Query psy6372
Match_columns 88
No_of_seqs 101 out of 1063
Neff 6.7
Searched_HMMs 46136
Date Sat Aug 17 00:48:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6372.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6372hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01721 Sm_D3 The eukaryotic S 99.9 6.7E-26 1.5E-30 136.1 9.8 70 9-78 1-70 (70)
2 PRK00737 small nuclear ribonuc 99.9 2.4E-25 5.2E-30 134.2 10.0 70 7-76 3-72 (72)
3 cd01726 LSm6 The eukaryotic Sm 99.9 2E-25 4.2E-30 132.9 9.4 67 9-75 1-67 (67)
4 cd01731 archaeal_Sm1 The archa 99.9 9.8E-25 2.1E-29 130.0 9.6 68 9-76 1-68 (68)
5 cd01722 Sm_F The eukaryotic Sm 99.9 7.6E-25 1.6E-29 130.7 8.8 68 8-75 1-68 (68)
6 cd01723 LSm4 The eukaryotic Sm 99.9 9.3E-25 2E-29 132.9 9.3 73 8-80 1-74 (76)
7 cd01724 Sm_D1 The eukaryotic S 99.9 1.6E-24 3.5E-29 135.8 10.2 73 9-81 2-74 (90)
8 cd01733 LSm10 The eukaryotic S 99.9 4.5E-24 9.7E-29 130.7 9.6 73 5-77 6-78 (78)
9 cd01719 Sm_G The eukaryotic Sm 99.9 1.1E-23 2.3E-28 127.2 9.4 71 9-79 1-71 (72)
10 cd01732 LSm5 The eukaryotic Sm 99.9 2E-23 4.4E-28 127.3 9.9 70 7-76 2-74 (76)
11 cd01725 LSm2 The eukaryotic Sm 99.9 2.3E-23 4.9E-28 128.2 9.1 75 9-83 2-78 (81)
12 cd01730 LSm3 The eukaryotic Sm 99.9 1.1E-22 2.5E-27 125.2 9.5 69 8-76 1-82 (82)
13 KOG3482|consensus 99.9 4.9E-23 1.1E-27 123.7 7.3 77 1-77 1-77 (79)
14 COG1958 LSM1 Small nuclear rib 99.9 2.1E-22 4.5E-27 123.0 10.1 74 3-76 2-79 (79)
15 PF01423 LSM: LSM domain ; In 99.9 2.5E-22 5.5E-27 118.4 10.0 66 11-76 1-67 (67)
16 smart00651 Sm snRNP Sm protein 99.9 3.1E-22 6.8E-27 117.9 9.4 66 11-76 1-67 (67)
17 cd01720 Sm_D2 The eukaryotic S 99.9 5.5E-22 1.2E-26 123.7 9.7 71 7-77 1-86 (87)
18 cd01729 LSm7 The eukaryotic Sm 99.9 8.8E-22 1.9E-26 121.2 9.8 68 11-78 5-80 (81)
19 cd00600 Sm_like The eukaryotic 99.9 7.1E-21 1.5E-25 110.6 8.7 63 13-75 1-63 (63)
20 cd01718 Sm_E The eukaryotic Sm 99.8 1.4E-20 3.1E-25 115.5 9.7 73 4-76 2-79 (79)
21 cd01717 Sm_B The eukaryotic Sm 99.8 1.2E-20 2.6E-25 115.3 9.2 66 11-76 3-78 (79)
22 cd01727 LSm8 The eukaryotic Sm 99.8 1.7E-20 3.7E-25 113.5 9.5 69 11-79 2-74 (74)
23 cd01728 LSm1 The eukaryotic Sm 99.8 4.9E-20 1.1E-24 111.9 9.9 68 9-76 3-73 (74)
24 KOG1783|consensus 99.8 2.4E-21 5.2E-26 116.4 1.6 74 5-78 3-76 (77)
25 cd06168 LSm9 The eukaryotic Sm 99.8 2.2E-19 4.9E-24 109.2 9.6 66 11-76 3-74 (75)
26 PTZ00138 small nuclear ribonuc 99.8 1.8E-18 3.9E-23 108.3 9.3 74 4-77 10-88 (89)
27 KOG1780|consensus 99.8 2.4E-18 5.2E-23 103.7 6.3 68 12-79 8-75 (77)
28 KOG3293|consensus 99.7 6.3E-18 1.4E-22 110.5 6.0 75 8-82 2-77 (134)
29 KOG3460|consensus 99.7 5.5E-18 1.2E-22 104.2 2.2 74 7-80 4-90 (91)
30 KOG3448|consensus 99.7 1.6E-16 3.5E-21 98.7 7.2 72 10-81 4-77 (96)
31 KOG3172|consensus 99.7 4.2E-16 9E-21 99.9 7.4 73 6-78 3-75 (119)
32 KOG1775|consensus 99.6 5E-16 1.1E-20 94.2 4.9 76 3-78 2-80 (84)
33 KOG3428|consensus 99.6 2.2E-14 4.8E-19 92.0 8.7 72 9-81 3-74 (109)
34 KOG1781|consensus 99.5 1.3E-15 2.8E-20 96.3 -0.4 73 10-82 19-99 (108)
35 KOG1784|consensus 99.3 9.9E-13 2.1E-17 82.2 3.9 72 11-82 3-78 (96)
36 KOG1774|consensus 99.3 2.6E-12 5.6E-17 78.9 4.0 71 7-77 11-86 (88)
37 KOG1782|consensus 99.3 8.3E-13 1.8E-17 86.4 1.0 72 11-82 12-86 (129)
38 KOG3168|consensus 99.3 8.1E-13 1.8E-17 90.5 0.3 67 11-77 7-83 (177)
39 KOG3459|consensus 98.8 9.7E-10 2.1E-14 70.8 -0.7 69 7-75 23-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 98.3 2.1E-06 4.5E-11 51.7 5.5 63 10-72 4-76 (77)
41 cd01739 LSm11_C The eukaryotic 98.2 1.9E-06 4.1E-11 51.1 3.2 36 18-53 8-47 (66)
42 PF12701 LSM14: Scd6-like Sm d 97.6 0.00053 1.2E-08 43.4 7.3 68 14-81 4-81 (96)
43 PF02237 BPL_C: Biotin protein 97.1 0.0046 9.9E-08 34.1 6.2 35 16-51 1-35 (48)
44 PF06372 Gemin6: Gemin6 protei 96.9 0.0025 5.3E-08 44.1 5.0 68 6-81 6-74 (166)
45 cd01736 LSm14_N LSm14 (also kn 96.8 0.0095 2.1E-07 36.2 6.5 59 14-72 2-71 (74)
46 PF11095 Gemin7: Gem-associate 96.7 0.014 3E-07 35.9 6.9 63 10-77 16-79 (80)
47 PF10842 DUF2642: Protein of u 96.5 0.022 4.9E-07 33.8 6.6 54 10-76 13-66 (66)
48 cd01716 Hfq Hfq, an abundant, 96.3 0.014 3.1E-07 34.2 4.8 34 12-45 3-38 (61)
49 cd01735 LSm12_N LSm12 belongs 96.2 0.019 4.1E-07 33.6 4.9 35 16-50 4-38 (61)
50 PRK14638 hypothetical protein; 96.2 0.017 3.6E-07 39.1 5.4 45 2-47 81-128 (150)
51 TIGR02383 Hfq RNA chaperone Hf 95.9 0.022 4.8E-07 33.3 4.2 35 11-45 6-42 (61)
52 PRK14639 hypothetical protein; 95.8 0.03 6.6E-07 37.4 5.4 44 2-46 69-115 (140)
53 COG1923 Hfq Uncharacterized ho 95.7 0.032 6.9E-07 34.0 4.7 38 11-49 10-49 (77)
54 PRK02001 hypothetical protein; 95.6 0.041 8.8E-07 37.4 5.4 45 2-47 71-118 (152)
55 PRK00395 hfq RNA-binding prote 95.5 0.032 6.9E-07 34.3 4.2 39 10-48 9-49 (79)
56 PRK14644 hypothetical protein; 95.3 0.047 1E-06 36.4 4.7 45 2-47 67-117 (136)
57 PRK14640 hypothetical protein; 94.5 0.12 2.7E-06 34.9 5.3 45 2-47 78-129 (152)
58 COG0779 Uncharacterized protei 94.5 0.17 3.8E-06 34.5 6.0 44 2-46 80-130 (153)
59 cd01734 YlxS_C YxlS is a Bacil 94.5 0.16 3.5E-06 30.7 5.3 44 2-46 6-56 (83)
60 PRK14091 RNA-binding protein H 94.5 0.12 2.7E-06 35.7 5.3 48 1-48 5-54 (165)
61 PF02576 DUF150: Uncharacteris 94.2 0.098 2.1E-06 34.6 4.3 44 2-46 68-118 (141)
62 PRK14633 hypothetical protein; 94.2 0.16 3.5E-06 34.2 5.3 45 2-47 75-126 (150)
63 PRK14645 hypothetical protein; 94.1 0.15 3.3E-06 34.6 5.0 43 2-46 83-128 (154)
64 PRK14642 hypothetical protein; 93.7 0.14 3E-06 36.3 4.3 44 2-46 81-140 (197)
65 PRK14643 hypothetical protein; 93.6 0.23 5E-06 34.1 5.2 40 2-41 85-131 (164)
66 PRK14632 hypothetical protein; 93.5 0.24 5.2E-06 34.2 5.3 45 2-47 79-133 (172)
67 PRK14636 hypothetical protein; 93.4 0.24 5.2E-06 34.4 5.1 44 2-46 79-129 (176)
68 PRK14091 RNA-binding protein H 93.4 0.93 2E-05 31.4 7.9 39 11-49 95-135 (165)
69 PRK14634 hypothetical protein; 93.3 0.27 5.8E-06 33.4 5.2 44 2-46 81-131 (155)
70 PRK00092 ribosome maturation p 93.2 0.3 6.4E-06 32.9 5.2 40 2-41 79-125 (154)
71 PRK14646 hypothetical protein; 93.0 0.33 7.1E-06 33.0 5.3 45 2-47 81-132 (155)
72 PRK14647 hypothetical protein; 92.9 0.35 7.6E-06 32.9 5.3 40 2-41 80-131 (159)
73 PRK14637 hypothetical protein; 92.1 0.48 1E-05 32.1 5.2 45 2-47 79-127 (151)
74 PRK14631 hypothetical protein; 92.1 0.48 1E-05 32.8 5.2 38 2-39 98-142 (174)
75 PRK06955 biotin--protein ligas 91.3 1.1 2.3E-05 33.2 6.6 50 16-69 247-296 (300)
76 PRK14641 hypothetical protein; 91.2 0.6 1.3E-05 32.4 4.9 38 2-39 85-129 (173)
77 KOG1073|consensus 91.1 0.76 1.6E-05 35.4 5.7 65 14-78 5-80 (361)
78 PRK11886 bifunctional biotin-- 88.8 2.5 5.4E-05 31.2 6.9 48 16-68 270-317 (319)
79 PRK14630 hypothetical protein; 87.6 1.8 3.8E-05 29.0 4.9 43 2-46 78-123 (143)
80 TIGR00121 birA_ligase birA, bi 87.5 3.4 7.3E-05 29.3 6.7 31 16-47 191-221 (237)
81 PRK14635 hypothetical protein; 87.4 3 6.5E-05 28.4 6.1 45 2-47 80-132 (162)
82 PRK13325 bifunctional biotin-- 86.2 5.4 0.00012 32.4 7.9 32 16-47 276-307 (592)
83 PF03614 Flag1_repress: Repres 83.3 2 4.3E-05 29.6 3.6 34 17-50 28-61 (165)
84 PRK09618 flgD flagellar basal 81.8 3 6.6E-05 28.1 4.0 26 14-39 88-113 (142)
85 COG0340 BirA Biotin-(acetyl-Co 81.3 10 0.00022 27.3 6.9 35 15-49 187-221 (238)
86 PF11607 DUF3247: Protein of u 80.2 2.9 6.3E-05 26.6 3.3 19 18-36 28-46 (101)
87 PRK08330 biotin--protein ligas 78.7 9.2 0.0002 27.1 5.9 34 15-49 185-219 (236)
88 PRK10898 serine endoprotease; 75.4 13 0.00028 28.1 6.2 33 18-50 101-133 (353)
89 PTZ00275 biotin-acetyl-CoA-car 74.2 9.2 0.0002 28.1 5.0 31 17-48 236-266 (285)
90 TIGR02038 protease_degS peripl 73.6 15 0.00033 27.6 6.2 32 19-50 102-133 (351)
91 PF07073 ROF: Modulator of Rho 72.9 3.8 8.2E-05 25.0 2.3 63 13-82 12-74 (80)
92 PF14563 DUF4444: Domain of un 72.6 5.8 0.00012 21.5 2.7 22 31-52 10-31 (42)
93 PRK11911 flgD flagellar basal 69.2 9.6 0.00021 25.7 3.8 27 14-40 89-115 (140)
94 PRK10139 serine endoprotease; 67.7 14 0.0003 29.0 5.0 33 18-50 114-146 (455)
95 PF03614 Flag1_repress: Repres 67.1 7 0.00015 26.9 2.9 24 17-40 119-142 (165)
96 PRK10942 serine endoprotease; 64.7 16 0.00034 28.8 4.8 32 18-49 135-166 (473)
97 PF10618 Tail_tube: Phage tail 63.3 16 0.00035 23.6 3.9 31 5-35 61-91 (119)
98 TIGR02037 degP_htrA_DO peripla 60.5 21 0.00046 27.3 4.8 32 19-50 82-113 (428)
99 PRK11625 Rho-binding antitermi 59.6 28 0.00061 21.4 4.3 25 13-37 18-42 (84)
100 TIGR02603 CxxCH_TIGR02603 puta 59.2 22 0.00048 23.0 4.1 30 19-49 58-87 (133)
101 PF06257 DUF1021: Protein of u 58.5 35 0.00077 20.6 4.6 31 11-41 10-44 (76)
102 TIGR03170 flgA_cterm flagella 56.1 17 0.00038 22.8 3.1 23 15-37 93-116 (122)
103 PF14153 Spore_coat_CotO: Spor 55.8 20 0.00043 25.2 3.6 34 9-42 122-158 (185)
104 PRK06792 flgD flagellar basal 55.8 21 0.00046 25.3 3.7 26 14-39 114-139 (190)
105 PRK08477 biotin--protein ligas 54.4 33 0.00071 24.3 4.6 35 15-50 172-206 (211)
106 PRK05163 rpsL 30S ribosomal pr 51.6 23 0.00051 23.4 3.2 26 14-39 46-71 (124)
107 smart00333 TUDOR Tudor domain. 51.6 37 0.0008 18.1 4.3 25 17-41 5-29 (57)
108 PF14485 DUF4431: Domain of un 51.4 21 0.00045 19.6 2.6 16 9-24 10-25 (48)
109 PRK06789 flagellar motor switc 51.2 34 0.00074 20.5 3.7 36 13-48 36-71 (74)
110 PF08661 Rep_fac-A_3: Replicat 50.5 7.9 0.00017 24.3 0.8 31 1-39 1-31 (109)
111 COG4466 Veg Uncharacterized pr 50.1 17 0.00037 22.3 2.2 39 11-49 12-55 (80)
112 PRK07018 flgA flagellar basal 46.7 26 0.00057 24.9 3.1 23 15-37 204-227 (235)
113 PF13437 HlyD_3: HlyD family s 44.6 68 0.0015 19.1 4.5 32 9-40 43-78 (105)
114 PF09465 LBR_tudor: Lamin-B re 42.4 66 0.0014 18.4 3.7 26 16-41 7-33 (55)
115 PF05954 Phage_GPD: Phage late 41.8 44 0.00095 23.4 3.7 27 13-39 23-49 (292)
116 PF05071 NDUFA12: NADH ubiquin 41.7 12 0.00026 23.6 0.7 17 33-49 1-17 (105)
117 PF05037 DUF669: Protein of un 41.0 23 0.0005 23.2 2.0 27 8-34 93-120 (141)
118 KOG3382|consensus 39.5 16 0.00035 24.7 1.0 28 25-52 39-66 (151)
119 PTZ00115 40S ribosomal protein 39.4 42 0.00091 25.1 3.2 35 14-50 142-176 (290)
120 KOG4401|consensus 38.8 45 0.00097 23.5 3.2 35 16-50 9-43 (184)
121 TIGR00567 3mg DNA-3-methyladen 38.4 88 0.0019 22.1 4.7 36 8-43 9-44 (192)
122 COG1363 FrvX Cellulase M and r 38.1 43 0.00092 25.8 3.3 27 14-40 93-119 (355)
123 COG1886 FliN Flagellar motor s 38.1 67 0.0014 21.1 3.8 34 14-47 101-134 (136)
124 PRK06005 flgA flagellar basal 37.9 49 0.0011 22.4 3.2 23 15-37 128-151 (160)
125 PRK10708 hypothetical protein; 36.7 47 0.001 19.2 2.5 26 17-42 3-28 (62)
126 TIGR00999 8a0102 Membrane Fusi 36.1 85 0.0018 21.8 4.4 27 17-43 141-167 (265)
127 PF12945 YcgR_2: Flagellar pro 35.8 88 0.0019 17.9 4.8 33 17-49 3-39 (87)
128 COG5316 Uncharacterized conser 35.5 1E+02 0.0022 24.4 5.0 45 6-51 70-114 (421)
129 KOG3493|consensus 35.2 33 0.00072 20.5 1.8 19 12-30 5-23 (73)
130 cd04479 RPA3 RPA3: A subfamily 34.5 1.1E+02 0.0025 18.8 5.5 19 7-25 4-22 (101)
131 PF11743 DUF3301: Protein of u 34.0 68 0.0015 19.9 3.2 24 55-78 73-96 (97)
132 COG4568 Rof Transcriptional an 33.3 68 0.0015 19.7 3.0 25 12-36 17-41 (84)
133 PRK04337 50S ribosomal protein 33.3 1.2E+02 0.0026 18.8 4.6 35 11-45 33-67 (87)
134 PRK12617 flgA flagellar basal 33.1 59 0.0013 23.1 3.1 23 15-37 183-206 (214)
135 PF02245 Pur_DNA_glyco: Methyl 32.7 89 0.0019 21.8 3.9 35 8-43 8-42 (184)
136 PRK08515 flgA flagellar basal 31.7 84 0.0018 22.3 3.8 23 15-37 193-215 (222)
137 PF10781 DSRB: Dextransucrase 30.8 60 0.0013 18.8 2.3 26 17-42 3-28 (62)
138 PRK12618 flgA flagellar basal 29.6 83 0.0018 20.8 3.2 23 15-37 109-132 (141)
139 PF01887 SAM_adeno_trans: S-ad 29.1 93 0.002 22.7 3.7 18 30-47 169-186 (258)
140 PRK06630 hypothetical protein; 29.0 31 0.00067 22.0 1.0 20 31-50 11-30 (99)
141 PF01052 SpoA: Surface present 28.8 1.2E+02 0.0026 17.3 3.9 34 17-50 41-74 (77)
142 PRK06804 flgA flagellar basal 28.5 80 0.0017 23.2 3.3 23 15-37 230-253 (261)
143 PRK09961 exoaminopeptidase; Pr 27.8 78 0.0017 23.8 3.2 23 14-36 90-112 (344)
144 PF09883 DUF2110: Uncharacteri 27.5 51 0.0011 23.9 2.0 15 28-42 75-89 (225)
145 PHA00446 hypothetical protein 27.4 52 0.0011 20.4 1.8 30 1-30 1-30 (89)
146 PF13144 SAF_2: SAF-like 27.3 1.1E+02 0.0024 20.6 3.7 23 15-37 167-190 (196)
147 COG2451 Ribosomal protein L35A 27.3 1.7E+02 0.0037 18.6 5.3 33 11-43 39-72 (100)
148 PF04452 Methyltrans_RNA: RNA 27.2 2.2E+02 0.0048 19.8 5.5 32 11-42 13-44 (225)
149 PF11305 DUF3107: Protein of u 26.9 92 0.002 18.7 2.8 19 62-80 48-66 (74)
150 cd01772 SAKS1_UBX SAKS1-like U 26.7 73 0.0016 18.7 2.4 23 17-39 3-25 (79)
151 TIGR03361 VI_Rhs_Vgr type VI s 26.1 1.2E+02 0.0026 23.8 4.0 27 13-39 42-72 (513)
152 PF08863 YolD: YolD-like prote 25.8 1.5E+02 0.0032 17.3 4.5 29 17-45 41-72 (92)
153 COG0265 DegQ Trypsin-like seri 25.3 1.7E+02 0.0036 21.7 4.5 31 18-48 95-125 (347)
154 PRK09864 putative peptidase; P 25.0 1E+02 0.0022 23.6 3.4 25 14-38 89-113 (356)
155 smart00166 UBX Domain present 24.8 68 0.0015 18.6 2.0 22 18-39 4-25 (80)
156 cd01767 UBX UBX (ubiquitin reg 24.3 1.1E+02 0.0024 17.5 2.8 21 19-39 3-23 (77)
157 PF05186 Dpy-30: Dpy-30 motif; 24.1 29 0.00063 18.4 0.2 14 4-17 24-37 (42)
158 PF00789 UBX: UBX domain; Int 23.7 1.4E+02 0.0031 17.1 3.2 21 19-39 7-27 (82)
159 PRK09798 antitoxin MazE; Provi 23.4 1.2E+02 0.0026 18.3 2.9 28 4-31 13-43 (82)
160 PLN02732 Probable NADH dehydro 23.0 76 0.0016 21.9 2.1 19 32-50 48-66 (159)
161 PRK08158 type III secretion sy 23.0 1.4E+02 0.003 22.6 3.7 37 13-49 259-295 (303)
162 PF01556 CTDII: DnaJ C termina 22.6 47 0.001 19.5 0.9 25 9-33 7-31 (81)
163 PF07076 DUF1344: Protein of u 22.4 1.1E+02 0.0023 17.9 2.4 23 30-52 4-27 (61)
164 PTZ00276 biotin/lipoate protei 22.4 1.3E+02 0.0029 21.4 3.4 23 26-48 209-231 (245)
165 PRK12786 flgA flagellar basal 22.3 1.2E+02 0.0026 23.1 3.3 23 15-37 286-309 (338)
166 PRK11713 16S ribosomal RNA met 22.2 2.1E+02 0.0045 20.2 4.3 31 11-41 26-56 (234)
167 PLN03095 NADH:ubiquinone oxido 21.9 54 0.0012 21.4 1.2 19 32-50 9-27 (115)
168 PF05343 Peptidase_M42: M42 gl 21.8 1.5E+02 0.0032 21.9 3.6 26 14-40 49-74 (292)
169 PF02736 Myosin_N: Myosin N-te 21.5 1.3E+02 0.0029 15.5 2.5 18 15-32 20-37 (42)
170 COG0048 RpsL Ribosomal protein 21.0 1.1E+02 0.0023 20.4 2.5 24 14-37 52-75 (129)
171 cd00540 AAG Alkyladenine DNA g 20.2 2.9E+02 0.0063 19.2 4.6 35 8-43 5-39 (179)
No 1
>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=99.94 E-value=6.7e-26 Score=136.07 Aligned_cols=70 Identities=29% Similarity=0.441 Sum_probs=65.1
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
|+.+|+++.|++|+|+|+||.+|+|+|.+||+|||++|+||.+...+++..+++.+||||++|+||++||
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 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence 7899999999999999999999999999999999999999998744445678999999999999999997
No 2
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.93 E-value=2.4e-25 Score=134.25 Aligned_cols=70 Identities=39% Similarity=0.557 Sum_probs=66.0
Q ss_pred CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372 7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~ 76 (88)
..|+.+|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.+..+++..++++.++|||++|++|.+
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence 5899999999999999999999999999999999999999999998777677899999999999999963
No 3
>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=99.93 E-value=2e-25 Score=132.85 Aligned_cols=67 Identities=46% Similarity=0.850 Sum_probs=63.8
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR 75 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~ 75 (88)
|++||++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..+++.+..++.++|||++|+||.
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence 8999999999999999999999999999999999999999999877777889999999999999984
No 4
>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=99.92 E-value=9.8e-25 Score=130.01 Aligned_cols=68 Identities=43% Similarity=0.527 Sum_probs=64.3
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~ 76 (88)
|+++|++++|++|+|+|++|+.|.|+|.+||+|||++|+||.+...+...+.++.++|||++|++|.+
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence 88999999999999999999999999999999999999999998766678899999999999999974
No 5
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.92 E-value=7.6e-25 Score=130.71 Aligned_cols=68 Identities=79% Similarity=1.246 Sum_probs=64.0
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR 75 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~ 75 (88)
.|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..++.....+|.++|||++|+||.
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 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence 58999999999999999999999999999999999999999999877766789999999999999983
No 6
>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=99.92 E-value=9.3e-25 Score=132.86 Aligned_cols=73 Identities=33% Similarity=0.440 Sum_probs=66.6
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEG 80 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d~~ 80 (88)
.|++||+++.|++|.|+|+||++|+|+|.+||+|||++|+||++.. +|+....++.+||||++|+||++||+.
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence 3899999999999999999999999999999999999999999873 454556789999999999999999864
No 7
>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=99.92 E-value=1.6e-24 Score=135.83 Aligned_cols=73 Identities=29% Similarity=0.322 Sum_probs=68.6
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
++.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++.+++....++.++|||++|+||++||+.+
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~ 74 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN 74 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence 6789999999999999999999999999999999999999999877767889999999999999999999863
No 8
>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=4.5e-24 Score=130.70 Aligned_cols=73 Identities=26% Similarity=0.302 Sum_probs=67.4
Q ss_pred CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372 5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
....+..||+++.|++|.|+|+||.+|+|+|.++|++||++|+||++..+++...+++.+||||++|+||++|
T Consensus 6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP 78 (78)
T cd01733 6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP 78 (78)
T ss_pred hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence 4567789999999999999999999999999999999999999999886665667899999999999999987
No 9
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.91 E-value=1.1e-23 Score=127.23 Aligned_cols=71 Identities=30% Similarity=0.387 Sum_probs=65.7
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE 79 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~ 79 (88)
|.++|+++++|+|.|+|++|+.|.|+|.+||+|||++|+||.|...+...+.+|.++|||++|++|.+.|.
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 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence 56789999999999999999999999999999999999999998766668899999999999999997753
No 10
>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=99.90 E-value=2e-23 Score=127.28 Aligned_cols=70 Identities=26% Similarity=0.385 Sum_probs=64.8
Q ss_pred CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cCeeeeeeceEEEeCCcEEEEEc
Q psy6372 7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~~~~v~IrG~~I~~I~~ 76 (88)
..|+++|+++++++|.|++++|+.+.|+|.+||+|||++|+||.|.. +++..+.+|.++|||++|.+|++
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 36999999999999999999999999999999999999999999986 44456889999999999999985
No 11
>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=99.90 E-value=2.3e-23 Score=128.24 Aligned_cols=75 Identities=23% Similarity=0.286 Sum_probs=66.5
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe--eeeeeceEEEeCCcEEEEEcCCCCCcc
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRCNNILYIRGAEEGDEE 83 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~--~~~~~~~v~IrG~~I~~I~~~d~~~~~ 83 (88)
|+.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||++..++. ....++.++|||++|+||++||+..|.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~ 78 (81)
T cd01725 2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT 78 (81)
T ss_pred hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence 789999999999999999999999999999999999999998774322 245678999999999999999987654
No 12
>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=99.89 E-value=1.1e-22 Score=125.21 Aligned_cols=69 Identities=22% Similarity=0.347 Sum_probs=62.8
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC-------------eeeeeeceEEEeCCcEEEE
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------------HCTGKLGEVLIRCNNILYI 74 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~~~~v~IrG~~I~~I 74 (88)
.|+++|+.+++++|.|+|++|+.+.|+|.+||+|||++|+||.|.+.+ ...+.+|.+||||++|++|
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 489999999999999999999999999999999999999999998632 1467899999999999998
Q ss_pred Ec
Q psy6372 75 RG 76 (88)
Q Consensus 75 ~~ 76 (88)
.+
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 63
No 13
>KOG3482|consensus
Probab=99.89 E-value=4.9e-23 Score=123.69 Aligned_cols=77 Identities=70% Similarity=1.142 Sum_probs=74.1
Q ss_pred CCCCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 1 m~~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
||+++|.+|.+||+.+.||+|.|+|+.|.+|.|+|++.|.+||+.|.+|+|..+|.....+|.++||-+||.||.-.
T Consensus 1 ~~a~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv 77 (79)
T KOG3482|consen 1 SSAKQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGV 77 (79)
T ss_pred CCCcccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecC
Confidence 79999999999999999999999999999999999999999999999999998998889999999999999999643
No 14
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.89 E-value=2.1e-22 Score=123.03 Aligned_cols=74 Identities=50% Similarity=0.684 Sum_probs=65.2
Q ss_pred CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe--cCee-eeeec-eEEEeCCcEEEEEc
Q psy6372 3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--DGHC-TGKLG-EVLIRCNNILYIRG 76 (88)
Q Consensus 3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~--~~~~-~~~~~-~v~IrG~~I~~I~~ 76 (88)
++....|+.+|+++++++|.|+|++|++|+|+|.+||+|||++|+||.+.. ++.. .+.++ .++|||++|++|.+
T Consensus 2 ~~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred CcccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 455678999999999999999999999999999999999999999999986 5544 34555 99999999999963
No 15
>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=99.89 E-value=2.5e-22 Score=118.41 Aligned_cols=66 Identities=44% Similarity=0.577 Sum_probs=62.5
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe-eeeeeceEEEeCCcEEEEEc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-CTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-~~~~~~~v~IrG~~I~~I~~ 76 (88)
.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+...+. +.++++.+||||++|++|++
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 3799999999999999999999999999999999999999998776 88999999999999999975
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.88 E-value=3.1e-22 Score=117.89 Aligned_cols=66 Identities=45% Similarity=0.646 Sum_probs=61.6
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC-eeeeeeceEEEeCCcEEEEEc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-HCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~v~IrG~~I~~I~~ 76 (88)
.+|++++|++|+|+|+||+.+.|+|.+||+|||++|+||.+...+ ...++++.+||||++|++|++
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 379999999999999999999999999999999999999998665 578999999999999999974
No 17
>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=99.88 E-value=5.5e-22 Score=123.75 Aligned_cols=71 Identities=13% Similarity=0.197 Sum_probs=63.0
Q ss_pred CCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe-------------eeeeeceEEEeCCcE
Q psy6372 7 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------------CTGKLGEVLIRCNNI 71 (88)
Q Consensus 7 ~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-------------~~~~~~~v~IrG~~I 71 (88)
..|+++|+.++ +++|.|+|++|+.+.|+|.+||+|||++|+||.|.+.+. ..+.+|.+||||++|
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V 80 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV 80 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence 36999999997 899999999999999999999999999999999975331 356789999999999
Q ss_pred EEEEcC
Q psy6372 72 LYIRGA 77 (88)
Q Consensus 72 ~~I~~~ 77 (88)
++|...
T Consensus 81 v~Is~~ 86 (87)
T cd01720 81 ILVLRN 86 (87)
T ss_pred EEEecC
Confidence 999753
No 18
>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=99.87 E-value=8.8e-22 Score=121.21 Aligned_cols=68 Identities=28% Similarity=0.335 Sum_probs=61.3
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC--------eeeeeeceEEEeCCcEEEEEcCC
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------HCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
.-|.++++|+|+|+|++|+.|.|+|.+||+||||+|++|+|...+ ...+.+|.++|||++|.+|.+.+
T Consensus 5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 449999999999999999999999999999999999999998543 24688999999999999998765
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=99.85 E-value=7.1e-21 Score=110.65 Aligned_cols=63 Identities=41% Similarity=0.523 Sum_probs=58.8
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR 75 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~ 75 (88)
|++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+...+...+.++.+||||++|++|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence 578899999999999999999999999999999999999876567899999999999999984
No 20
>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=99.85 E-value=1.4e-20 Score=115.54 Aligned_cols=73 Identities=23% Similarity=0.323 Sum_probs=64.5
Q ss_pred CCCCCcHHHHhhcCCC--EEEEEEc--CccEEEEEEEEecCCcceEEcceEEEec-CeeeeeeceEEEeCCcEEEEEc
Q psy6372 4 PLPCNPKPFLNLLTGK--SVICKLK--WGHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 4 ~~~~~p~~~L~~~i~k--~V~V~L~--~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~v~IrG~~I~~I~~ 76 (88)
++-..|+..|.+++++ +|.|+++ +|+.+.|+|.|||+|||++|+||.|... +...+.+|.++|||++|.+|++
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence 3456799999999999 7888887 8999999999999999999999999864 4567889999999999999973
No 21
>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=99.85 E-value=1.2e-20 Score=115.33 Aligned_cols=66 Identities=26% Similarity=0.283 Sum_probs=59.5
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC----------eeeeeeceEEEeCCcEEEEEc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----------HCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~----------~~~~~~~~v~IrG~~I~~I~~ 76 (88)
+-|.+++|++|+|+|++|+.+.|+|.+||+|||++|+||.|.+.. ...+.+|+++|||++|++|.+
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 468899999999999999999999999999999999999997521 246889999999999999974
No 22
>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=99.85 E-value=1.7e-20 Score=113.48 Aligned_cols=69 Identities=26% Similarity=0.194 Sum_probs=62.1
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec----CeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----GHCTGKLGEVLIRCNNILYIRGAEE 79 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~~~~v~IrG~~I~~I~~~d~ 79 (88)
+.|.++++++|+|.|++|+.|.|+|.+||+|||++|++|.|... +...+.+|.++|||++|.+|.+.|+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~ 74 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE 74 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence 56899999999999999999999999999999999999998742 3356789999999999999998764
No 23
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=4.9e-20 Score=111.87 Aligned_cols=68 Identities=29% Similarity=0.270 Sum_probs=60.7
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cC-e-eeeeeceEEEeCCcEEEEEc
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DG-H-CTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~-~-~~~~~~~v~IrG~~I~~I~~ 76 (88)
++..|.++++|+|.|.|++|+.|.|+|.+||+|||++|+||.|.. .+ + ..+.+|.++|||++|.+|..
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 467899999999999999999999999999999999999999874 22 1 46789999999999999974
No 24
>KOG1783|consensus
Probab=99.82 E-value=2.4e-21 Score=116.39 Aligned_cols=74 Identities=43% Similarity=0.743 Sum_probs=70.5
Q ss_pred CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372 5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
....|.+||++.+||+|.|+|.+|..|+|+|.++|.+||+.|+.+.+..+|+.+++++..||||++|.||....
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~ 76 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK 76 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence 66789999999999999999999999999999999999999999999999999999999999999999998653
No 25
>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=99.81 E-value=2.2e-19 Score=109.20 Aligned_cols=66 Identities=26% Similarity=0.278 Sum_probs=60.7
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC------eeeeeeceEEEeCCcEEEEEc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG------HCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~------~~~~~~~~v~IrG~~I~~I~~ 76 (88)
+.|++++|++|+|+|+|||.|.|+|.+||++||++|+||.|.+.. ...+.+|+++|||++|.+|..
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 568999999999999999999999999999999999999998632 468899999999999999975
No 26
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.78 E-value=1.8e-18 Score=108.28 Aligned_cols=74 Identities=24% Similarity=0.297 Sum_probs=62.8
Q ss_pred CCCCCcHHHHhhcCCC--EEEEEEcC--ccEEEEEEEEecCCcceEEcceEEEec-CeeeeeeceEEEeCCcEEEEEcC
Q psy6372 4 PLPCNPKPFLNLLTGK--SVICKLKW--GHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 4 ~~~~~p~~~L~~~i~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
+.-..|+.++.+++++ +|.|++.+ ++.+.|+|.+||+|||++|+||+|... +...+.+|.++|||++|.+|.+.
T Consensus 10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcC
Confidence 3456799999999875 47777767 599999999999999999999999854 34578999999999999999753
No 27
>KOG1780|consensus
Probab=99.76 E-value=2.4e-18 Score=103.68 Aligned_cols=68 Identities=31% Similarity=0.386 Sum_probs=62.0
Q ss_pred HHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE 79 (88)
Q Consensus 12 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~ 79 (88)
.|+++.+|++.++|..||..+|.|.+||.|||++|+++.|.........++.++|||++|+.+...+.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeeccc
Confidence 79999999999999999999999999999999999999998544457889999999999999987653
No 28
>KOG3293|consensus
Probab=99.73 E-value=6.3e-18 Score=110.48 Aligned_cols=75 Identities=29% Similarity=0.394 Sum_probs=69.7
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEGDE 82 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d~~~~ 82 (88)
.|+.+|..+-++++.|+|+||.+|.|-|+.||.+|||.|.++.++. ++.+...+++++|||++|.|+.+||+..+
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid 77 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIID 77 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHH
Confidence 5999999999999999999999999999999999999999999985 56678889999999999999999997643
No 29
>KOG3460|consensus
Probab=99.70 E-value=5.5e-18 Score=104.22 Aligned_cols=74 Identities=22% Similarity=0.289 Sum_probs=66.2
Q ss_pred CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cC----------eeeeeeceEEEeCCcEEE
Q psy6372 7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DG----------HCTGKLGEVLIRCNNILY 73 (88)
Q Consensus 7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~----------~~~~~~~~v~IrG~~I~~ 73 (88)
..|+++|+-.++.+|.|+++++++++|+|++||+|.|++|.|+.++. ++ ...+.+..+||||++|.+
T Consensus 4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil 83 (91)
T KOG3460|consen 4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL 83 (91)
T ss_pred cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence 57999999999999999999999999999999999999999999863 11 256789999999999999
Q ss_pred EEcCCCC
Q psy6372 74 IRGAEEG 80 (88)
Q Consensus 74 I~~~d~~ 80 (88)
|.+|-..
T Consensus 84 vspp~~~ 90 (91)
T KOG3460|consen 84 VSPPLRL 90 (91)
T ss_pred EcCcccC
Confidence 9988653
No 30
>KOG3448|consensus
Probab=99.68 E-value=1.6e-16 Score=98.73 Aligned_cols=72 Identities=24% Similarity=0.309 Sum_probs=63.9
Q ss_pred HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe--eeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~--~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
.+|+++++|+.|.|+|+|+-.+.|+|.++|+|.|+.|.|.....+.+ .-.++..+||||+.|+||.+|.+.-
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~v 77 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAV 77 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHH
Confidence 47899999999999999999999999999999999999999774432 3567789999999999999998754
No 31
>KOG3172|consensus
Probab=99.66 E-value=4.2e-16 Score=99.95 Aligned_cols=73 Identities=26% Similarity=0.388 Sum_probs=68.0
Q ss_pred CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372 6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
...|+.+|+..-|.-|++++..|..|+|+|...+++||++|+|++.+..+.....+++|||||++|+|+.+||
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPd 75 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPD 75 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECch
Confidence 4579999999999999999999999999999999999999999998855556889999999999999999997
No 32
>KOG1775|consensus
Probab=99.63 E-value=5e-16 Score=94.24 Aligned_cols=76 Identities=25% Similarity=0.378 Sum_probs=67.9
Q ss_pred CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372 3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
+.....|++++.+++|.+|.|.+++++++.|+|.+||+|.|++|+|++|+- +|+...+++++++.|++|....+.-
T Consensus 2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG 80 (84)
T KOG1775|consen 2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG 80 (84)
T ss_pred ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence 345678999999999999999999999999999999999999999999872 4556778999999999999987654
No 33
>KOG3428|consensus
Probab=99.57 E-value=2.2e-14 Score=91.99 Aligned_cols=72 Identities=29% Similarity=0.302 Sum_probs=66.6
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
...||+++.+.+|+|+|+||+..+|++.++|.+||..|.++.-+.+| ++.++...+|||++|+|+.+||.-.
T Consensus 3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~ 74 (109)
T KOG3428|consen 3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLN 74 (109)
T ss_pred HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcC
Confidence 46799999999999999999999999999999999999999988777 6789999999999999999998753
No 34
>KOG1781|consensus
Probab=99.52 E-value=1.3e-15 Score=96.30 Aligned_cols=73 Identities=32% Similarity=0.317 Sum_probs=64.2
Q ss_pred HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEE-ec-------CeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-ID-------GHCTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~-------~~~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
.-.|.++++|+|+|++..||+..|+|.+||+.||++|+++.|+ ++ +...|++|++.+||..++.|.+.|.-|
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 4468999999999999999999999999999999999999986 22 125699999999999999999887655
Q ss_pred c
Q psy6372 82 E 82 (88)
Q Consensus 82 ~ 82 (88)
|
T Consensus 99 ~ 99 (108)
T KOG1781|consen 99 E 99 (108)
T ss_pred h
Confidence 4
No 35
>KOG1784|consensus
Probab=99.34 E-value=9.9e-13 Score=82.17 Aligned_cols=72 Identities=24% Similarity=0.183 Sum_probs=64.4
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe----cCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----DGHCTGKLGEVLIRCNNILYIRGAEEGDE 82 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~----~~~~~~~~~~v~IrG~~I~~I~~~d~~~~ 82 (88)
+-|.++++++|.|.+.|||.+.|+|.+||+..||.|+++-+.. .+.....+|..+|||+||..|.+.||+-+
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d 78 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD 78 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence 4588999999999999999999999999999999999999863 35567788999999999999999988754
No 36
>KOG1774|consensus
Probab=99.30 E-value=2.6e-12 Score=78.89 Aligned_cols=71 Identities=28% Similarity=0.381 Sum_probs=58.7
Q ss_pred CCcHHHHhhcCCC--EEEEEEcC--ccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcC
Q psy6372 7 CNPKPFLNLLTGK--SVICKLKW--GHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 7 ~~p~~~L~~~i~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
..|+.++..++.. +|.|+|.+ |..+.|.+.+||+|||++|++|+|.. +.+.-+.+|.++++|++|..|...
T Consensus 11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeec
Confidence 4688888888764 58888876 78999999999999999999999874 232334899999999999999754
No 37
>KOG1782|consensus
Probab=99.28 E-value=8.3e-13 Score=86.38 Aligned_cols=72 Identities=26% Similarity=0.337 Sum_probs=62.2
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCe--eeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGH--CTGKLGEVLIRCNNILYIRGAEEGDE 82 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~--~~~~~~~v~IrG~~I~~I~~~d~~~~ 82 (88)
.-|.+++++++.|-|+|||.+.|.|.|||+|.|++|.+|.|.. -++ .....|.++|||.||+.+...|.+-|
T Consensus 12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE 86 (129)
T KOG1782|consen 12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE 86 (129)
T ss_pred hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence 3488899999999999999999999999999999999999863 121 34566899999999999988887777
No 38
>KOG3168|consensus
Probab=99.26 E-value=8.1e-13 Score=90.49 Aligned_cols=67 Identities=27% Similarity=0.288 Sum_probs=59.4
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe----------cCeeeeeeceEEEeCCcEEEEEcC
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~----------~~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
+-|-++++.+++|.++||++|.|++.+||.|||++|.+|.|.+ ++.+.+-+++|++||++|++....
T Consensus 7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence 4567789999999999999999999999999999999999853 244789999999999999998753
No 39
>KOG3459|consensus
Probab=98.76 E-value=9.7e-10 Score=70.81 Aligned_cols=69 Identities=14% Similarity=0.230 Sum_probs=59.3
Q ss_pred CCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-------cCe------eeeeeceEEEeCCcE
Q psy6372 7 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGH------CTGKLGEVLIRCNNI 71 (88)
Q Consensus 7 ~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-------~~~------~~~~~~~v~IrG~~I 71 (88)
..|++++.+.. ..+|.|-++|++..-|.+.+||.|.|++|+|+.+.+ +|. ..++++.+||||++|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 47888888886 578999999999999999999999999999999854 122 267899999999999
Q ss_pred EEEE
Q psy6372 72 LYIR 75 (88)
Q Consensus 72 ~~I~ 75 (88)
+.+.
T Consensus 103 I~v~ 106 (114)
T KOG3459|consen 103 ILVL 106 (114)
T ss_pred EEEE
Confidence 8875
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=98.31 E-value=2.1e-06 Score=51.71 Aligned_cols=63 Identities=19% Similarity=0.309 Sum_probs=41.7
Q ss_pred HHHHhhcCCCEEEEEEcCccEEEEEEEEecC---CcceEEcceEEEecC----e---eeeeeceEEEeCCcEE
Q psy6372 10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDG---YMNCQLASTEEIIDG----H---CTGKLGEVLIRCNNIL 72 (88)
Q Consensus 10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~---~mNlvL~d~~e~~~~----~---~~~~~~~v~IrG~~I~ 72 (88)
.-++..++|++|.|+++||..|.|.|.+++. .+.++|+.+...... . .....+.++|+++.|+
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 3467889999999999999999999999998 899999988875322 1 2345566777776654
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=98.18 E-value=1.9e-06 Score=51.07 Aligned_cols=36 Identities=22% Similarity=0.236 Sum_probs=30.8
Q ss_pred CCEEEEEEcCc----cEEEEEEEEecCCcceEEcceEEEe
Q psy6372 18 GKSVICKLKWG----HEYKGILVSTDGYMNCQLASTEEII 53 (88)
Q Consensus 18 ~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~d~~e~~ 53 (88)
+++|+|.++.- -.++|.|.+||+|||++|.|+.|..
T Consensus 8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y 47 (66)
T cd01739 8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY 47 (66)
T ss_pred CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence 57888888763 4788999999999999999999874
No 42
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=97.61 E-value=0.00053 Score=43.44 Aligned_cols=68 Identities=19% Similarity=0.228 Sum_probs=54.3
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEE-ecCe--------eeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEI-IDGH--------CTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~-~~~~--------~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
..++|++|.+..+++-.|.|+|..+|. ...+.|.|+..+ .++. ....++.+..||+.|.-+.+.+...
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~ 81 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP 81 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence 368999999999999999999999995 789999999865 2221 2346789999999999987765443
No 43
>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=97.05 E-value=0.0046 Score=34.06 Aligned_cols=35 Identities=17% Similarity=0.119 Sum_probs=29.9
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEE
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEE 51 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e 51 (88)
.+|++|++.+ ++..++|+..++|++-.|+++....
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 3799999999 6777799999999999999875543
No 44
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=96.89 E-value=0.0025 Score=44.07 Aligned_cols=68 Identities=26% Similarity=0.302 Sum_probs=45.7
Q ss_pred CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372 6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD 81 (88)
Q Consensus 6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~ 81 (88)
...|+. +..|++|.|.|.+.| +++.|-|..+|+ .-|++|-+..+ +++ . .--+|.|..|..|...++.+
T Consensus 6 ~~~p~~-~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~--~--sv~~I~ghaVk~vevl~~~~ 74 (166)
T PF06372_consen 6 KKSPLE-WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGK--R--SVKVIMGHAVKSVEVLSEGD 74 (166)
T ss_dssp HS-HHH-HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS---E--EEEEE-GGGEEEEEEEE---
T ss_pred hCCHHH-HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCc--e--eEEEEEccceEEEEEccCCc
Confidence 345554 468999999999999 999999999995 68899886664 222 2 24689999999998877643
No 45
>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=96.81 E-value=0.0095 Score=36.16 Aligned_cols=59 Identities=17% Similarity=0.229 Sum_probs=46.5
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC-----e----eeeeeceEEEeCCcEE
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG-----H----CTGKLGEVLIRCNNIL 72 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~-----~----~~~~~~~v~IrG~~I~ 72 (88)
..++|+++.+..+.+-.|.|+|.++| +..-+.|.|+..+ .+| . ...-++.+..||+.|.
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk 71 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK 71 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence 36899999999999999999999999 4577889998865 221 1 3445678888988775
No 46
>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=96.72 E-value=0.014 Score=35.95 Aligned_cols=63 Identities=22% Similarity=0.202 Sum_probs=46.8
Q ss_pred HHHHhhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372 10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA 77 (88)
Q Consensus 10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~ 77 (88)
+.+|..+.|++|.+.|.++.+..|++.++|. ..|+..+|-+ ++=| ..+.-.+|..-|.++...
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-TPlG----v~~eAlLR~~DVi~~~f~ 79 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-TPLG----VQPEALLRCSDVISISFD 79 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-TTTT----EEEEEEEEGGGEEEEEE-
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-CCcc----cChhheeecCCEEEEEec
Confidence 5678889999999999999999999999994 5777666554 2223 246789999999998754
No 47
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=96.51 E-value=0.022 Score=33.80 Aligned_cols=54 Identities=26% Similarity=0.384 Sum_probs=41.0
Q ss_pred HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372 10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG 76 (88)
Q Consensus 10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~ 76 (88)
.+.|++++|++|.|++-.|+. +|+|.++-+.- ++|+.. + ..+|||=.+|++|.+
T Consensus 13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~-----~------~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN-----G------TPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC-----C------cEEEEEeeeEEEEcC
Confidence 468999999999999987766 99999998543 343322 2 367899889988853
No 48
>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=96.30 E-value=0.014 Score=34.16 Aligned_cols=34 Identities=29% Similarity=0.267 Sum_probs=28.3
Q ss_pred HHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372 12 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ 45 (88)
Q Consensus 12 ~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv 45 (88)
||+.+. ..+|+|-|.||-.++|.+.+||+|+=+.
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll 38 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLL 38 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence 555554 5679999999999999999999998444
No 49
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=96.17 E-value=0.019 Score=33.61 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=29.8
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
.+|.+|++++..|..++|.+.+||...++.+-.+.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~ 38 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCP 38 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECc
Confidence 47999999999999999999999988777654433
No 50
>PRK14638 hypothetical protein; Provisional
Probab=96.16 E-value=0.017 Score=39.09 Aligned_cols=45 Identities=22% Similarity=0.102 Sum_probs=36.0
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
||+...-|+ .-+..++|++|.|++.+++.++|+|.++|+. ++.|.
T Consensus 81 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 666666665 4566789999999999999999999999974 35554
No 51
>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=95.86 E-value=0.022 Score=33.34 Aligned_cols=35 Identities=31% Similarity=0.354 Sum_probs=28.8
Q ss_pred HHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372 11 PFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ 45 (88)
Q Consensus 11 ~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv 45 (88)
.||..+. +.+|+|-|.||-.++|.+.+||+|+=+.
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll 42 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL 42 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence 3565553 5779999999999999999999998444
No 52
>PRK14639 hypothetical protein; Provisional
Probab=95.82 E-value=0.03 Score=37.43 Aligned_cols=44 Identities=23% Similarity=0.193 Sum_probs=35.7
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+..++|+.|.|++.+++.+.|+|.++|+. ++.|
T Consensus 69 SSPGl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 69 SSPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 566666665 4567889999999999999999999999984 4555
No 53
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=95.74 E-value=0.032 Score=34.04 Aligned_cols=38 Identities=34% Similarity=0.443 Sum_probs=30.4
Q ss_pred HHHhhc--CCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 11 PFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 11 ~~L~~~--i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
.||.++ -+.+|.|-|.||-..+|.+.+||+|. +.|++.
T Consensus 10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~~ 49 (77)
T COG1923 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV-VLLKNT 49 (77)
T ss_pred HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEcC
Confidence 466655 46789999999999999999999997 444443
No 54
>PRK02001 hypothetical protein; Validated
Probab=95.62 E-value=0.041 Score=37.42 Aligned_cols=45 Identities=20% Similarity=0.177 Sum_probs=36.1
Q ss_pred CCCCCCCcHH---HHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPKP---FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~~---~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
||+.-.-|+. -+..++|+.|.|++.+++.+.|+|.++|+. ++.|.
T Consensus 71 SSPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~ 118 (152)
T PRK02001 71 GSAGLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE 118 (152)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence 6666666654 556779999999999999999999999975 35553
No 55
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.53 E-value=0.032 Score=34.26 Aligned_cols=39 Identities=28% Similarity=0.341 Sum_probs=31.3
Q ss_pred HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372 10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 10 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
-.||..+. +.+|+|-|.||-.++|.+.+||+|.=+.-.+
T Consensus 9 d~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 9 DPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred HHHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 35666664 6779999999999999999999998555434
No 56
>PRK14644 hypothetical protein; Provisional
Probab=95.25 E-value=0.047 Score=36.41 Aligned_cols=45 Identities=18% Similarity=0.025 Sum_probs=35.6
Q ss_pred CCCCCCCcHH--HHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPKP--FLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~~--~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~ 47 (88)
||+.-.-|+. -+..++|+.|.|+|++. +.+.|+|.++|+. ++.|.
T Consensus 67 SSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 67 SSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred ECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 5666666654 47788999999999887 9999999999974 46554
No 57
>PRK14640 hypothetical protein; Provisional
Probab=94.52 E-value=0.12 Score=34.88 Aligned_cols=45 Identities=20% Similarity=0.310 Sum_probs=34.8
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
||+...-|+ .-+.+++|+.|.|+| .+.+.++|+|.++|+. ++.|.
T Consensus 78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 78 SSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 666666665 456678999999999 5679999999999975 35553
No 58
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.50 E-value=0.17 Score=34.48 Aligned_cols=44 Identities=27% Similarity=0.395 Sum_probs=35.9
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+..++|+.|.|+| .+.+.+.|+|.++|+.. +++
T Consensus 80 SSPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 80 SSPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred eCCCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 666666665 466777999999999 78899999999999887 444
No 59
>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=94.49 E-value=0.16 Score=30.74 Aligned_cols=44 Identities=32% Similarity=0.381 Sum_probs=33.8
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc---Cc-cEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+..++|+.|.|+++ +| +.+.|.|.++|+. ++.|
T Consensus 6 SSPGl~RpL~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 6 SSPGAERPLKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 666666665 4566779999999997 55 6899999999985 3444
No 60
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=94.49 E-value=0.12 Score=35.66 Aligned_cols=48 Identities=23% Similarity=0.194 Sum_probs=35.0
Q ss_pred CCCCCCCCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372 1 MSTPLPCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 1 m~~~~~~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
|++.....--.||..+. ..+|+|-|.||-.++|++.+||+|.=+.-.+
T Consensus 5 m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~ 54 (165)
T PRK14091 5 MAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD 54 (165)
T ss_pred ccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence 44333333356788775 4568999999999999999999998444434
No 61
>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=94.23 E-value=0.098 Score=34.57 Aligned_cols=44 Identities=30% Similarity=0.345 Sum_probs=29.4
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+..++|+.|.|+++ +.+.+.|+|.++|+ -.++|
T Consensus 68 SSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 68 SSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp E--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred eCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 677767776 4678889999999994 45899999999998 33444
No 62
>PRK14633 hypothetical protein; Provisional
Probab=94.16 E-value=0.16 Score=34.24 Aligned_cols=45 Identities=24% Similarity=0.214 Sum_probs=34.6
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL~ 47 (88)
||+.-.-|+ .-+.+++|++|.|+++ +.+.++|+|.++++. ++.|.
T Consensus 75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 666666665 4556779999999993 569999999999885 45553
No 63
>PRK14645 hypothetical protein; Provisional
Probab=94.07 E-value=0.15 Score=34.62 Aligned_cols=43 Identities=16% Similarity=0.313 Sum_probs=33.7
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+.+++|+.|.|++ +++.+.|+|.++|+. .+.|
T Consensus 83 SSPGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 83 ESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 666666675 455677999999986 789999999999975 3554
No 64
>PRK14642 hypothetical protein; Provisional
Probab=93.65 E-value=0.14 Score=36.33 Aligned_cols=44 Identities=20% Similarity=0.264 Sum_probs=34.7
Q ss_pred CCCCCCCcHH---HHhhcCCCEEEEEEc-------------CccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPKP---FLNLLTGKSVICKLK-------------WGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~~---~L~~~i~k~V~V~L~-------------~g~~~~G~L~~~D~~mNlvL 46 (88)
||+-..-|+. -+.+++|+.|.|+|+ +.+.++|+|.++|+. ++.|
T Consensus 81 SSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 81 SSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 6666666764 556779999999998 679999999999975 4544
No 65
>PRK14643 hypothetical protein; Provisional
Probab=93.56 E-value=0.23 Score=34.07 Aligned_cols=40 Identities=15% Similarity=0.003 Sum_probs=32.6
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcC----ccEEEEEEEEecCC
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKW----GHEYKGILVSTDGY 41 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~----g~~~~G~L~~~D~~ 41 (88)
||+.-.-|+ .-+..++|+.|.|+|++ .+.+.|+|.++|..
T Consensus 85 SSPGleRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 85 SSSGIEKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred cCCCCCCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 666666665 46678899999999965 59999999999965
No 66
>PRK14632 hypothetical protein; Provisional
Probab=93.53 E-value=0.24 Score=34.20 Aligned_cols=45 Identities=20% Similarity=0.283 Sum_probs=34.8
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcC-------ccEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKW-------GHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~-------g~~~~G~L~~~D~~mNlvL~ 47 (88)
||+...-|+ .-+..++|+.|.|+|.+ .+.+.|+|.++|+. ++.|.
T Consensus 79 SSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 79 SSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 666666665 45677899999999975 58999999999874 45554
No 67
>PRK14636 hypothetical protein; Provisional
Probab=93.40 E-value=0.24 Score=34.35 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=33.7
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc---Cc-cEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL 46 (88)
||+.-.-|+ .-+..++|+.|.|+|+ +| +.++|+|.++|+. ++.|
T Consensus 79 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 79 SSPGIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 566666665 4566789999999997 45 7999999999874 3554
No 68
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=93.35 E-value=0.93 Score=31.39 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=31.1
Q ss_pred HHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 11 PFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 11 ~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
.||..+. ..+|+|-|.||-.++|.+.+||+|.=+.-.+.
T Consensus 95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 4677664 56799999999999999999999985554443
No 69
>PRK14634 hypothetical protein; Provisional
Probab=93.32 E-value=0.27 Score=33.39 Aligned_cols=44 Identities=16% Similarity=0.150 Sum_probs=33.6
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL 46 (88)
||+...-|+ .-+..++|+.|.|+|.+. +.+.|+|.++|+.. +.|
T Consensus 81 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~-v~l 131 (155)
T PRK14634 81 SSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH-LQI 131 (155)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE-EEE
Confidence 666666665 456678999999999742 89999999999753 555
No 70
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=93.17 E-value=0.3 Score=32.87 Aligned_cols=40 Identities=30% Similarity=0.428 Sum_probs=32.4
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCC
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGY 41 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~ 41 (88)
||+...-|+ .-+..++|+.|.|++ .+++.+.|+|.++|+.
T Consensus 79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~ 125 (154)
T PRK00092 79 SSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE 125 (154)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence 666666665 457788999999997 5678999999999984
No 71
>PRK14646 hypothetical protein; Provisional
Probab=93.04 E-value=0.33 Score=32.96 Aligned_cols=45 Identities=13% Similarity=0.060 Sum_probs=34.5
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~ 47 (88)
||+.-.-|+ .-+..++|+.|.|+|++. +.++|+|.++|+. ++.|.
T Consensus 81 SSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 81 SSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 666666665 456778999999999653 7889999999985 45553
No 72
>PRK14647 hypothetical protein; Provisional
Probab=92.92 E-value=0.35 Score=32.87 Aligned_cols=40 Identities=18% Similarity=0.076 Sum_probs=31.9
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc---------CccEEEEEEEEecCC
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK---------WGHEYKGILVSTDGY 41 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---------~g~~~~G~L~~~D~~ 41 (88)
||+...-|+ .-+..++|+.|.|+|+ +.+.+.|+|.++|+.
T Consensus 80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~ 131 (159)
T PRK14647 80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG 131 (159)
T ss_pred cCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence 666666665 4567789999999995 359999999999963
No 73
>PRK14637 hypothetical protein; Provisional
Probab=92.14 E-value=0.48 Score=32.07 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=33.1
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCccEE-EEEEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEY-KGILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~ 47 (88)
||+...-|+ .-+..++|+.|.|++.+.+.+ +|+|.++|+. ++.|.
T Consensus 79 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 79 SSPGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred eCCCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 666666665 456777999999999544556 7999999985 45554
No 74
>PRK14631 hypothetical protein; Provisional
Probab=92.12 E-value=0.48 Score=32.84 Aligned_cols=38 Identities=24% Similarity=0.245 Sum_probs=31.0
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEec
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTD 39 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D 39 (88)
||+.-.-|+ .-+..++|+.|.|+|. +.+.++|+|.++|
T Consensus 98 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 98 SSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 666666665 4667789999999996 4599999999998
No 75
>PRK06955 biotin--protein ligase; Provisional
Probab=91.29 E-value=1.1 Score=33.19 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=36.4
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCC
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCN 69 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~ 69 (88)
++|++|+|...+++.+.|++.++|+...|+++... |......|.|.+|..
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~~----g~~~~~sGeV~~~~~ 296 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDTPA----GRQAIAAGDVSLREA 296 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEeCC----CeEEEEEEEEEEecc
Confidence 57999999776778899999999999999985322 212344566666544
No 76
>PRK14641 hypothetical protein; Provisional
Probab=91.21 E-value=0.6 Score=32.37 Aligned_cols=38 Identities=21% Similarity=0.175 Sum_probs=30.3
Q ss_pred CCCCCCCcHH---HHhhcCCCEEEEEEcC----ccEEEEEEEEec
Q psy6372 2 STPLPCNPKP---FLNLLTGKSVICKLKW----GHEYKGILVSTD 39 (88)
Q Consensus 2 ~~~~~~~p~~---~L~~~i~k~V~V~L~~----g~~~~G~L~~~D 39 (88)
||+...-|+. -+.+++|+.|.|+|.+ .+.++|+|.+++
T Consensus 85 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 85 SSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 5666666654 5677799999999976 468999999996
No 77
>KOG1073|consensus
Probab=91.06 E-value=0.76 Score=35.39 Aligned_cols=65 Identities=18% Similarity=0.168 Sum_probs=51.3
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC-----e----eeeeeceEEEeCCcEEEEEcCC
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG-----H----CTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~-----~----~~~~~~~v~IrG~~I~~I~~~d 78 (88)
..+||+.|.+.-+++..|.|.|..+| +..-|-|.+|-.+ .++ . ...-++.++.||+.|.-+.+-+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~ 80 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE 80 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence 46899999999999999999999999 7788999998533 211 1 1226789999999999766543
No 78
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=88.84 E-value=2.5 Score=31.16 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=34.7
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeC
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC 68 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG 68 (88)
+.|++|++... +..+.|++.++|+...|+++.. .+......|.+.+++
T Consensus 270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~~----g~~~~~~~gev~~~~ 317 (319)
T PRK11886 270 FLGREVKLIIG-DKEISGIARGIDEQGALLLEDD----GVEKPFNGGEISLRS 317 (319)
T ss_pred ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEeC----CcEEEEEEeEEEEec
Confidence 57999999874 5679999999999999999621 112334556666654
No 79
>PRK14630 hypothetical protein; Provisional
Probab=87.59 E-value=1.8 Score=29.05 Aligned_cols=43 Identities=16% Similarity=0.132 Sum_probs=32.0
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL 46 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL 46 (88)
||+.-.-|+ .-+..++|++|.|+|.. ...+|+|.++|+.. +.|
T Consensus 78 SSPGldRpL~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d~~-i~l 123 (143)
T PRK14630 78 STPGINRKIKSDREFKIFEGKKIKLMLDN-DFEEGFILEAKADS-FIF 123 (143)
T ss_pred eCCCCCCcCCCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeCCE-EEE
Confidence 666666665 45667799999999965 44599999999843 444
No 80
>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=87.52 E-value=3.4 Score=29.26 Aligned_cols=31 Identities=23% Similarity=0.099 Sum_probs=27.1
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
.+|++|++...+ ..+.|+..++|+...|+++
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 469999998754 5799999999999999996
No 81
>PRK14635 hypothetical protein; Provisional
Probab=87.37 E-value=3 Score=28.40 Aligned_cols=45 Identities=20% Similarity=0.193 Sum_probs=33.1
Q ss_pred CCCCCCCcH---HHHhhcCCCEEEEEEc--CccEEEE---EEEEecCCcceEEc
Q psy6372 2 STPLPCNPK---PFLNLLTGKSVICKLK--WGHEYKG---ILVSTDGYMNCQLA 47 (88)
Q Consensus 2 ~~~~~~~p~---~~L~~~i~k~V~V~L~--~g~~~~G---~L~~~D~~mNlvL~ 47 (88)
||+.-.-|+ .-+..++|+.|.|++. ++..++| +|.++|+. ++.|.
T Consensus 80 SSPGldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~ 132 (162)
T PRK14635 80 SSAGAERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE 132 (162)
T ss_pred cCCCCCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence 666666665 4567789999999985 4678888 99999975 45443
No 82
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=86.17 E-value=5.4 Score=32.39 Aligned_cols=32 Identities=22% Similarity=0.219 Sum_probs=28.5
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
+.|++|.+...++..+.|+..++|+...|.|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 57999999766777899999999999999996
No 83
>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=83.28 E-value=2 Score=29.58 Aligned_cols=34 Identities=15% Similarity=-0.042 Sum_probs=31.1
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
-+-+|+|.+.||..+.|.+.+|+.--|.+|..+.
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 4678999999999999999999999999998766
No 84
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=81.76 E-value=3 Score=28.14 Aligned_cols=26 Identities=27% Similarity=0.230 Sum_probs=24.0
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
..++||.|.+...+|..++|++.++-
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46899999999999999999999986
No 85
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=81.30 E-value=10 Score=27.32 Aligned_cols=35 Identities=29% Similarity=0.213 Sum_probs=31.8
Q ss_pred hcCCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 15 LLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 15 ~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
..+|++|+++..++....|+..++|....|+++..
T Consensus 187 ~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 187 LSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred ccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 34899999999999999999999999999998766
No 86
>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=80.18 E-value=2.9 Score=26.58 Aligned_cols=19 Identities=21% Similarity=0.263 Sum_probs=15.2
Q ss_pred CCEEEEEEcCccEEEEEEE
Q psy6372 18 GKSVICKLKWGHEYKGILV 36 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~ 36 (88)
+.+|.++|+||+.+.||+.
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 4689999999999999974
No 87
>PRK08330 biotin--protein ligase; Provisional
Probab=78.71 E-value=9.2 Score=27.05 Aligned_cols=34 Identities=24% Similarity=0.182 Sum_probs=27.3
Q ss_pred hcCCCEEEEEEcCccEE-EEEEEEecCCcceEEcce
Q psy6372 15 LLTGKSVICKLKWGHEY-KGILVSTDGYMNCQLAST 49 (88)
Q Consensus 15 ~~i~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~d~ 49 (88)
.++|++|++.. ++..+ .|+..++|+...|+++..
T Consensus 185 ~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 185 MILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 35799999976 55565 699999999999988643
No 88
>PRK10898 serine endoprotease; Provisional
Probab=75.36 E-value=13 Score=28.08 Aligned_cols=33 Identities=18% Similarity=0.389 Sum_probs=28.7
Q ss_pred CCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
...+.|.+.+|+.|.+++.++|...+|-+-.+.
T Consensus 101 a~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 101 ADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CCEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 367899999999999999999999998776554
No 89
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=74.17 E-value=9.2 Score=28.11 Aligned_cols=31 Identities=16% Similarity=-0.061 Sum_probs=27.1
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
+|++|.|.. ++..+.|++.++|+...|+++.
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 799999975 5689999999999999998863
No 90
>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=73.55 E-value=15 Score=27.58 Aligned_cols=32 Identities=19% Similarity=0.369 Sum_probs=28.1
Q ss_pred CEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 19 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
..+.|.+.+|+.+.+++.++|...++-+-.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 46899999999999999999999998886554
No 91
>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=72.85 E-value=3.8 Score=25.01 Aligned_cols=63 Identities=22% Similarity=0.223 Sum_probs=27.4
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE 82 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~~ 82 (88)
|..+-+-+|+++|+||..+.|+-. |=..|- +-+|+.. -...-+...||=+.|..+.+..+-++
T Consensus 12 iAC~~~~~v~L~l~dG~~~~g~A~--dt~~~~---~k~E~L~--l~~~~~~~~i~Ld~I~~~~al~~nPh 74 (80)
T PF07073_consen 12 IACMYRYPVKLTLKDGEQIEGKAL--DTRTNA---KKEECLV--LEQDGGEQEIRLDQIASMSALTDNPH 74 (80)
T ss_dssp HHHTTTT-EEEE-TTT--EEESS---EEE------SSS-EEE--EEETTEEEEESTT--SEEE----ETT
T ss_pred HHHhcCCeEEEEEeCCCEEEEEEE--EEEEec---CceEEEE--EecCCcEEEEEhhheeeeeecCCCCe
Confidence 456678999999999999999832 222221 1111100 00011345677778877776555444
No 92
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=72.62 E-value=5.8 Score=21.51 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=14.8
Q ss_pred EEEEEEEecCCcceEEcceEEE
Q psy6372 31 YKGILVSTDGYMNCQLASTEEI 52 (88)
Q Consensus 31 ~~G~L~~~D~~mNlvL~d~~e~ 52 (88)
.+|++.++|+...+.|++...+
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 6899999999999999876643
No 93
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=69.20 E-value=9.6 Score=25.68 Aligned_cols=27 Identities=19% Similarity=0.089 Sum_probs=23.5
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecC
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDG 40 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~ 40 (88)
..++||.|.....+|..++|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 368999999888999999999998763
No 94
>PRK10139 serine endoprotease; Provisional
Probab=67.72 E-value=14 Score=28.97 Aligned_cols=33 Identities=18% Similarity=0.344 Sum_probs=28.6
Q ss_pred CCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
...+.|++.||+.|.+++.++|....|-+-.+.
T Consensus 114 a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 114 AQKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CCEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 367999999999999999999999988775553
No 95
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=67.11 E-value=7 Score=26.91 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=22.2
Q ss_pred CCCEEEEEEcCccEEEEEEEEecC
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDG 40 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~ 40 (88)
-|+.|+|-+.+||.+.|+-.++|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 488999999999999999999985
No 96
>PRK10942 serine endoprotease; Provisional
Probab=64.74 E-value=16 Score=28.82 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=27.9
Q ss_pred CCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
...+.|.+.+|+.|.+++.+.|...+|-|-..
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999999877644
No 97
>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=63.32 E-value=16 Score=23.63 Aligned_cols=31 Identities=19% Similarity=0.037 Sum_probs=26.7
Q ss_pred CCCCcHHHHhhcCCCEEEEEEcCccEEEEEE
Q psy6372 5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGIL 35 (88)
Q Consensus 5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L 35 (88)
.+..|...|....+-+|.+++.||+.|.+.=
T Consensus 61 ~~~~~~~~i~~~~~~tvt~e~~nG~~y~l~~ 91 (119)
T PF10618_consen 61 TKDTDVDDINDITDATVTFELDNGKVYVLSN 91 (119)
T ss_pred CCCCCHHHHhCCcccEEEEEecCCcEEEecC
Confidence 3567888999999999999999999997753
No 98
>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=60.49 E-value=21 Score=27.33 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=28.1
Q ss_pred CEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 19 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
..+.|.+.+|+.|.+++.++|...++.|-...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 57899999999999999999999998876554
No 99
>PRK11625 Rho-binding antiterminator; Provisional
Probab=59.62 E-value=28 Score=21.40 Aligned_cols=25 Identities=16% Similarity=0.024 Sum_probs=20.8
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEE
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVS 37 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~ 37 (88)
|...-+.+|.++|+||..+.|+-..
T Consensus 18 lAC~~~~~l~l~l~dGe~~~g~A~D 42 (84)
T PRK11625 18 LACQHHLMLTLELKDGEVLQAKASD 42 (84)
T ss_pred HHHhcCCeEEEEECCCCEEEEEEEe
Confidence 4455789999999999999998744
No 100
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=59.23 E-value=22 Score=22.98 Aligned_cols=30 Identities=20% Similarity=0.205 Sum_probs=22.2
Q ss_pred CEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 19 KSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 19 k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
....|.++||+.+.|.+.+=|+. .+.|.++
T Consensus 58 ~~~~v~~~dG~~~~G~~~~e~~~-~~~l~~~ 87 (133)
T TIGR02603 58 EAYRVTLKDGRILSGIVASETAD-GVTVKMP 87 (133)
T ss_pred ccEEEEECCCCEEEEEEEecCCC-eEEEEcC
Confidence 34899999999999999985533 3555443
No 101
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=58.52 E-value=35 Score=20.61 Aligned_cols=31 Identities=32% Similarity=0.254 Sum_probs=22.3
Q ss_pred HHHhhcCCCEEEEEEcCcc----EEEEEEEEecCC
Q psy6372 11 PFLNLLTGKSVICKLKWGH----EYKGILVSTDGY 41 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~----~~~G~L~~~D~~ 41 (88)
..|.+.+|++|.++.+.|| +-.|+|...=+.
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~tYPs 44 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEETYPS 44 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE-SS
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEeecCc
Confidence 4688999999999999994 678999876543
No 102
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=56.07 E-value=17 Score=22.78 Aligned_cols=23 Identities=22% Similarity=0.329 Sum_probs=19.5
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
..+|..|+|. +..|+.++|++.+
T Consensus 93 g~~G~~I~V~N~~s~k~i~~~V~~ 116 (122)
T TIGR03170 93 GAVGDQIRVRNLSSGKIISGIVTG 116 (122)
T ss_pred cCCCCEEEEEECCCCCEEEEEEeC
Confidence 4578999999 7899999998875
No 103
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=55.83 E-value=20 Score=25.16 Aligned_cols=34 Identities=26% Similarity=0.415 Sum_probs=25.1
Q ss_pred cHHHHhhcCC--CEEEEEE-cCccEEEEEEEEecCCc
Q psy6372 9 PKPFLNLLTG--KSVICKL-KWGHEYKGILVSTDGYM 42 (88)
Q Consensus 9 p~~~L~~~i~--k~V~V~L-~~g~~~~G~L~~~D~~m 42 (88)
-+.||..+-+ -+|.|.+ .++..|+|.+.++|.-.
T Consensus 122 KI~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~~ 158 (185)
T PF14153_consen 122 KIDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEGE 158 (185)
T ss_pred HHHHHHhCcccCCCCceEEEeCCceEEEEEEeccCCE
Confidence 3567777765 3466666 45799999999999763
No 104
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=55.81 E-value=21 Score=25.28 Aligned_cols=26 Identities=19% Similarity=0.115 Sum_probs=22.9
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
..++||.|.+.-.+|..+.|++.++.
T Consensus 114 ~slIGK~V~~~~~dG~~vtG~V~sV~ 139 (190)
T PRK06792 114 MKFLGKYVRGVSNDGKQVTGQVETVR 139 (190)
T ss_pred HHhcCcEEEEEcCCCCEEEEEEEEEE
Confidence 36799999998889999999999876
No 105
>PRK08477 biotin--protein ligase; Provisional
Probab=54.41 E-value=33 Score=24.26 Aligned_cols=35 Identities=9% Similarity=-0.196 Sum_probs=29.2
Q ss_pred hcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 15 LLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 15 ~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
-.+|+.|+|. .+++.++|+..++|+..-|++....
T Consensus 172 ~~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 172 FEKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKK 206 (211)
T ss_pred HHcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEE
Confidence 3579999987 5789999999999999988876544
No 106
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=51.63 E-value=23 Score=23.43 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=20.1
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
++++-|-++|.|.||+.++.-+=+..
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheEEEEEeCCCCEEEEEcCCCC
Confidence 45667889999999999987665544
No 107
>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=51.60 E-value=37 Score=18.11 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=21.7
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCC
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGY 41 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~ 41 (88)
.|..+.+...+|.-|+|++.++++.
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 5777888878899999999999975
No 108
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=51.41 E-value=21 Score=19.59 Aligned_cols=16 Identities=31% Similarity=0.405 Sum_probs=13.1
Q ss_pred cHHHHhhcCCCEEEEE
Q psy6372 9 PKPFLNLLTGKSVICK 24 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~ 24 (88)
-...+++++||+|+|.
T Consensus 10 ~~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 10 DYSYLKSLLGKRVSVT 25 (48)
T ss_pred hhHHHHHhcCCeEEEE
Confidence 3567788999999986
No 109
>PRK06789 flagellar motor switch protein; Validated
Probab=51.21 E-value=34 Score=20.55 Aligned_cols=36 Identities=19% Similarity=0.199 Sum_probs=29.0
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
|.+..+.+|.|.+++-...+|.+..+|+.+=+.+.+
T Consensus 36 Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGVRIte 71 (74)
T PRK06789 36 LENSTKNTVRLMLENEEIGTGKILTKNGKMYVEIVE 71 (74)
T ss_pred eCCcCCCCEEEEECCEEEeEEeEEEECCEEEEEEEE
Confidence 467788889999988888999999999877666543
No 110
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=50.47 E-value=7.9 Score=24.29 Aligned_cols=31 Identities=32% Similarity=0.442 Sum_probs=20.8
Q ss_pred CCCCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 1 m~~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
|++..|-.--+.|+++.||+|++. |++.+++
T Consensus 1 M~~~~pRVn~~~L~~~~gk~Vriv--------Gkv~~~~ 31 (109)
T PF08661_consen 1 MDAPTPRVNGSMLSQFVGKTVRIV--------GKVESVD 31 (109)
T ss_dssp GGS--EEE-GGGGGGGTTSEEEEE--------EEEEEE-
T ss_pred CCCCcceECHHHHHhhCCCeEEEE--------EEEeeEc
Confidence 666666666789999999999864 5566665
No 111
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.13 E-value=17 Score=22.29 Aligned_cols=39 Identities=23% Similarity=0.272 Sum_probs=25.6
Q ss_pred HHHhhcCCCEEEEEEcCccEE----EEEEEEec-CCcceEEcce
Q psy6372 11 PFLNLLTGKSVICKLKWGHEY----KGILVSTD-GYMNCQLAST 49 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~----~G~L~~~D-~~mNlvL~d~ 49 (88)
.-+.+.+|++|.+++++||.= .|.|...= ..+=+-|++.
T Consensus 12 ~~i~ah~G~~v~lk~ngGRKk~~~r~G~L~EtYpSvFIiel~~d 55 (80)
T COG4466 12 ESIDAHLGERVTLKANGGRKKTIERSGILIETYPSVFIIELDQD 55 (80)
T ss_pred HHHHhccCcEEEEEecCCceeeehhceEEeeecCcEEEEEeccc
Confidence 457888999999999999643 46665443 3333444433
No 112
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=46.68 E-value=26 Score=24.90 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=20.2
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
..+|..|+|+ +..|+.+.|++.+
T Consensus 204 G~~Gd~IrVrN~~Sgk~i~g~V~~ 227 (235)
T PRK07018 204 GAVGQQIRVRNMASGQVVSGIVTG 227 (235)
T ss_pred CCCCCeEEEEECCCCCEEEEEEeC
Confidence 4579999999 9999999999875
No 113
>PF13437 HlyD_3: HlyD family secretion protein
Probab=44.58 E-value=68 Score=19.12 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=25.6
Q ss_pred cHHHHhhc--CCCEEEEEEcCc--cEEEEEEEEecC
Q psy6372 9 PKPFLNLL--TGKSVICKLKWG--HEYKGILVSTDG 40 (88)
Q Consensus 9 p~~~L~~~--i~k~V~V~L~~g--~~~~G~L~~~D~ 40 (88)
|-..+..+ .|..|.+.+.++ ..+.|++..++.
T Consensus 43 ~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 43 PEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 44555565 699999999855 699999999998
No 114
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=42.41 E-value=66 Score=18.35 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=18.8
Q ss_pred cCCCEEEEEEcCccEE-EEEEEEecCC
Q psy6372 16 LTGKSVICKLKWGHEY-KGILVSTDGY 41 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~-~G~L~~~D~~ 41 (88)
..|..|.+.--++..| .|++.+||.-
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~ 33 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSK 33 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETT
T ss_pred cCCCEEEEECCCCCcEEEEEEEEeccc
Confidence 4689999999887665 9999999964
No 115
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=41.81 E-value=44 Score=23.38 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=22.9
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
+..++|++|.|.+...+.++|.+.+++
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 345999999999998999999998885
No 116
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=41.69 E-value=12 Score=23.60 Aligned_cols=17 Identities=35% Similarity=0.434 Sum_probs=15.5
Q ss_pred EEEEEecCCcceEEcce
Q psy6372 33 GILVSTDGYMNCQLAST 49 (88)
Q Consensus 33 G~L~~~D~~mNlvL~d~ 49 (88)
|+|+|.|.+.|.--++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999988777
No 117
>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=40.99 E-value=23 Score=23.21 Aligned_cols=27 Identities=41% Similarity=0.759 Sum_probs=21.7
Q ss_pred CcHHHHhhcCCCEEEEEEcCc-cEEEEE
Q psy6372 8 NPKPFLNLLTGKSVICKLKWG-HEYKGI 34 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g-~~~~G~ 34 (88)
..-.++..++||+++|.++.. ..+.|.
T Consensus 93 sl~~~~~~l~gk~l~V~v~~~~~e~nGk 120 (141)
T PF05037_consen 93 SLEQFLNQLLGKPLRVTVKWEENEYNGK 120 (141)
T ss_pred cHHHHHHHHcCCeeEEEecccccCCCCc
Confidence 345788899999999999887 677774
No 118
>KOG3382|consensus
Probab=39.45 E-value=16 Score=24.69 Aligned_cols=28 Identities=18% Similarity=0.200 Sum_probs=21.5
Q ss_pred EcCccEEEEEEEEecCCcceEEcceEEE
Q psy6372 25 LKWGHEYKGILVSTDGYMNCQLASTEEI 52 (88)
Q Consensus 25 L~~g~~~~G~L~~~D~~mNlvL~d~~e~ 52 (88)
++++-.-.|||++.|+|.|=--+|-...
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~~~f 66 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENNDYF 66 (151)
T ss_pred Hhcccccceeeeeecccccchhccccee
Confidence 3455666799999999999888776543
No 119
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=39.38 E-value=42 Score=25.08 Aligned_cols=35 Identities=17% Similarity=0.004 Sum_probs=25.0
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
.+++-|-++|.|.||+.++.-+=+.. | ||.=-+.+
T Consensus 142 NSA~RKvarVrLsNGk~VtAyIPGeG-H-nLQEHs~V 176 (290)
T PTZ00115 142 NSGLRKVARVRLSTGRTVTVYIPGIG-H-NLNTHSVV 176 (290)
T ss_pred CccccceEEEEecCCCEEEEEcCCCC-c-ccccCCEE
Confidence 45677889999999999988776655 3 55533333
No 120
>KOG4401|consensus
Probab=38.75 E-value=45 Score=23.53 Aligned_cols=35 Identities=14% Similarity=-0.080 Sum_probs=30.5
Q ss_pred cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
.+|-.|.|..-+|....|.+.+||-.-+...-++.
T Consensus 9 avg~~v~~~t~~e~~~~G~Vyafd~~~k~l~~~~~ 43 (184)
T KOG4401|consen 9 AVGSCVEIGTEDEKFAVGEVYAFDLTTKDLFLGTP 43 (184)
T ss_pred EEEEEEEecccccceeeeEEEEEEcccCeeEeccc
Confidence 46889999999999999999999988777776666
No 121
>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=38.42 E-value=88 Score=22.06 Aligned_cols=36 Identities=28% Similarity=0.501 Sum_probs=30.7
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcc
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMN 43 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mN 43 (88)
.+..+=++++||.+.-++.+|....|.++....|.-
T Consensus 9 ~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G 44 (192)
T TIGR00567 9 DAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMG 44 (192)
T ss_pred CHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccC
Confidence 456777899999999888888888999999998864
No 122
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=38.14 E-value=43 Score=25.79 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=22.8
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecC
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDG 40 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~ 40 (88)
+-+.|++|+|...+|+.|.|++-+.=.
T Consensus 93 ~~~~gq~v~i~t~~g~~i~GvIg~~p~ 119 (355)
T COG1363 93 QVLEGQRVTIHTDKGKKIRGVIGSKPP 119 (355)
T ss_pred hhccCcEEEEEeCCCcEEeeeEcccCc
Confidence 456899999999999999999984443
No 123
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=38.08 E-value=67 Score=21.14 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=24.7
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~ 47 (88)
.+..|..|.|-.++-..-+|-++-+|+.+=+.+.
T Consensus 101 d~~~~~~VdI~vNg~~Ig~GEvVvvd~~~GVrIt 134 (136)
T COG1886 101 DKLAGEPVDILVNGRLIGRGEVVVVDDKFGVRIT 134 (136)
T ss_pred CCcCCCceEEEECCEEEEEEeEEEECCeEEEEEE
Confidence 4566777887777777788888888877655554
No 124
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=37.86 E-value=49 Score=22.40 Aligned_cols=23 Identities=13% Similarity=0.205 Sum_probs=19.2
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
..+|..|+|+ +..|+.++|++.+
T Consensus 128 G~~Gd~IrVrN~~Sgkiv~g~V~~ 151 (160)
T PRK06005 128 GAAGDLIRVRNVDSGVIVSGTVLA 151 (160)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3578999999 8899999998764
No 125
>PRK10708 hypothetical protein; Provisional
Probab=36.73 E-value=47 Score=19.24 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=22.9
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCc
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYM 42 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~m 42 (88)
++-+|+|++-.|..-.|++.++..|.
T Consensus 3 vnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 3 VNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred cccEEEEecCCCccccceEEEEeecc
Confidence 56789999999999999999998774
No 126
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=36.14 E-value=85 Score=21.76 Aligned_cols=27 Identities=11% Similarity=0.085 Sum_probs=23.4
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCcc
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYMN 43 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~mN 43 (88)
.|.+|.|.+.+|..+.|++..+++..+
T Consensus 141 ~g~~v~i~~~~~~~~~g~v~~I~~~~~ 167 (265)
T TIGR00999 141 KGSKATVLLENGRPLPARVDYVGPEVD 167 (265)
T ss_pred CCCEEEEEECCCCEEEEEEEEEccccC
Confidence 589999999889999999999986543
No 127
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=35.83 E-value=88 Score=17.90 Aligned_cols=33 Identities=12% Similarity=0.170 Sum_probs=23.0
Q ss_pred CCCEEEEEEcCc----cEEEEEEEEecCCcceEEcce
Q psy6372 17 TGKSVICKLKWG----HEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 17 i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~d~ 49 (88)
+|.+|.|++.++ ..|.-++.++++.-.+.++--
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P 39 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMP 39 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE--
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcC
Confidence 688999999554 359999999998855665544
No 128
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=35.50 E-value=1e+02 Score=24.37 Aligned_cols=45 Identities=20% Similarity=0.124 Sum_probs=35.3
Q ss_pred CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEE
Q psy6372 6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEE 51 (88)
Q Consensus 6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e 51 (88)
...|-.++.+++||.|+- =++|++++++|.+=|.-.=+.+.+-.+
T Consensus 70 l~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~ 114 (421)
T COG5316 70 LLSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVE 114 (421)
T ss_pred ccCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEE
Confidence 346778899999999999 899999999999988655455444443
No 129
>KOG3493|consensus
Probab=35.22 E-value=33 Score=20.47 Aligned_cols=19 Identities=32% Similarity=0.190 Sum_probs=15.1
Q ss_pred HHhhcCCCEEEEEEcCccE
Q psy6372 12 FLNLLTGKSVICKLKWGHE 30 (88)
Q Consensus 12 ~L~~~i~k~V~V~L~~g~~ 30 (88)
.+++.+||+|+|+-...-+
T Consensus 5 ~~nDrLGKKVRvKCn~dDt 23 (73)
T KOG3493|consen 5 VLNDRLGKKVRVKCNTDDT 23 (73)
T ss_pred hhhhhcCceEEEEeCCccc
Confidence 5788899999999876544
No 130
>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=34.47 E-value=1.1e+02 Score=18.80 Aligned_cols=19 Identities=21% Similarity=0.095 Sum_probs=14.6
Q ss_pred CCcHHHHhhcCCCEEEEEE
Q psy6372 7 CNPKPFLNLLTGKSVICKL 25 (88)
Q Consensus 7 ~~p~~~L~~~i~k~V~V~L 25 (88)
-.-.+.|++++||+|++.-
T Consensus 4 rVn~~~L~~f~gk~V~ivG 22 (101)
T cd04479 4 RINGAMLSQFVGKTVRIVG 22 (101)
T ss_pred eeCHHHHHhhCCCEEEEEE
Confidence 3445789999999998753
No 131
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=34.03 E-value=68 Score=19.88 Aligned_cols=24 Identities=8% Similarity=0.090 Sum_probs=21.0
Q ss_pred CeeeeeeceEEEeCCcEEEEEcCC
Q psy6372 55 GHCTGKLGEVLIRCNNILYIRGAE 78 (88)
Q Consensus 55 ~~~~~~~~~v~IrG~~I~~I~~~d 78 (88)
....+.-|.+.+.|..+..|.+|+
T Consensus 73 ~G~~ry~G~l~m~G~~l~~v~lpp 96 (97)
T PF11743_consen 73 DGEDRYQGELVMLGRRLISVELPP 96 (97)
T ss_pred CChhcceEEEEEECCeeeEEEcCC
Confidence 336788899999999999999986
No 132
>COG4568 Rof Transcriptional antiterminator [Transcription]
Probab=33.32 E-value=68 Score=19.72 Aligned_cols=25 Identities=20% Similarity=0.064 Sum_probs=20.8
Q ss_pred HHhhcCCCEEEEEEcCccEEEEEEE
Q psy6372 12 FLNLLTGKSVICKLKWGHEYKGILV 36 (88)
Q Consensus 12 ~L~~~i~k~V~V~L~~g~~~~G~L~ 36 (88)
.|..+-.-+++.+|++|..+.|.-.
T Consensus 17 ElACl~hl~l~L~lkdGev~~a~A~ 41 (84)
T COG4568 17 ELACLHHLPLTLELKDGEVLQAKAS 41 (84)
T ss_pred HHHHhhhceEEEEEcCCeEEEEEeh
Confidence 4566778899999999999999744
No 133
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=33.32 E-value=1.2e+02 Score=18.81 Aligned_cols=35 Identities=29% Similarity=0.303 Sum_probs=29.2
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQ 45 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlv 45 (88)
+.-.-++||+|.-.-+.|+.+.|++.---.....+
T Consensus 33 ~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvV 67 (87)
T PRK04337 33 EEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEV 67 (87)
T ss_pred HHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceE
Confidence 34466899999999999999999998877776666
No 134
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=33.10 E-value=59 Score=23.14 Aligned_cols=23 Identities=13% Similarity=0.044 Sum_probs=19.5
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
...|..|+|+ +..|+.+.|++.+
T Consensus 183 G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 183 AGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred CCCCCEEEEEECCCCCEEEEEEeC
Confidence 3578999999 7999999999864
No 135
>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=32.73 E-value=89 Score=21.82 Aligned_cols=35 Identities=23% Similarity=0.428 Sum_probs=25.7
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcc
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMN 43 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mN 43 (88)
.+..+=++++||.+..++.++. +.|.++....|.-
T Consensus 8 ~~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g 42 (184)
T PF02245_consen 8 DTVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLG 42 (184)
T ss_dssp BHHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-S
T ss_pred CHHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccC
Confidence 3566778999999999999888 9999998877654
No 136
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.72 E-value=84 Score=22.28 Aligned_cols=23 Identities=22% Similarity=0.062 Sum_probs=19.9
Q ss_pred hcCCCEEEEEEcCccEEEEEEEE
Q psy6372 15 LLTGKSVICKLKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~L~~g~~~~G~L~~ 37 (88)
..+|..|+|+-..|+.+.|++.+
T Consensus 193 G~~Gd~IrVrN~Sgkii~g~V~~ 215 (222)
T PRK08515 193 GNLGDIIQAKNKSNKILKAKVLS 215 (222)
T ss_pred CCCCCEEEEEeCCCCEEEEEEec
Confidence 45799999999889999999875
No 137
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=30.79 E-value=60 Score=18.81 Aligned_cols=26 Identities=15% Similarity=0.342 Sum_probs=22.7
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCc
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYM 42 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~m 42 (88)
++-+|+|++-.|..-.|++.++..|.
T Consensus 3 vnD~VtVKTDG~~rR~G~ilavE~F~ 28 (62)
T PF10781_consen 3 VNDRVTVKTDGGPRREGVILAVEPFN 28 (62)
T ss_pred cccEEEEecCCcccccceEEEEeecc
Confidence 56789999999999999999998774
No 138
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.58 E-value=83 Score=20.83 Aligned_cols=23 Identities=13% Similarity=0.066 Sum_probs=18.6
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
...|..|+|+ +..|+.++|++.+
T Consensus 109 G~~Gd~IrV~N~~S~riV~g~V~~ 132 (141)
T PRK12618 109 GGVGDEIRVMNLSSRTTVSGRIAA 132 (141)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 3578899995 7889999998865
No 139
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=29.12 E-value=93 Score=22.70 Aligned_cols=18 Identities=17% Similarity=0.209 Sum_probs=16.6
Q ss_pred EEEEEEEEecCCcceEEc
Q psy6372 30 EYKGILVSTDGYMNCQLA 47 (88)
Q Consensus 30 ~~~G~L~~~D~~mNlvL~ 47 (88)
.++|.+..+|.|-|+++.
T Consensus 169 ~i~g~Vi~iD~FGNlitn 186 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITN 186 (258)
T ss_dssp EEEEEEEEEETTSEEEEE
T ss_pred eEEEEEEEECccCCeeeC
Confidence 899999999999999864
No 140
>PRK06630 hypothetical protein; Provisional
Probab=29.00 E-value=31 Score=22.01 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=17.1
Q ss_pred EEEEEEEecCCcceEEcceE
Q psy6372 31 YKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 31 ~~G~L~~~D~~mNlvL~d~~ 50 (88)
..|+|+|-|.+.|---++..
T Consensus 11 r~G~lVG~D~~GNkYYE~~~ 30 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESRN 30 (99)
T ss_pred ccCeEeEEeCCCChhcccCC
Confidence 47999999999999888743
No 141
>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=28.76 E-value=1.2e+02 Score=17.30 Aligned_cols=34 Identities=12% Similarity=0.206 Sum_probs=26.6
Q ss_pred CCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~ 50 (88)
.+..|.+...+-..++|.+..++++.=+.+.+..
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 5678888888789999999999987766665543
No 142
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.53 E-value=80 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.114 Sum_probs=19.7
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
...|..|+|+ +..|+.++|++.+
T Consensus 230 G~~Gd~IrVrN~~SgkvV~a~V~~ 253 (261)
T PRK06804 230 GRKGELIKVKNLSSGRVVTATVDG 253 (261)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4578999999 8999999999875
No 143
>PRK09961 exoaminopeptidase; Provisional
Probab=27.80 E-value=78 Score=23.81 Aligned_cols=23 Identities=13% Similarity=0.001 Sum_probs=20.0
Q ss_pred hhcCCCEEEEEEcCccEEEEEEE
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILV 36 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~ 36 (88)
+.+.+++|+|..++|+.+.|++.
T Consensus 90 ~~~~~~~v~i~~~~g~~i~Gvi~ 112 (344)
T PRK09961 90 AARQLQPVRITTREECKIPGLLN 112 (344)
T ss_pred cccCCCEEEEEeCCCCEeeEEEC
Confidence 45689999999999988999994
No 144
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.54 E-value=51 Score=23.94 Aligned_cols=15 Identities=40% Similarity=0.499 Sum_probs=13.7
Q ss_pred ccEEEEEEEEecCCc
Q psy6372 28 GHEYKGILVSTDGYM 42 (88)
Q Consensus 28 g~~~~G~L~~~D~~m 42 (88)
|.+|.|+|.++|+--
T Consensus 75 Ge~y~G~l~s~~~~G 89 (225)
T PF09883_consen 75 GETYVGTLISWDEDG 89 (225)
T ss_pred CceEEEEEEeecccc
Confidence 999999999999764
No 145
>PHA00446 hypothetical protein
Probab=27.43 E-value=52 Score=20.39 Aligned_cols=30 Identities=7% Similarity=-0.158 Sum_probs=23.1
Q ss_pred CCCCCCCCcHHHHhhcCCCEEEEEEcCccE
Q psy6372 1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHE 30 (88)
Q Consensus 1 m~~~~~~~p~~~L~~~i~k~V~V~L~~g~~ 30 (88)
||-....++++.--+.-+++|.|..+||+.
T Consensus 1 i~~~~nTIrlsDT~Dq~~RrVHINVRngKv 30 (89)
T PHA00446 1 IKFVANTIRLSDTADQWARRVHINVRNGKV 30 (89)
T ss_pred CCCccceeecCccHHhhhheEEEEeeCCeE
Confidence 455566677777777889999999999964
No 146
>PF13144 SAF_2: SAF-like
Probab=27.30 E-value=1.1e+02 Score=20.64 Aligned_cols=23 Identities=17% Similarity=0.170 Sum_probs=19.1
Q ss_pred hcCCCEEEEEEcC-ccEEEEEEEE
Q psy6372 15 LLTGKSVICKLKW-GHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~L~~-g~~~~G~L~~ 37 (88)
..+|..|+|+-.+ |+.++|++.+
T Consensus 167 G~~G~~I~V~N~~S~k~v~g~V~~ 190 (196)
T PF13144_consen 167 GALGDTIRVKNLSSGKIVQGRVIG 190 (196)
T ss_pred CCCCCEEEEEECCCCCEEEEEEec
Confidence 4579999999855 9999999875
No 147
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=27.29 E-value=1.7e+02 Score=18.60 Aligned_cols=33 Identities=30% Similarity=0.347 Sum_probs=26.4
Q ss_pred HHHhhcCCCEEEEEEcC-ccEEEEEEEEecCCcc
Q psy6372 11 PFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMN 43 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~-g~~~~G~L~~~D~~mN 43 (88)
+.-+.++|+.|.-+-++ |+.+.|++.-.-...-
T Consensus 39 ~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsG 72 (100)
T COG2451 39 EEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSG 72 (100)
T ss_pred HHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcc
Confidence 44577899998888888 9999999987765544
No 148
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=27.16 E-value=2.2e+02 Score=19.81 Aligned_cols=32 Identities=22% Similarity=0.180 Sum_probs=25.1
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCCc
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYM 42 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~m 42 (88)
.+|+.-.|..|.|-..+|..|.+++...++..
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~ 44 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKS 44 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSE
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcE
Confidence 35566689999999999999999999999764
No 149
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=26.92 E-value=92 Score=18.71 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=16.2
Q ss_pred ceEEEeCCcEEEEEcCCCC
Q psy6372 62 GEVLIRCNNILYIRGAEEG 80 (88)
Q Consensus 62 ~~v~IrG~~I~~I~~~d~~ 80 (88)
..++|+++.|.||.+..+.
T Consensus 48 r~~lVp~~~iaYVeiG~~~ 66 (74)
T PF11305_consen 48 RRVLVPAASIAYVEIGSEE 66 (74)
T ss_pred CEEEEECCcEEEEEEcCCC
Confidence 4789999999999987654
No 150
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=26.73 E-value=73 Score=18.71 Aligned_cols=23 Identities=17% Similarity=0.188 Sum_probs=18.8
Q ss_pred CCCEEEEEEcCccEEEEEEEEec
Q psy6372 17 TGKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 17 i~k~V~V~L~~g~~~~G~L~~~D 39 (88)
-..+|.|.|-||..+.+++.+-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~ 25 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKARE 25 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCC
Confidence 45689999999999999887544
No 151
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=26.12 E-value=1.2e+02 Score=23.79 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=22.6
Q ss_pred HhhcCCCEEEEEEc--Cc--cEEEEEEEEec
Q psy6372 13 LNLLTGKSVICKLK--WG--HEYKGILVSTD 39 (88)
Q Consensus 13 L~~~i~k~V~V~L~--~g--~~~~G~L~~~D 39 (88)
+.+++|++|.|.+. +| +.+.|.+.++.
T Consensus 42 ~~~llG~~v~l~i~~~~~~~r~f~GiVt~~~ 72 (513)
T TIGR03361 42 LEDLLGQPATLTLGRDGGGPRYFHGIVTRFE 72 (513)
T ss_pred HHHHcCCeEEEEEEeCCCceEEEEEEEEEEE
Confidence 67789999999995 23 77999999986
No 152
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=25.82 E-value=1.5e+02 Score=17.30 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=22.5
Q ss_pred CCCEEEEEEcC-c--cEEEEEEEEecCCcceE
Q psy6372 17 TGKSVICKLKW-G--HEYKGILVSTDGYMNCQ 45 (88)
Q Consensus 17 i~k~V~V~L~~-g--~~~~G~L~~~D~~mNlv 45 (88)
-+..|+|+.-+ | ..++|++..+|...+.+
T Consensus 41 ~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l 72 (92)
T PF08863_consen 41 ENQPVTITYYEDGYYQSVTGTIHKIDEINRTL 72 (92)
T ss_pred CCCEEEEEEEECCeeEEEEEEEEEEcCCCCEE
Confidence 47788888854 4 78999999999776544
No 153
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.27 E-value=1.7e+02 Score=21.65 Aligned_cols=31 Identities=19% Similarity=0.222 Sum_probs=25.3
Q ss_pred CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
..++.+.+.+|+.+.+.+.+.|...-+-+-.
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlk 125 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLK 125 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEE
Confidence 4678899999999999999999876555433
No 154
>PRK09864 putative peptidase; Provisional
Probab=25.00 E-value=1e+02 Score=23.58 Aligned_cols=25 Identities=16% Similarity=0.229 Sum_probs=20.7
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEe
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVST 38 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~ 38 (88)
+.+.+++|+|..++|..+.|++-.-
T Consensus 89 ~~l~~q~V~i~t~~g~~v~GVig~~ 113 (356)
T PRK09864 89 QSMLNHRVTIRTHKGVKIPGVIGSV 113 (356)
T ss_pred cccCCCEEEEEeCCCCEEEEEEeCC
Confidence 4578999999999997789998553
No 155
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=24.83 E-value=68 Score=18.65 Aligned_cols=22 Identities=18% Similarity=0.093 Sum_probs=18.4
Q ss_pred CCEEEEEEcCccEEEEEEEEec
Q psy6372 18 GKSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 18 ~k~V~V~L~~g~~~~G~L~~~D 39 (88)
..+|.|.|-||..+.+++..-|
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~ 25 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSD 25 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCC
Confidence 3689999999999999987644
No 156
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=24.31 E-value=1.1e+02 Score=17.53 Aligned_cols=21 Identities=19% Similarity=0.185 Sum_probs=17.3
Q ss_pred CEEEEEEcCccEEEEEEEEec
Q psy6372 19 KSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 19 k~V~V~L~~g~~~~G~L~~~D 39 (88)
.+|.|.|-||..+.+++..-|
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~ 23 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTH 23 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCC
Confidence 479999999999999876444
No 157
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=24.11 E-value=29 Score=18.44 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=9.8
Q ss_pred CCCCCcHHHHhhcC
Q psy6372 4 PLPCNPKPFLNLLT 17 (88)
Q Consensus 4 ~~~~~p~~~L~~~i 17 (88)
.+|..|+.||..++
T Consensus 24 ~rP~DPi~~La~~L 37 (42)
T PF05186_consen 24 ERPEDPIEFLAEYL 37 (42)
T ss_dssp H--SSHHHHHHHHH
T ss_pred HCCCChHHHHHHHH
Confidence 46899999998764
No 158
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=23.72 E-value=1.4e+02 Score=17.09 Aligned_cols=21 Identities=14% Similarity=0.186 Sum_probs=17.5
Q ss_pred CEEEEEEcCccEEEEEEEEec
Q psy6372 19 KSVICKLKWGHEYKGILVSTD 39 (88)
Q Consensus 19 k~V~V~L~~g~~~~G~L~~~D 39 (88)
.+|.|.|-||..++.++..-|
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~ 27 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSD 27 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTS
T ss_pred EEEEEECCCCCEEEEEECCcc
Confidence 478999999999999987544
No 159
>PRK09798 antitoxin MazE; Provisional
Probab=23.45 E-value=1.2e+02 Score=18.27 Aligned_cols=28 Identities=21% Similarity=0.203 Sum_probs=21.6
Q ss_pred CCCCCcHHHHhhc---CCCEEEEEEcCccEE
Q psy6372 4 PLPCNPKPFLNLL---TGKSVICKLKWGHEY 31 (88)
Q Consensus 4 ~~~~~p~~~L~~~---i~k~V~V~L~~g~~~ 31 (88)
...-.|..+|..+ .|..|.|+..+|+.+
T Consensus 13 ~~vRIPk~~l~~l~l~~g~~vei~v~~~~ii 43 (82)
T PRK09798 13 PAVRIPATLMQALNLNIDDEVKIDLVDGKLI 43 (82)
T ss_pred ceEEcCHHHHHHcCCCCCCEEEEEEECCEEE
Confidence 3445788888775 689999999988765
No 160
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=22.96 E-value=76 Score=21.86 Aligned_cols=19 Identities=21% Similarity=0.158 Sum_probs=16.5
Q ss_pred EEEEEEecCCcceEEcceE
Q psy6372 32 KGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 32 ~G~L~~~D~~mNlvL~d~~ 50 (88)
.|+|++.|.+.|---++..
T Consensus 48 ~G~lVG~D~~GNkYYE~~~ 66 (159)
T PLN02732 48 GATLVGVDKFGNKYYQKLG 66 (159)
T ss_pred CcEEEEecCCCCeeeecCC
Confidence 4999999999999887764
No 161
>PRK08158 type III secretion system protein SpaO; Validated
Probab=22.96 E-value=1.4e+02 Score=22.61 Aligned_cols=37 Identities=16% Similarity=0.050 Sum_probs=28.1
Q ss_pred HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAST 49 (88)
Q Consensus 13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~ 49 (88)
|....+.+|.|..++-...+|.|+.+|+.+=+.+.+.
T Consensus 259 L~~~~~~~V~I~vNg~lva~GELV~v~~~lGVrIt~i 295 (303)
T PRK08158 259 LPTNAELNVEIRANGALLGNGELVQMDDTLGVEIHEW 295 (303)
T ss_pred CCCCCCCceEEEECCEEEEEEEEEEECCEEEEEEEEE
Confidence 3456788888888888888899988888776666544
No 162
>PF01556 CTDII: DnaJ C terminal domain; InterPro: IPR002939 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. This domain consists of the C-terminal region of the DnaJ protein. The function of this domain is unknown. It is found associated with IPR001623 from INTERPRO and IPR001305 from INTERPRO. ; GO: 0051082 unfolded protein binding, 0006457 protein folding; PDB: 2Q2G_A 2QLD_A 3AGX_A 3AGZ_A 3AGY_A 3I38_J 3LZ8_B 2B26_B 1C3G_A 1XAO_B ....
Probab=22.61 E-value=47 Score=19.47 Aligned_cols=25 Identities=20% Similarity=0.153 Sum_probs=17.5
Q ss_pred cHHHHhhcCCCEEEEEEcCccEEEE
Q psy6372 9 PKPFLNLLTGKSVICKLKWGHEYKG 33 (88)
Q Consensus 9 p~~~L~~~i~k~V~V~L~~g~~~~G 33 (88)
++++..++.|..+.|.+-+|+.++=
T Consensus 7 ~I~l~~al~G~~i~i~~l~g~~~~i 31 (81)
T PF01556_consen 7 PISLKEALLGGTISIPTLDGKTIKI 31 (81)
T ss_dssp EEEHHHHHH-EEEEEE-TTS-EEEE
T ss_pred EeCHHHHhCCCEEEEECCCCCEEEE
Confidence 5678888999999999998866553
No 163
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=22.35 E-value=1.1e+02 Score=17.85 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=19.2
Q ss_pred EEEEEEEEecC-CcceEEcceEEE
Q psy6372 30 EYKGILVSTDG-YMNCQLASTEEI 52 (88)
Q Consensus 30 ~~~G~L~~~D~-~mNlvL~d~~e~ 52 (88)
...|++.++|. .+-|+|+|-.-+
T Consensus 4 ~veG~I~~id~~~~titLdDGksy 27 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSY 27 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEE
Confidence 46899999994 588999998865
No 164
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=22.35 E-value=1.3e+02 Score=21.42 Aligned_cols=23 Identities=4% Similarity=-0.130 Sum_probs=19.8
Q ss_pred cCccEEEEEEEEecCCcceEEcc
Q psy6372 26 KWGHEYKGILVSTDGYMNCQLAS 48 (88)
Q Consensus 26 ~~g~~~~G~L~~~D~~mNlvL~d 48 (88)
.++..+.|+..++|+...|+++.
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~ 231 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRR 231 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEE
Confidence 36678899999999999999864
No 165
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.28 E-value=1.2e+02 Score=23.08 Aligned_cols=23 Identities=17% Similarity=0.120 Sum_probs=19.1
Q ss_pred hcCCCEEEEE-EcCccEEEEEEEE
Q psy6372 15 LLTGKSVICK-LKWGHEYKGILVS 37 (88)
Q Consensus 15 ~~i~k~V~V~-L~~g~~~~G~L~~ 37 (88)
..+|..|+|. +..|+.++|++.+
T Consensus 286 G~~Gd~IrV~N~~S~kiv~g~V~g 309 (338)
T PRK12786 286 GAEGDVVRVLNLQSKRTVTGTVTG 309 (338)
T ss_pred cCCCCEEEEEECCCCCEEEEEEec
Confidence 3578899996 8899999999875
No 166
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=22.16 E-value=2.1e+02 Score=20.15 Aligned_cols=31 Identities=19% Similarity=0.094 Sum_probs=26.4
Q ss_pred HHHhhcCCCEEEEEEcCccEEEEEEEEecCC
Q psy6372 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGY 41 (88)
Q Consensus 11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~ 41 (88)
.+|+.-.|..|.|...+|..|.|++..+|..
T Consensus 26 ~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~ 56 (234)
T PRK11713 26 RVLRLKEGDELRLFDGDGGEYLAEITEIGKK 56 (234)
T ss_pred hhccCCCCCEEEEEeCCCCEEEEEEEEecCc
Confidence 4566678999999988999999999999863
No 167
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=21.94 E-value=54 Score=21.38 Aligned_cols=19 Identities=26% Similarity=0.308 Sum_probs=16.4
Q ss_pred EEEEEEecCCcceEEcceE
Q psy6372 32 KGILVSTDGYMNCQLASTE 50 (88)
Q Consensus 32 ~G~L~~~D~~mNlvL~d~~ 50 (88)
.|+|++.|.+.|---++..
T Consensus 9 ~g~lVG~D~~GNkYYE~~~ 27 (115)
T PLN03095 9 AGRLVGEDEFGNKYYENPS 27 (115)
T ss_pred cceEeEEcCCCCeeeEcCC
Confidence 7999999999999887653
No 168
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=21.81 E-value=1.5e+02 Score=21.87 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=21.0
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEEecC
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVSTDG 40 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~ 40 (88)
+.+.+++|+|..++| .+.|++-.--.
T Consensus 49 ~~l~gq~v~i~~~~g-~i~Gvig~~~~ 74 (292)
T PF05343_consen 49 RVLPGQRVRIHTRDG-DIPGVIGSKPP 74 (292)
T ss_dssp GGTTTEEEEEEETTE-EEEEEEEE--G
T ss_pred cccCCCEEEEEcCCc-EEEEEEcCCCC
Confidence 457899999999999 99999966533
No 169
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=21.46 E-value=1.3e+02 Score=15.54 Aligned_cols=18 Identities=28% Similarity=0.224 Sum_probs=13.5
Q ss_pred hcCCCEEEEEEcCccEEE
Q psy6372 15 LLTGKSVICKLKWGHEYK 32 (88)
Q Consensus 15 ~~i~k~V~V~L~~g~~~~ 32 (88)
+.-|..|+|++.+|++.+
T Consensus 20 ~~~g~~vtV~~~~G~~~t 37 (42)
T PF02736_consen 20 EEEGDKVTVKTEDGKEVT 37 (42)
T ss_dssp EEESSEEEEEETTTEEEE
T ss_pred EEcCCEEEEEECCCCEEE
Confidence 445788999999987643
No 170
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=21.02 E-value=1.1e+02 Score=20.43 Aligned_cols=24 Identities=21% Similarity=0.142 Sum_probs=18.5
Q ss_pred hhcCCCEEEEEEcCccEEEEEEEE
Q psy6372 14 NLLTGKSVICKLKWGHEYKGILVS 37 (88)
Q Consensus 14 ~~~i~k~V~V~L~~g~~~~G~L~~ 37 (88)
++++-|-++|.|.||++++.-+=+
T Consensus 52 NSAlRK~~RVrL~NG~~VtAyiPg 75 (129)
T COG0048 52 NSALRKVARVRLINGKEVTAYIPG 75 (129)
T ss_pred ChhhheeEEEEeeCCcEEEEEcCC
Confidence 355667899999999998876543
No 171
>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=20.19 E-value=2.9e+02 Score=19.17 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=28.8
Q ss_pred CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcc
Q psy6372 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMN 43 (88)
Q Consensus 8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mN 43 (88)
.+..+=++++||.+.-.+. +..+.|.++....|.-
T Consensus 5 ~~~~vA~~LLGk~Lv~~~~-~~~~~grIvEtEAY~G 39 (179)
T cd00540 5 DTVEVARDLLGKVLVRRLP-GGILSGRIVETEAYLG 39 (179)
T ss_pred CHHHHHHHhCCCEEEEECC-CCEEEEEEEEEeccCC
Confidence 4567788999999987775 6689999999998853
Done!