Query psy5557
Match_columns 213
No_of_seqs 120 out of 1171
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 20:34:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5557.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5557hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01729 LSm7 The eukaryotic Sm 99.9 1.5E-22 3.2E-27 151.4 9.2 74 106-179 2-80 (81)
2 cd01728 LSm1 The eukaryotic Sm 99.9 5.9E-22 1.3E-26 146.6 9.8 71 108-178 4-74 (74)
3 cd01727 LSm8 The eukaryotic Sm 99.9 6.5E-22 1.4E-26 144.9 9.2 72 109-180 2-74 (74)
4 cd01719 Sm_G The eukaryotic Sm 99.9 2.2E-21 4.8E-26 142.2 8.9 69 109-180 3-71 (72)
5 cd01732 LSm5 The eukaryotic Sm 99.9 3.8E-21 8.3E-26 142.7 9.9 71 107-177 4-74 (76)
6 cd01717 Sm_B The eukaryotic Sm 99.8 3.4E-21 7.4E-26 142.4 8.9 68 109-176 3-77 (79)
7 cd01730 LSm3 The eukaryotic Sm 99.8 3.4E-21 7.4E-26 143.6 8.6 72 106-177 1-82 (82)
8 cd01731 archaeal_Sm1 The archa 99.8 6.2E-21 1.3E-25 137.1 8.5 67 108-177 2-68 (68)
9 PRK00737 small nuclear ribonuc 99.8 2.3E-20 5E-25 136.2 8.8 69 106-177 4-72 (72)
10 cd06168 LSm9 The eukaryotic Sm 99.8 1.2E-19 2.6E-24 134.6 9.5 69 108-176 2-73 (75)
11 PF01423 LSM: LSM domain ; In 99.8 2.3E-19 5E-24 126.6 8.8 67 109-177 1-67 (67)
12 cd01726 LSm6 The eukaryotic Sm 99.8 1.7E-19 3.7E-24 129.7 8.1 67 107-176 1-67 (67)
13 cd01722 Sm_F The eukaryotic Sm 99.8 2.3E-19 5E-24 129.5 8.5 67 107-176 2-68 (68)
14 smart00651 Sm snRNP Sm protein 99.8 3.2E-19 6.9E-24 125.7 8.7 66 110-177 2-67 (67)
15 cd01720 Sm_D2 The eukaryotic S 99.8 3.9E-19 8.4E-24 135.5 9.3 71 107-177 3-85 (87)
16 cd01718 Sm_E The eukaryotic Sm 99.8 8.5E-19 1.8E-23 131.8 8.6 70 106-177 6-79 (79)
17 COG1958 LSM1 Small nuclear rib 99.8 1.8E-18 3.8E-23 127.6 9.0 71 107-177 8-79 (79)
18 cd00600 Sm_like The eukaryotic 99.7 7.4E-18 1.6E-22 116.9 8.4 63 111-176 1-63 (63)
19 cd01723 LSm4 The eukaryotic Sm 99.7 1E-17 2.3E-22 123.3 8.6 73 107-181 2-74 (76)
20 cd01721 Sm_D3 The eukaryotic S 99.7 2.1E-17 4.6E-22 120.2 8.7 69 108-179 2-70 (70)
21 KOG1780|consensus 99.7 7.4E-18 1.6E-22 126.2 5.7 69 109-180 7-75 (77)
22 cd01724 Sm_D1 The eukaryotic S 99.7 5.7E-17 1.2E-21 123.8 10.0 73 108-183 3-75 (90)
23 KOG1782|consensus 99.7 3.4E-18 7.5E-23 138.3 0.1 74 110-183 13-86 (129)
24 KOG1784|consensus 99.7 2.2E-17 4.7E-22 128.0 4.4 85 109-193 3-88 (96)
25 PTZ00138 small nuclear ribonuc 99.7 1.9E-16 4.1E-21 121.6 8.3 75 102-178 10-88 (89)
26 cd01733 LSm10 The eukaryotic S 99.7 3E-16 6.4E-21 117.0 8.9 75 100-177 3-77 (78)
27 cd01725 LSm2 The eukaryotic Sm 99.7 4.3E-16 9.4E-21 116.4 8.9 77 108-185 3-79 (81)
28 KOG1781|consensus 99.6 2E-17 4.3E-22 129.9 -0.0 81 102-182 13-98 (108)
29 KOG3482|consensus 99.6 6.7E-16 1.5E-20 115.7 5.8 70 107-179 9-78 (79)
30 KOG3460|consensus 99.5 2.8E-15 6.1E-20 114.9 1.3 74 105-178 4-87 (91)
31 KOG3168|consensus 99.5 1.6E-14 3.5E-19 122.2 1.8 74 108-181 6-86 (177)
32 KOG1783|consensus 99.4 1.6E-14 3.5E-19 108.2 0.7 71 105-178 5-75 (77)
33 KOG1775|consensus 99.4 1.8E-13 4E-18 103.6 3.6 70 109-178 10-79 (84)
34 KOG3293|consensus 99.2 5.4E-11 1.2E-15 96.9 5.8 77 107-185 3-79 (134)
35 KOG1774|consensus 99.1 1.2E-10 2.6E-15 89.2 4.9 71 107-179 17-87 (88)
36 KOG3448|consensus 98.9 3E-09 6.6E-14 82.6 5.5 76 109-186 5-81 (96)
37 KOG3428|consensus 98.6 3.8E-07 8.3E-12 72.9 9.1 70 108-181 4-73 (109)
38 KOG3172|consensus 98.5 3.1E-07 6.8E-12 73.7 7.8 76 110-188 9-84 (119)
39 KOG3459|consensus 98.0 8.7E-07 1.9E-11 71.2 -0.6 61 116-176 36-106 (114)
40 PF14438 SM-ATX: Ataxin 2 SM d 97.8 3.6E-05 7.8E-10 56.2 5.3 64 110-173 6-76 (77)
41 cd01739 LSm11_C The eukaryotic 97.4 0.00011 2.3E-09 54.5 2.8 36 117-152 9-48 (66)
42 PF02237 BPL_C: Biotin protein 96.9 0.0047 1E-07 41.8 6.2 48 114-168 1-48 (48)
43 PF11095 Gemin7: Gem-associate 96.5 0.021 4.6E-07 43.7 8.0 62 107-176 15-77 (80)
44 PF12701 LSM14: Scd6-like Sm d 96.3 0.028 6.1E-07 43.9 8.0 71 112-182 4-81 (96)
45 PF11600 CAF-1_p150: Chromatin 96.0 0.11 2.4E-06 44.9 11.2 12 108-119 179-190 (216)
46 PF06372 Gemin6: Gemin6 protei 95.8 0.028 6E-07 48.0 6.5 63 109-181 10-73 (166)
47 cd01716 Hfq Hfq, an abundant, 95.0 0.038 8.2E-07 40.3 4.1 31 116-146 11-41 (61)
48 TIGR02383 Hfq RNA chaperone Hf 94.8 0.047 1E-06 39.9 4.0 31 116-146 15-45 (61)
49 PRK00395 hfq RNA-binding prote 94.5 0.057 1.2E-06 41.3 4.0 33 115-147 18-50 (79)
50 cd01736 LSm14_N LSm14 (also kn 94.4 0.19 4.2E-06 38.0 6.6 63 112-174 2-72 (74)
51 cd01735 LSm12_N LSm12 belongs 93.9 0.13 2.7E-06 37.5 4.7 34 114-147 4-37 (61)
52 PRK14638 hypothetical protein; 92.7 0.29 6.2E-06 40.7 5.5 36 109-145 93-128 (150)
53 COG1923 Hfq Uncharacterized ho 91.8 0.26 5.6E-06 37.7 3.8 32 115-146 18-49 (77)
54 PRK14639 hypothetical protein; 91.7 0.45 9.7E-06 39.1 5.5 35 109-144 81-115 (140)
55 PRK02001 hypothetical protein; 90.7 0.63 1.4E-05 39.0 5.5 35 109-144 83-117 (152)
56 TIGR02794 tolA_full TolA prote 89.4 1.8 4E-05 40.4 8.1 14 134-147 259-272 (346)
57 cd01734 YlxS_C YxlS is a Bacil 89.3 1.1 2.5E-05 33.2 5.4 35 109-144 18-56 (83)
58 PF10842 DUF2642: Protein of u 89.0 2.5 5.3E-05 31.3 6.9 53 109-177 14-66 (66)
59 PRK14091 RNA-binding protein H 88.9 0.58 1.3E-05 40.2 4.0 33 115-147 103-135 (165)
60 PRK14644 hypothetical protein; 88.5 1.2 2.5E-05 36.7 5.4 35 110-145 79-117 (136)
61 PRK14091 RNA-binding protein H 88.2 0.68 1.5E-05 39.8 4.0 32 116-147 24-55 (165)
62 PRK14640 hypothetical protein; 87.9 1.4 3E-05 36.6 5.6 36 109-145 90-129 (152)
63 PRK14633 hypothetical protein; 87.6 1.5 3.3E-05 36.4 5.6 37 108-145 86-126 (150)
64 PF11600 CAF-1_p150: Chromatin 87.0 19 0.00042 31.1 12.5 12 104-115 179-190 (216)
65 PF02576 DUF150: Uncharacteris 86.5 1.6 3.5E-05 35.1 5.1 36 108-144 79-118 (141)
66 PRK06955 biotin--protein ligas 86.2 2.5 5.3E-05 38.2 6.7 37 110-146 243-279 (300)
67 PRK14636 hypothetical protein; 86.1 1.8 4E-05 37.0 5.5 35 109-144 91-129 (176)
68 PRK14642 hypothetical protein; 85.5 2.1 4.6E-05 37.6 5.7 36 108-144 92-140 (197)
69 PRK14632 hypothetical protein; 85.1 2.2 4.8E-05 36.2 5.5 36 109-145 91-133 (172)
70 PF03614 Flag1_repress: Repres 84.8 2 4.4E-05 36.9 5.1 37 111-147 24-60 (165)
71 PRK14645 hypothetical protein; 84.6 2.5 5.4E-05 35.4 5.5 34 109-144 95-128 (154)
72 PRK11886 bifunctional biotin-- 84.5 2.9 6.3E-05 37.5 6.3 35 110-145 266-300 (319)
73 TIGR00121 birA_ligase birA, bi 84.2 3.6 7.9E-05 35.5 6.5 37 108-145 185-221 (237)
74 PRK14647 hypothetical protein; 83.0 3.3 7.1E-05 34.6 5.6 35 109-144 92-135 (159)
75 PRK14634 hypothetical protein; 82.3 3.5 7.5E-05 34.5 5.5 36 108-144 92-131 (155)
76 PRK00092 ribosome maturation p 82.1 3.8 8.3E-05 33.7 5.6 30 109-138 91-124 (154)
77 PRK14646 hypothetical protein; 82.1 3.6 7.7E-05 34.4 5.5 35 109-144 93-131 (155)
78 KOG2412|consensus 81.9 10 0.00022 38.3 9.3 40 35-74 211-251 (591)
79 PRK08330 biotin--protein ligas 81.3 6.4 0.00014 34.0 7.0 37 110-147 182-219 (236)
80 PRK14643 hypothetical protein; 80.9 3.7 8.1E-05 34.7 5.2 31 109-139 97-131 (164)
81 COG0340 BirA Biotin-(acetyl-Co 80.9 5.3 0.00012 35.4 6.4 41 107-147 181-221 (238)
82 COG0779 Uncharacterized protei 80.6 4.5 9.9E-05 34.1 5.6 33 108-140 91-127 (153)
83 PRK14631 hypothetical protein; 80.2 4.8 0.00011 34.4 5.7 36 108-144 109-150 (174)
84 KOG1144|consensus 78.8 12 0.00027 39.6 9.0 18 65-82 238-255 (1064)
85 KOG3054|consensus 78.1 17 0.00037 33.8 8.9 14 11-24 99-112 (299)
86 PRK13325 bifunctional biotin-- 78.0 5.7 0.00012 39.6 6.3 38 109-146 271-308 (592)
87 PRK14637 hypothetical protein; 75.8 6.7 0.00015 32.7 5.3 37 108-145 90-127 (151)
88 PF14153 Spore_coat_CotO: Spor 75.3 12 0.00026 32.5 6.9 63 103-178 118-183 (185)
89 KOG1073|consensus 74.3 12 0.00026 35.8 7.2 71 111-181 4-82 (361)
90 KOG0163|consensus 74.1 41 0.0009 36.0 11.3 17 100-116 1005-1021(1259)
91 PTZ00275 biotin-acetyl-CoA-car 73.1 7.7 0.00017 35.0 5.3 37 109-146 230-266 (285)
92 PTZ00266 NIMA-related protein 72.2 48 0.001 35.7 11.5 10 195-204 646-655 (1021)
93 PRK14641 hypothetical protein; 71.4 7.1 0.00015 33.5 4.5 29 109-137 97-129 (173)
94 KOG1144|consensus 70.4 16 0.00034 38.8 7.4 8 119-126 308-315 (1064)
95 PRK10898 serine endoprotease; 70.2 16 0.00034 33.8 6.8 31 117-147 102-132 (353)
96 PF05262 Borrelia_P83: Borreli 69.8 1.2E+02 0.0027 30.1 15.8 25 117-141 360-385 (489)
97 PRK09510 tolA cell envelope in 66.2 96 0.0021 30.0 11.3 12 134-145 300-311 (387)
98 PRK10942 serine endoprotease; 66.0 17 0.00037 35.1 6.3 32 116-147 135-166 (473)
99 PF14563 DUF4444: Domain of un 65.0 7.6 0.00016 26.7 2.7 20 129-148 10-29 (42)
100 PRK10139 serine endoprotease; 64.6 25 0.00053 33.8 7.1 31 117-147 115-145 (455)
101 TIGR02038 protease_degS peripl 60.9 14 0.0003 34.0 4.6 31 117-147 102-132 (351)
102 PRK14630 hypothetical protein; 60.4 21 0.00045 29.5 5.1 34 109-144 90-123 (143)
103 KOG3382|consensus 60.4 4.5 9.8E-05 34.2 1.2 25 123-147 39-63 (151)
104 PF05071 NDUFA12: NADH ubiquin 60.2 4.9 0.00011 31.5 1.3 17 131-147 1-17 (105)
105 PRK14635 hypothetical protein; 58.0 26 0.00055 29.4 5.3 35 109-144 92-131 (162)
106 KOG3054|consensus 57.1 36 0.00077 31.7 6.4 9 163-171 246-254 (299)
107 TIGR02603 CxxCH_TIGR02603 puta 56.4 20 0.00043 28.6 4.2 28 118-146 59-86 (133)
108 KOG3634|consensus 56.4 41 0.00088 32.3 6.8 48 90-145 151-198 (361)
109 PF11607 DUF3247: Protein of u 54.0 25 0.00054 28.2 4.3 60 116-180 28-94 (101)
110 PF07073 ROF: Modulator of Rho 52.8 17 0.00036 27.7 3.1 63 112-184 13-75 (80)
111 PRK08477 biotin--protein ligas 51.5 29 0.00062 30.3 4.7 36 111-147 170-205 (211)
112 PF03614 Flag1_repress: Repres 50.2 17 0.00036 31.4 3.0 24 115-138 119-142 (165)
113 TIGR02037 degP_htrA_DO peripla 50.2 26 0.00056 32.8 4.5 31 117-147 82-112 (428)
114 PF08863 YolD: YolD-like prote 49.2 71 0.0015 23.1 5.9 42 103-144 27-73 (92)
115 PF03122 Herpes_MCP: Herpes vi 48.5 5.8 0.00013 43.5 0.0 56 118-174 249-304 (1354)
116 PRK09618 flgD flagellar basal 48.4 68 0.0015 26.9 6.3 29 109-137 85-113 (142)
117 TIGR02794 tolA_full TolA prote 47.2 2.4E+02 0.0053 26.5 10.4 7 110-116 233-239 (346)
118 PLN02732 Probable NADH dehydro 46.8 14 0.0003 31.7 2.0 17 131-147 49-65 (159)
119 PF07946 DUF1682: Protein of u 45.7 1.2E+02 0.0026 27.8 8.0 8 84-91 307-314 (321)
120 PF07317 YcgR: Flagellar regul 42.6 62 0.0014 25.0 4.9 69 104-181 7-77 (108)
121 KOG0163|consensus 41.3 1.8E+02 0.0039 31.5 9.2 12 163-174 1044-1055(1259)
122 KOG0544|consensus 38.5 31 0.00067 27.9 2.7 16 195-210 55-70 (108)
123 COG4942 Membrane-bound metallo 38.1 39 0.00085 33.0 3.8 16 161-176 376-391 (420)
124 PF05085 DUF685: Protein of un 37.9 1.8E+02 0.004 27.0 7.8 42 112-153 165-206 (265)
125 PF06257 DUF1021: Protein of u 37.5 91 0.002 23.7 4.9 39 104-144 5-47 (76)
126 PF07202 Tcp10_C: T-complex pr 37.2 35 0.00076 29.4 3.0 34 113-146 141-178 (179)
127 PTZ00276 biotin/lipoate protei 37.2 60 0.0013 28.5 4.6 24 124-147 209-232 (245)
128 PF01887 SAM_adeno_trans: S-ad 36.7 42 0.00091 30.2 3.6 20 128-147 169-188 (258)
129 PRK06630 hypothetical protein; 35.6 19 0.00041 28.9 1.0 19 129-147 11-29 (99)
130 smart00333 TUDOR Tudor domain. 34.3 1.1E+02 0.0024 20.1 4.5 25 115-139 5-29 (57)
131 PRK11625 Rho-binding antitermi 33.9 1.7E+02 0.0038 22.5 6.0 52 114-176 21-72 (84)
132 KOG3168|consensus 33.7 1.1E+02 0.0024 26.8 5.5 76 108-183 42-126 (177)
133 COG0094 RplE Ribosomal protein 32.4 16 0.00035 31.9 0.2 63 113-180 98-162 (180)
134 PLN03095 NADH:ubiquinone oxido 31.7 25 0.00055 28.6 1.2 19 129-147 8-26 (115)
135 PRK11911 flgD flagellar basal 30.8 98 0.0021 26.0 4.6 27 112-138 89-115 (140)
136 CHL00078 rpl5 ribosomal protei 29.5 16 0.00035 31.5 -0.3 67 111-181 97-164 (181)
137 COG5439 Uncharacterized conser 29.3 19 0.0004 29.2 0.1 73 116-196 7-92 (112)
138 PF08830 DUF1806: Protein of u 29.3 1.9E+02 0.0042 23.8 5.8 24 105-128 6-31 (114)
139 PHA00672 hypothetical protein 27.2 1.9E+02 0.004 24.7 5.6 27 121-149 52-78 (152)
140 PF12869 tRNA_anti-like: tRNA_ 25.3 57 0.0012 25.4 2.2 20 128-147 124-143 (144)
141 PRK11637 AmiB activator; Provi 25.2 1E+02 0.0022 29.0 4.1 17 161-177 384-400 (428)
142 COG0265 DegQ Trypsin-like seri 24.9 1.1E+02 0.0025 27.5 4.3 32 116-147 95-126 (347)
143 PF05735 TSP_C: Thrombospondin 24.9 1.4E+02 0.003 26.6 4.6 31 118-148 4-41 (201)
144 PRK05163 rpsL 30S ribosomal pr 24.6 83 0.0018 26.1 3.1 26 112-137 46-71 (124)
145 PRK00010 rplE 50S ribosomal pr 23.8 19 0.00042 30.9 -0.8 67 111-181 96-163 (179)
146 PRK08183 NADH dehydrogenase; V 23.7 41 0.0009 28.0 1.1 18 130-147 25-42 (133)
147 PF14485 DUF4431: Domain of un 23.6 1.1E+02 0.0025 21.0 3.1 36 105-145 8-43 (48)
148 COG4466 Veg Uncharacterized pr 23.1 1.1E+02 0.0024 23.7 3.3 26 103-128 6-31 (80)
149 KOG4401|consensus 22.7 1E+02 0.0023 27.1 3.5 35 114-148 9-43 (184)
150 PF11743 DUF3301: Protein of u 22.5 1.8E+02 0.0039 22.4 4.4 41 136-177 54-94 (97)
151 PF12945 YcgR_2: Flagellar pro 22.3 2E+02 0.0043 20.2 4.4 32 115-146 3-38 (87)
152 cd01772 SAKS1_UBX SAKS1-like U 22.3 65 0.0014 23.5 1.9 25 114-138 2-26 (79)
153 cd04479 RPA3 RPA3: A subfamily 22.2 1.8E+02 0.0039 22.3 4.4 23 109-139 8-30 (101)
154 PF13365 Trypsin_2: Trypsin-li 22.0 3E+02 0.0065 19.5 6.4 33 115-147 29-64 (120)
No 1
>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=99.88 E-value=1.5e-22 Score=151.38 Aligned_cols=74 Identities=26% Similarity=0.326 Sum_probs=65.1
Q ss_pred HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-c----cceeccceeeeecCcEEEEEeec
Q psy5557 106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-Q----YGDIPRGIFIIRGENVVLMGEVV 179 (213)
Q Consensus 106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-~----~~er~LGlVlIRGnnIV~I~~iD 179 (213)
|....|.+++|++|+|.|+|||.|.|+|+|||+||||||++|+|+++.++ . ...+.+|+++|||+||++|+++|
T Consensus 2 ~~~~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~ 80 (81)
T cd01729 2 ESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD 80 (81)
T ss_pred cchhhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence 45677999999999999999999999999999999999999999986432 1 13567999999999999999775
No 2
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=5.9e-22 Score=146.58 Aligned_cols=71 Identities=58% Similarity=0.949 Sum_probs=64.7
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i 178 (213)
...|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||+|+++.++.+..+++|+++||||||++|+.+
T Consensus 4 ~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~~ 74 (74)
T cd01728 4 TASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGEI 74 (74)
T ss_pred hHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEcC
Confidence 56799999999999999999999999999999999999999998765545578899999999999999863
No 3
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.87 E-value=6.5e-22 Score=144.85 Aligned_cols=72 Identities=26% Similarity=0.504 Sum_probs=64.1
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC-CccceeccceeeeecCcEEEEEeecc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG-NQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~-n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
..|..|+|++|+|+|+||+.|.|+|.|||+||||||++|+|++... ..+..+.+|+++|||+||++|+++|.
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 4689999999999999999999999999999999999999987543 23346689999999999999999874
No 4
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=2.2e-21 Score=142.24 Aligned_cols=69 Identities=28% Similarity=0.454 Sum_probs=62.5
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
.+|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||.|++. ++ ..+.+|.++|||+||++|+++|.
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~-~~--~~~~lg~v~IRG~~I~~i~~~~~ 71 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNS-GG--EKNNIGMVVIRGNSIVMLEALER 71 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEcc-CC--ceeEeceEEECCCEEEEEEcccc
Confidence 57999999999999999999999999999999999999999863 22 25678999999999999999874
No 5
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=3.8e-21 Score=142.73 Aligned_cols=71 Identities=13% Similarity=0.156 Sum_probs=62.9
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
+.+.|..++|++|+|.|+||+.|.|+|.|||+||||||+||.|++...+....+.+|.+|||||||++|++
T Consensus 4 P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p 74 (76)
T cd01732 4 PLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP 74 (76)
T ss_pred hHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence 46789999999999999999999999999999999999999999854432235679999999999999986
No 6
>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=3.4e-21 Score=142.39 Aligned_cols=68 Identities=26% Similarity=0.335 Sum_probs=60.8
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-------ccceeccceeeeecCcEEEEE
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-------~~~er~LGlVlIRGnnIV~I~ 176 (213)
+.|..|+|++|+|.|+|||.|.|+|.|||+||||||+||.|+++... ....+++|++||||+||++|+
T Consensus 3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~ 77 (79)
T cd01717 3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMT 77 (79)
T ss_pred chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEE
Confidence 67999999999999999999999999999999999999999875432 123578999999999999997
No 7
>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=99.85 E-value=3.4e-21 Score=143.64 Aligned_cols=72 Identities=21% Similarity=0.250 Sum_probs=62.5
Q ss_pred HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----------ccceeccceeeeecCcEEEE
Q psy5557 106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----------QYGDIPRGIFIIRGENVVLM 175 (213)
Q Consensus 106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----------~~~er~LGlVlIRGnnIV~I 175 (213)
++...|..+++++|+|.|+|||.|.|+|.|||+||||||+||.|+++... ....+.+|++||||+||++|
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 35678899999999999999999999999999999999999999985421 11256899999999999999
Q ss_pred Ee
Q psy5557 176 GE 177 (213)
Q Consensus 176 ~~ 177 (213)
++
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 74
No 8
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.84 E-value=6.2e-21 Score=137.10 Aligned_cols=67 Identities=25% Similarity=0.261 Sum_probs=60.8
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
...|..++|++|+|.|+||+.|.|+|.|||+||||+|+||+|++..+ ..+.+|.++|||+||++|++
T Consensus 2 ~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 2 LDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGE---PVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred hHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCC---eEeEcCcEEEeCCEEEEEcC
Confidence 57899999999999999999999999999999999999999986533 25679999999999999974
No 9
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.83 E-value=2.3e-20 Score=136.19 Aligned_cols=69 Identities=26% Similarity=0.252 Sum_probs=61.2
Q ss_pred HHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 106 EKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 106 E~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
-+...|..++|++|.|.|+||+.|.|+|.|||+||||+|+||.|++. +. ..+.+|.++|||+||++|++
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~--~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-GE--VVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcC-CC--eEeEcCcEEEeCCEEEEEcC
Confidence 36789999999999999999999999999999999999999999753 22 24679999999999999964
No 10
>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=1.2e-19 Score=134.57 Aligned_cols=69 Identities=20% Similarity=0.247 Sum_probs=61.8
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC---ccceeccceeeeecCcEEEEE
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN---QYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n---~~~er~LGlVlIRGnnIV~I~ 176 (213)
.+.|..|||++|+|.|+|||.|.|+|.|||+||||||+||.|++.... ....+.+|+++|||++|++|.
T Consensus 2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~ 73 (75)
T cd06168 2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIE 73 (75)
T ss_pred HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEE
Confidence 367999999999999999999999999999999999999999986432 234778999999999999997
No 11
>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=99.80 E-value=2.3e-19 Score=126.64 Aligned_cols=67 Identities=31% Similarity=0.371 Sum_probs=60.6
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
++|..++|++|+|.|+||++|.|+|.|||+||||+|.||.++...+. ..+++|.+||||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~--~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGP--EKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTES--EEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCC--cEeECcEEEEECCEEEEEEC
Confidence 57999999999999999999999999999999999999999865432 36789999999999999975
No 12
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.80 E-value=1.7e-19 Score=129.66 Aligned_cols=67 Identities=24% Similarity=0.258 Sum_probs=59.0
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~ 176 (213)
+..+|..++|++|.|.|+||+.|.|+|.|||+||||+|+||.+... +. ....+|.++|||++|++|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~-~~--~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVN-GQ--LKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeC-Cc--eeeEeCCEEEECCEEEEEC
Confidence 3578999999999999999999999999999999999999988643 22 2457899999999999984
No 13
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.80 E-value=2.3e-19 Score=129.50 Aligned_cols=67 Identities=27% Similarity=0.232 Sum_probs=59.4
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~ 176 (213)
+...|..++|++|+|.|+||++|.|+|.|||+||||+|+||.++.. ++ ....+|.++|||+||++|.
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~-~~--~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-GK--STGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeC-Cc--cccCcCcEEEECCEEEEEC
Confidence 4678999999999999999999999999999999999999998753 22 2457899999999999983
No 14
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.80 E-value=3.2e-19 Score=125.66 Aligned_cols=66 Identities=27% Similarity=0.316 Sum_probs=59.6
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
+|.+++|++|+|.|+||+.|.|+|.|||+||||+|+||.++...+ ...+.+|.++|||++|++|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~--~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--EKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCC--cEEeEeCCEEEcCCEEEEEeC
Confidence 689999999999999999999999999999999999999987542 236789999999999999973
No 15
>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=99.79 E-value=3.9e-19 Score=135.46 Aligned_cols=71 Identities=20% Similarity=0.225 Sum_probs=60.7
Q ss_pred HHHHHHhhc--CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----------ccceeccceeeeecCcEEE
Q psy5557 107 KKNKKAEEQ--NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----------QYGDIPRGIFIIRGENVVL 174 (213)
Q Consensus 107 ~~~~L~~~L--gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----------~~~er~LGlVlIRGnnIV~ 174 (213)
+...|...+ +++|+|.|++|+.|.|+|.|||.||||+|+||.|.+.... ....+++|.||||||||++
T Consensus 3 Pl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~Vv~ 82 (87)
T cd01720 3 PLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSVIL 82 (87)
T ss_pred hHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEEEE
Confidence 466788887 8999999999999999999999999999999999875422 0124578999999999999
Q ss_pred EEe
Q psy5557 175 MGE 177 (213)
Q Consensus 175 I~~ 177 (213)
|++
T Consensus 83 Is~ 85 (87)
T cd01720 83 VLR 85 (87)
T ss_pred Eec
Confidence 975
No 16
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=8.5e-19 Score=131.80 Aligned_cols=70 Identities=19% Similarity=0.272 Sum_probs=59.3
Q ss_pred HHHHHHHhhcCC--eEEEEec--CCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 106 EKKNKKAEEQNR--QQGLYPN--QKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 106 E~~~~L~~~LgK--rV~V~Lk--DGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
-+...|.+|+++ +|.|.|. +|+.|.|+|.|||+||||||+||+|++..+. ..+.+|.++||||||++|++
T Consensus 6 ~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~--~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 6 QPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTK--TRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCc--eEeEcCcEEEeCCEEEEEcC
Confidence 357789999999 5666665 9999999999999999999999999975332 25678999999999999974
No 17
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.77 E-value=1.8e-18 Score=127.56 Aligned_cols=71 Identities=27% Similarity=0.279 Sum_probs=59.9
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCcc-ceeccceeeeecCcEEEEEe
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQY-GDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~-~er~LGlVlIRGnnIV~I~~ 177 (213)
+...|..++|++|.|.|+||++|.|+|+|||+||||+|+||.|++..+... .....|.++|||+||++|.+
T Consensus 8 ~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred cHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence 468899999999999999999999999999999999999999987412111 13345599999999999963
No 18
>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=99.74 E-value=7.4e-18 Score=116.94 Aligned_cols=63 Identities=30% Similarity=0.415 Sum_probs=56.7
Q ss_pred HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~ 176 (213)
|..++|++|+|.|.||+.|.|+|.|||+||||+|++|.++...+ ..+.+|.++|||++|++|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~---~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEG---KKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCC---cEEECCeEEEECCEEEEEC
Confidence 57899999999999999999999999999999999999886542 3568999999999999983
No 19
>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=99.74 E-value=1e-17 Score=123.34 Aligned_cols=73 Identities=18% Similarity=0.126 Sum_probs=62.4
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
+...|..++|++|.|.|+||+.|.|+|.|||.||||+|.||.+...++.. ...+|.+||||++|.||...|..
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~--~~~~~~v~IRG~~I~~i~~p~~~ 74 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDK--FWKMPECYIRGNTIKYLRVPDEI 74 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcE--eeeCCcEEEeCCEEEEEEcCHHH
Confidence 46789999999999999999999999999999999999999876443332 23468999999999999876654
No 20
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.72 E-value=2.1e-17 Score=120.19 Aligned_cols=69 Identities=13% Similarity=0.011 Sum_probs=60.2
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV 179 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD 179 (213)
...|..++|++|+|.|+||.+|.|+|.+||.||||+|.||.+...++. ...+|.+||||+||.||..+|
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~---~~~~~~v~IRG~nI~~v~lPd 70 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGR---VSQLEQVYIRGSKIRFFILPD 70 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCc---EeEcCcEEEeCCEEEEEEeCC
Confidence 568999999999999999999999999999999999999976543332 346799999999999998664
No 21
>KOG1780|consensus
Probab=99.72 E-value=7.4e-18 Score=126.24 Aligned_cols=69 Identities=28% Similarity=0.425 Sum_probs=61.7
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
..|..|++++|.|.|++||.++|+|+|||.||||||++|+|...++. ...+|.++|||++|+++.++|.
T Consensus 7 PeLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~---~~~ig~~vIrgnsiv~~eaL~~ 75 (77)
T KOG1780|consen 7 PELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGD---KNNIGMVVIRGNSIVMVEALER 75 (77)
T ss_pred chHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCC---cceeeeEEEeccEEEEEeeccc
Confidence 37999999999999999999999999999999999999999854332 3468999999999999998763
No 22
>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=99.71 E-value=5.7e-17 Score=123.81 Aligned_cols=73 Identities=16% Similarity=0.101 Sum_probs=64.0
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN 183 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d 183 (213)
..+|..++|++|+|.|+||.+|.|+|.+||.||||+|+||.++...+. ...+|.++|||+||.||..+|....
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~---~~~~~~v~IRG~nI~yi~lPd~l~~ 75 (90)
T cd01724 3 VRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRN---PVPLDTLSIRGNNIRYFILPDSLNL 75 (90)
T ss_pred hHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCc---eeEcceEEEeCCEEEEEEcCCcCCc
Confidence 568999999999999999999999999999999999999987754322 4568999999999999998877633
No 23
>KOG1782|consensus
Probab=99.68 E-value=3.4e-18 Score=138.26 Aligned_cols=74 Identities=55% Similarity=0.807 Sum_probs=71.2
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccc
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVN 183 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d 183 (213)
.|..++++.|.|.|+|||.+.|+|+|||||.|+||.+|+|+++.++.|..+..|.++|||.||++++.+|.+..
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE 86 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE 86 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence 48899999999999999999999999999999999999999999999999999999999999999999998876
No 24
>KOG1784|consensus
Probab=99.68 E-value=2.2e-17 Score=127.96 Aligned_cols=85 Identities=27% Similarity=0.446 Sum_probs=74.7
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC-ccceeccceeeeecCcEEEEEeeccccccccc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN-QYGDIPRGIFIIRGENVVLMGEVVTVVNVKVI 187 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n-~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~~ 187 (213)
+.|.+|+|++|.|++.|||.+.|+|.|||+..||+|++|.|++++.. ...+..+|+.+|||+||.+|+++|+.+|..+.
T Consensus 3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d~~ld 82 (96)
T KOG1784|consen 3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELDSRLD 82 (96)
T ss_pred hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhhhhhh
Confidence 46899999999999999999999999999999999999999987532 34577899999999999999999999887776
Q ss_pred cCCCCC
Q psy5557 188 KGGDSG 193 (213)
Q Consensus 188 eg~~~g 193 (213)
-.--++
T Consensus 83 ~tkir~ 88 (96)
T KOG1784|consen 83 LTKIRA 88 (96)
T ss_pred hhhccc
Confidence 544444
No 25
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.67 E-value=1.9e-16 Score=121.58 Aligned_cols=75 Identities=17% Similarity=0.238 Sum_probs=59.2
Q ss_pred hhhHHHHHHHHhhcCCe--EEEEecC--CeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 102 KKKEEKKNKKAEEQNRQ--QGLYPNQ--KRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 102 ~~keE~~~~L~~~LgKr--V~V~LkD--GR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
+.-..++..|..++..+ |.|.+.| ++.|.|+|.|||+||||||+||.|++..+. ..+.+|.+|||||||++|++
T Consensus 10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~--~~~~lG~ilIRGnnV~~I~~ 87 (89)
T PTZ00138 10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKN--TRKDLGRILLKGDNITLIMA 87 (89)
T ss_pred eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCc--eeeEcCeEEEcCCEEEEEEc
Confidence 34455677888888654 5555546 589999999999999999999999865332 25679999999999999986
Q ss_pred e
Q psy5557 178 V 178 (213)
Q Consensus 178 i 178 (213)
.
T Consensus 88 ~ 88 (89)
T PTZ00138 88 A 88 (89)
T ss_pred C
Confidence 4
No 26
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.67 E-value=3e-16 Score=116.98 Aligned_cols=75 Identities=16% Similarity=0.115 Sum_probs=64.1
Q ss_pred hhhhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 100 QKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 100 ~~~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
+.+.......+|..+.|++|.|.|+||..|.|+|.+||.||||+|+||.+.. .+. ....+|.++|||+||.||..
T Consensus 3 ~~~~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~-~~~--~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 3 RTLLENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID-RNG--KQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred cchhhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc-CCC--ceeECCcEEEECCEEEEEEc
Confidence 4566677888999999999999999999999999999999999999997543 222 13468999999999999974
No 27
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.66 E-value=4.3e-16 Score=116.43 Aligned_cols=77 Identities=17% Similarity=0.076 Sum_probs=63.4
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccccc
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVK 185 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s 185 (213)
.++|.+++|++|.|.|+||.+|.|+|.+||.||||+|+||..... +.......++.++|||++|.||..+|..+|..
T Consensus 3 ~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~-~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~~ 79 (81)
T cd01725 3 FSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDP-EKYPHMLSVKNCFIRGSVVRYVQLPADEVDTE 79 (81)
T ss_pred hHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcC-CCcccccccCeEEEECCEEEEEEeChhHcCcc
Confidence 468999999999999999999999999999999999999965522 11111235689999999999999888776643
No 28
>KOG1781|consensus
Probab=99.64 E-value=2e-17 Score=129.89 Aligned_cols=81 Identities=23% Similarity=0.271 Sum_probs=71.1
Q ss_pred hhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCc-----cceeccceeeeecCcEEEEE
Q psy5557 102 KKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQ-----YGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 102 ~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~-----~~er~LGlVlIRGnnIV~I~ 176 (213)
+.+.|.+..|..|+++.|+|.+.+||..+|+|.|||+.|||||+||+|++.++.. ...+.+|++++||..|++|+
T Consensus 13 ~~kkEsilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlis 92 (108)
T KOG1781|consen 13 KPKKESILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLIS 92 (108)
T ss_pred ccchhHHhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEc
Confidence 3456789999999999999999999999999999999999999999999865431 12478999999999999999
Q ss_pred eecccc
Q psy5557 177 EVVTVV 182 (213)
Q Consensus 177 ~iD~~~ 182 (213)
+.|...
T Consensus 93 p~dG~e 98 (108)
T KOG1781|consen 93 PADGSE 98 (108)
T ss_pred CCcchh
Confidence 987654
No 29
>KOG3482|consensus
Probab=99.62 E-value=6.7e-16 Score=115.72 Aligned_cols=70 Identities=24% Similarity=0.162 Sum_probs=63.0
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV 179 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD 179 (213)
+..+|+.+.|++|.|.|.+|..|.|+|++.|.||||.|.+|.|++.. . ....+|.++||+|||.+|..++
T Consensus 9 PKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG-~--~~g~lGEilIRCNNvlyi~gv~ 78 (79)
T KOG3482|consen 9 PKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDG-V--STGNLGEILIRCNNVLYIRGVP 78 (79)
T ss_pred chHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcc-c--ccccceeEEEEeccEEEEecCC
Confidence 46799999999999999999999999999999999999999998753 2 2567999999999999998654
No 30
>KOG3460|consensus
Probab=99.52 E-value=2.8e-15 Score=114.86 Aligned_cols=74 Identities=22% Similarity=0.259 Sum_probs=64.4
Q ss_pred HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCC----c------cceeccceeeeecCcEEE
Q psy5557 105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGN----Q------YGDIPRGIFIIRGENVVL 174 (213)
Q Consensus 105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n----~------~~er~LGlVlIRGnnIV~ 174 (213)
+++...|.-+|+-+|+|.|+++|.+.|+|.+||+|.||||.|+.|.+..-+ . ...+.+.++||||++|++
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 568889999999999999999999999999999999999999998775311 1 235678999999999999
Q ss_pred EEee
Q psy5557 175 MGEV 178 (213)
Q Consensus 175 I~~i 178 (213)
|++.
T Consensus 84 vspp 87 (91)
T KOG3460|consen 84 VSPP 87 (91)
T ss_pred EcCc
Confidence 9875
No 31
>KOG3168|consensus
Probab=99.46 E-value=1.6e-14 Score=122.23 Aligned_cols=74 Identities=26% Similarity=0.315 Sum_probs=62.7
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC-------CccceeccceeeeecCcEEEEEeecc
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG-------NQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~-------n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
-+.|.++||.+++|+++|||+|+|+|.+||.||||||.||.|+.... ...+.+-||+|++||.|||+++.-+.
T Consensus 6 sskml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegp 85 (177)
T KOG3168|consen 6 SSKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGP 85 (177)
T ss_pred hhHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCC
Confidence 36789999999999999999999999999999999999998865321 12346789999999999999987543
Q ss_pred c
Q psy5557 181 V 181 (213)
Q Consensus 181 ~ 181 (213)
.
T Consensus 86 p 86 (177)
T KOG3168|consen 86 P 86 (177)
T ss_pred C
Confidence 3
No 32
>KOG1783|consensus
Probab=99.44 E-value=1.6e-14 Score=108.21 Aligned_cols=71 Identities=23% Similarity=0.205 Sum_probs=62.8
Q ss_pred HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557 105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178 (213)
Q Consensus 105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i 178 (213)
+.+-++|..++|++|.|.|.+|-.|.|+|.|+|.||||.|+.|.|+.. +. ..+++|.+||||+||.+|+..
T Consensus 5 ~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~n-gq--l~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVN-GQ--LKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred cCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhc-Cc--ccccccceeeccccEEEEEec
Confidence 456789999999999999999999999999999999999999988752 22 356789999999999999864
No 33
>KOG1775|consensus
Probab=99.40 E-value=1.8e-13 Score=103.56 Aligned_cols=70 Identities=14% Similarity=0.171 Sum_probs=60.2
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i 178 (213)
.-+-..||.+|+|++++.+.|.|||+|||.|.|+||.|++||...........++.+++.||||+++-+.
T Consensus 10 EliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG 79 (84)
T KOG1775|consen 10 ELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG 79 (84)
T ss_pred HHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence 3456789999999999999999999999999999999999997665432345789999999999998653
No 34
>KOG3293|consensus
Probab=99.15 E-value=5.4e-11 Score=96.95 Aligned_cols=77 Identities=18% Similarity=0.177 Sum_probs=66.7
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccccccc
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVK 185 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s 185 (213)
++.-|...-+.+|.|.|.+|-+|.|+|+.+|.+|||.|.+++.+..++..+ -.+..+.|||++|-||...|.++|..
T Consensus 3 PLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf--~r~pEcYirGttIkylri~d~iid~v 79 (134)
T KOG3293|consen 3 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKF--FRMPECYIRGTTIKYLRIPDEIIDKV 79 (134)
T ss_pred chhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCce--eecceeEEecceeEEEeccHHHHHHH
Confidence 356788888999999999999999999999999999999999887655543 24688999999999999999887644
No 35
>KOG1774|consensus
Probab=99.09 E-value=1.2e-10 Score=89.17 Aligned_cols=71 Identities=18% Similarity=0.215 Sum_probs=55.0
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeec
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV 179 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD 179 (213)
+-.+|++...-.||..=+-|-.+.|.++|||.||||||++|.|.....+. ...+|.+++.||||.+|...+
T Consensus 17 Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~--rk~lGRilLKGDnItli~~~~ 87 (88)
T KOG1774|consen 17 IFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKS--RKELGRILLKGDNITLIQSAG 87 (88)
T ss_pred HHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccC--CCccccEEEcCCcEEEEeecC
Confidence 34566666666666666678999999999999999999999886433222 347999999999999998654
No 36
>KOG3448|consensus
Probab=98.88 E-value=3e-09 Score=82.63 Aligned_cols=76 Identities=20% Similarity=0.197 Sum_probs=59.7
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCcc-ceeccceeeeecCcEEEEEeecccccccc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQY-GDIPRGIFIIRGENVVLMGEVVTVVNVKV 186 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~-~er~LGlVlIRGnnIV~I~~iD~~~d~s~ 186 (213)
+++..++|+.|.|.|.++-.+.|||.|+|+|+||-|.|.. +.+...| .-..+..+||||+.|-||.......+..+
T Consensus 5 sfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~--v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~vdtql 81 (96)
T KOG3448|consen 5 SFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDIS--VTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAVDTQL 81 (96)
T ss_pred HHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeE--eeCcccCCCeeeeeeEEEeccEEEEEEeChhHHHHHH
Confidence 5788999999999999999999999999999999999974 2222222 12346779999999999987654444433
No 37
>KOG3428|consensus
Probab=98.58 E-value=3.8e-07 Score=72.90 Aligned_cols=70 Identities=17% Similarity=0.084 Sum_probs=59.4
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
..+|..+.+.+|.|.|.+|....|++.+.|.+||..|.++.=. ..+ ....+-.++|||+||=|+-..|..
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t-~~~---~pv~l~~lsirgnniRy~~lpD~l 73 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMT-VKG---EPVRLDTLSIRGNNIRYYILPDSL 73 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEe-cCC---CceeEEEEEeecceEEEEEccCCc
Confidence 5689999999999999999999999999999999999998522 222 245688999999999999887654
No 38
>KOG3172|consensus
Probab=98.55 E-value=3.1e-07 Score=73.74 Aligned_cols=76 Identities=16% Similarity=0.084 Sum_probs=62.6
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccccccccc
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNVKVIK 188 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~s~~e 188 (213)
.|...-|.-|.|.+..|..|.|.|.-.|++||++|+|++=...++. ...+..|||||+.|-++-.+|-...+++..
T Consensus 9 lLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~---vs~le~V~IRGS~IRFlvlPdmLKnAPmFk 84 (119)
T KOG3172|consen 9 LLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGR---VSQLEQVFIRGSKIRFLVLPDMLKNAPMFK 84 (119)
T ss_pred eeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCc---ceeeeeEEEecCeEEEEECchHhhcCcccc
Confidence 4566778899999999999999999999999999999865433322 335788999999999999988887766554
No 39
>KOG3459|consensus
Probab=98.02 E-value=8.7e-07 Score=71.17 Aligned_cols=61 Identities=23% Similarity=0.273 Sum_probs=52.0
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecC----Cc-----c-ceeccceeeeecCcEEEEE
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVG----NQ-----Y-GDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~----n~-----~-~er~LGlVlIRGnnIV~I~ 176 (213)
+.+|.|.++|++.+.|.+.|||-|.|++|.++.|.+..- .. . ..+++|.+|||||+|+.+.
T Consensus 36 ~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsvI~v~ 106 (114)
T KOG3459|consen 36 NTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSVILVL 106 (114)
T ss_pred CceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeEEEEE
Confidence 678999999999999999999999999999998877431 11 1 2678999999999999886
No 40
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.84 E-value=3.6e-05 Score=56.20 Aligned_cols=64 Identities=13% Similarity=0.075 Sum_probs=39.5
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecC---cCceEecceEEEeecC---Cc-cceeccceeeeecCcEE
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQ---FANLVLHKTIERIHVG---NQ-YGDIPRGIFIIRGENVV 173 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq---~mNLVLsDavEri~~~---n~-~~er~LGlVlIRGnnIV 173 (213)
.+..++|.+|.|++.||..|.|+|.+++. -+.++|..|....... .. ........++|.++.|+
T Consensus 6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 46789999999999999999999999998 8899998875432211 11 11234567888887775
No 41
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.44 E-value=0.00011 Score=54.49 Aligned_cols=36 Identities=19% Similarity=0.217 Sum_probs=29.1
Q ss_pred CeEEEEec--CC--eEEEEEEEEecCcCceEecceEEEee
Q psy5557 117 RQQGLYPN--QK--RTLIGYLRSVDQFANLVLHKTIERIH 152 (213)
Q Consensus 117 KrV~V~Lk--DG--R~~~GtL~gFDq~mNLVLsDavEri~ 152 (213)
.+|.|.++ +| -.++|.|++||.|+||+|.|+.|.+.
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhc
Confidence 56666664 44 38999999999999999999998654
No 42
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=96.87 E-value=0.0047 Score=41.79 Aligned_cols=48 Identities=15% Similarity=0.184 Sum_probs=36.1
Q ss_pred hcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeee
Q psy5557 114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIR 168 (213)
Q Consensus 114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIR 168 (213)
++|++|+|.+ ++..+.|++.|+|.+..|+|......+ ...+.|.|++|
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g~~------~~i~sGdv~~r 48 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDGSI------RTISSGDVSLR 48 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTEEE------EEESSSEEEEE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCCCE------EEEEEEEEEeC
Confidence 4899999999 667779999999999999997653311 12344666665
No 43
>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=96.47 E-value=0.021 Score=43.66 Aligned_cols=62 Identities=8% Similarity=0.018 Sum_probs=46.9
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~ 176 (213)
=+..|..+.|++|.+.|-++.+..|+|.|+|. ..|+..++-. .+- ..+...+||++.|++++
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~----TPl----Gv~~eAlLR~~DVi~~~ 77 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ----TPL----GVQPEALLRCSDVISIS 77 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE----TTT----TEEEEEEEEGGGEEEEE
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC----CCc----ccChhheeecCCEEEEE
Confidence 45668888899999999999999999999994 5577776642 221 12467999999999986
No 44
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=96.29 E-value=0.028 Score=43.94 Aligned_cols=71 Identities=14% Similarity=0.112 Sum_probs=53.3
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCC----c--cceeccceeeeecCcEEEEEeecccc
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGN----Q--YGDIPRGIFIIRGENVVLMGEVVTVV 182 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n----~--~~er~LGlVlIRGnnIV~I~~iD~~~ 182 (213)
..|||++|.++.+++-.|.|+|..+|. ..+|.|.++.-+=..+- . -....+..|++||+.|--+..++...
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 468999999999999999999999995 78999999864322110 0 01124688999999999998776553
No 45
>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair [].P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].
Probab=96.05 E-value=0.11 Score=44.92 Aligned_cols=12 Identities=0% Similarity=0.027 Sum_probs=8.2
Q ss_pred HHHHHhhcCCeE
Q psy5557 108 KNKKAEEQNRQQ 119 (213)
Q Consensus 108 ~~~L~~~LgKrV 119 (213)
...|.+|+.++.
T Consensus 179 q~~~~~FF~k~~ 190 (216)
T PF11600_consen 179 QARITSFFKKPK 190 (216)
T ss_pred HHHHHHHhCCCC
Confidence 667788876544
No 46
>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=95.84 E-value=0.028 Score=48.01 Aligned_cols=63 Identities=16% Similarity=0.200 Sum_probs=45.2
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
..+..|+++.|.|.+.| ++|.|.|.++|+ ..||||.+..+ +. ....-+|-|..|-.|..++..
T Consensus 10 ~~~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~----~~sv~~I~ghaVk~vevl~~~ 73 (166)
T PF06372_consen 10 LEWQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DG----KRSVKVIMGHAVKSVEVLSEG 73 (166)
T ss_dssp HHHHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS-----EEEEEE-GGGEEEEEEEE--
T ss_pred HHHHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CC----ceeEEEEEccceEEEEEccCC
Confidence 56789999999999999 999999999995 67999976432 11 124689999999999988754
No 47
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.05 E-value=0.038 Score=40.32 Aligned_cols=31 Identities=23% Similarity=0.278 Sum_probs=27.9
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
..+|.|.|.||-.+.|.+.|||+|+=|+-.+
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll~~~ 41 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLLESD 41 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEEEEC
Confidence 6789999999999999999999999777655
No 48
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=94.81 E-value=0.047 Score=39.86 Aligned_cols=31 Identities=19% Similarity=0.250 Sum_probs=27.8
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
..+|.|.|.+|-.+.|.+.|||.|+=|+-.+
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~~~ 45 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLESQ 45 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEEEC
Confidence 6789999999999999999999999777654
No 49
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.52 E-value=0.057 Score=41.34 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=29.2
Q ss_pred cCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
-..+|.|.|.+|-.+.|.+.|||.|+=|+..+-
T Consensus 18 ~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~g 50 (79)
T PRK00395 18 ERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTG 50 (79)
T ss_pred cCCCEEEEEeCCcEEEEEEEEEccEEEEEEECC
Confidence 378899999999999999999999998776554
No 50
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=94.35 E-value=0.19 Score=38.02 Aligned_cols=63 Identities=13% Similarity=0.117 Sum_probs=44.5
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEecC-cCceEecceEEEeecCCc---c----ceeccceeeeecCcEEE
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVDQ-FANLVLHKTIERIHVGNQ---Y----GDIPRGIFIIRGENVVL 174 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq-~mNLVLsDavEri~~~n~---~----~er~LGlVlIRGnnIV~ 174 (213)
..|||++|.++.+.+-.|.|+|.++|. -.-|.|.|+..+=..+.. . ....+..++.||+.|--
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 468999999999999999999999995 456778887543211110 0 11235678888887753
No 51
>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=93.93 E-value=0.13 Score=37.52 Aligned_cols=34 Identities=15% Similarity=0.117 Sum_probs=30.3
Q ss_pred hcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
.+|..|.+.+..|..|.|.+.+||.-.+|++-.|
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 5899999999999999999999998888776554
No 52
>PRK14638 hypothetical protein; Provisional
Probab=92.68 E-value=0.29 Score=40.69 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=30.7
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs 145 (213)
..+..++|+.|.|+|.+++.|+|+|.++|.- +|+|.
T Consensus 93 ~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~ 128 (150)
T PRK14638 93 KDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS 128 (150)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 4678999999999999999999999999963 45553
No 53
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=91.76 E-value=0.26 Score=37.72 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=27.1
Q ss_pred cCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
-+.+|.|.|.||-.+.|.+.|||+|.=|+=++
T Consensus 18 ~~i~VtIfLvNG~~L~G~V~sfD~f~VlL~~~ 49 (77)
T COG1923 18 EKIPVTIFLVNGFKLQGQVESFDNFVVLLKNT 49 (77)
T ss_pred cCCeEEEEEEcCEEEEEEEEeeeeEEEEEEcC
Confidence 36789999999999999999999997554433
No 54
>PRK14639 hypothetical protein; Provisional
Probab=91.69 E-value=0.45 Score=39.11 Aligned_cols=35 Identities=26% Similarity=0.319 Sum_probs=30.6
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|.|.+++.|.|+|.++|. .+++|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~-~~i~l 115 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDD-ENITL 115 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeC-CEEEE
Confidence 467899999999999999999999999998 35555
No 55
>PRK02001 hypothetical protein; Validated
Probab=90.66 E-value=0.63 Score=39.00 Aligned_cols=35 Identities=17% Similarity=0.328 Sum_probs=30.1
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|.|.+++.|.|+|.+||.- +++|
T Consensus 83 ~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 83 RQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 4577899999999999999999999999974 4444
No 56
>TIGR02794 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.
Probab=89.37 E-value=1.8 Score=40.41 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=8.7
Q ss_pred EEecCcCceEecce
Q psy5557 134 RSVDQFANLVLHKT 147 (213)
Q Consensus 134 ~gFDq~mNLVLsDa 147 (213)
..++.|.++|-.-.
T Consensus 259 ~ev~~Y~a~I~~~I 272 (346)
T TIGR02794 259 SEVDKYAAIIQQAI 272 (346)
T ss_pred chHHHHHHHHHHHH
Confidence 34577887765544
No 57
>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=89.32 E-value=1.1 Score=33.18 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=28.7
Q ss_pred HHHHhhcCCeEEEEec---CC-eEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPN---QK-RTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~Lk---DG-R~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|.|. +| +.|.|+|.++|.- +++|
T Consensus 18 ~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l 56 (83)
T cd01734 18 ADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL 56 (83)
T ss_pred HHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence 4678899999999996 55 6999999999984 4444
No 58
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=88.96 E-value=2.5 Score=31.31 Aligned_cols=53 Identities=17% Similarity=0.152 Sum_probs=40.0
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
+.|++++|++|.|.+..|.. .|+|.+.... .|+|+.+ -..++||=..|++|.+
T Consensus 14 q~lq~liG~~vvV~T~~g~v-~G~L~~V~pD-hIvl~~~--------------~~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 14 QTLQSLIGQRVVVQTTRGSV-RGILVDVKPD-HIVLEEN--------------GTPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHhcCCEEEEEEcCCcE-EEEEEeecCC-EEEEEeC--------------CcEEEEEeeeEEEEcC
Confidence 57999999999999988776 9999998743 2344332 1457888888888753
No 59
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.87 E-value=0.58 Score=40.24 Aligned_cols=33 Identities=15% Similarity=0.198 Sum_probs=29.3
Q ss_pred cCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 115 QNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
-..+|.|.|.+|-.+.|.+.|||.|+=|+..+.
T Consensus 103 ~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g 135 (165)
T PRK14091 103 SGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG 135 (165)
T ss_pred cCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 377899999999999999999999998777665
No 60
>PRK14644 hypothetical protein; Provisional
Probab=88.46 E-value=1.2 Score=36.68 Aligned_cols=35 Identities=11% Similarity=0.126 Sum_probs=30.3
Q ss_pred HHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEec
Q psy5557 110 KKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVLs 145 (213)
.+..++|..|.|.|.+. +.|.|+|.++|. .+|+|.
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~-~~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNP-ETITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeC-CEEEEE
Confidence 68899999999999877 899999999997 456664
No 61
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=88.24 E-value=0.68 Score=39.84 Aligned_cols=32 Identities=16% Similarity=0.225 Sum_probs=28.1
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..+|.|.|.+|-.+.|.+.|||+|.=|+..+.
T Consensus 24 k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~g 55 (165)
T PRK14091 24 KTPVTMFLVKGVKLQGIITWFDNFSILLRRDG 55 (165)
T ss_pred CCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence 67899999999999999999999987776554
No 62
>PRK14640 hypothetical protein; Provisional
Probab=87.88 E-value=1.4 Score=36.56 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=29.6
Q ss_pred HHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEec
Q psy5557 109 NKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 109 ~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVLs 145 (213)
..+..++|+.|.|+| .+++.|.|+|.++|.. ++.|.
T Consensus 90 ~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 90 AQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 467899999999999 5669999999999974 45553
No 63
>PRK14633 hypothetical protein; Provisional
Probab=87.57 E-value=1.5 Score=36.35 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=30.0
Q ss_pred HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEec
Q psy5557 108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVLs 145 (213)
...+..++|+.|.|++ .+++.|+|+|.++|.. +|.|.
T Consensus 86 ~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 86 IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred HHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 3567899999999998 4679999999999874 55553
No 64
>PF11600 CAF-1_p150: Chromatin assembly factor 1 complex p150 subunit, N-terminal; InterPro: IPR021644 P150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair [].P150 is the HP1 interaction site of CAF-1 and lies within the N-terminal region of the protein [].
Probab=86.99 E-value=19 Score=31.10 Aligned_cols=12 Identities=0% Similarity=-0.108 Sum_probs=6.2
Q ss_pred hHHHHHHHHhhc
Q psy5557 104 KEEKKNKKAEEQ 115 (213)
Q Consensus 104 keE~~~~L~~~L 115 (213)
.-.+.+|+..-.
T Consensus 179 q~~~~~FF~k~~ 190 (216)
T PF11600_consen 179 QARITSFFKKPK 190 (216)
T ss_pred HHHHHHHhCCCC
Confidence 445556665433
No 65
>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=86.50 E-value=1.6 Score=35.15 Aligned_cols=36 Identities=19% Similarity=0.224 Sum_probs=27.2
Q ss_pred HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcCceEe
Q psy5557 108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~mNLVL 144 (213)
...+..++|+.|.|.+ .+.+.|.|+|.++|. .+|+|
T Consensus 79 ~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l 118 (141)
T PF02576_consen 79 PRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL 118 (141)
T ss_dssp HHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred HHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence 3578899999999999 345799999999998 45555
No 66
>PRK06955 biotin--protein ligase; Provisional
Probab=86.23 E-value=2.5 Score=38.22 Aligned_cols=37 Identities=16% Similarity=0.179 Sum_probs=31.5
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
...-++|+.|.|...++..+.|++.|+|..+.|+|..
T Consensus 243 ~~~~~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 243 ALHAYAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred HHhhcCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 3445789999998777788999999999999999953
No 67
>PRK14636 hypothetical protein; Provisional
Probab=86.09 E-value=1.8 Score=36.96 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=28.9
Q ss_pred HHHHhhcCCeEEEEec---CC-eEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPN---QK-RTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~Lk---DG-R~~~GtL~gFDq~mNLVL 144 (213)
..+..++|+.|.|+|. +| +.|+|+|.++|.- +++|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 5678999999999997 55 6999999999873 4554
No 68
>PRK14642 hypothetical protein; Provisional
Probab=85.49 E-value=2.1 Score=37.56 Aligned_cols=36 Identities=6% Similarity=0.056 Sum_probs=29.9
Q ss_pred HHHHHhhcCCeEEEEec-------------CCeEEEEEEEEecCcCceEe
Q psy5557 108 KNKKAEEQNRQQGLYPN-------------QKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~Lk-------------DGR~~~GtL~gFDq~mNLVL 144 (213)
...+..++|..|.|+|. +.+.|.|+|.++|.. +|.|
T Consensus 92 ~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 92 EQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 35678899999999997 679999999999974 4444
No 69
>PRK14632 hypothetical protein; Provisional
Probab=85.06 E-value=2.2 Score=36.23 Aligned_cols=36 Identities=25% Similarity=0.274 Sum_probs=29.4
Q ss_pred HHHHhhcCCeEEEEecC-------CeEEEEEEEEecCcCceEec
Q psy5557 109 NKKAEEQNRQQGLYPNQ-------KRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkD-------GR~~~GtL~gFDq~mNLVLs 145 (213)
..+..++|+.|.|+|.+ .+.|.|+|.++|. .+|+|.
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~-~~i~l~ 133 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEG-DTVVLR 133 (172)
T ss_pred HHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeC-CEEEEE
Confidence 46789999999999975 5799999999986 355553
No 70
>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=84.79 E-value=2 Score=36.85 Aligned_cols=37 Identities=8% Similarity=-0.006 Sum_probs=32.9
Q ss_pred HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
...+-+-+|+|++.||.+|.|.+.||++--|+||+-+
T Consensus 24 f~r~~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~ 60 (165)
T PF03614_consen 24 FWRFNDIPVRVVSENGQVFCMYVSGFMSKENKILAPD 60 (165)
T ss_pred HHHhcCCceEEEecCCcEEEEEEeccCcccCEEeccC
Confidence 3445688999999999999999999999999999776
No 71
>PRK14645 hypothetical protein; Provisional
Probab=84.62 E-value=2.5 Score=35.43 Aligned_cols=34 Identities=6% Similarity=0.061 Sum_probs=28.3
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|.+ +++.|.|+|.+||.- +|+|
T Consensus 95 ~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l 128 (154)
T PRK14645 95 RHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF 128 (154)
T ss_pred HHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence 467789999999986 889999999999974 4444
No 72
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=84.50 E-value=2.9 Score=37.54 Aligned_cols=35 Identities=23% Similarity=0.278 Sum_probs=29.4
Q ss_pred HHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557 110 KKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs 145 (213)
...-++|+.|.|... +..+.|++.|+|..+.|+|.
T Consensus 266 ~~~~~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~ 300 (319)
T PRK11886 266 KLDLFLGREVKLIIG-DKEISGIARGIDEQGALLLE 300 (319)
T ss_pred HhccccCCeEEEEeC-CcEEEEEEEEECCCceEEEE
Confidence 344578999999874 45799999999999999995
No 73
>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=84.15 E-value=3.6 Score=35.51 Aligned_cols=37 Identities=22% Similarity=0.282 Sum_probs=30.5
Q ss_pred HHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs 145 (213)
-.....++|++|.|...+ ..+.|++.|+|..+.|+|.
T Consensus 185 ~~~~~~~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 185 WEKLSAHIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred HHHhhhccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 344556789999998754 5699999999999999996
No 74
>PRK14647 hypothetical protein; Provisional
Probab=83.00 E-value=3.3 Score=34.58 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=28.1
Q ss_pred HHHHhhcCCeEEEEec---------CCeEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPN---------QKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~Lk---------DGR~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|+|. +.+.|+|+|.++|. .+++|
T Consensus 92 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~-~~v~l 135 (159)
T PRK14647 92 ADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD-GVVTI 135 (159)
T ss_pred HHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC-CEEEE
Confidence 5678999999999994 35899999999996 34444
No 75
>PRK14634 hypothetical protein; Provisional
Probab=82.34 E-value=3.5 Score=34.46 Aligned_cols=36 Identities=11% Similarity=0.054 Sum_probs=28.6
Q ss_pred HHHHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEe
Q psy5557 108 KNKKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVL 144 (213)
...+..++|+.|.|.|.+. +.|.|+|.++|.- +|.|
T Consensus 92 ~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 92 DRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 3567899999999998632 7999999999973 4545
No 76
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=82.07 E-value=3.8 Score=33.68 Aligned_cols=30 Identities=17% Similarity=0.177 Sum_probs=26.9
Q ss_pred HHHHhhcCCeEEEEe----cCCeEEEEEEEEecC
Q psy5557 109 NKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQ 138 (213)
Q Consensus 109 ~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq 138 (213)
..+..++|+.|.|.| .+++.|.|+|.++|.
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 567899999999997 677899999999998
No 77
>PRK14646 hypothetical protein; Provisional
Probab=82.06 E-value=3.6 Score=34.37 Aligned_cols=35 Identities=20% Similarity=0.088 Sum_probs=28.5
Q ss_pred HHHHhhcCCeEEEEecCC----eEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVL 144 (213)
..+..++|..|.|.|.+. +.|.|+|.+||.- +|.|
T Consensus 93 ~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 93 RDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred HHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 467899999999999543 7899999999984 5555
No 78
>KOG2412|consensus
Probab=81.86 E-value=10 Score=38.33 Aligned_cols=40 Identities=25% Similarity=0.513 Sum_probs=16.6
Q ss_pred HHHHHhhHHHHHHHHHHHH-HHHHHHHHhHHHHHHHhhHHH
Q psy5557 35 EEKKQKKKEEKKQKKKEKK-EEKEEKKEKKKEEKKQKKEEE 74 (213)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 74 (213)
..+.|+..+++++.+-+++ +..+|+.+.++.++..+++.+
T Consensus 211 qi~~~~~~~e~kr~Eaerk~~~~qEe~Rqk~d~~~~~~eqe 251 (591)
T KOG2412|consen 211 QIRERKERSEEKREEAERKRRAHQEELRQKEDEEAELQEQE 251 (591)
T ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 3344444555555554433 223333344443333333333
No 79
>PRK08330 biotin--protein ligase; Provisional
Probab=81.30 E-value=6.4 Score=34.04 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=29.6
Q ss_pred HHHhhcCCeEEEEecCCeEE-EEEEEEecCcCceEecce
Q psy5557 110 KKAEEQNRQQGLYPNQKRTL-IGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 110 ~L~~~LgKrV~V~LkDGR~~-~GtL~gFDq~mNLVLsDa 147 (213)
....++|++|.|.. ++..+ .|++.|+|..+.|+|...
T Consensus 182 ~~~~~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~~ 219 (236)
T PRK08330 182 GRSMILGKRVKIIG-DGEILVEGIAEDIDEFGALILRLD 219 (236)
T ss_pred HHHHhcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEEC
Confidence 34467899999986 56665 699999999999999643
No 80
>PRK14643 hypothetical protein; Provisional
Probab=80.89 E-value=3.7 Score=34.71 Aligned_cols=31 Identities=13% Similarity=0.130 Sum_probs=26.9
Q ss_pred HHHHhhcCCeEEEEecC----CeEEEEEEEEecCc
Q psy5557 109 NKKAEEQNRQQGLYPNQ----KRTLIGYLRSVDQF 139 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkD----GR~~~GtL~gFDq~ 139 (213)
..+..++|..|.|.|.+ .+.|.|+|.++|.-
T Consensus 97 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~ 131 (164)
T PRK14643 97 EELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN 131 (164)
T ss_pred HHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence 56789999999999965 58999999999964
No 81
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=80.87 E-value=5.3 Score=35.43 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=35.5
Q ss_pred HHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 107 KKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 107 ~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
.-..+..++|++|++.+.++..+.|+..++|..+.|+|...
T Consensus 181 ~~~~~~~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 181 RWRARSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred HHHHHhccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 34455667999999999999999999999999999999876
No 82
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.64 E-value=4.5 Score=34.14 Aligned_cols=33 Identities=12% Similarity=0.071 Sum_probs=29.8
Q ss_pred HHHHHhhcCCeEEEEe----cCCeEEEEEEEEecCcC
Q psy5557 108 KNKKAEEQNRQQGLYP----NQKRTLIGYLRSVDQFA 140 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~L----kDGR~~~GtL~gFDq~m 140 (213)
...+..|+|..|.|.| .+++.|.|+|.++|.-+
T Consensus 91 ~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~ 127 (153)
T COG0779 91 AEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET 127 (153)
T ss_pred HHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe
Confidence 3567899999999999 88999999999999877
No 83
>PRK14631 hypothetical protein; Provisional
Probab=80.20 E-value=4.8 Score=34.38 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=29.1
Q ss_pred HHHHHhhcCCeEEEEec----CCeEEEEEEEEec--CcCceEe
Q psy5557 108 KNKKAEEQNRQQGLYPN----QKRTLIGYLRSVD--QFANLVL 144 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~Lk----DGR~~~GtL~gFD--q~mNLVL 144 (213)
...+..|+|+.|.|+|. +.+.|+|+|.++| . .+|.|
T Consensus 109 ~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~-~~v~l 150 (174)
T PRK14631 109 LEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLEN-EEIQV 150 (174)
T ss_pred HHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCC-CEEEE
Confidence 45788999999999995 5599999999998 4 34444
No 84
>KOG1144|consensus
Probab=78.75 E-value=12 Score=39.56 Aligned_cols=18 Identities=39% Similarity=0.739 Sum_probs=7.7
Q ss_pred HHHHHhhHHHHhhHHHHH
Q psy5557 65 EEKKQKKEEEKDKKKEEK 82 (213)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~ 82 (213)
||+-+.+++|.+.-.+++
T Consensus 238 EE~~r~eeEEer~~ee~E 255 (1064)
T KOG1144|consen 238 EERLRREEEEERRREEEE 255 (1064)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444444444444444333
No 85
>KOG3054|consensus
Probab=78.13 E-value=17 Score=33.76 Aligned_cols=14 Identities=43% Similarity=0.743 Sum_probs=7.4
Q ss_pred cccccchhhhhhhH
Q psy5557 11 ISPRIGKRKKKKKE 24 (213)
Q Consensus 11 ~~~~~~~~~~~~~~ 24 (213)
.+-.+|+++..|-+
T Consensus 99 ~~~kigkkK~aKle 112 (299)
T KOG3054|consen 99 LQAKIGKKKEAKLE 112 (299)
T ss_pred hhhhhhhHHHHHHH
Confidence 34455666655533
No 86
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=78.00 E-value=5.7 Score=39.60 Aligned_cols=38 Identities=16% Similarity=0.216 Sum_probs=31.8
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
..+.-++|++|.|...++..+.|+..|+|..+.|+|..
T Consensus 271 ~~~~~~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 271 QAANRDHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred HHhhccCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 34445789999998777788999999999999999963
No 87
>PRK14637 hypothetical protein; Provisional
Probab=75.84 E-value=6.7 Score=32.71 Aligned_cols=37 Identities=14% Similarity=0.103 Sum_probs=28.1
Q ss_pred HHHHHhhcCCeEEEEecCCeEE-EEEEEEecCcCceEec
Q psy5557 108 KNKKAEEQNRQQGLYPNQKRTL-IGYLRSVDQFANLVLH 145 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~LkDGR~~-~GtL~gFDq~mNLVLs 145 (213)
...+..++|+.|.|.|.+...| +|+|.++|.. +++|.
T Consensus 90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 3567899999999999444455 7999999874 55553
No 88
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=75.29 E-value=12 Score=32.46 Aligned_cols=63 Identities=11% Similarity=0.056 Sum_probs=41.7
Q ss_pred hhHHHHHHHHhhcCC--eEEEE-ecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEee
Q psy5557 103 KKEEKKNKKAEEQNR--QQGLY-PNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 178 (213)
Q Consensus 103 ~keE~~~~L~~~LgK--rV~V~-LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~i 178 (213)
-..|.+.+|.++.+. +|.+. .+++..|.|++++||.- -|+|... ++ ...+.|.-+.|++|..+
T Consensus 118 ~~~EKI~fL~~~P~~lp~i~C~i~t~~~~Y~G~I~~~~~~-~v~i~~~------~~------~~~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 118 NIEEKIDFLINLPHHLPPIKCEIETKDKSYRGIILSYDEG-EVSIMPF------NQ------GEEIEIPIDDITSIKMI 183 (185)
T ss_pred cHHHHHHHHHhCcccCCCCceEEEeCCceEEEEEEeccCC-EEEEecc------CC------CcceEeehhheeeeeec
Confidence 357899999988754 33333 37889999999999964 1222111 11 25567777888888765
No 89
>KOG1073|consensus
Probab=74.35 E-value=12 Score=35.76 Aligned_cols=71 Identities=14% Similarity=0.052 Sum_probs=51.0
Q ss_pred HHhhcCCeEEEEecCCeEEEEEEEEec-CcCceEecceEEE----eecCCc---cceeccceeeeecCcEEEEEeeccc
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGYLRSVD-QFANLVLHKTIER----IHVGNQ---YGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~GtL~gFD-q~mNLVLsDavEr----i~~~n~---~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
...|||+.|.++-+...-|.|+|.-+| +-.=|-|.+|--+ ...+.. .-...+.-||.||+.|-.|...+..
T Consensus 4 ~t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~~p 82 (361)
T KOG1073|consen 4 VTSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQETP 82 (361)
T ss_pred ccccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeeccCc
Confidence 357999999999999999999999999 7778888887221 111111 0111357799999999977765543
No 90
>KOG0163|consensus
Probab=74.07 E-value=41 Score=35.97 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=8.1
Q ss_pred hhhhhHHHHHHHHhhcC
Q psy5557 100 QKKKKEEKKNKKAEEQN 116 (213)
Q Consensus 100 ~~~~keE~~~~L~~~Lg 116 (213)
|.|--.+..+.|.+.-|
T Consensus 1005 qer~D~~la~RlA~sd~ 1021 (1259)
T KOG0163|consen 1005 QERRDHELALRLANSDG 1021 (1259)
T ss_pred HHHHHHHHHHHHhhccC
Confidence 33444455555555444
No 91
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=73.06 E-value=7.7 Score=34.98 Aligned_cols=37 Identities=14% Similarity=0.283 Sum_probs=30.5
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
....-++|+.|.|.. ++..+.|++.|+|..+.|+|..
T Consensus 230 ~~~~~~~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 230 TPRLLYKDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred HHHhccCCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 344456899999975 6689999999999999999964
No 92
>PTZ00266 NIMA-related protein kinase; Provisional
Probab=72.18 E-value=48 Score=35.73 Aligned_cols=10 Identities=0% Similarity=-0.386 Sum_probs=4.0
Q ss_pred cccccccCCC
Q psy5557 195 KWLRGVKQGV 204 (213)
Q Consensus 195 ~~~rg~~q~~ 204 (213)
.|+-++-||+
T Consensus 646 ~~~~~~~~~~ 655 (1021)
T PTZ00266 646 GMGNARAPPP 655 (1021)
T ss_pred ccccccCCCC
Confidence 3334444443
No 93
>PRK14641 hypothetical protein; Provisional
Probab=71.40 E-value=7.1 Score=33.45 Aligned_cols=29 Identities=14% Similarity=0.178 Sum_probs=25.1
Q ss_pred HHHHhhcCCeEEEEecC----CeEEEEEEEEec
Q psy5557 109 NKKAEEQNRQQGLYPNQ----KRTLIGYLRSVD 137 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkD----GR~~~GtL~gFD 137 (213)
..+..++|+.|.|+|.+ .+.|+|+|.++|
T Consensus 97 ~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 97 RQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 46788999999999965 469999999995
No 94
>KOG1144|consensus
Probab=70.41 E-value=16 Score=38.84 Aligned_cols=8 Identities=0% Similarity=-0.151 Sum_probs=3.6
Q ss_pred EEEEecCC
Q psy5557 119 QGLYPNQK 126 (213)
Q Consensus 119 V~V~LkDG 126 (213)
+.|...||
T Consensus 308 ~~va~kdg 315 (1064)
T KOG1144|consen 308 LPVADKDG 315 (1064)
T ss_pred CCCCcccC
Confidence 44444444
No 95
>PRK10898 serine endoprotease; Provisional
Probab=70.18 E-value=16 Score=33.83 Aligned_cols=31 Identities=19% Similarity=0.174 Sum_probs=27.6
Q ss_pred CeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 117 RQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 117 KrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..|+|++.||+.|.+.++++|...+|-|-.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5789999999999999999999999977655
No 96
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=69.78 E-value=1.2e+02 Score=30.13 Aligned_cols=25 Identities=12% Similarity=-0.040 Sum_probs=15.2
Q ss_pred CeEE-EEecCCeEEEEEEEEecCcCc
Q psy5557 117 RQQG-LYPNQKRTLIGYLRSVDQFAN 141 (213)
Q Consensus 117 KrV~-V~LkDGR~~~GtL~gFDq~mN 141 (213)
.+|+ +.+.|--++.|.|+-+|.-.-
T Consensus 360 ~p~f~Lkv~d~~~~ls~LvllD~~tg 385 (489)
T PF05262_consen 360 KPVFGLKVLDPNHYLSELVLLDSDTG 385 (489)
T ss_pred CceeEEEEecCCCcceeEEEEeCCCC
Confidence 4555 444444467788888886543
No 97
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=66.21 E-value=96 Score=29.98 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=7.0
Q ss_pred EEecCcCceEec
Q psy5557 134 RSVDQFANLVLH 145 (213)
Q Consensus 134 ~gFDq~mNLVLs 145 (213)
...|.|..+|-.
T Consensus 300 ~ev~~Y~a~Ira 311 (387)
T PRK09510 300 ADIDQYAGQIKS 311 (387)
T ss_pred cchhhHHHHHHH
Confidence 345677776644
No 98
>PRK10942 serine endoprotease; Provisional
Probab=65.99 E-value=17 Score=35.08 Aligned_cols=32 Identities=9% Similarity=0.064 Sum_probs=27.8
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
...|.|++.||+.|.+.++++|...+|-|-..
T Consensus 135 a~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 135 ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CCEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 35789999999999999999999999877643
No 99
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=64.98 E-value=7.6 Score=26.75 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=14.1
Q ss_pred EEEEEEEecCcCceEecceE
Q psy5557 129 LIGYLRSVDQFANLVLHKTI 148 (213)
Q Consensus 129 ~~GtL~gFDq~mNLVLsDav 148 (213)
.+|+|.|+|..+.|+|.+..
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~ 29 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDD 29 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS
T ss_pred cceeEEeeccccceEEEeCC
Confidence 68999999999999998763
No 100
>PRK10139 serine endoprotease; Provisional
Probab=64.63 E-value=25 Score=33.85 Aligned_cols=31 Identities=16% Similarity=0.199 Sum_probs=27.6
Q ss_pred CeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 117 RQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 117 KrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..|.|++.||+.|.+.++|+|....|-|-.+
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5789999999999999999999999877554
No 101
>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=60.89 E-value=14 Score=34.02 Aligned_cols=31 Identities=19% Similarity=0.155 Sum_probs=27.5
Q ss_pred CeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 117 RQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 117 KrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..+.|.+.||+.|.++++++|...+|-|-.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv 132 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKI 132 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 3688999999999999999999999988654
No 102
>PRK14630 hypothetical protein; Provisional
Probab=60.43 E-value=21 Score=29.50 Aligned_cols=34 Identities=6% Similarity=0.115 Sum_probs=26.7
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVL 144 (213)
..+..++|+.|.|.|.+ ..+.|+|.++|. .++.|
T Consensus 90 ~df~r~~G~~v~V~l~~-~~~~G~L~~~~d-~~i~l 123 (143)
T PRK14630 90 REFKIFEGKKIKLMLDN-DFEEGFILEAKA-DSFIF 123 (143)
T ss_pred HHHHHhCCCEEEEEEcC-cceEEEEEEEeC-CEEEE
Confidence 46789999999999955 456999999987 44444
No 103
>KOG3382|consensus
Probab=60.40 E-value=4.5 Score=34.23 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=20.0
Q ss_pred ecCCeEEEEEEEEecCcCceEecce
Q psy5557 123 PNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 123 LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
++..-.-+|||+|.|.|+|=...|-
T Consensus 39 yrtd~~kiGTLVG~DkfGNkYyen~ 63 (151)
T KOG3382|consen 39 YRTDDHKIGTLVGVDKFGNKYYENN 63 (151)
T ss_pred Hhcccccceeeeeecccccchhccc
Confidence 3455566899999999999887775
No 104
>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=60.23 E-value=4.9 Score=31.47 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=15.3
Q ss_pred EEEEEecCcCceEecce
Q psy5557 131 GYLRSVDQFANLVLHKT 147 (213)
Q Consensus 131 GtL~gFDq~mNLVLsDa 147 (213)
|+|+|.|.|+|....+-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 89999999999988765
No 105
>PRK14635 hypothetical protein; Provisional
Probab=58.00 E-value=26 Score=29.41 Aligned_cols=35 Identities=11% Similarity=-0.059 Sum_probs=27.5
Q ss_pred HHHHhhcCCeEEEEec--CCeEEEE---EEEEecCcCceEe
Q psy5557 109 NKKAEEQNRQQGLYPN--QKRTLIG---YLRSVDQFANLVL 144 (213)
Q Consensus 109 ~~L~~~LgKrV~V~Lk--DGR~~~G---tL~gFDq~mNLVL 144 (213)
..+..++|..|.|.+. ++..|.| +|.++|.- ++.|
T Consensus 92 ~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l 131 (162)
T PRK14635 92 EDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVEL 131 (162)
T ss_pred HHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEE
Confidence 4678999999999875 4678887 99999974 4544
No 106
>KOG3054|consensus
Probab=57.11 E-value=36 Score=31.71 Aligned_cols=9 Identities=33% Similarity=0.486 Sum_probs=4.1
Q ss_pred ceeeeecCc
Q psy5557 163 GIFIIRGEN 171 (213)
Q Consensus 163 GlVlIRGnn 171 (213)
|.|==||..
T Consensus 246 GVmDDRGKf 254 (299)
T KOG3054|consen 246 GVMDDRGKF 254 (299)
T ss_pred eeecCCCce
Confidence 444445553
No 107
>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=56.45 E-value=20 Score=28.57 Aligned_cols=28 Identities=14% Similarity=0.116 Sum_probs=20.9
Q ss_pred eEEEEecCCeEEEEEEEEecCcCceEecc
Q psy5557 118 QQGLYPNQKRTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 118 rV~V~LkDGR~~~GtL~gFDq~mNLVLsD 146 (213)
.+.|.|.||+.|+|+|++=| ...++|.+
T Consensus 59 ~~~v~~~dG~~~~G~~~~e~-~~~~~l~~ 86 (133)
T TIGR02603 59 AYRVTLKDGRILSGIVASET-ADGVTVKM 86 (133)
T ss_pred cEEEEECCCCEEEEEEEecC-CCeEEEEc
Confidence 47899999999999998855 33444444
No 108
>KOG3634|consensus
Probab=56.42 E-value=41 Score=32.30 Aligned_cols=48 Identities=15% Similarity=0.246 Sum_probs=26.4
Q ss_pred HHHhhHHHHHhhhhhHHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557 90 KKQKKKEEKKQKKKKEEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 90 ~~~~~~~~~~~~~~keE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs 145 (213)
.++.+.+|++-.|...+...+-..-.++..+|.-.+ ..||.|+||+-.
T Consensus 151 e~r~r~~Eek~Rr~~m~~~~~~~~~~gknftvakk~--------a~~~~fgn~~qa 198 (361)
T KOG3634|consen 151 ERRIRLEEEKSRRQEMMAGRFAEDDAGKNFTVAKKG--------AQNDGFGNIVQA 198 (361)
T ss_pred HHHHHHHHHHHHHHHHHhcCcCcccccCcceeeccc--------ccchhHHHHHHH
Confidence 344555555555555544444444444444443322 679999999754
No 109
>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=53.98 E-value=25 Score=28.22 Aligned_cols=60 Identities=12% Similarity=0.078 Sum_probs=29.3
Q ss_pred CCeEEEEecCCeEEEEEEEE-------ecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecc
Q psy5557 116 NRQQGLYPNQKRTLIGYLRS-------VDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~g-------FDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
+-+|.+.|.||+.+.||+.- +|...|==+.-.. ++.... ...-.-.|.=|.|+.|.++..
T Consensus 28 e~~V~l~L~DGs~l~Gtv~vrPtvQ~frD~~~~EG~Ng~l-RlD~~D----~~~~~~~iWlD~I~~V~pl~~ 94 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVAVRPTVQQFRDAQEREGINGQL-RLDDLD----APQEPHWIWLDQIAKVHPLPL 94 (101)
T ss_dssp T-EEEEEETTS-EEEEEECC---EEEEE-TT--EEEEEEE-EEE-SS----TT-SEEEEEGGGEEEEEE---
T ss_pred cceEEEEEcCCCeeeeeeccccchhhhhCcccccCccceE-EecCCC----CcccceeehhhhhhheeeCCC
Confidence 56899999999999999742 2333322221111 111110 111225677788888887653
No 110
>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=52.82 E-value=17 Score=27.66 Aligned_cols=63 Identities=17% Similarity=0.086 Sum_probs=30.7
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeecccccc
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTVVNV 184 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~~d~ 184 (213)
.=+-+.+|.++|.||..+.|+ +.|-..|- +-.|++.-. ..-|...||=+.|+.|.+.+.+..+
T Consensus 13 AC~~~~~v~L~l~dG~~~~g~--A~dt~~~~---~k~E~L~l~-----~~~~~~~i~Ld~I~~~~al~~nPhF 75 (80)
T PF07073_consen 13 ACMYRYPVKLTLKDGEQIEGK--ALDTRTNA---KKEECLVLE-----QDGGEQEIRLDQIASMSALTDNPHF 75 (80)
T ss_dssp HHTTTT-EEEE-TTT--EEES--S-EEE------SSS-EEEEE-----ETTEEEEESTT--SEEE----ETTT
T ss_pred HHhcCCeEEEEEeCCCEEEEE--EEEEEEec---CceEEEEEe-----cCCcEEEEEhhheeeeeecCCCCee
Confidence 334578999999999999998 33333331 223333211 1236788999999999987766443
No 111
>PRK08477 biotin--protein ligase; Provisional
Probab=51.48 E-value=29 Score=30.31 Aligned_cols=36 Identities=3% Similarity=-0.069 Sum_probs=30.5
Q ss_pred HHhhcCCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..-.+++.|.|.. +++.+.|+..++|..+.|++..-
T Consensus 170 ~~~~~~~~v~v~~-~~~~~~g~a~~I~~~G~L~v~~~ 205 (211)
T PRK08477 170 LEFEKSKSFSFHI-DGKLVSLKDAELLEDGSILINGK 205 (211)
T ss_pred HHHHcCCEEEEEE-CCEEEEEEEeeECCCCeEEECCE
Confidence 3457899999874 78999999999999999988764
No 112
>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=50.18 E-value=17 Score=31.42 Aligned_cols=24 Identities=21% Similarity=0.314 Sum_probs=21.8
Q ss_pred cCCeEEEEecCCeEEEEEEEEecC
Q psy5557 115 QNRQQGLYPNQKRTLIGYLRSVDQ 138 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~GtL~gFDq 138 (213)
.|+-|+|.|.|||.+.|.-.|.|.
T Consensus 119 qg~sIrVyM~DgR~ieG~stGvna 142 (165)
T PF03614_consen 119 QGKSIRVYMADGREIEGKSTGVNA 142 (165)
T ss_pred CCCeEEEEEcCCcEEEeeecccce
Confidence 478899999999999999999884
No 113
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=50.15 E-value=26 Score=32.80 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=27.8
Q ss_pred CeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 117 RQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 117 KrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
..+.|++.||+.|.+++.++|.+.+|.|-..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 4688999999999999999999999988665
No 114
>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=49.16 E-value=71 Score=23.06 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=30.3
Q ss_pred hhHHHHHHHHhhc--CCeEEEEe-cCC--eEEEEEEEEecCcCceEe
Q psy5557 103 KKEEKKNKKAEEQ--NRQQGLYP-NQK--RTLIGYLRSVDQFANLVL 144 (213)
Q Consensus 103 ~keE~~~~L~~~L--gKrV~V~L-kDG--R~~~GtL~gFDq~mNLVL 144 (213)
..++....|...+ +..|.|+. .+| ..++|++..||...+.+.
T Consensus 27 ~leei~~~l~~a~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~ 73 (92)
T PF08863_consen 27 QLEEINEKLSEAYQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLK 73 (92)
T ss_pred HHHHHHHHHHHHhcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEE
Confidence 3455666666554 77888877 445 789999999998876655
No 115
>PF03122 Herpes_MCP: Herpes virus major capsid protein; InterPro: IPR000912 The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces []. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1NO7_B.
Probab=48.52 E-value=5.8 Score=43.48 Aligned_cols=56 Identities=21% Similarity=0.218 Sum_probs=0.0
Q ss_pred eEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEE
Q psy5557 118 QQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVL 174 (213)
Q Consensus 118 rV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~ 174 (213)
+.+=++.+|+.+.|.|++.|.-|+.+|+---. +.+..-.....+|.++|+|+|.|.
T Consensus 249 ~~Tytt~~G~~v~GVlvTT~~V~q~Ll~~l~~-i~~~~v~~PatYg~~Vi~geNlVT 304 (1354)
T PF03122_consen 249 RSTYTTSSGRPVDGVLVTTANVMQKLLNLLGQ-ISDTSVSVPATYGEFVISGENLVT 304 (1354)
T ss_dssp ---------------------------------------------------------
T ss_pred cceeecCCCCEeceEEeccHHHHHHHHHHHhh-hccceeecchhheeeeecCccHHH
Confidence 34445689999999999999999888766543 322121234568999999999764
No 116
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=48.43 E-value=68 Score=26.95 Aligned_cols=29 Identities=17% Similarity=0.140 Sum_probs=25.8
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEec
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVD 137 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFD 137 (213)
.....+||+.|.+...+|..++|+..++.
T Consensus 85 ~~a~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 85 TKYSELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHHHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 45578999999999999999999999886
No 117
>TIGR02794 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.
Probab=47.18 E-value=2.4e+02 Score=26.50 Aligned_cols=7 Identities=0% Similarity=-0.121 Sum_probs=3.3
Q ss_pred HHHhhcC
Q psy5557 110 KKAEEQN 116 (213)
Q Consensus 110 ~L~~~Lg 116 (213)
.|.+++|
T Consensus 233 ~~~d~~g 239 (346)
T TIGR02794 233 ELGDIFG 239 (346)
T ss_pred hhhhhhc
Confidence 3455544
No 118
>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
Probab=46.84 E-value=14 Score=31.71 Aligned_cols=17 Identities=35% Similarity=0.428 Sum_probs=15.7
Q ss_pred EEEEEecCcCceEecce
Q psy5557 131 GYLRSVDQFANLVLHKT 147 (213)
Q Consensus 131 GtL~gFDq~mNLVLsDa 147 (213)
|+|+|-|.|+|-...+.
T Consensus 49 G~lVG~D~~GNkYYE~~ 65 (159)
T PLN02732 49 ATLVGVDKFGNKYYQKL 65 (159)
T ss_pred cEEEEecCCCCeeeecC
Confidence 99999999999988876
No 119
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=45.71 E-value=1.2e+02 Score=27.79 Aligned_cols=8 Identities=63% Similarity=0.754 Sum_probs=3.1
Q ss_pred HhHHHHHH
Q psy5557 84 QKKKEEKK 91 (213)
Q Consensus 84 ~~~~~~~~ 91 (213)
|++-+|++
T Consensus 307 QrK~eeKe 314 (321)
T PF07946_consen 307 QRKYEEKE 314 (321)
T ss_pred HHHHHHHH
Confidence 44443333
No 120
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=42.64 E-value=62 Score=25.01 Aligned_cols=69 Identities=10% Similarity=0.083 Sum_probs=42.5
Q ss_pred hHHHHHHHHhhcCC--eEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 104 KEEKKNKKAEEQNR--QQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 104 keE~~~~L~~~LgK--rV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
..+....|..+++. .|+|...+|..|.=+|.+.|.-.|.++=|+- . +. .....++.++.+++++..|..
T Consensus 7 p~eI~~~Lr~L~~~~~~l~v~~~~g~~f~T~iL~VD~~~~~l~lD~~---~-~~-----~~n~~~l~a~~~~~~a~~~gV 77 (108)
T PF07317_consen 7 PREILAVLRDLAKQRSPLTVRHPRGQSFITSILAVDPDRGTLVLDEG---S-DE-----EENQRLLNAEELTFVAELDGV 77 (108)
T ss_dssp HHHHHHHHHHHHHTT--EEEETT-SSEEEE-EEEEETTTTEEEEE-----B-SG-----GGHHHHHTT--EEEEEEETTE
T ss_pred HHHHHHHHHHHHhCCCeEEEEeCCCCEEEEEEEEEeCCCCEEEEEcC---C-Ch-----HHHHHHhcCCcEEEEEEeCCe
Confidence 45677788888754 5555657777799999999988877665542 1 11 124467778888887766544
No 121
>KOG0163|consensus
Probab=41.32 E-value=1.8e+02 Score=31.47 Aligned_cols=12 Identities=42% Similarity=0.540 Sum_probs=7.5
Q ss_pred ceeeeecCcEEE
Q psy5557 163 GIFIIRGENVVL 174 (213)
Q Consensus 163 GlVlIRGnnIV~ 174 (213)
..++|||.||..
T Consensus 1044 ~k~l~r~~~v~a 1055 (1259)
T KOG0163|consen 1044 NKMLIRSENVRA 1055 (1259)
T ss_pred ccccccchhhhH
Confidence 445777777653
No 122
>KOG0544|consensus
Probab=38.49 E-value=31 Score=27.94 Aligned_cols=16 Identities=31% Similarity=0.626 Sum_probs=13.4
Q ss_pred cccccccCCCcccccc
Q psy5557 195 KWLRGVKQGVDQLSLA 210 (213)
Q Consensus 195 ~~~rg~~q~~~~~~~~ 210 (213)
.--|||-+||.|||+-
T Consensus 55 eVIkGwdegv~qmsvG 70 (108)
T KOG0544|consen 55 EVIKGWDEGVAQMSVG 70 (108)
T ss_pred ceeechhhcchhcccc
Confidence 4579999999999974
No 123
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=38.05 E-value=39 Score=33.02 Aligned_cols=16 Identities=38% Similarity=0.729 Sum_probs=9.2
Q ss_pred ccceeeeecCcEEEEE
Q psy5557 161 PRGIFIIRGENVVLMG 176 (213)
Q Consensus 161 ~LGlVlIRGnnIV~I~ 176 (213)
..|..|..|..|..++
T Consensus 376 ~~G~~V~AGepIa~~G 391 (420)
T COG4942 376 NPGQFVKAGEPIALVG 391 (420)
T ss_pred cCCCEeecCCchhhcc
Confidence 4455556666555555
No 124
>PF05085 DUF685: Protein of unknown function (DUF685); InterPro: IPR007777 This family consists of uncharacterised proteins from Borrelia species. There is some evidence to suggest that the proteins may be outer surface proteins.
Probab=37.87 E-value=1.8e+02 Score=26.97 Aligned_cols=42 Identities=12% Similarity=0.043 Sum_probs=29.7
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeec
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHV 153 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~ 153 (213)
.+|-|+.+.|.|.++..++=++.-.+..-.|-|+=-++..+.
T Consensus 165 ~~YkNK~i~I~Le~~~dvtLif~Ks~Dd~pIYLdIdi~i~h~ 206 (265)
T PF05085_consen 165 SDYKNKAITIDLENNSDVTLIFYKSYDDDPIYLDIDIEIEHS 206 (265)
T ss_pred hhccCceEEEEeccCCcEEEEEcccCCCCcEEEEEEEEEEEc
Confidence 467899999999988888777766666556666544444333
No 125
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=37.50 E-value=91 Score=23.65 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=28.1
Q ss_pred hHHHHHHHHhhcCCeEEEEecCCe----EEEEEEEEecCcCceEe
Q psy5557 104 KEEKKNKKAEEQNRQQGLYPNQKR----TLIGYLRSVDQFANLVL 144 (213)
Q Consensus 104 keE~~~~L~~~LgKrV~V~LkDGR----~~~GtL~gFDq~mNLVL 144 (213)
...+...|..++|++|.|+.+.|| .-.|+|... |-||..
T Consensus 5 l~~Ik~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t--YPsvFv 47 (76)
T PF06257_consen 5 LADIKKELESHVGKRVKLKANKGRKKIIEREGVLEET--YPSVFV 47 (76)
T ss_dssp HHHHHHHHHHTTTSEEEEEE--SSS--S-EEEEEEEE---SSEEE
T ss_pred HHHHHHHHHHcCCCEEEEEEcCCceEEEEEEEEEEee--cCcEEE
Confidence 356788999999999999999996 678998865 445544
No 126
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=37.18 E-value=35 Score=29.43 Aligned_cols=34 Identities=18% Similarity=0.144 Sum_probs=28.2
Q ss_pred hhcCCeEEEEecCC----eEEEEEEEEecCcCceEecc
Q psy5557 113 EEQNRQQGLYPNQK----RTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 113 ~~LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVLsD 146 (213)
.|.|-.|.++..|| ++-.|.|+.=|..+||||+.
T Consensus 141 eyPDGTvk~vy~dG~qet~y~~gr~r~kd~~g~~~~d~ 178 (179)
T PF07202_consen 141 EYPDGTVKTVYPDGRQETRYASGRVRIKDKDGNVIMDT 178 (179)
T ss_pred EcCCCCEEEEecCCCEEEEeCCCcEEEecCCCCEEecC
Confidence 46788888888888 56779999999999999863
No 127
>PTZ00276 biotin/lipoate protein ligase; Provisional
Probab=37.18 E-value=60 Score=28.54 Aligned_cols=24 Identities=8% Similarity=0.173 Sum_probs=20.7
Q ss_pred cCCeEEEEEEEEecCcCceEecce
Q psy5557 124 NQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 124 kDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
.++..+.|++.|+|..+.|+|...
T Consensus 209 ~~~~~~~G~~~gId~~G~Lvv~~~ 232 (245)
T PTZ00276 209 TGRDPEELTALSLNEWGHLIVRRP 232 (245)
T ss_pred cCCcEEEEEEEEECCCCeEEEEEC
Confidence 467788999999999999999653
No 128
>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=36.72 E-value=42 Score=30.20 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=18.0
Q ss_pred EEEEEEEEecCcCceEecce
Q psy5557 128 TLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 128 ~~~GtL~gFDq~mNLVLsDa 147 (213)
.+.|...-+|.|+||+++=.
T Consensus 169 ~i~g~Vi~iD~FGNlitnI~ 188 (258)
T PF01887_consen 169 GIRGEVIYIDHFGNLITNIS 188 (258)
T ss_dssp EEEEEEEEEETTSEEEEEEE
T ss_pred eEEEEEEEECccCCeeeCCC
Confidence 89999999999999998654
No 129
>PRK06630 hypothetical protein; Provisional
Probab=35.65 E-value=19 Score=28.86 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=16.8
Q ss_pred EEEEEEEecCcCceEecce
Q psy5557 129 LIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 129 ~~GtL~gFDq~mNLVLsDa 147 (213)
..|+|+|-|.|+|-...+.
T Consensus 11 r~G~lVG~D~~GNkYYE~~ 29 (99)
T PRK06630 11 FFHKKVGEDEFLNQYYESR 29 (99)
T ss_pred ccCeEeEEeCCCChhcccC
Confidence 4799999999999988775
No 130
>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=34.30 E-value=1.1e+02 Score=20.07 Aligned_cols=25 Identities=8% Similarity=-0.148 Sum_probs=20.7
Q ss_pred cCCeEEEEecCCeEEEEEEEEecCc
Q psy5557 115 QNRQQGLYPNQKRTLIGYLRSVDQF 139 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~GtL~gFDq~ 139 (213)
+|..|.+...||..|.|++.+++..
T Consensus 5 ~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 5 VGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCEEEEEeCCCCEEEEEEEEECCC
Confidence 4666777767999999999999975
No 131
>PRK11625 Rho-binding antiterminator; Provisional
Probab=33.89 E-value=1.7e+02 Score=22.49 Aligned_cols=52 Identities=13% Similarity=0.097 Sum_probs=36.4
Q ss_pred hcCCeEEEEecCCeEEEEEEEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEE
Q psy5557 114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMG 176 (213)
Q Consensus 114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~ 176 (213)
.-+.+|.+.|.||..+.|+- .|-+. .+-+|++.-+. .-+...||=|.|++|+
T Consensus 21 ~~~~~l~l~l~dGe~~~g~A--~D~~~----~~k~EyL~l~~-----~g~~~~iRLD~I~s~~ 72 (84)
T PRK11625 21 QHHLMLTLELKDGEVLQAKA--SDLVS----RKNVEYLVVEA-----AGETRELRLDKIASFS 72 (84)
T ss_pred hcCCeEEEEECCCCEEEEEE--Eeeec----CCceEEEEEEc-----CCCEEEEEeeeEeecc
Confidence 35789999999999999986 45443 35567664322 1255678888888887
No 132
>KOG3168|consensus
Probab=33.66 E-value=1.1e+02 Score=26.77 Aligned_cols=76 Identities=9% Similarity=-0.035 Sum_probs=51.4
Q ss_pred HHHHHhhcCCeEEEE-ecCCeEEEEEEEEecCcCceEecceEEEeecCCcc------ceeccceeeeecCcEEE--EEee
Q psy5557 108 KNKKAEEQNRQQGLY-PNQKRTLIGYLRSVDQFANLVLHKTIERIHVGNQY------GDIPRGIFIIRGENVVL--MGEV 178 (213)
Q Consensus 108 ~~~L~~~LgKrV~V~-LkDGR~~~GtL~gFDq~mNLVLsDavEri~~~n~~------~er~LGlVlIRGnnIV~--I~~i 178 (213)
++++..|.+.+-.+. ++++.+..+....+|---|||+--|.+.-..+..+ ...-.|...+-|-.|.. ++..
T Consensus 42 l~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVegppp~s~s~~~v~ag~~~g~G~ar~~Grgip~~~~~~a 121 (177)
T KOG3168|consen 42 LQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVEGPPPPSDSFRRVPAGAARGPGIARVAGRGIPSGPLGQA 121 (177)
T ss_pred HHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEeccCCCCCccccccccccccCCcccccccCCCccCCCcccC
Confidence 456677777776666 89999999999999999999998776543222211 13345777777777776 5544
Q ss_pred ccccc
Q psy5557 179 VTVVN 183 (213)
Q Consensus 179 D~~~d 183 (213)
-..++
T Consensus 122 ~~gLt 126 (177)
T KOG3168|consen 122 PEGLT 126 (177)
T ss_pred CCCCc
Confidence 44443
No 133
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=32.40 E-value=16 Score=31.93 Aligned_cols=63 Identities=24% Similarity=0.268 Sum_probs=40.1
Q ss_pred hhcCCeEEEEecCCeEEEEEE-EEecCcCceEecceEEEeec-CCccceeccceeeeecCcEEEEEeecc
Q psy5557 113 EEQNRQQGLYPNQKRTLIGYL-RSVDQFANLVLHKTIERIHV-GNQYGDIPRGIFIIRGENVVLMGEVVT 180 (213)
Q Consensus 113 ~~LgKrV~V~LkDGR~~~GtL-~gFDq~mNLVLsDavEri~~-~n~~~er~LGlVlIRGnnIV~I~~iD~ 180 (213)
.+|++-+.|.|--=|-|.|.= .|||.++|..+.=. |++.. +-.| + ...-|+|=+|+.+.....
T Consensus 98 eFL~rl~~i~lPrvrdfrGls~~sFDg~GN~sfGI~-E~i~FPei~y-D---~~~~i~GMdi~ivtta~~ 162 (180)
T COG0094 98 EFLDRLLNIALPRVRDFRGLSPKSFDGRGNYSFGIK-EQIIFPEIDY-D---PIIGIRGMDITIVTTAKG 162 (180)
T ss_pred HHHHHHHHhhccccccccCCCccccCCCCceEecch-heeecCcccc-C---ccCCccCceEEEEecCCC
Confidence 344444466665456677655 89999999999766 44433 3333 2 234489999888876544
No 134
>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional
Probab=31.74 E-value=25 Score=28.64 Aligned_cols=19 Identities=26% Similarity=0.319 Sum_probs=16.6
Q ss_pred EEEEEEEecCcCceEecce
Q psy5557 129 LIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 129 ~~GtL~gFDq~mNLVLsDa 147 (213)
-.|+|+|.|.|+|-...+.
T Consensus 8 r~g~lVG~D~~GNkYYE~~ 26 (115)
T PLN03095 8 RAGRLVGEDEFGNKYYENP 26 (115)
T ss_pred ecceEeEEcCCCCeeeEcC
Confidence 4799999999999988764
No 135
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=30.81 E-value=98 Score=25.98 Aligned_cols=27 Identities=15% Similarity=0.064 Sum_probs=23.6
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEecC
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVDQ 138 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFDq 138 (213)
..+||+.|.....+|..++|++.++..
T Consensus 89 ~~lIGk~V~~~~~~g~~~tG~V~sV~~ 115 (140)
T PRK11911 89 VNFIGKDIKGVSLNGEVISGKVESVQQ 115 (140)
T ss_pred HHhhCceeEEEecCCCEEEEEEEEEEE
Confidence 479999999888999999999987764
No 136
>CHL00078 rpl5 ribosomal protein L5
Probab=29.54 E-value=16 Score=31.51 Aligned_cols=67 Identities=21% Similarity=0.154 Sum_probs=40.6
Q ss_pred HHhhcCCeEEEEecCCeEEEEE-EEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGY-LRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~Gt-L~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
+-.+|++-|.+.|-.=+.|.|. ..+||.++|+.+.=....+++.-.| --...|+|=+|..+.....+
T Consensus 97 my~FL~kli~~vlPrirdf~Gi~~~sfd~~Gn~sfGi~e~~~FPEi~~----d~~~~i~G~~Itivtta~t~ 164 (181)
T CHL00078 97 MYAFLDRLINLALPRIRDFQGLSPKSFDGHGNYNLGLKEQLMFPEIDY----DKIDQIRGMDISIVTTAKTD 164 (181)
T ss_pred HHHHHHHHHHHhcccccccccccccccCCCceEEECcchhccCCCccc----CccCCcCCCeEEEEEeeCCH
Confidence 3344454456666555677765 7899999988876542222222122 12456899999888765443
No 137
>COG5439 Uncharacterized conserved protein [Function unknown]
Probab=29.33 E-value=19 Score=29.20 Aligned_cols=73 Identities=14% Similarity=0.252 Sum_probs=44.6
Q ss_pred CCeEEEEecCCeEEEEEEE-----EecCcCceEec----ceEEEeecCCccceeccceeeeecCcEEEEEeec----ccc
Q psy5557 116 NRQQGLYPNQKRTLIGYLR-----SVDQFANLVLH----KTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVV----TVV 182 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~-----gFDq~mNLVLs----DavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD----~~~ 182 (213)
|.||++.=.| .+|.|+++ +|-+-||++|+ ||.+.+.+ --|+-|++.+-|-+++-.. .-.
T Consensus 7 DYRvw~E~~d-iyFdG~mRL~s~eayaPIm~l~~~~L~a~ps~mtin-------L~gL~FLNSSGInlLakftievRk~p 78 (112)
T COG5439 7 DYRVWFEEAD-IYFDGFMRLESMEAYAPIMNLMLEILSADPSEMTIN-------LEGLEFLNSSGINLLAKFTIEVRKKP 78 (112)
T ss_pred ceEEEeccCc-eEEeeEEecccccccchHHHHHHHHHhcChHHhEEe-------cccceeecccchHHHHhhhhhhhcCC
Confidence 6778877655 88889875 56777888765 44443321 1377777777766655422 113
Q ss_pred ccccccCCCCCCcc
Q psy5557 183 NVKVIKGGDSGKKW 196 (213)
Q Consensus 183 d~s~~eg~~~g~~~ 196 (213)
|.++..-|++-.||
T Consensus 79 d~~fvvrGs~~ipW 92 (112)
T COG5439 79 DTSFVVRGSKNIPW 92 (112)
T ss_pred CceEEEecCCCCcc
Confidence 45555556666666
No 138
>PF08830 DUF1806: Protein of unknown function (DUF1806); InterPro: IPR014934 This entry consists of bacterial uncharacterised proteins. The structure of one of the proteins has been solved and it adopts a beta barrel-like structure. ; PDB: 1NJH_A.
Probab=29.28 E-value=1.9e+02 Score=23.76 Aligned_cols=24 Identities=17% Similarity=-0.035 Sum_probs=16.4
Q ss_pred HHHHHHHHhhcCCeEEEEe--cCCeE
Q psy5557 105 EEKKNKKAEEQNRQQGLYP--NQKRT 128 (213)
Q Consensus 105 eE~~~~L~~~LgKrV~V~L--kDGR~ 128 (213)
+.-...|.++.|++|+|.| ++|-+
T Consensus 6 ~~VQ~~l~~~~~~~vYlHlETTnGAY 31 (114)
T PF08830_consen 6 EEVQALLDSFANKDVYLHLETTNGAY 31 (114)
T ss_dssp HHHHHHHHHTTTS-EEEEEEEEE---
T ss_pred HHHHHHHHHhcCCceEEEEeecCchh
Confidence 4556789999999999987 56643
No 139
>PHA00672 hypothetical protein
Probab=27.22 E-value=1.9e+02 Score=24.71 Aligned_cols=27 Identities=19% Similarity=0.186 Sum_probs=21.7
Q ss_pred EEecCCeEEEEEEEEecCcCceEecceEE
Q psy5557 121 LYPNQKRTLIGYLRSVDQFANLVLHKTIE 149 (213)
Q Consensus 121 V~LkDGR~~~GtL~gFDq~mNLVLsDavE 149 (213)
|++--|-.++|.+.-||.+ |+++--.-
T Consensus 52 i~IPkGt~LtG~~hkf~~~--ii~sG~it 78 (152)
T PHA00672 52 IRIPAGVALTGALIKVSTV--LIFSGHAT 78 (152)
T ss_pred EeccCceeeeeeeeEeeEE--EEecccEE
Confidence 5667899999999999999 77765543
No 140
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=25.35 E-value=57 Score=25.41 Aligned_cols=20 Identities=15% Similarity=0.223 Sum_probs=7.8
Q ss_pred EEEEEEEEecCcCceEecce
Q psy5557 128 TLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 128 ~~~GtL~gFDq~mNLVLsDa 147 (213)
++.|++.|||-..++.|++|
T Consensus 124 ti~G~~~g~~~~~~v~l~~c 143 (144)
T PF12869_consen 124 TIKGICTGYSLMGVVMLDDC 143 (144)
T ss_dssp EEEEE-----SSS-EEEE--
T ss_pred EEEEEEEeeecCCcEEeecc
Confidence 45678888875557777766
No 141
>PRK11637 AmiB activator; Provisional
Probab=25.16 E-value=1e+02 Score=29.04 Aligned_cols=17 Identities=24% Similarity=0.485 Sum_probs=11.1
Q ss_pred ccceeeeecCcEEEEEe
Q psy5557 161 PRGIFIIRGENVVLMGE 177 (213)
Q Consensus 161 ~LGlVlIRGnnIV~I~~ 177 (213)
..|..|=.|+.|.+|+.
T Consensus 384 ~~G~~V~~G~~ig~~g~ 400 (428)
T PRK11637 384 SVGAQVRAGQPIALVGS 400 (428)
T ss_pred CCcCEECCCCeEEeecC
Confidence 45666667777766653
No 142
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.94 E-value=1.1e+02 Score=27.54 Aligned_cols=32 Identities=16% Similarity=0.150 Sum_probs=25.7
Q ss_pred CCeEEEEecCCeEEEEEEEEecCcCceEecce
Q psy5557 116 NRQQGLYPNQKRTLIGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 116 gKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDa 147 (213)
...+.|.+.||+.|.+.++|+|...-|.+-..
T Consensus 95 a~~i~v~l~dg~~~~a~~vg~d~~~dlavlki 126 (347)
T COG0265 95 AEEITVTLADGREVPAKLVGKDPISDLAVLKI 126 (347)
T ss_pred cceEEEEeCCCCEEEEEEEecCCccCEEEEEe
Confidence 45788889999999999999998776655443
No 143
>PF05735 TSP_C: Thrombospondin C-terminal region; InterPro: IPR008859 Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers []. EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin. The globular C-terminal domain is a beta sandwich of two curved antiparallel beta-sheets []. The fold is an elaboration of the jelly role topology, with strand B3-B7, B11 and B14-B15 forming the eight-stranded jelly roll motif. The function of the C-terminal domain is not yet known.; GO: 0005509 calcium ion binding, 0007155 cell adhesion, 0005576 extracellular region; PDB: 1UX6_A 1YO8_A 2RHP_A 3FBY_C.
Probab=24.85 E-value=1.4e+02 Score=26.57 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=22.5
Q ss_pred eEEEEecCCeEEE-------EEEEEecCcCceEecceE
Q psy5557 118 QQGLYPNQKRTLI-------GYLRSVDQFANLVLHKTI 148 (213)
Q Consensus 118 rV~V~LkDGR~~~-------GtL~gFDq~mNLVLsDav 148 (213)
+.+++..+|+++. |.++|.|.|.++-++-+.
T Consensus 4 P~W~v~~~G~ev~Qt~NsdP~l~ig~~~~~~vdf~GT~ 41 (201)
T PF05735_consen 4 PNWVVSNQGAEVVQTLNSDPGLAIGPDNFGGVDFSGTF 41 (201)
T ss_dssp --EEEECCCTEEEE-SS-SSEEEEEEEEESSEEEEEEE
T ss_pred CceEEecCCeEEEEeccCCCeEEEccceecceEEEEEE
Confidence 4567777776665 778888989888887774
No 144
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=24.65 E-value=83 Score=26.14 Aligned_cols=26 Identities=4% Similarity=0.042 Sum_probs=19.7
Q ss_pred HhhcCCeEEEEecCCeEEEEEEEEec
Q psy5557 112 AEEQNRQQGLYPNQKRTLIGYLRSVD 137 (213)
Q Consensus 112 ~~~LgKrV~V~LkDGR~~~GtL~gFD 137 (213)
++.+-+-+.|.|.+|+.++..+=|..
T Consensus 46 NSA~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 46 NSALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred CchhheEEEEEeCCCCEEEEEcCCCC
Confidence 45567788999999998887666655
No 145
>PRK00010 rplE 50S ribosomal protein L5; Validated
Probab=23.77 E-value=19 Score=30.91 Aligned_cols=67 Identities=22% Similarity=0.172 Sum_probs=40.1
Q ss_pred HHhhcCCeEEEEecCCeEEEEE-EEEecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEeeccc
Q psy5557 111 KAEEQNRQQGLYPNQKRTLIGY-LRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVVTV 181 (213)
Q Consensus 111 L~~~LgKrV~V~LkDGR~~~Gt-L~gFDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~iD~~ 181 (213)
+.++|++=+.+.|-.-+.|.|. ..+||.++|+.+.=-...+.+.-.| --..-|+|=+|..+....++
T Consensus 96 my~FL~kli~~vlPrirdf~Gi~~~sfD~~Gn~sfGi~e~~~FPei~y----d~~~~i~G~~Itivtta~t~ 163 (179)
T PRK00010 96 MYEFLDRLINIALPRVRDFRGLSPKSFDGRGNYTLGIKEQIIFPEIDY----DKIDKIRGMDITIVTTAKTD 163 (179)
T ss_pred HHHHHHHHHHHhcccccccccccccccCCCceEEECcchhhcCCCccc----CccCCcCCceEEEEeccCCH
Confidence 3344444456666666777776 6799999988876332122222112 12356889999888765443
No 146
>PRK08183 NADH dehydrogenase; Validated
Probab=23.69 E-value=41 Score=27.97 Aligned_cols=18 Identities=22% Similarity=0.285 Sum_probs=15.8
Q ss_pred EEEEEEecCcCceEecce
Q psy5557 130 IGYLRSVDQFANLVLHKT 147 (213)
Q Consensus 130 ~GtL~gFDq~mNLVLsDa 147 (213)
.|+|+|.|.|+|-...+.
T Consensus 25 ~g~lVG~D~~GNkYYE~~ 42 (133)
T PRK08183 25 KGERVGEDEFGNVYYRTK 42 (133)
T ss_pred cCeEeEecCCCCeeeecC
Confidence 699999999999988664
No 147
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=23.56 E-value=1.1e+02 Score=20.98 Aligned_cols=36 Identities=8% Similarity=0.066 Sum_probs=23.5
Q ss_pred HHHHHHHHhhcCCeEEEEecCCeEEEEEEEEecCcCceEec
Q psy5557 105 EEKKNKKAEEQNRQQGLYPNQKRTLIGYLRSVDQFANLVLH 145 (213)
Q Consensus 105 eE~~~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLs 145 (213)
++..+.+..++|++|.|+ |..|-+. +=..|.+++|+
T Consensus 8 ~~~~~~~~~~~Gk~V~V~---G~l~~a~--t~hH~Tpvll~ 43 (48)
T PF14485_consen 8 EEDYSYLKSLLGKRVSVT---GKLFHAH--TGHHHTPVLLD 43 (48)
T ss_pred hhhhHHHHHhcCCeEEEE---EEEeecc--CcccCCceeee
Confidence 355678888999999987 4433321 22356677776
No 148
>COG4466 Veg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.06 E-value=1.1e+02 Score=23.72 Aligned_cols=26 Identities=19% Similarity=0.115 Sum_probs=21.8
Q ss_pred hhHHHHHHHHhhcCCeEEEEecCCeE
Q psy5557 103 KKEEKKNKKAEEQNRQQGLYPNQKRT 128 (213)
Q Consensus 103 ~keE~~~~L~~~LgKrV~V~LkDGR~ 128 (213)
+.-.+...|..++|.+|.+++++||.
T Consensus 6 ki~~IK~~i~ah~G~~v~lk~ngGRK 31 (80)
T COG4466 6 KIVDIKESIDAHLGERVTLKANGGRK 31 (80)
T ss_pred HHHHHHHHHHhccCcEEEEEecCCce
Confidence 34456788999999999999999974
No 149
>KOG4401|consensus
Probab=22.66 E-value=1e+02 Score=27.12 Aligned_cols=35 Identities=9% Similarity=0.025 Sum_probs=31.6
Q ss_pred hcCCeEEEEecCCeEEEEEEEEecCcCceEecceE
Q psy5557 114 EQNRQQGLYPNQKRTLIGYLRSVDQFANLVLHKTI 148 (213)
Q Consensus 114 ~LgKrV~V~LkDGR~~~GtL~gFDq~mNLVLsDav 148 (213)
.+|-.|.|.+-+|....|.+++||--.++..-+|.
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 46788999999999999999999999888888886
No 150
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=22.51 E-value=1.8e+02 Score=22.38 Aligned_cols=41 Identities=12% Similarity=0.148 Sum_probs=27.2
Q ss_pred ecCcCceEecceEEEeecCCccceeccceeeeecCcEEEEEe
Q psy5557 136 VDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 177 (213)
Q Consensus 136 FDq~mNLVLsDavEri~~~n~~~er~LGlVlIRGnnIV~I~~ 177 (213)
-|...-+.+..++..-++.+. ..++-|.+++.|..|..|..
T Consensus 54 r~~~g~~~~~r~y~FEFS~~G-~~ry~G~l~m~G~~l~~v~l 94 (97)
T PF11743_consen 54 RDSRGRLRWRRVYQFEFSSDG-EDRYQGELVMLGRRLISVEL 94 (97)
T ss_pred cCCCCCeEEEEEEEEEEeCCC-hhcceEEEEEECCeeeEEEc
Confidence 345566666666443333222 26788999999999998874
No 151
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=22.30 E-value=2e+02 Score=20.19 Aligned_cols=32 Identities=6% Similarity=0.028 Sum_probs=22.8
Q ss_pred cCCeEEEEecCC----eEEEEEEEEecCcCceEecc
Q psy5557 115 QNRQQGLYPNQK----RTLIGYLRSVDQFANLVLHK 146 (213)
Q Consensus 115 LgKrV~V~LkDG----R~~~GtL~gFDq~mNLVLsD 146 (213)
+|.+|.|.+.++ ..|...|.|++..-.|+++-
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~ 38 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISM 38 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE-
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEc
Confidence 688899988443 36999999999886666643
No 152
>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=22.25 E-value=65 Score=23.52 Aligned_cols=25 Identities=12% Similarity=0.037 Sum_probs=20.7
Q ss_pred hcCCeEEEEecCCeEEEEEEEEecC
Q psy5557 114 EQNRQQGLYPNQKRTLIGYLRSVDQ 138 (213)
Q Consensus 114 ~LgKrV~V~LkDGR~~~GtL~gFDq 138 (213)
|-..+|.|.|-||..+.++|.+-|.
T Consensus 2 ~~~~~i~iRlp~G~~~~~~F~~~~t 26 (79)
T cd01772 2 YTETRIQIRLLDGTTLKQTFKAREQ 26 (79)
T ss_pred CcEEEEEEECCCCCEEEEEeCCCCh
Confidence 4567899999999999999876553
No 153
>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=22.18 E-value=1.8e+02 Score=22.28 Aligned_cols=23 Identities=13% Similarity=0.079 Sum_probs=16.6
Q ss_pred HHHHhhcCCeEEEEecCCeEEEEEEEEecCc
Q psy5557 109 NKKAEEQNRQQGLYPNQKRTLIGYLRSVDQF 139 (213)
Q Consensus 109 ~~L~~~LgKrV~V~LkDGR~~~GtL~gFDq~ 139 (213)
..|..|+|++|++. |.+.++|.-
T Consensus 8 ~~L~~f~gk~V~iv--------GkV~~~~~~ 30 (101)
T cd04479 8 AMLSQFVGKTVRIV--------GKVEKVDGD 30 (101)
T ss_pred HHHHhhCCCEEEEE--------EEEEEecCC
Confidence 47899999999876 555555543
No 154
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=21.98 E-value=3e+02 Score=19.55 Aligned_cols=33 Identities=18% Similarity=0.074 Sum_probs=28.1
Q ss_pred cCCeEEEEecCCeEEE--EEEEEecCc-CceEecce
Q psy5557 115 QNRQQGLYPNQKRTLI--GYLRSVDQF-ANLVLHKT 147 (213)
Q Consensus 115 LgKrV~V~LkDGR~~~--GtL~gFDq~-mNLVLsDa 147 (213)
.+..|.+.+.++..+. +.+..+|.. .+|-|-.+
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~All~v 64 (120)
T PF13365_consen 29 DNSSVEVVFPDGRRVPPVAEVVYFDPDDYDLALLKV 64 (120)
T ss_dssp TCSEEEEEETTSCEEETEEEEEEEETT-TTEEEEEE
T ss_pred CCCEEEEEecCCCEEeeeEEEEEECCccccEEEEEE
Confidence 5678999999998888 999999998 88877554
Done!