Aligned_cols=67 Identities=39% Similarity=0.649 Sum_probs=61.9
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~l 71 (150)
.+|+++++++|+|+|+||++|+|+|.+||.||||+|+||+++..+..+...++.+||||++|+||++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence 4899999999999999999999999999999999999999998765345789999999999999985
No 17
>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=1.6e-19 Score=124.92 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=63.6
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCcc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~ 74 (150)
|-++|+++++|+|.|+|++|++|+|+|.+||+||||+|+||+|+..+ ....+++.++|||++|.+|..-|.
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~-~~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSG-GEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccC-CceeEeceEEECCCEEEEEEcccc
Confidence 55789999999999999999999999999999999999999998633 344789999999999999986554
No 18
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification]
Probab=99.80 E-value=1.9e-19 Score=129.51 Aligned_cols=89 Identities=28% Similarity=0.567 Sum_probs=80.0
Q ss_pred CChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCe-eeecCeEEEecCeEEEEecCccccchH
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDR-FWRMPECYIRGNTIKYLRVPDEVIDKV 79 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~-~~~l~~v~IRGnnIryI~lPd~lld~~ 79 (150)
|+.++|+++++++.|+|||||+..+.|+|.++|+|+|+.|.|+..++++.-+ ...+..|||||+.|+||++|.+.+|..
T Consensus 1 mLFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtq 80 (96)
T KOG3448|consen 1 MLFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQ 80 (96)
T ss_pred CchHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHH
Confidence 8999999999999999999999999999999999999999999998765432 245778999999999999999999999
Q ss_pred HHHhhhhcCC
Q 031941 80 QEETKSRSDR 89 (150)
Q Consensus 80 ~~~~~~~~~~ 89 (150)
..++.++++.
T Consensus 81 ll~da~R~e~ 90 (96)
T KOG3448|consen 81 LLQDAARREA 90 (96)
T ss_pred HHHHHHHHHH
Confidence 8888877643
No 19
>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=99.78 E-value=1.3e-18 Score=114.82 Aligned_cols=63 Identities=35% Similarity=0.524 Sum_probs=58.1
Q ss_pred HhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|+++++++|+|+|+|+++|.|+|.+||.|||++|+||+++..+.. +.+++.+||||++|+||+
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~-~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGK-KRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCc-EEECCeEEEECCEEEEEC
Confidence 578999999999999999999999999999999999999876644 478999999999999985
No 20
>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=99.77 E-value=1.8e-18 Score=121.97 Aligned_cols=69 Identities=22% Similarity=0.380 Sum_probs=61.4
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCC------------CeeeecCeEEEecCeEEEE
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDG------------DRFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g------------~~~~~l~~v~IRGnnIryI 69 (150)
-|+.||+.+++|+|+|+|+++++|.|+|.+||.||||+|+||+|+.... +....++.+||||++|.+|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 3999999999999999999999999999999999999999999985321 1235789999999999998
Q ss_pred e
Q 031941 70 R 70 (150)
Q Consensus 70 ~ 70 (150)
+
T Consensus 81 ~ 81 (82)
T cd01730 81 S 81 (82)
T ss_pred C
Confidence 5
No 21
>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=99.76 E-value=3.7e-18 Score=122.44 Aligned_cols=70 Identities=21% Similarity=0.294 Sum_probs=61.3
Q ss_pred ChHHHHhhcC--CCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCC------------eeeecCeEEEecCeEE
Q 031941 2 LPLSLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD------------RFWRMPECYIRGNTIK 67 (150)
Q Consensus 2 lPl~lL~~l~--gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~------------~~~~l~~v~IRGnnIr 67 (150)
=|+++|++++ +++|.|+|+++++|.|+|.+||.||||+|+||+|+..... ....++.|||||++|.
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv 81 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVI 81 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEE
Confidence 4999999997 8999999999999999999999999999999999753321 2346899999999999
Q ss_pred EEec
Q 031941 68 YLRV 71 (150)
Q Consensus 68 yI~l 71 (150)
||+-
T Consensus 82 ~Is~ 85 (87)
T cd01720 82 LVLR 85 (87)
T ss_pred EEec
Confidence 9864
No 22
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=99.75 E-value=2e-18 Score=120.29 Aligned_cols=68 Identities=37% Similarity=0.573 Sum_probs=63.9
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
.|-.||+.+.+|+|.|+||.|.+|+|+|+++|.||||.|.+++|+ .+|...-++++++||.|||.||.
T Consensus 8 NPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~-idG~~~g~lGEilIRCNNvlyi~ 75 (79)
T KOG3482|consen 8 NPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEY-IDGVSTGNLGEILIRCNNVLYIR 75 (79)
T ss_pred CchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhh-hcccccccceeEEEEeccEEEEe
Confidence 488999999999999999999999999999999999999999997 47776678999999999999995
No 23
>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=99.75 E-value=1e-17 Score=118.28 Aligned_cols=71 Identities=18% Similarity=0.278 Sum_probs=61.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCC-------CeeeecCeEEEecCeEEEEecCc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDG-------DRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g-------~~~~~l~~v~IRGnnIryI~lPd 73 (150)
++.-|+++++|+|.|.|+++++|.|+|.+||+||||+|+||+|+..+. +....++.++|||+||.+|...+
T Consensus 3 ~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 3 SILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred chhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 345699999999999999999999999999999999999999986432 13367999999999999997654
No 24
>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=99.74 E-value=1.4e-17 Score=117.63 Aligned_cols=69 Identities=14% Similarity=0.231 Sum_probs=61.8
Q ss_pred ChHHHHhhcCCC--eEEEEEc--CCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 2 LPLSLLKTAQGH--PMLVELK--NGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 2 lPl~lL~~l~gk--~V~VeLK--nG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
.|+.+|.+++.+ +|.|+|+ ++.+|+|+|.+||+||||+|+||+|+...+++..+++.++|||+||.+|+
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~ 78 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQ 78 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEc
Confidence 699999999998 7888887 99999999999999999999999998643444468999999999999987
No 25
>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=99.69 E-value=1.6e-16 Score=111.07 Aligned_cols=67 Identities=21% Similarity=0.280 Sum_probs=58.7
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccC---------CCeeeecCeEEEecCeEEEEec
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD---------GDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~---------g~~~~~l~~v~IRGnnIryI~l 71 (150)
+-|.++++++|.|+|+++++|.|+|.+||.||||+|+||+|+... ..+...++.+||||++|.+|.+
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 458899999999999999999999999999999999999997521 1233579999999999999975
No 26
>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=99.68 E-value=2.4e-16 Score=109.84 Aligned_cols=69 Identities=22% Similarity=0.237 Sum_probs=60.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCC--eeeecCeEEEecCeEEEEec
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGD--RFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~--~~~~l~~v~IRGnnIryI~l 71 (150)
++..|.++++|+|.|.|+++++|.|+|.+||+||||+|+||+|+..+++ ....++.++|||++|.+|.+
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 4778999999999999999999999999999999999999998754332 22568999999999999864
No 27
>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=99.68 E-value=2.6e-16 Score=108.90 Aligned_cols=69 Identities=22% Similarity=0.172 Sum_probs=60.7
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEcc---CCCeeeecCeEEEecCeEEEEecCc
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK---DGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~---~g~~~~~l~~v~IRGnnIryI~lPd 73 (150)
+.|+++++++|.|.|++++.|.|+|.+||+||||+|++|+|+.. ++.....++.++|||++|.+|..-|
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 57899999999999999999999999999999999999999753 2333357999999999999998655
No 28
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=99.66 E-value=1.8e-17 Score=115.45 Aligned_cols=71 Identities=31% Similarity=0.534 Sum_probs=66.5
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCc
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd 73 (150)
.|.+||++.+|++|.|+|.++..|+|+|.++|.||||.|+.++|.. +++...+++.+||||++|.||+..+
T Consensus 6 ~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~-ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 6 MPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV-NGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred CcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh-cCcccccccceeeccccEEEEEecc
Confidence 4889999999999999999999999999999999999999999985 8887789999999999999998653
No 29
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.64 E-value=1.7e-15 Score=109.25 Aligned_cols=70 Identities=13% Similarity=0.209 Sum_probs=59.8
Q ss_pred ChHHHHhhcCC--CeEEEEEcC--CCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031941 2 LPLSLLKTAQG--HPMLVELKN--GETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~g--k~V~VeLKn--G~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~l 71 (150)
.|+.+|.+++. .+|.|+|++ +++|+|+|.+||.||||+|+||+|+..+.+....++.++|||+||.||+.
T Consensus 14 ~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 14 QPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred CCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEc
Confidence 58999999985 567777767 48999999999999999999999986444444689999999999999975
No 30
>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=99.60 E-value=6.2e-15 Score=102.98 Aligned_cols=67 Identities=21% Similarity=0.206 Sum_probs=59.9
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccC-----CCeeeecCeEEEecCeEEEEec
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKD-----GDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~-----g~~~~~l~~v~IRGnnIryI~l 71 (150)
+.|+++++++|.|.|++|+.|.|+|.+||.+|||+|+||.|+... ..+...++.++|||++|..|++
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 578999999999999999999999999999999999999998643 1234689999999999999975
No 31
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification]
Probab=99.53 E-value=1.5e-14 Score=101.02 Aligned_cols=67 Identities=30% Similarity=0.443 Sum_probs=61.5
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
+.|+++++|++.|+|..++.+.|+|.+||.||||+|++++|...++++ ..++.++|||++|..+..-
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~-~~ig~~vIrgnsiv~~eaL 73 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDK-NNIGMVVIRGNSIVMVEAL 73 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCc-ceeeeEEEeccEEEEEeec
Confidence 389999999999999999999999999999999999999999877765 6899999999999987543
No 32
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=99.42 E-value=9.7e-14 Score=97.72 Aligned_cols=70 Identities=27% Similarity=0.538 Sum_probs=64.5
Q ss_pred CChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEc--cCCCeeeecCeEEEecCeEEEEe
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS--KDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~--~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
.+|+.++.+++|++|.|.+|+++++.|+|++||.|.|++|+||+++. +++....+++.+++.||+|..+.
T Consensus 6 llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLv 77 (84)
T KOG1775|consen 6 LLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLV 77 (84)
T ss_pred cccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEe
Confidence 47999999999999999999999999999999999999999999864 56777789999999999999764
No 33
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification]
Probab=99.37 E-value=1.8e-13 Score=97.72 Aligned_cols=73 Identities=23% Similarity=0.345 Sum_probs=63.0
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEcc--CCC----------eeeecCeEEEecCeEEEE
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK--DGD----------RFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~--~g~----------~~~~l~~v~IRGnnIryI 69 (150)
-|++||+-++..+|.|+|++++++.|+|.+||+|+|++|.||+++.. +.+ ....++.+||||++|.+|
T Consensus 5 ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vilv 84 (91)
T KOG3460|consen 5 EPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVILV 84 (91)
T ss_pred ccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEEE
Confidence 49999999999999999999999999999999999999999987642 221 124688999999999999
Q ss_pred ecCcc
Q 031941 70 RVPDE 74 (150)
Q Consensus 70 ~lPd~ 74 (150)
..|-.
T Consensus 85 spp~~ 89 (91)
T KOG3460|consen 85 SPPLR 89 (91)
T ss_pred cCccc
Confidence 88743
No 34
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=99.18 E-value=2.8e-11 Score=86.19 Aligned_cols=70 Identities=17% Similarity=0.280 Sum_probs=59.3
Q ss_pred ChHHHHhhcC--CCeEEEEEcC--CCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEec
Q 031941 2 LPLSLLKTAQ--GHPMLVELKN--GETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRV 71 (150)
Q Consensus 2 lPl~lL~~l~--gk~V~VeLKn--G~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~l 71 (150)
.|+.++..++ -.+|.|+|.. +..++|.+++||+|||++|++|++.+...+.-..++.++++|+||..|+-
T Consensus 12 ~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~ 85 (88)
T KOG1774|consen 12 QPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQS 85 (88)
T ss_pred CcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEee
Confidence 5888888876 5688999977 78999999999999999999999987554432479999999999999874
No 35
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.86 E-value=2.9e-09 Score=77.30 Aligned_cols=82 Identities=23% Similarity=0.204 Sum_probs=69.5
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEcc---CCCeeeecCeEEEecCeEEEEecCccccchHHH
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK---DGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~---~g~~~~~l~~v~IRGnnIryI~lPd~lld~~~~ 81 (150)
+-|..+++++|.|-+.+|+.+.|+|.+||+..||.|+++-+... .+.+...++..+|||+||..|-+-|+.+|+.++
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld 82 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD 82 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence 45889999999999999999999999999999999999987542 333446789999999999999999998888666
Q ss_pred Hhhhh
Q 031941 82 ETKSR 86 (150)
Q Consensus 82 ~~~~~ 86 (150)
..+-|
T Consensus 83 ~tkir 87 (96)
T KOG1784|consen 83 LTKIR 87 (96)
T ss_pred hhhcc
Confidence 55433
No 36
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.82 E-value=5.1e-10 Score=82.24 Aligned_cols=72 Identities=18% Similarity=0.253 Sum_probs=61.8
Q ss_pred HHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCC-------CeeeecCeEEEecCeEEEEecCccc
Q 031941 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDG-------DRFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g-------~~~~~l~~v~IRGnnIryI~lPd~l 75 (150)
+--|.+++.|+|.|++..|+++.|+|.+||+.||++|+|++|+..|- ++..+|+.+.+||..+..|+..|-.
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~ 97 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGS 97 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcch
Confidence 34588999999999999999999999999999999999999876432 1236899999999999998876654
No 37
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=98.69 E-value=2.5e-09 Score=85.07 Aligned_cols=71 Identities=24% Similarity=0.311 Sum_probs=60.6
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEc---------cCCCeeeecCeEEEecCeEEEEecCccc
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTS---------KDGDRFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~---------~~g~~~~~l~~v~IRGnnIryI~lPd~l 75 (150)
+-|-+++|.++.|.|+++++|.|++.+||.|||++|.||+|.. .++++...|..|++||+||...++.+-.
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegpp 86 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPP 86 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCC
Confidence 4466789999999999999999999999999999999998743 2445557799999999999998876544
No 38
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=98.67 E-value=4.1e-09 Score=80.07 Aligned_cols=68 Identities=26% Similarity=0.317 Sum_probs=57.6
Q ss_pred HHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCee--eecCeEEEecCeEEEEecCc
Q 031941 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRF--WRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~--~~l~~v~IRGnnIryI~lPd 73 (150)
-|.+++.++|.|-|++|+.+.|+|.+||+|-|++|++|++..--++.+ ...+..+|||.||..|-..|
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid 82 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEID 82 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCC
Confidence 377888999999999999999999999999999999999865434332 35678999999999997544
No 39
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.98 E-value=2.7e-05 Score=53.65 Aligned_cols=45 Identities=24% Similarity=0.351 Sum_probs=37.6
Q ss_pred HHHHhhcCCCeEEEEEcCCCEEEEEEEEecC---ccceEEccEEEEcc
Q 031941 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDT---WMNIHLREVICTSK 48 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~---~MNI~L~dv~~t~~ 48 (150)
+.++.+++|++|.|.++||..|+|+|.+++. -+.++|+.|.....
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~ 51 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPK 51 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccc
Confidence 5688999999999999999999999999998 89999999998754
No 40
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification]
Probab=97.80 E-value=3.6e-06 Score=63.02 Aligned_cols=68 Identities=21% Similarity=0.341 Sum_probs=55.8
Q ss_pred hHHHHhhcC--CCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEcc------CCCe------eeecCeEEEecCeEEE
Q 031941 3 PLSLLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSK------DGDR------FWRMPECYIRGNTIKY 68 (150)
Q Consensus 3 Pl~lL~~l~--gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~------~g~~------~~~l~~v~IRGnnIry 68 (150)
|+++|..++ ..+|+|-++|...+.|.+.+||-|.|++|+|+.+... ++.. -..++.+||||++|..
T Consensus 25 pls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~ 104 (114)
T KOG3459|consen 25 PLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVIL 104 (114)
T ss_pred chhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEE
Confidence 778888776 7899999999999999999999999999999987431 2221 1357899999999877
Q ss_pred Ee
Q 031941 69 LR 70 (150)
Q Consensus 69 I~ 70 (150)
+.
T Consensus 105 v~ 106 (114)
T KOG3459|consen 105 VL 106 (114)
T ss_pred EE
Confidence 64
No 41
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.33 E-value=0.00019 Score=49.43 Aligned_cols=38 Identities=24% Similarity=0.267 Sum_probs=31.5
Q ss_pred CCeEEEEEcCC----CEEEEEEEEecCccceEEccEEEEccC
Q 031941 12 GHPMLVELKNG----ETYNGHLVNCDTWMNIHLREVICTSKD 49 (150)
Q Consensus 12 gk~V~VeLKnG----~~~~G~L~~~D~~MNI~L~dv~~t~~~ 49 (150)
.++|.|.++.- -.++|.|++||.||||.|.||+|+...
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 57788888553 478899999999999999999998643
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.19 E-value=0.0022 Score=46.88 Aligned_cols=68 Identities=25% Similarity=0.225 Sum_probs=55.8
Q ss_pred hhcCCCeEEEEEcCCCEEEEEEEEecC-ccceEEccEEEEccCCCe--------eeecCeEEEecCeEEEEecCccc
Q 031941 8 KTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDR--------FWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~~D~-~MNI~L~dv~~t~~~g~~--------~~~l~~v~IRGnnIryI~lPd~l 75 (150)
..++|++|.+..|++..|+|+|..+|. .-.|.|+||...-.++.+ ...++.+..||+.|+-|.+-+.-
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~ 80 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPP 80 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCC
Confidence 468999999999999999999999996 679999999987554421 13588999999999999875544
No 43
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=97.18 E-value=0.0012 Score=54.11 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=4.9
Q ss_pred HHhhcCCCeE
Q 031941 6 LLKTAQGHPM 15 (150)
Q Consensus 6 lL~~l~gk~V 15 (150)
||..+++.-|
T Consensus 59 flh~Cegd~V 68 (215)
T KOG3262|consen 59 FLHMCEGDLV 68 (215)
T ss_pred hhhhcCCceE
Confidence 4555555444
No 44
>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=96.78 E-value=0.0058 Score=43.52 Aligned_cols=64 Identities=20% Similarity=0.285 Sum_probs=50.9
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCc-cceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTW-MNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~-MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
.|.+|.++.+++|.+.|...+++.++..+||.. .|+.++|-.- +=| ..++..||.+-|..+++.
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T--PlG----v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT--PLG----VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET--TTT----EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC--Ccc----cChhheeecCCEEEEEec
Confidence 467889999999999999999999999999964 6888887553 333 457899999999999874
No 45
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.13 E-value=0.014 Score=39.53 Aligned_cols=36 Identities=22% Similarity=0.377 Sum_probs=29.9
Q ss_pred HHhhcC--CCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 6 LLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 6 lL~~l~--gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
||+.+. ..+|+|-|.||..+.|.+.+||.|+=+.-.
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~ 40 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLLES 40 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEEEE
Confidence 455553 789999999999999999999999865543
No 46
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.96 E-value=0.019 Score=39.03 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=29.8
Q ss_pred HHhhc--CCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 6 LLKTA--QGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 6 lL~~l--~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
||+.+ ...+|+|-|.||..+.|.+.+||.|+=+.-.
T Consensus 7 fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll~~ 44 (61)
T TIGR02383 7 FLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLES 44 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEEEE
Confidence 45555 3789999999999999999999999866543
No 47
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=95.87 E-value=0.06 Score=44.25 Aligned_cols=7 Identities=29% Similarity=0.572 Sum_probs=3.3
Q ss_pred EecCccc
Q 031941 69 LRVPDEV 75 (150)
Q Consensus 69 I~lPd~l 75 (150)
++-|+.|
T Consensus 126 fi~p~Kl 132 (215)
T KOG3262|consen 126 FIDPDKL 132 (215)
T ss_pred Eeccccc
Confidence 3345555
No 48
>PTZ00146 fibrillarin; Provisional
Probab=95.73 E-value=0.028 Score=48.42 Aligned_cols=7 Identities=43% Similarity=0.819 Sum_probs=2.6
Q ss_pred CCCCCCC
Q 031941 137 GKPGGSR 143 (150)
Q Consensus 137 ~~~~~~~ 143 (150)
+++|+.+
T Consensus 44 ~~~~~~~ 50 (293)
T PTZ00146 44 GGRGGGG 50 (293)
T ss_pred CCCCCCC
Confidence 3333333
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.63 E-value=0.028 Score=39.99 Aligned_cols=37 Identities=19% Similarity=0.361 Sum_probs=30.1
Q ss_pred HHhhc--CCCeEEEEEcCCCEEEEEEEEecCccceEEcc
Q 031941 6 LLKTA--QGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 6 lL~~l--~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~d 42 (150)
||+.+ ...+|+|-|.||..+.|.+.+||.|+=+...+
T Consensus 11 fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 11 FLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 44444 37899999999999999999999998665433
No 50
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=95.49 E-value=0.068 Score=37.63 Aligned_cols=62 Identities=24% Similarity=0.211 Sum_probs=48.1
Q ss_pred hhcCCCeEEEEEcCCCEEEEEEEEecCc-cceEEccEEEEccCCCe---------eeecCeEEEecCeEEEE
Q 031941 8 KTAQGHPMLVELKNGETYNGHLVNCDTW-MNIHLREVICTSKDGDR---------FWRMPECYIRGNTIKYL 69 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~~D~~-MNI~L~dv~~t~~~g~~---------~~~l~~v~IRGnnIryI 69 (150)
.+++|++|.+-.|.+..|+|+|.++|.. --|.|+||...-.++.+ ...++.+..||+.|+-+
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkDL 73 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKDL 73 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccccc
Confidence 3689999999999999999999999965 57889999987554422 12366677888877643
No 51
>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=95.24 E-value=0.092 Score=33.16 Aligned_cols=31 Identities=19% Similarity=0.155 Sum_probs=27.8
Q ss_pred CCCeEEEEEcCCCEEEEEEEEecCccceEEcc
Q 031941 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~d 42 (150)
+|++|+|++ ++..++|+...+|+.-.|.|+.
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEE
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEE
Confidence 689999999 7777899999999999998865
No 52
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=94.66 E-value=0.075 Score=42.48 Aligned_cols=63 Identities=24% Similarity=0.263 Sum_probs=43.7
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecC-ccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccc
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~-~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~l 75 (150)
..+..|++|.|.|.+.| ++|.|.|..+|+ .-||+|-+-.+ +++ . ..-+|-|.+|+.|.+-++-
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e---~~~--~--sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE---DGK--R--SVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T---TS---E--EEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc---CCc--e--eEEEEEccceEEEEEccCC
Confidence 35678999999999999 999999999996 56888875443 332 2 2478999999999876553
No 53
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.82 E-value=0.1 Score=46.28 Aligned_cols=70 Identities=23% Similarity=0.228 Sum_probs=55.1
Q ss_pred HHhhcCCCeEEEEEcCCCEEEEEEEEecC-ccceEEccEEEEccCCCee---------eecCeEEEecCeEEEEecCccc
Q 031941 6 LLKTAQGHPMLVELKNGETYNGHLVNCDT-WMNIHLREVICTSKDGDRF---------WRMPECYIRGNTIKYLRVPDEV 75 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~~D~-~MNI~L~dv~~t~~~g~~~---------~~l~~v~IRGnnIryI~lPd~l 75 (150)
+...++|++|.+--|++..|+|+|..+|. -.=|-|++|..+-.++.+. ..++.|+.||+.|+-|++-+..
T Consensus 3 ~~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 3 LVTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred cccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 45678999999999999999999999994 5689999997654433210 1578899999999988765533
No 54
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=93.59 E-value=0.75 Score=31.60 Aligned_cols=53 Identities=26% Similarity=0.414 Sum_probs=39.1
Q ss_pred HHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
+..|++++|++|.|++-.|+. +|+|.++.... |+|+. .+ ..+|||=..|.+|.
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~------~~------~~~~IR~~~IV~v~ 65 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEE------NG------TPFFIRIAQIVWVM 65 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEe------CC------cEEEEEeeeEEEEc
Confidence 567999999999999977776 99999986431 23322 12 24788888888875
No 55
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.46 E-value=0.15 Score=36.10 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=28.1
Q ss_pred HHHhhc--CCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 5 SLLKTA--QGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 5 ~lL~~l--~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
.||.++ ...+|+|-|.||..+.|.+.+||.|.=
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~V 44 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFVV 44 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEEE
Confidence 456555 478999999999999999999999963
No 56
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=91.62 E-value=0.38 Score=38.55 Aligned_cols=37 Identities=24% Similarity=0.440 Sum_probs=30.0
Q ss_pred HHhhc--CCCeEEEEEcCCCEEEEEEEEecCccceEEcc
Q 031941 6 LLKTA--QGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 6 lL~~l--~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~d 42 (150)
||+.+ ...+|+|-|.||-.++|++.+||.|+=|...+
T Consensus 96 fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~ 134 (165)
T PRK14091 96 FLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERD 134 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 44444 37899999999999999999999998665444
No 57
>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=91.30 E-value=1 Score=30.48 Aligned_cols=31 Identities=13% Similarity=0.127 Sum_probs=27.4
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEE
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L 40 (150)
.+|..|.+++-.|.+++|.|.+||...++.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lI 34 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLI 34 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEE
Confidence 4799999999999999999999998776553
No 58
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=90.84 E-value=0.5 Score=37.87 Aligned_cols=37 Identities=19% Similarity=0.316 Sum_probs=30.1
Q ss_pred HHhhcC--CCeEEEEEcCCCEEEEEEEEecCccceEEcc
Q 031941 6 LLKTAQ--GHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 6 lL~~l~--gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~d 42 (150)
||+.+. ..+|+|-|.||..++|++.+||.|.=|...+
T Consensus 16 fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 16 FLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred HHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 455553 6889999999999999999999998655544
No 59
>PRK14639 hypothetical protein; Provisional
Probab=88.72 E-value=1 Score=34.62 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=29.9
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L 40 (150)
.-++.++|++|.|+|++...+.|+|.++|.. ++.|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4577899999999999999999999999873 4444
No 60
>PRK14638 hypothetical protein; Provisional
Probab=87.79 E-value=1 Score=35.11 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=29.5
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L 40 (150)
.-+..++|++|.|+|++.+.++|+|.++|.. +++|
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 4567889999999999999999999999863 3444
No 61
>PRK02001 hypothetical protein; Validated
Probab=87.47 E-value=1.4 Score=34.53 Aligned_cols=35 Identities=31% Similarity=0.401 Sum_probs=29.4
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L 40 (150)
.-+..++|+.|.|.|.+...|.|+|.++|.. +++|
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 3467889999999999999999999999875 3444
No 62
>PRK14644 hypothetical protein; Provisional
Probab=83.03 E-value=2.8 Score=32.23 Aligned_cols=35 Identities=23% Similarity=0.312 Sum_probs=29.4
Q ss_pred HHhhcCCCeEEEEEcCC----CEEEEEEEEecCccceEEc
Q 031941 6 LLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG----~~~~G~L~~~D~~MNI~L~ 41 (150)
-+..++|+.|.|+|++. ..+.|+|.++|.. ++.|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 47889999999999887 9999999999873 45554
No 63
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.75 E-value=4.5 Score=31.88 Aligned_cols=33 Identities=18% Similarity=0.290 Sum_probs=29.4
Q ss_pred HHHHhhcCCCeEEEEE----cCCCEEEEEEEEecCcc
Q 031941 4 LSLLKTAQGHPMLVEL----KNGETYNGHLVNCDTWM 36 (150)
Q Consensus 4 l~lL~~l~gk~V~VeL----KnG~~~~G~L~~~D~~M 36 (150)
..-+..++|+.|.|+| .+.+.++|+|..+|..+
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3567888999999999 78999999999999876
No 64
>PRK14642 hypothetical protein; Provisional
Probab=81.27 E-value=3.4 Score=33.87 Aligned_cols=69 Identities=14% Similarity=0.145 Sum_probs=43.9
Q ss_pred HHHhhcCCCeEEEEEc-------------CCCEEEEEEEEecCccceEE--ccEEEEccCC------CeeeecCeEEEec
Q 031941 5 SLLKTAQGHPMLVELK-------------NGETYNGHLVNCDTWMNIHL--REVICTSKDG------DRFWRMPECYIRG 63 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK-------------nG~~~~G~L~~~D~~MNI~L--~dv~~t~~~g------~~~~~l~~v~IRG 63 (150)
.-+..++|+.|.|.|+ +.+.|+|+|.++|.. +++| ++.-+- +++ +.+..+..+-|-=
T Consensus 93 ~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l~~~~~~~~-k~g~~~~k~~~~~~~~~~~~~~ 170 (197)
T PRK14642 93 QDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQIVWSDEPPV-KPGQRVSKKRVPAPLQALGFTL 170 (197)
T ss_pred HHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEEEEeecccC-CCccccccccccccceeEEeeh
Confidence 4567889999999998 779999999999874 4444 322111 111 1112334566666
Q ss_pred CeEEEEecCccc
Q 031941 64 NTIKYLRVPDEV 75 (150)
Q Consensus 64 nnIryI~lPd~l 75 (150)
+.|++..|...+
T Consensus 171 ~eik~a~l~p~~ 182 (197)
T PRK14642 171 DELREARLAPIV 182 (197)
T ss_pred hheeeEEEEEEE
Confidence 777777665543
No 65
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=81.19 E-value=6.3 Score=30.40 Aligned_cols=30 Identities=20% Similarity=0.350 Sum_probs=26.3
Q ss_pred HHHhhcCCCeEEEEE----cCCCEEEEEEEEecC
Q 031941 5 SLLKTAQGHPMLVEL----KNGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeL----KnG~~~~G~L~~~D~ 34 (150)
.-++.++|+.|.|+| .+...++|+|.++|.
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 457789999999997 567899999999987
No 66
>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=80.92 E-value=3.4 Score=28.68 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=26.2
Q ss_pred HHHhhcCCCeEEEEEc---CC-CEEEEEEEEecCc
Q 031941 5 SLLKTAQGHPMLVELK---NG-ETYNGHLVNCDTW 35 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---nG-~~~~G~L~~~D~~ 35 (150)
.-+..++|+.|.|+|+ ++ +.+.|.|.++|..
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 4567889999999997 55 6899999999874
No 67
>PRK14640 hypothetical protein; Provisional
Probab=79.99 E-value=4.2 Score=31.61 Aligned_cols=35 Identities=20% Similarity=0.262 Sum_probs=28.6
Q ss_pred HHHhhcCCCeEEEEE----cCCCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVEL----KNGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeL----KnG~~~~G~L~~~D~~MNI~L 40 (150)
.-++.++|+.|.|.| .+.+.++|+|.++|.. ++.|
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 456789999999999 5679999999999874 3444
No 68
>PRK14632 hypothetical protein; Provisional
Probab=76.59 E-value=5.7 Score=31.61 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=28.4
Q ss_pred HHHhhcCCCeEEEEEcC-------CCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKN-------GETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn-------G~~~~G~L~~~D~~MNI~L 40 (150)
.-++.++|+.|.|+|++ .+.|.|+|.++|.. +|.|
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l 132 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVL 132 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEE
Confidence 45678999999999976 57999999999863 4444
No 69
>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=76.20 E-value=4.9 Score=30.39 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=23.8
Q ss_pred HHHhhcCCCeEEEEEc----CCCEEEEEEEEecC
Q 031941 5 SLLKTAQGHPMLVELK----NGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK----nG~~~~G~L~~~D~ 34 (150)
.-+..++|++|.|+|+ +.+.+.|+|.++|.
T Consensus 80 ~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 80 RDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp HHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred HHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 4678899999999994 55799999999998
No 70
>PRK14636 hypothetical protein; Provisional
Probab=75.52 E-value=5.8 Score=31.73 Aligned_cols=35 Identities=20% Similarity=0.371 Sum_probs=27.9
Q ss_pred HHHhhcCCCeEEEEEc---CC-CEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELK---NG-ETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---nG-~~~~G~L~~~D~~MNI~L 40 (150)
.-+..++|++|.|+|+ ++ +.++|+|.++|.. ++.|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 4567889999999997 45 7999999999873 3443
No 71
>PRK11625 Rho-binding antiterminator; Provisional
Probab=73.35 E-value=24 Score=25.22 Aligned_cols=55 Identities=18% Similarity=0.171 Sum_probs=33.6
Q ss_pred HhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|..+.+.+|.++|+||++++|+. .|-+.+ +.+++...+.. -....||=++|..|+
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A--~D~~~~---~k~EyL~l~~~----g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKA--SDLVSR---KNVEYLVVEAA----GETRELRLDKIASFS 72 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEE--EeeecC---CceEEEEEEcC----CCEEEEEeeeEeecc
Confidence 44557899999999999999987 454543 44444322110 123455555555555
No 72
>PRK14647 hypothetical protein; Provisional
Probab=73.27 E-value=7.8 Score=30.26 Aligned_cols=30 Identities=17% Similarity=0.142 Sum_probs=25.9
Q ss_pred HHHhhcCCCeEEEEEc---------CCCEEEEEEEEecC
Q 031941 5 SLLKTAQGHPMLVELK---------NGETYNGHLVNCDT 34 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK---------nG~~~~G~L~~~D~ 34 (150)
.-++.++|++|.|+|+ +.+.+.|+|.++|.
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 4577899999999995 35899999999986
No 73
>PRK14633 hypothetical protein; Provisional
Probab=73.02 E-value=6.4 Score=30.56 Aligned_cols=35 Identities=14% Similarity=0.137 Sum_probs=28.3
Q ss_pred HHHhhcCCCeEEEEEc----CCCEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELK----NGETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK----nG~~~~G~L~~~D~~MNI~L 40 (150)
.-+..++|++|.|+|+ +.+.++|+|.++|.. ++.|
T Consensus 87 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 87 IQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 4567889999999994 669999999999874 4444
No 74
>PRK14643 hypothetical protein; Provisional
Probab=71.83 E-value=8.2 Score=30.54 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=28.5
Q ss_pred HHHhhcCCCeEEEEEcC----CCEEEEEEEEecCc-cceEE
Q 031941 5 SLLKTAQGHPMLVELKN----GETYNGHLVNCDTW-MNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn----G~~~~G~L~~~D~~-MNI~L 40 (150)
.-++.++|++|.|.|+. ...++|+|.++|.- ..|.|
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 45678899999999965 69999999999864 34433
No 75
>PRK14645 hypothetical protein; Provisional
Probab=71.79 E-value=6.6 Score=30.75 Aligned_cols=30 Identities=17% Similarity=0.188 Sum_probs=25.9
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCc
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~ 35 (150)
.-+..++|++|.|.+ +...++|+|.++|..
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 456788999999986 789999999999874
No 76
>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=71.31 E-value=4.1 Score=28.81 Aligned_cols=30 Identities=30% Similarity=0.405 Sum_probs=18.2
Q ss_pred HHhhcCCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
.|..+...+|.++||||++++|+ +.|...|
T Consensus 11 EiAC~~~~~v~L~l~dG~~~~g~--A~dt~~~ 40 (80)
T PF07073_consen 11 EIACMYRYPVKLTLKDGEQIEGK--ALDTRTN 40 (80)
T ss_dssp HHHHTTTT-EEEE-TTT--EEES--S-EEE--
T ss_pred HHHHhcCCeEEEEEeCCCEEEEE--EEEEEEe
Confidence 35667899999999999999997 4444444
No 77
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=70.46 E-value=3.3 Score=31.82 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=10.1
Q ss_pred EEecCccccchHH
Q 031941 68 YLRVPDEVIDKVQ 80 (150)
Q Consensus 68 yI~lPd~lld~~~ 80 (150)
|++||++++-+..
T Consensus 80 yL~LP~eivP~T~ 92 (124)
T PTZ00034 80 YLHLPPDVFPATH 92 (124)
T ss_pred HhCCCcccCchhh
Confidence 6889999977655
No 78
>PRK14634 hypothetical protein; Provisional
Probab=70.21 E-value=7.7 Score=30.31 Aligned_cols=35 Identities=17% Similarity=0.355 Sum_probs=27.6
Q ss_pred HHHhhcCCCeEEEEEcCC----CEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG----~~~~G~L~~~D~~MNI~L 40 (150)
.-++.++|+.|.|+|++. +.|+|+|.++|.. +|.|
T Consensus 93 ~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 93 RDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 456788999999999743 7999999999874 3444
No 79
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=69.97 E-value=18 Score=34.05 Aligned_cols=26 Identities=8% Similarity=0.127 Sum_probs=14.8
Q ss_pred ecCeEEEecCeEEEEecCccccchHHH
Q 031941 55 RMPECYIRGNTIKYLRVPDEVIDKVQE 81 (150)
Q Consensus 55 ~l~~v~IRGnnIryI~lPd~lld~~~~ 81 (150)
.++.+-|. ++-.||.+|+.+.+.+..
T Consensus 518 ~ig~i~i~-~~~s~v~~~~~~~~~~~~ 543 (629)
T PRK11634 518 YIGNIKLF-ASHSTIELPKGMPGEVLQ 543 (629)
T ss_pred hCCcEEEe-CCceEEEcChhhHHHHHH
Confidence 34444444 234678888877555443
No 80
>PRK14637 hypothetical protein; Provisional
Probab=69.82 E-value=11 Score=29.43 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=26.4
Q ss_pred HHHhhcCCCeEEEEEcCCCEE-EEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNGETY-NGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~-~G~L~~~D~~MNI~L 40 (150)
.-+..++|+.|.|+|.+...+ +|+|.++|.. ++.|
T Consensus 91 ~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 91 AEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred HHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 456788999999999544455 7999999874 3444
No 81
>PRK06955 biotin--protein ligase; Provisional
Probab=68.41 E-value=18 Score=30.67 Aligned_cols=32 Identities=16% Similarity=0.099 Sum_probs=27.9
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
+++++|+|...++.+++|++.++|..-.|+|+
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 56999999876778899999999999888875
No 82
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=68.37 E-value=13 Score=37.43 Aligned_cols=18 Identities=22% Similarity=0.811 Sum_probs=14.2
Q ss_pred EEEE-EEEecCccceEEcc
Q 031941 25 YNGH-LVNCDTWMNIHLRE 42 (150)
Q Consensus 25 ~~G~-L~~~D~~MNI~L~d 42 (150)
.-|. |+-+|+|.++.++.
T Consensus 1074 sdgq~IV~VDdWIklqIsh 1092 (1282)
T KOG0921|consen 1074 SDGQGIVRVDDWIKLQISH 1092 (1282)
T ss_pred ccCcceEEeeceeeEeccH
Confidence 3466 88899999998863
No 83
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=68.35 E-value=15 Score=28.75 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=23.9
Q ss_pred hhcCCCeEEEEEcCCCEEEEEEEEec
Q 031941 8 KTAQGHPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 8 ~~l~gk~V~VeLKnG~~~~G~L~~~D 33 (150)
.+++||.|++++.++..+.|++.++.
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46789999999999999999999986
No 84
>PRK14646 hypothetical protein; Provisional
Probab=68.10 E-value=9.1 Score=29.91 Aligned_cols=35 Identities=29% Similarity=0.326 Sum_probs=27.8
Q ss_pred HHHhhcCCCeEEEEEcCC----CEEEEEEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELKNG----ETYNGHLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG----~~~~G~L~~~D~~MNI~L 40 (150)
.-++.++|++|.|+|++. ..++|+|.++|.. +|+|
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 457788999999999643 7889999999874 4444
No 85
>PRK14641 hypothetical protein; Provisional
Probab=61.75 E-value=12 Score=29.92 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=24.7
Q ss_pred HHHhhcCCCeEEEEEcC----CCEEEEEEEEec
Q 031941 5 SLLKTAQGHPMLVELKN----GETYNGHLVNCD 33 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKn----G~~~~G~L~~~D 33 (150)
.-++.++|+.|.|.|++ .+.++|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 45778899999999976 468999999995
No 86
>PRK14631 hypothetical protein; Provisional
Probab=61.05 E-value=14 Score=29.55 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=25.9
Q ss_pred HHHHhhcCCCeEEEEEc----CCCEEEEEEEEec
Q 031941 4 LSLLKTAQGHPMLVELK----NGETYNGHLVNCD 33 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLK----nG~~~~G~L~~~D 33 (150)
..-++.++|+.|.|+|+ +.+.|+|+|.++|
T Consensus 109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 34578899999999995 5599999999998
No 87
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=60.22 E-value=8.2 Score=29.82 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=8.3
Q ss_pred ecCeEEEec-CeEEEEecCc
Q 031941 55 RMPECYIRG-NTIKYLRVPD 73 (150)
Q Consensus 55 ~l~~v~IRG-nnIryI~lPd 73 (150)
+|.+|.+-- +-=+|+.+|+
T Consensus 39 ~L~~Vi~ts~Dgdkf~r~pE 58 (134)
T KOG3293|consen 39 HLREVICTSEDGDKFFRMPE 58 (134)
T ss_pred chheeEEeccCCCceeecce
Confidence 344444332 2334555554
No 88
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=60.17 E-value=42 Score=29.75 Aligned_cols=13 Identities=15% Similarity=0.386 Sum_probs=7.1
Q ss_pred EecCeEEEEecCc
Q 031941 61 IRGNTIKYLRVPD 73 (150)
Q Consensus 61 IRGnnIryI~lPd 73 (150)
-.|..|.+|...|
T Consensus 341 ~~G~ai~l~~~~d 353 (456)
T PRK10590 341 ATGEALSLVCVDE 353 (456)
T ss_pred CCeeEEEEecHHH
Confidence 3455666665443
No 89
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=59.90 E-value=30 Score=32.54 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=28.0
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
++|++|.|...+..+++|+..++|..-.|.|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 57999999766777899999999999998885
No 90
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=57.59 E-value=35 Score=28.81 Aligned_cols=31 Identities=13% Similarity=0.109 Sum_probs=27.0
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
+.|+.|+|.. ++.+++|++..+|..-.|+|+
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLE 300 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEE
Confidence 4699999987 446799999999999999885
No 91
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=56.37 E-value=28 Score=26.04 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=24.1
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEE
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGH 28 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~ 28 (150)
+|+..|+.+.+-+|+.||.||.+|...
T Consensus 64 ~~~~~i~~~~~~tvt~e~~nG~~y~l~ 90 (119)
T PF10618_consen 64 TDVDDINDITDATVTFELDNGKVYVLS 90 (119)
T ss_pred CCHHHHhCCcccEEEEEecCCcEEEec
Confidence 478889999999999999999999754
No 92
>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=55.24 E-value=26 Score=26.00 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=15.4
Q ss_pred CCeEEEEEcCCCEEEEEEE
Q 031941 12 GHPMLVELKNGETYNGHLV 30 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~ 30 (150)
...|.++|++|+.+.||+.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 5789999999999999874
No 93
>PRK08330 biotin--protein ligase; Provisional
Probab=52.33 E-value=54 Score=26.60 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=26.2
Q ss_pred hcCCCeEEEEEcCCCEE-EEEEEEecCccceEEcc
Q 031941 9 TAQGHPMLVELKNGETY-NGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~-~G~L~~~D~~MNI~L~d 42 (150)
.+.+++|+|.. ++.++ +|++.++|..-.|.|+.
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 35799999976 45554 79999999998888863
No 94
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=50.68 E-value=28 Score=25.90 Aligned_cols=21 Identities=24% Similarity=0.358 Sum_probs=18.4
Q ss_pred CeEEEEEcCCCEEEEEEEEec
Q 031941 13 HPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~~D 33 (150)
..+.|.|+||+++.|.|..=|
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~ 78 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASET 78 (133)
T ss_pred ccEEEEECCCCEEEEEEEecC
Confidence 458999999999999998855
No 95
>PRK14635 hypothetical protein; Provisional
Probab=50.32 E-value=39 Score=26.44 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=26.6
Q ss_pred HHHhhcCCCeEEEEEc--CCCEEEE---EEEEecCccceEE
Q 031941 5 SLLKTAQGHPMLVELK--NGETYNG---HLVNCDTWMNIHL 40 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLK--nG~~~~G---~L~~~D~~MNI~L 40 (150)
.-+..++|+.|.|++. ++..+.| +|.++|.. ++.|
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 3467889999999986 4578887 99999864 4444
No 96
>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=49.88 E-value=50 Score=26.77 Aligned_cols=31 Identities=16% Similarity=0.083 Sum_probs=26.8
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
+++++|+|...+ .++.|++.++|..-.|.|+
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 469999998755 5799999999999999886
No 97
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=48.94 E-value=67 Score=25.04 Aligned_cols=26 Identities=19% Similarity=0.219 Sum_probs=23.1
Q ss_pred hcCCCeEEEEEcCCCEEEEEEEEecC
Q 031941 9 TAQGHPMLVELKNGETYNGHLVNCDT 34 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~~G~L~~~D~ 34 (150)
+++||.|+..+.++..+.|++.++..
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEE
Confidence 68999999888999999999998864
No 98
>PRK14630 hypothetical protein; Provisional
Probab=47.98 E-value=32 Score=26.53 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=24.4
Q ss_pred HHHhhcCCCeEEEEEcCCCEEEEEEEEecCc
Q 031941 5 SLLKTAQGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~ 35 (150)
.-++.++|++|.|.|+.- ..+|+|.++|..
T Consensus 90 ~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~ 119 (143)
T PRK14630 90 REFKIFEGKKIKLMLDND-FEEGFILEAKAD 119 (143)
T ss_pred HHHHHhCCCEEEEEEcCc-ceEEEEEEEeCC
Confidence 456788999999999664 459999999873
No 99
>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=43.91 E-value=35 Score=27.31 Aligned_cols=34 Identities=18% Similarity=0.063 Sum_probs=31.0
Q ss_pred CCCeEEEEEcCCCEEEEEEEEecCccceEEccEE
Q 031941 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~ 44 (150)
-.-+|.|.+.|+.++.+.+..++.--|.+|.-+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 4689999999999999999999999999987665
No 100
>PF07833 Cu_amine_oxidN1: Copper amine oxidase N-terminal domain; InterPro: IPR012854 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents a domain found at the N-terminal of certain copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix [, ]. ; PDB: 1SPU_A 2WGQ_A 2WO0_A 1JRQ_A 1QAF_B 1D6U_B 1QAL_A 2WOF_A 1OAC_B 1QAK_A ....
Probab=43.42 E-value=64 Score=21.39 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=17.2
Q ss_pred CChHHHHhhcCCCeEEEEEcCCC
Q 031941 1 MLPLSLLKTAQGHPMLVELKNGE 23 (150)
Q Consensus 1 MlPl~lL~~l~gk~V~VeLKnG~ 23 (150)
|+|+.+|.+++|-.|...-++.+
T Consensus 6 ~vPl~~i~~~lg~~v~~d~~~~~ 28 (93)
T PF07833_consen 6 YVPLRFIAEALGAKVSWDNKTKT 28 (93)
T ss_dssp EEEHHHHHHHHT-EEEEETTTTE
T ss_pred EEEHHHHHHHcCCEEEEEcCCcE
Confidence 68999999999998877544443
No 101
>PRK10898 serine endoprotease; Provisional
Probab=43.42 E-value=46 Score=28.94 Aligned_cols=60 Identities=15% Similarity=0.289 Sum_probs=39.7
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecC--eEEEecCeEEEEecCcc
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMP--ECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~--~v~IRGnnIryI~lPd~ 74 (150)
...+.|.+.++++|..+|+.+|..++|-|=.+... + -++..+. ...-.|+.|..|-.|-.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~~~--~-l~~~~l~~~~~~~~G~~V~aiG~P~g 162 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKINAT--N-LPVIPINPKRVPHIGDVVLAIGNPYN 162 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEcCC--C-CCeeeccCcCcCCCCCEEEEEeCCCC
Confidence 36789999999999999999999999877655421 1 0111121 12335667777766643
No 102
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=41.09 E-value=56 Score=26.66 Aligned_cols=35 Identities=20% Similarity=0.459 Sum_probs=30.0
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
++.+=+.|+||.+..++.++..+.|.|+.+..|+-
T Consensus 10 ~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 10 AVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred HHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 35566788999999999999888999999999974
No 103
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=39.97 E-value=89 Score=19.15 Aligned_cols=25 Identities=20% Similarity=0.407 Sum_probs=21.6
Q ss_pred CCCeEEEEEcCCCEEEEEEEEecCc
Q 031941 11 QGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~~D~~ 35 (150)
.|+.|.+...++.-|.+++++++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5778888888999999999999964
No 104
>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=37.12 E-value=65 Score=27.89 Aligned_cols=58 Identities=14% Similarity=0.222 Sum_probs=38.2
Q ss_pred CeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeec--CeEEEecCeEEEEecCc
Q 031941 13 HPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRM--PECYIRGNTIKYLRVPD 73 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l--~~v~IRGnnIryI~lPd 73 (150)
..+.|.+.+++.+.++++.+|...+|-|=.+.... -++..+ ..-+-.|+.|..|-.|-
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~~~~---~~~~~l~~s~~~~~G~~V~aiG~P~ 161 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIEGDN---LPTIPVNLDRPPHVGDVVLAIGNPY 161 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEecCCC---CceEeccCcCccCCCCEEEEEeCCC
Confidence 46899999999999999999999998876554321 011111 11233466666666664
No 105
>PRK10139 serine endoprotease; Provisional
Probab=35.81 E-value=68 Score=29.00 Aligned_cols=61 Identities=13% Similarity=0.201 Sum_probs=40.3
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecC--eEEEecCeEEEEecCcc
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMP--ECYIRGNTIKYLRVPDE 74 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~--~v~IRGnnIryI~lPd~ 74 (150)
...|.|.|.|+++|..+|+.+|...+|-|=.+... +.-++..+. .-+--|..|..|--|-.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~~~--~~l~~~~lg~s~~~~~G~~V~aiG~P~g 176 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNP--SKLTQIAIADSDKLRVGDFAVAVGNPFG 176 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEecCC--CCCceeEecCccccCCCCEEEEEecCCC
Confidence 46899999999999999999999998877555421 111112222 12334777777777644
No 106
>PF13437 HlyD_3: HlyD family secretion protein
Probab=35.64 E-value=80 Score=21.64 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=26.5
Q ss_pred ChHHHHhhc--CCCeEEEEEcCC--CEEEEEEEEecC
Q 031941 2 LPLSLLKTA--QGHPMLVELKNG--ETYNGHLVNCDT 34 (150)
Q Consensus 2 lPl~lL~~l--~gk~V~VeLKnG--~~~~G~L~~~D~ 34 (150)
+|-..+..+ .|..|+|.+.++ ..+.|+|..++.
T Consensus 42 v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 42 VPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 455666676 699999999855 699999999988
No 107
>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=34.82 E-value=71 Score=28.13 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=28.1
Q ss_pred CeEEEEEcCCCEEEEEEEEecCccceEEccEE
Q 031941 13 HPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~ 44 (150)
..+.|.+.++++|..+|+.+|..++|-|=.+.
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57889999999999999999999998776554
No 108
>cd01343 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins.
Probab=34.17 E-value=1.3e+02 Score=24.91 Aligned_cols=52 Identities=13% Similarity=0.202 Sum_probs=35.0
Q ss_pred eEEEEEcCCCEEEEEEEEecCccceEEccEEEEccCCCeeeecCeEEEecCeEEEE
Q 031941 14 PMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYL 69 (150)
Q Consensus 14 ~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI 69 (150)
.+.+.|.++..+.|.+...+ -+|.|.+-..+...++ ..+..+.+.+..|.|-
T Consensus 74 ~~~~~l~~~s~l~G~i~~~~--~~v~l~~~s~W~~tg~--S~v~~L~l~~g~v~f~ 125 (233)
T cd01343 74 LAELLLGGNAAWTGAIQGLN--ATVSLNLNSVWTLTGD--SNVNNLTLNGGTVDFN 125 (233)
T ss_pred eEEEEEcCCCEEEeEEeccc--ceEEEcCCCEEEEeCC--cccceeEecCCEEEec
Confidence 68899999999999999988 4566662222223344 2466777776666654
No 109
>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=33.58 E-value=1.9e+02 Score=21.66 Aligned_cols=57 Identities=12% Similarity=0.107 Sum_probs=41.2
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCccc-eEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWMN-IHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~MN-I~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
|-+|.|.-=...-.+|.+..+|..-| ++++.+....++|.+ -++.|.-+||.++.|-
T Consensus 45 GD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~----~e~pIh~SnV~l~~l~ 102 (114)
T TIGR01080 45 GDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTE----VPVPIHPSNVMITKLN 102 (114)
T ss_pred CCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECCCCeE----EEeeechHHeEEEecc
Confidence 56666666555667899999996655 888888887777632 3566888888887653
No 110
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=33.51 E-value=73 Score=25.75 Aligned_cols=34 Identities=15% Similarity=0.482 Sum_probs=25.8
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
++.+=+.|+||.+..++.++. +.|.|+.+..|+-
T Consensus 9 ~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 9 TVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp HHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred HHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 466778899999999999888 9999999988775
No 111
>PRK10942 serine endoprotease; Provisional
Probab=33.33 E-value=76 Score=28.83 Aligned_cols=32 Identities=22% Similarity=0.439 Sum_probs=27.8
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCccceEEccE
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWMNIHLREV 43 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv 43 (150)
...|.|.|.++++|..+++..|...+|-|=.+
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999999876544
No 112
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=33.25 E-value=69 Score=29.16 Aligned_cols=8 Identities=13% Similarity=0.044 Sum_probs=3.6
Q ss_pred cCeEEEec
Q 031941 56 MPECYIRG 63 (150)
Q Consensus 56 l~~v~IRG 63 (150)
...|.+|.
T Consensus 317 ~~~I~vr~ 324 (419)
T KOG0116|consen 317 EGGIQVRS 324 (419)
T ss_pred ccceEEec
Confidence 34445543
No 113
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=33.00 E-value=91 Score=26.37 Aligned_cols=31 Identities=16% Similarity=0.084 Sum_probs=26.4
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEc
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLR 41 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~ 41 (150)
..++.|+|.. ++..+.|++..+|..-.|+|+
T Consensus 235 ~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~ 265 (285)
T PTZ00275 235 YKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLL 265 (285)
T ss_pred cCCCEEEEEe-CCCEEEEEEEEECCCCeEEEE
Confidence 3699999976 568899999999998888775
No 114
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=32.54 E-value=87 Score=22.40 Aligned_cols=16 Identities=13% Similarity=0.071 Sum_probs=13.3
Q ss_pred HHHHhhcCCCeEEEEE
Q 031941 4 LSLLKTAQGHPMLVEL 19 (150)
Q Consensus 4 l~lL~~l~gk~V~VeL 19 (150)
-++|+++++++|+|.-
T Consensus 7 ~~~L~~f~gk~V~ivG 22 (101)
T cd04479 7 GAMLSQFVGKTVRIVG 22 (101)
T ss_pred HHHHHhhCCCEEEEEE
Confidence 4689999999998763
No 115
>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=32.50 E-value=50 Score=26.45 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=23.0
Q ss_pred CCCeEEEEEcCCCEEEEEEEEecCc
Q 031941 11 QGHPMLVELKNGETYNGHLVNCDTW 35 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~~D~~ 35 (150)
+++.|.|.+.+|++++|+-.++|+.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccceE
Confidence 5899999999999999999999864
No 116
>PRK06789 flagellar motor switch protein; Validated
Probab=31.52 E-value=83 Score=21.94 Aligned_cols=36 Identities=19% Similarity=0.296 Sum_probs=26.8
Q ss_pred HhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEcc
Q 031941 7 LKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLRE 42 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~d 42 (150)
|.++.+.+|.|.+.+-..-+|.|+.+|..+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 455667888888888888888888888876665543
No 117
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=29.72 E-value=67 Score=23.03 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=22.7
Q ss_pred HHhhcCCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 6 LLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 6 lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
.|..+..-+++.+||+|..|++.- -|-+.|
T Consensus 17 ElACl~hl~l~L~lkdGev~~a~A--~d~~~r 46 (84)
T COG4568 17 ELACLHHLPLTLELKDGEVLQAKA--SDLQRR 46 (84)
T ss_pred HHHHhhhceEEEEEcCCeEEEEEe--hhhhhh
Confidence 355667889999999999999964 444444
No 118
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=29.08 E-value=1.2e+02 Score=25.23 Aligned_cols=34 Identities=18% Similarity=0.187 Sum_probs=31.0
Q ss_pred cCCCeEEEEEcCCCEEEEEEEEecCccceEEccE
Q 031941 10 AQGHPMLVELKNGETYNGHLVNCDTWMNIHLREV 43 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv 43 (150)
.+|++|++++.++.++.|+...+|..-.|+|+..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4799999999999999999999999999988765
No 119
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=28.58 E-value=1.6e+02 Score=19.28 Aligned_cols=31 Identities=29% Similarity=0.406 Sum_probs=21.8
Q ss_pred cCCCEEEEEEEEe---cCccceEEccEEEEccCC
Q 031941 20 KNGETYNGHLVNC---DTWMNIHLREVICTSKDG 50 (150)
Q Consensus 20 KnG~~~~G~L~~~---D~~MNI~L~dv~~t~~~g 50 (150)
++-.++.|.|..| |.-+=.+|+|++....+.
T Consensus 3 k~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~~~~ 36 (52)
T PF02751_consen 3 KNKLSFKGHLDTYRFCDNVWTFILKNVEFKMEDN 36 (52)
T ss_dssp --EEEEEEEEEEEEEETTEEEEEEEEEEEEEE-S
T ss_pred ceeEEEEEeeeEEEeeCcEEEEEEcCEEEEEecC
Confidence 4556788988764 887888999999875333
No 120
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=28.25 E-value=84 Score=25.82 Aligned_cols=26 Identities=12% Similarity=0.120 Sum_probs=22.8
Q ss_pred hcCCCeEEEEEcCCCEEEEEEEEecC
Q 031941 9 TAQGHPMLVELKNGETYNGHLVNCDT 34 (150)
Q Consensus 9 ~l~gk~V~VeLKnG~~~~G~L~~~D~ 34 (150)
+++||.|.+.-.++..+.|++.++.-
T Consensus 115 slIGK~V~~~~~dG~~vtG~V~sV~~ 140 (190)
T PRK06792 115 KFLGKYVRGVSNDGKQVTGQVETVRL 140 (190)
T ss_pred HhcCcEEEEEcCCCCEEEEEEEEEEE
Confidence 67999999988899999999998763
No 121
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=27.83 E-value=54 Score=20.77 Aligned_cols=22 Identities=23% Similarity=0.300 Sum_probs=14.7
Q ss_pred EEEEEEEecCccceEEccEEEE
Q 031941 25 YNGHLVNCDTWMNIHLREVICT 46 (150)
Q Consensus 25 ~~G~L~~~D~~MNI~L~dv~~t 46 (150)
..|+..++|+.+.+.|++...+
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 6899999999999999886544
No 122
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=27.72 E-value=65 Score=25.80 Aligned_cols=27 Identities=22% Similarity=0.511 Sum_probs=23.1
Q ss_pred HhhcCCCeEEEEEcCCCEEEEEEEEec
Q 031941 7 LKTAQGHPMLVELKNGETYNGHLVNCD 33 (150)
Q Consensus 7 L~~l~gk~V~VeLKnG~~~~G~L~~~D 33 (150)
+..++|++|.|.|.....++|++..++
T Consensus 23 ~~~~~G~~v~v~i~~~~~~~G~v~~~~ 49 (292)
T PF05954_consen 23 LKDLLGKPVTVRIGSERVFSGYVTSVE 49 (292)
T ss_dssp CGGTTT-EEEEEETTEEEEEEEEEEEE
T ss_pred hhHhCCCEEEEEEeeeeEeccEEEEEE
Confidence 355899999999999999999999985
No 123
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=27.51 E-value=1.4e+02 Score=23.72 Aligned_cols=35 Identities=17% Similarity=0.219 Sum_probs=26.8
Q ss_pred hHHHHhhc-CCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 3 PLSLLKTA-QGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l-~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
|-..+..+ .|.+|.|.+.++.+|.|+|..++...+
T Consensus 132 ~~~~~~~i~~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 132 PAKDVSRIRKGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CHHHHhhCCCCCEEEEEECCCCEEEEEEEEEccccC
Confidence 44444444 489999999989999999999987543
No 124
>PF07752 S-layer: S-layer protein; InterPro: IPR006457 This domain is found tandemly duplicated in a most members of a paralogous family in the archaeon Methanosarcina acetivorans str. C2A. This domain is clearly related to the central region of a family of archaeal S-layer proteins described in IPR006454 from INTERPRO.
Probab=27.31 E-value=2.8e+02 Score=23.63 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=19.4
Q ss_pred CCCeEEEEE-cCCCEEEEEEEEecCc
Q 031941 11 QGHPMLVEL-KNGETYNGHLVNCDTW 35 (150)
Q Consensus 11 ~gk~V~VeL-KnG~~~~G~L~~~D~~ 35 (150)
-|.+|.+|| |||..+.=.+++....
T Consensus 137 dG~kv~leL~KdG~~Vd~~ii~~~~~ 162 (259)
T PF07752_consen 137 DGNKVWLELYKDGEEVDSKIISPGSD 162 (259)
T ss_pred CCCEEEEEEEECCeEEEeEEEcCCCC
Confidence 478999988 9998888877776443
No 125
>KOG3199 consensus Nicotinamide mononucleotide adenylyl transferase [Coenzyme transport and metabolism]
Probab=27.20 E-value=21 Score=30.11 Aligned_cols=68 Identities=22% Similarity=0.401 Sum_probs=44.5
Q ss_pred CeEEEEEcCCCEEEEEEEEec-----CccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCccccchHHHHh
Q 031941 13 HPMLVELKNGETYNGHLVNCD-----TWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEET 83 (150)
Q Consensus 13 k~V~VeLKnG~~~~G~L~~~D-----~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd~lld~~~~~~ 83 (150)
.-+.+..+.|.-+.=+|.+.| ..-|++.+|.++.+ .-.-.++..++-||-+|+|+ +||.+++.+.+..
T Consensus 156 yGl~cv~r~gsD~~~~i~~~d~i~~~~~~~l~ikn~~~~N--~ISStklr~ai~r~~SVkYl-~PD~Vi~yI~~h~ 228 (234)
T KOG3199|consen 156 YGLVCVTREGSDVENFLSSHDIILEKRRNILHIKNEIVPN--DISSTKLRQAIRRGQSVKYL-TPDSVIEYIREHN 228 (234)
T ss_pred CcEEEEeccCCCHHHHHhccHHHHHhhcceEEEeeeeecC--CcchHHHHHHHHcCCeeEee-CcHHHHHHHHHhh
Confidence 344455566665555666655 12378888877742 22224677888899999987 7888888766544
No 126
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=26.59 E-value=1.9e+02 Score=26.50 Aligned_cols=44 Identities=16% Similarity=0.183 Sum_probs=36.7
Q ss_pred ChHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccceEEccEEEE
Q 031941 2 LPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICT 46 (150)
Q Consensus 2 lPl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~~t 46 (150)
.|-.++.+++||.|+- =|+|++++++|.+-|.-.-+.+.+-++.
T Consensus 72 s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v 115 (421)
T COG5316 72 SPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEV 115 (421)
T ss_pred CchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEE
Confidence 4778999999999999 8999999999999998766666665553
No 127
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=26.50 E-value=2.7e+02 Score=21.15 Aligned_cols=57 Identities=18% Similarity=0.176 Sum_probs=41.0
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCccc-eEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWMN-IHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~MN-I~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
|-.|.|.-=...=-+|++..+|.--| ++++.+....++|.+ -++.|.=+||.++.+.
T Consensus 49 GD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~~----~e~pIh~SNV~l~~l~ 106 (120)
T PRK01191 49 GDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKADGTE----VPRPIHPSNVMITKLD 106 (120)
T ss_pred CCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECCCCeE----EEcccchhHeEEEeCc
Confidence 45555555444556799999997766 888999988777732 3577888888887653
No 128
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=25.30 E-value=1.5e+02 Score=23.91 Aligned_cols=34 Identities=15% Similarity=0.441 Sum_probs=28.4
Q ss_pred hHHHHhhcCCCeEEEEEcCCCEEEEEEEEecCccc
Q 031941 3 PLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMN 37 (150)
Q Consensus 3 Pl~lL~~l~gk~V~VeLKnG~~~~G~L~~~D~~MN 37 (150)
++.+=+.|+||.+..++. +.++.|.|+.+..|+-
T Consensus 6 ~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 6 TVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred HHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 466778899999988775 6689999999999964
No 129
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=25.04 E-value=93 Score=22.33 Aligned_cols=36 Identities=17% Similarity=0.134 Sum_probs=27.1
Q ss_pred ceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCc
Q 031941 37 NIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 37 NI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd 73 (150)
.+.=.-.-|.+.+|+. ..-+++.+.|..+.-|.+|+
T Consensus 61 ~~~r~y~FEFS~~G~~-ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 61 RWRRVYQFEFSSDGED-RYQGELVMLGRRLISVELPP 96 (97)
T ss_pred EEEEEEEEEEeCCChh-cceEEEEEECCeeeEEEcCC
Confidence 3333344456677775 67899999999999999996
No 130
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=24.80 E-value=69 Score=20.40 Aligned_cols=30 Identities=27% Similarity=0.367 Sum_probs=20.6
Q ss_pred HHHHhhcCCCeEEEEEcCCCEEEEEEEEec---CccceEEc
Q 031941 4 LSLLKTAQGHPMLVELKNGETYNGHLVNCD---TWMNIHLR 41 (150)
Q Consensus 4 l~lL~~l~gk~V~VeLKnG~~~~G~L~~~D---~~MNI~L~ 41 (150)
++.+++++||+|.|. |+|.-.. -+..+.|+
T Consensus 11 ~~~~~~~~Gk~V~V~--------G~l~~a~t~hH~Tpvll~ 43 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT--------GKLFHAHTGHHHTPVLLD 43 (48)
T ss_pred hHHHHHhcCCeEEEE--------EEEeeccCcccCCceeee
Confidence 567888999999986 5555544 23466665
No 131
>PRK07228 N-ethylammeline chlorohydrolase; Provisional
Probab=22.84 E-value=1.4e+02 Score=26.05 Aligned_cols=35 Identities=14% Similarity=0.144 Sum_probs=18.8
Q ss_pred cceEEccEEEEccCCCeeeecCeEEEecCeEEEEe
Q 031941 36 MNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLR 70 (150)
Q Consensus 36 MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~ 70 (150)
|++.|++++.++.+......-..|.|.+..|..|.
T Consensus 1 ~~~~i~~~~vi~~~~~~~~~~g~V~I~dg~I~~vg 35 (445)
T PRK07228 1 MTILIKNAGIVTMNAKREIVDGDVLIEDDRIAAVG 35 (445)
T ss_pred CeEEEEccEEEecCCCcEecccEEEEECCEEEEec
Confidence 55666666555443322233345666666666664
No 132
>PF03287 Pox_C7_F8A: Poxvirus C7/F8A protein; InterPro: IPR004967 This family includes Poxvirus C7 and F8A proteins.; GO: 0016032 viral reproduction
Probab=22.46 E-value=1.2e+02 Score=24.05 Aligned_cols=54 Identities=24% Similarity=0.294 Sum_probs=31.0
Q ss_pred EEEEEecCcc---ceEEccEEEEccCCCeeeecCeEEEe---cCeEEEEecCccc-cchHHHH
Q 031941 27 GHLVNCDTWM---NIHLREVICTSKDGDRFWRMPECYIR---GNTIKYLRVPDEV-IDKVQEE 82 (150)
Q Consensus 27 G~L~~~D~~M---NI~L~dv~~t~~~g~~~~~l~~v~IR---GnnIryI~lPd~l-ld~~~~~ 82 (150)
|+...+|-|+ ||.|++|.... |++.-..=.+-+. =-++++|.-||+- ++.++..
T Consensus 2 Gi~He~dIfiVde~ialkn~~L~k--GdsYGC~I~lk~~~~K~i~f~~Il~pdwseI~~vKpi 62 (149)
T PF03287_consen 2 GITHELDIFIVDENIALKNVELHK--GDSYGCTIKLKSKETKKINFIFILRPDWSEIDEVKPI 62 (149)
T ss_pred ceeEEEEEEEEeCceeeceeeccc--CcccCEEEEEEeCCccEEEEEEEEccChhhcccccce
Confidence 5667778766 99999999863 4321100011111 1166777778875 5655544
No 133
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=22.42 E-value=2.7e+02 Score=21.81 Aligned_cols=57 Identities=11% Similarity=0.161 Sum_probs=42.2
Q ss_pred CCeEEEEEcCCCEEEEEEEEecCcc-ceEEccEEEEccCCCeeeecCeEEEecCeEEEEecC
Q 031941 12 GHPMLVELKNGETYNGHLVNCDTWM-NIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVP 72 (150)
Q Consensus 12 gk~V~VeLKnG~~~~G~L~~~D~~M-NI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lP 72 (150)
|-+|.|.-=...=-+|.++.+|.-- -++++.+.....++++ -++.|--+||.++.+.
T Consensus 50 GD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~----~e~PIh~SNV~iv~l~ 107 (143)
T PTZ00194 50 DDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP----VQIGIHPSNVIITKLK 107 (143)
T ss_pred CCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE----eecCcCchheEEEccc
Confidence 5556665544444569999999655 5999999998878765 3788888999887654
No 134
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=21.37 E-value=1.5e+02 Score=19.52 Aligned_cols=34 Identities=15% Similarity=0.402 Sum_probs=26.1
Q ss_pred CCCeEEEEEcCCCEEEEEEEEecCccceEEccEE
Q 031941 11 QGHPMLVELKNGETYNGHLVNCDTWMNIHLREVI 44 (150)
Q Consensus 11 ~gk~V~VeLKnG~~~~G~L~~~D~~MNI~L~dv~ 44 (150)
....|.|.+.+-..+.|.|..++..+=+.+.+..
T Consensus 41 ~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~~ 74 (77)
T PF01052_consen 41 ADEPVELRVNGQPIFRGELGRVNGRLAVRITELI 74 (77)
T ss_dssp SSTEEEEEETTEEEEEEEEEEETTEEEEEEEEE-
T ss_pred CCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEc
Confidence 3578888887778889999988888777776654
No 135
>PF14262 DUF4353: Domain of unknown function (DUF4353)
Probab=21.27 E-value=2.9e+02 Score=23.57 Aligned_cols=58 Identities=14% Similarity=0.297 Sum_probs=38.8
Q ss_pred cCCCeEEEEEcCCCEEEEEEE------Ee--cCccceEEccEEEEccCCCeeeecCeEEEecCeEEEEecCc
Q 031941 10 AQGHPMLVELKNGETYNGHLV------NC--DTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPD 73 (150)
Q Consensus 10 l~gk~V~VeLKnG~~~~G~L~------~~--D~~MNI~L~dv~~t~~~g~~~~~l~~v~IRGnnIryI~lPd 73 (150)
..+..|+|.-..--++.|+|. .. +....|+|++|..+..++- -++|.-..=.+|.|++
T Consensus 4 v~~~~vtIt~~GtY~lsGs~~~g~i~V~a~~~~~v~lvL~gv~it~~~~a------~I~v~~a~k~~i~la~ 69 (264)
T PF14262_consen 4 VSGSTVTITKAGTYVLSGSLSDGQIVVDAGDTDKVRLVLDGVSITNSSGA------AIYVKSADKVFITLAE 69 (264)
T ss_pred EeCCEEEEcCCEEEEEEEEccCcEEEEEcCCCceEEEEECCeEEeCCCCC------CEEEEeCCeEEEEEcC
Confidence 346777777655566677665 33 3567899999999875543 3566666666677776
No 136
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.19 E-value=62 Score=24.39 Aligned_cols=25 Identities=32% Similarity=0.558 Sum_probs=20.0
Q ss_pred HHHhhcCCCeEEEEEcCC-CEEEEEE
Q 031941 5 SLLKTAQGHPMLVELKNG-ETYNGHL 29 (150)
Q Consensus 5 ~lL~~l~gk~V~VeLKnG-~~~~G~L 29 (150)
.++..+++|+|.|+++.. ..+.|..
T Consensus 96 ~~~~~l~gk~l~V~v~~~~~e~nGk~ 121 (141)
T PF05037_consen 96 QFLNQLLGKPLRVTVKWEENEYNGKT 121 (141)
T ss_pred HHHHHHcCCeeEEEecccccCCCCcE
Confidence 467888899999999988 6666643
No 137
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=20.09 E-value=3.1e+02 Score=25.89 Aligned_cols=22 Identities=14% Similarity=0.078 Sum_probs=12.3
Q ss_pred EEEecCeEEEEecCccc--cchHH
Q 031941 59 CYIRGNTIKYLRVPDEV--IDKVQ 80 (150)
Q Consensus 59 v~IRGnnIryI~lPd~l--ld~~~ 80 (150)
.-|.+..|--|.|-|.. +|..+
T Consensus 512 ~~~~~~~ig~i~i~~~~s~v~~~~ 535 (629)
T PRK11634 512 GDISSRYIGNIKLFASHSTIELPK 535 (629)
T ss_pred cCCChhhCCcEEEeCCceEEEcCh
Confidence 34556666666666555 44433
Done!