Query 032228
Match_columns 145
No_of_seqs 113 out of 674
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:18:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032228hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00208 translation initiatio 100.0 7.8E-54 1.7E-58 330.4 16.1 145 1-145 1-145 (145)
2 PTZ00329 eukaryotic translatio 100.0 1.3E-53 2.8E-58 332.1 15.8 131 1-137 1-131 (155)
3 KOG3403 Translation initiation 100.0 4.7E-47 1E-51 287.1 6.6 145 1-145 1-145 (145)
4 TIGR00523 eIF-1A eukaryotic/ar 100.0 1.2E-36 2.5E-41 222.0 13.3 98 14-111 1-99 (99)
5 PRK04012 translation initiatio 100.0 3.7E-36 8E-41 219.8 13.4 95 17-111 6-100 (100)
6 smart00652 eIF1a eukaryotic tr 100.0 6.4E-36 1.4E-40 211.7 12.1 83 28-110 1-83 (83)
7 cd04456 S1_IF1A_like S1_IF1A_l 100.0 2.2E-33 4.7E-38 196.9 11.3 77 33-109 1-78 (78)
8 cd05793 S1_IF1A S1_IF1A: Trans 100.0 8.6E-33 1.9E-37 193.3 11.3 77 33-109 1-77 (77)
9 cd05792 S1_eIF1AD_like S1_eIF1 100.0 1.1E-32 2.4E-37 193.7 10.6 77 33-109 1-78 (78)
10 COG0361 InfA Translation initi 100.0 1.2E-28 2.6E-33 172.1 9.2 72 28-99 3-75 (75)
11 PF01176 eIF-1a: Translation i 99.9 3.6E-27 7.7E-32 159.4 7.5 65 30-94 1-65 (65)
12 TIGR00008 infA translation ini 99.9 7.4E-25 1.6E-29 150.6 9.5 62 33-94 6-68 (68)
13 PRK12442 translation initiatio 99.9 5.4E-24 1.2E-28 152.3 10.0 64 33-96 8-72 (87)
14 KOG2925 Predicted translation 99.9 1.5E-25 3.3E-30 174.4 1.4 100 17-116 7-110 (167)
15 CHL00010 infA translation init 99.8 1.5E-18 3.2E-23 121.4 9.1 66 33-98 8-74 (78)
16 PRK00276 infA translation init 99.8 3.9E-18 8.5E-23 117.2 9.2 64 33-96 8-72 (72)
17 cd04451 S1_IF1 S1_IF1: Transla 99.5 5.2E-14 1.1E-18 94.0 8.5 62 33-94 2-64 (64)
18 cd04466 S1_YloQ_GTPase S1_YloQ 98.3 5.9E-06 1.3E-10 54.4 7.3 59 35-96 2-61 (68)
19 PRK00098 GTPase RsgA; Reviewed 97.1 0.0023 4.9E-08 53.8 7.7 47 35-82 2-49 (298)
20 PRK12289 GTPase RsgA; Reviewed 97.1 0.0023 5E-08 55.6 7.5 62 29-91 4-72 (352)
21 PRK12288 GTPase RsgA; Reviewed 96.7 0.0084 1.8E-07 52.0 7.9 58 34-95 40-99 (347)
22 cd01854 YjeQ_engC YjeQ/EngC. 96.5 0.0084 1.8E-07 50.1 6.9 57 36-96 1-58 (287)
23 PRK01889 GTPase RsgA; Reviewed 95.2 0.069 1.5E-06 46.2 6.9 63 31-99 26-93 (356)
24 cd00164 S1_like S1_like: Ribos 94.7 0.15 3.3E-06 31.3 5.8 57 35-92 2-63 (65)
25 cd05685 S1_Tex S1_Tex: The C-t 91.2 1.3 2.9E-05 27.7 6.3 59 32-92 2-66 (68)
26 TIGR00638 Mop molybdenum-pteri 89.3 2.1 4.6E-05 27.5 6.2 55 30-84 5-62 (69)
27 PF03459 TOBE: TOBE domain; I 88.7 0.94 2E-05 29.0 4.1 55 29-83 2-59 (64)
28 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 87.9 2 4.3E-05 29.1 5.5 64 29-94 4-77 (86)
29 PHA02945 interferon resistance 87.1 5.9 0.00013 28.7 7.8 66 26-93 6-79 (88)
30 COG1162 Predicted GTPases [Gen 85.5 2.1 4.5E-05 37.1 5.6 60 34-97 5-68 (301)
31 cd04454 S1_Rrp4_like S1_Rrp4_l 84.7 6.2 0.00013 26.5 6.7 63 28-92 3-71 (82)
32 PF02736 Myosin_N: Myosin N-te 82.8 4 8.7E-05 25.0 4.6 33 27-60 7-39 (42)
33 COG1093 SUI2 Translation initi 81.5 2.8 6.1E-05 35.9 4.7 75 27-101 7-91 (269)
34 PF11948 DUF3465: Protein of u 81.2 7.7 0.00017 30.0 6.6 62 34-95 41-111 (131)
35 PF15057 DUF4537: Domain of un 80.3 7 0.00015 29.2 6.1 50 34-84 15-68 (124)
36 PF01455 HupF_HypC: HupF/HypC 77.9 19 0.00041 24.4 8.6 56 35-103 6-63 (68)
37 cd05705 S1_Rrp5_repeat_hs14 S1 77.6 19 0.0004 24.2 7.6 60 32-92 5-72 (74)
38 TIGR03689 pup_AAA proteasome A 76.7 5 0.00011 36.9 5.1 54 27-82 102-155 (512)
39 COG0048 RpsL Ribosomal protein 76.5 5 0.00011 30.9 4.3 45 46-93 58-105 (129)
40 PRK10413 hydrogenase 2 accesso 76.1 8.4 0.00018 27.3 5.1 59 35-102 6-67 (82)
41 TIGR00074 hypC_hupF hydrogenas 75.8 13 0.00027 26.0 5.9 56 35-103 6-61 (76)
42 PTZ00248 eukaryotic translatio 74.2 16 0.00034 31.9 7.3 78 27-105 13-101 (319)
43 cd05707 S1_Rrp5_repeat_sc11 S1 73.2 21 0.00045 22.9 6.1 59 33-92 3-66 (68)
44 PF04076 BOF: Bacterial OB fol 72.7 13 0.00029 27.2 5.6 48 33-81 38-85 (103)
45 cd05791 S1_CSL4 S1_CSL4: CSL4, 72.6 8.8 0.00019 27.1 4.5 58 28-86 3-76 (92)
46 KOG2107 Uncharacterized conser 72.2 8.5 0.00018 31.1 4.8 48 41-106 100-147 (179)
47 cd04479 RPA3 RPA3: A subfamily 71.5 12 0.00025 26.9 5.0 31 33-64 19-49 (101)
48 PRK03987 translation initiatio 71.3 21 0.00046 30.0 7.3 65 28-93 5-77 (262)
49 PRK11642 exoribonuclease R; Pr 71.1 39 0.00085 32.9 9.8 46 71-116 186-240 (813)
50 CHL00051 rps12 ribosomal prote 71.1 7.2 0.00016 29.9 4.0 34 46-82 52-85 (123)
51 cd05689 S1_RPS1_repeat_ec4 S1_ 70.8 25 0.00054 22.6 7.0 62 29-92 2-70 (72)
52 PRK10409 hydrogenase assembly 70.7 18 0.00039 26.1 5.8 54 35-102 6-66 (90)
53 cd04452 S1_IF2_alpha S1_IF2_al 70.5 26 0.00056 22.6 7.1 61 32-94 5-73 (76)
54 PTZ00454 26S protease regulato 70.3 14 0.0003 32.8 6.2 54 30-84 64-117 (398)
55 cd00319 Ribosomal_S12_like Rib 69.5 8.3 0.00018 28.3 3.9 33 46-81 37-69 (95)
56 PF03749 SfsA: Sugar fermentat 68.6 44 0.00094 27.4 8.4 65 45-111 5-88 (215)
57 smart00316 S1 Ribosomal protei 68.1 25 0.00053 21.4 7.7 62 32-94 4-70 (72)
58 PF00717 Peptidase_S24: Peptid 67.7 2.5 5.4E-05 27.1 0.8 24 71-95 11-34 (70)
59 cd05696 S1_Rrp5_repeat_hs4 S1_ 67.7 30 0.00064 22.8 6.1 57 36-92 7-68 (71)
60 TIGR00981 rpsL_bact ribosomal 65.9 10 0.00022 29.1 3.9 34 46-82 52-85 (124)
61 PRK05163 rpsL 30S ribosomal pr 65.5 11 0.00024 28.9 4.0 34 46-82 52-85 (124)
62 cd05790 S1_Rrp40 S1_Rrp40: Rrp 65.4 22 0.00048 25.2 5.3 55 29-86 4-65 (86)
63 PF09038 53-BP1_Tudor: Tumour 65.0 18 0.00039 27.7 5.0 37 36-84 22-58 (122)
64 PLN00207 polyribonucleotide nu 64.3 23 0.0005 35.0 6.8 65 28-95 750-822 (891)
65 cd03368 Ribosomal_S12 S12-like 63.9 12 0.00026 28.1 3.8 34 46-82 50-83 (108)
66 PRK04163 exosome complex RNA-b 62.6 26 0.00056 28.8 6.0 78 27-105 59-161 (235)
67 PF08661 Rep_fac-A_3: Replicat 62.6 25 0.00054 25.2 5.3 33 34-66 23-56 (109)
68 cd04482 RPA2_OBF_like RPA2_OBF 62.4 14 0.0003 26.0 3.8 38 45-82 19-59 (91)
69 cd05690 S1_RPS1_repeat_ec5 S1_ 61.4 38 0.00083 21.3 6.1 59 33-92 3-67 (69)
70 PF00164 Ribosom_S12_S23: Ribo 61.0 13 0.00028 28.4 3.6 51 32-85 27-87 (122)
71 PRK08059 general stress protei 60.8 56 0.0012 24.0 7.0 65 31-96 8-77 (123)
72 cd05692 S1_RPS1_repeat_hs4 S1_ 60.4 37 0.00081 20.8 7.1 59 33-93 3-66 (69)
73 PRK07899 rpsA 30S ribosomal pr 60.3 48 0.001 30.4 7.8 64 31-95 294-362 (486)
74 cd05704 S1_Rrp5_repeat_hs13 S1 59.7 47 0.001 21.8 6.5 57 32-91 5-67 (72)
75 CHL00141 rpl24 ribosomal prote 59.6 14 0.00031 26.0 3.4 32 68-99 6-37 (83)
76 smart00318 SNc Staphylococcal 59.2 27 0.00058 25.3 5.0 75 33-108 2-103 (138)
77 cd06530 S26_SPase_I The S26 Ty 59.1 11 0.00025 25.1 2.8 24 71-94 14-40 (85)
78 PF04717 Phage_base_V: Phage-r 58.2 44 0.00094 22.4 5.6 56 44-99 10-72 (79)
79 TIGR02063 RNase_R ribonuclease 58.1 1.1E+02 0.0025 28.8 10.1 84 32-115 121-225 (709)
80 COG0298 HypC Hydrogenase matur 58.0 34 0.00073 24.5 5.1 55 35-102 6-63 (82)
81 cd05698 S1_Rrp5_repeat_hs6_sc5 57.8 46 0.001 21.1 7.1 59 33-93 3-67 (70)
82 PF11302 DUF3104: Protein of u 57.6 14 0.00031 26.0 3.1 45 69-119 4-55 (75)
83 PF12857 TOBE_3: TOBE-like dom 57.1 49 0.0011 21.2 6.0 53 29-82 2-58 (58)
84 COG0509 GcvH Glycine cleavage 56.8 7 0.00015 30.2 1.6 40 59-98 3-48 (131)
85 cd04721 BAH_plant_1 BAH, or Br 56.4 18 0.00038 27.3 3.7 48 66-113 3-66 (130)
86 PRK10676 DNA-binding transcrip 55.6 33 0.00072 28.5 5.6 53 31-83 199-254 (263)
87 PRK07252 hypothetical protein; 55.4 83 0.0018 23.3 7.5 63 32-95 5-72 (120)
88 TIGR00156 conserved hypothetic 54.8 43 0.00093 25.6 5.6 49 33-82 61-109 (126)
89 PRK01191 rpl24p 50S ribosomal 54.3 19 0.00041 27.4 3.6 32 68-99 43-74 (120)
90 TIGR02754 sod_Ni_protease nick 53.6 18 0.0004 24.5 3.2 26 71-96 12-40 (90)
91 cd04508 TUDOR Tudor domains ar 53.5 25 0.00055 20.9 3.5 31 30-60 10-42 (48)
92 TIGR02696 pppGpp_PNP guanosine 53.2 36 0.00077 33.0 6.0 62 29-92 645-716 (719)
93 TIGR00230 sfsA sugar fermentat 52.0 56 0.0012 27.2 6.3 74 34-111 10-100 (232)
94 cd04472 S1_PNPase S1_PNPase: P 51.7 56 0.0012 20.2 6.7 58 33-92 3-65 (68)
95 PRK12281 rplX 50S ribosomal pr 51.3 21 0.00045 24.8 3.1 31 69-99 5-35 (76)
96 cd05697 S1_Rrp5_repeat_hs5 S1_ 51.0 63 0.0014 20.6 6.5 60 33-93 3-67 (69)
97 PF04014 Antitoxin-MazE: Antid 50.2 4.4 9.5E-05 25.0 -0.4 30 54-83 4-33 (47)
98 TIGR00358 3_prime_RNase VacB a 50.0 1.5E+02 0.0033 27.9 9.5 45 71-115 120-173 (654)
99 PTZ00361 26 proteosome regulat 49.5 50 0.0011 29.8 6.1 51 31-82 103-153 (438)
100 PRK05054 exoribonuclease II; P 48.7 1.7E+02 0.0037 27.6 9.6 46 71-116 122-177 (644)
101 cd05708 S1_Rrp5_repeat_sc12 S1 48.7 69 0.0015 20.4 7.4 63 32-95 4-72 (77)
102 PRK10053 hypothetical protein; 48.6 57 0.0012 25.0 5.4 48 33-81 65-112 (130)
103 PF08402 TOBE_2: TOBE domain; 48.5 65 0.0014 20.0 5.7 52 31-83 15-69 (75)
104 PTZ00115 40S ribosomal protein 48.2 27 0.00058 30.1 3.9 33 46-81 148-180 (290)
105 COG1098 VacB Predicted RNA bin 48.2 34 0.00074 26.4 4.1 61 32-94 7-72 (129)
106 PRK13806 rpsA 30S ribosomal pr 47.9 80 0.0017 28.6 7.2 65 30-95 292-362 (491)
107 TIGR01439 lp_hng_hel_AbrB loop 47.6 13 0.00028 21.8 1.4 25 58-82 8-32 (43)
108 cd06462 Peptidase_S24_S26 The 47.1 24 0.00052 22.7 2.8 28 71-98 14-41 (84)
109 PRK00347 putative DNA-binding 46.3 1.2E+02 0.0025 25.2 7.3 49 33-85 7-59 (234)
110 cd04453 S1_RNase_E S1_RNase_E: 46.1 98 0.0021 21.4 6.7 54 32-85 9-71 (88)
111 PTZ00194 60S ribosomal protein 46.0 28 0.0006 27.3 3.4 31 68-98 44-74 (143)
112 smart00743 Agenet Tudor-like d 44.5 52 0.0011 20.7 4.1 23 31-53 16-39 (61)
113 PF08605 Rad9_Rad53_bind: Fung 43.2 75 0.0016 24.3 5.4 45 35-82 26-71 (131)
114 cd04719 BAH_Orc1p_animal BAH, 42.9 24 0.00051 26.8 2.5 25 69-93 2-27 (128)
115 cd05693 S1_Rrp5_repeat_hs1_sc1 42.0 1.2E+02 0.0027 21.4 6.8 67 31-98 4-97 (100)
116 TIGR01080 rplX_A_E ribosomal p 41.5 39 0.00085 25.3 3.5 31 68-98 39-69 (114)
117 PF08922 DUF1905: Domain of un 40.6 33 0.00072 23.6 2.8 47 35-81 32-80 (80)
118 PRK00004 rplX 50S ribosomal pr 40.2 36 0.00078 24.9 3.1 31 69-99 3-33 (105)
119 PF10017 Methyltransf_33: Hist 39.9 1.5E+02 0.0032 21.8 6.5 67 33-112 47-114 (127)
120 PRK08582 hypothetical protein; 39.8 1.6E+02 0.0036 22.2 8.5 63 32-96 7-74 (139)
121 smart00333 TUDOR Tudor domain. 38.8 76 0.0016 19.4 4.1 27 34-60 19-46 (57)
122 PF07039 DUF1325: SGF29 tudor- 38.2 54 0.0012 24.8 3.9 61 33-94 19-96 (130)
123 PRK02693 apocytochrome f; Revi 38.2 1.8E+02 0.004 25.5 7.5 70 10-81 180-252 (312)
124 cd05706 S1_Rrp5_repeat_sc10 S1 37.9 1.1E+02 0.0023 19.6 8.3 61 32-93 5-70 (73)
125 COG1489 SfsA DNA-binding prote 37.8 1.6E+02 0.0035 24.8 6.9 55 36-91 10-64 (235)
126 COG0198 RplX Ribosomal protein 37.7 48 0.001 24.6 3.4 31 68-98 2-32 (104)
127 TIGR00717 rpsA ribosomal prote 37.6 1.4E+02 0.0031 26.6 7.1 65 31-96 360-430 (516)
128 KOG1999 RNA polymerase II tran 37.6 81 0.0018 31.8 5.8 76 19-96 520-607 (1024)
129 TIGR02062 RNase_B exoribonucle 37.4 3E+02 0.0065 26.0 9.4 45 71-115 119-173 (639)
130 PRK05807 hypothetical protein; 36.9 1.8E+02 0.0039 21.8 7.5 62 31-95 6-72 (136)
131 smart00739 KOW KOW (Kyprides, 36.1 69 0.0015 16.7 3.4 24 71-94 2-25 (28)
132 TIGR01079 rplX_bact ribosomal 35.7 43 0.00093 24.5 2.9 30 70-99 3-32 (104)
133 cd04471 S1_RNase_R S1_RNase_R: 35.4 1.2E+02 0.0027 19.5 7.5 62 33-95 4-82 (83)
134 PRK10676 DNA-binding transcrip 35.3 85 0.0018 26.1 4.9 46 31-76 127-176 (263)
135 cd04487 RecJ_OBF2_like RecJ_OB 34.9 1.3E+02 0.0028 20.3 5.0 40 43-82 13-55 (73)
136 COG1222 RPT1 ATP-dependent 26S 34.7 2.4E+02 0.0053 25.7 7.9 80 30-110 70-170 (406)
137 cd05695 S1_Rrp5_repeat_hs3 S1_ 34.0 1.3E+02 0.0028 19.3 6.2 58 33-91 3-63 (66)
138 TIGR00982 S23_S12_E_A ribosoma 34.0 88 0.0019 24.5 4.5 35 46-81 64-99 (139)
139 PRK09521 exosome complex RNA-b 33.9 2.3E+02 0.005 22.1 7.9 58 27-85 60-133 (189)
140 PRK08577 hypothetical protein; 33.9 36 0.00079 25.2 2.3 24 59-82 15-38 (136)
141 PF13533 Biotin_lipoyl_2: Biot 33.7 66 0.0014 20.0 3.2 35 57-101 5-39 (50)
142 cd06529 S24_LexA-like Peptidas 33.7 32 0.0007 22.2 1.8 12 71-82 14-25 (81)
143 PF09902 DUF2129: Uncharacteri 33.3 42 0.00091 23.2 2.3 22 88-109 2-23 (71)
144 cd05691 S1_RPS1_repeat_ec6 S1_ 32.9 1.3E+02 0.0028 18.9 6.7 60 33-93 3-67 (73)
145 cd05687 S1_RPS1_repeat_ec1_hs1 32.8 1.3E+02 0.0028 19.0 6.1 59 33-92 3-66 (70)
146 PRK06676 rpsA 30S ribosomal pr 32.4 2.4E+02 0.0052 24.3 7.4 64 31-95 278-346 (390)
147 PRK13806 rpsA 30S ribosomal pr 32.2 2.1E+02 0.0047 25.9 7.4 65 31-96 380-449 (491)
148 cd05795 Ribosomal_P0_L10e Ribo 32.2 64 0.0014 25.2 3.5 41 59-110 134-175 (175)
149 PF13986 DUF4224: Domain of un 32.2 25 0.00055 22.2 1.0 16 93-108 14-29 (47)
150 PRK06299 rpsA 30S ribosomal pr 32.1 1.8E+02 0.0039 26.5 6.9 64 31-95 374-443 (565)
151 PRK04211 rps12P 30S ribosomal 32.0 97 0.0021 24.4 4.4 49 32-81 46-105 (145)
152 COG2063 FlgH Flagellar basal b 31.7 1.1E+02 0.0023 25.8 4.9 35 32-66 147-186 (230)
153 PF03079 ARD: ARD/ARD' family; 31.5 70 0.0015 25.0 3.6 31 42-82 100-130 (157)
154 TIGR03591 polynuc_phos polyrib 31.5 1.2E+02 0.0027 28.8 5.9 60 29-91 616-682 (684)
155 cd06395 PB1_Map2k5 PB1 domain 30.0 19 0.00042 26.0 0.3 12 134-145 43-54 (91)
156 TIGR03027 pepcterm_export puta 30.0 43 0.00092 25.6 2.2 22 62-83 143-164 (165)
157 PRK06299 rpsA 30S ribosomal pr 29.9 2.7E+02 0.006 25.2 7.7 65 31-96 461-530 (565)
158 COG0539 RpsA Ribosomal protein 29.7 1.7E+02 0.0036 27.6 6.3 67 28-95 275-346 (541)
159 cd04461 S1_Rrp5_repeat_hs8_sc7 29.6 1.7E+02 0.0037 19.3 7.2 68 24-93 7-81 (83)
160 COG2996 Predicted RNA-bindinin 29.5 2E+02 0.0043 25.1 6.3 64 34-101 77-143 (287)
161 PF12859 Apc1: Anaphase-promot 29.5 88 0.0019 22.4 3.6 36 42-78 6-41 (105)
162 CHL00037 petA cytochrome f 29.1 3E+02 0.0064 24.3 7.3 71 9-81 186-260 (320)
163 PRK12269 bifunctional cytidyla 29.1 2.5E+02 0.0055 27.8 7.7 67 29-96 751-825 (863)
164 PF08940 DUF1918: Domain of un 29.0 1.1E+02 0.0024 20.5 3.7 30 31-60 18-51 (58)
165 cd03367 Ribosomal_S23 S12-like 28.4 62 0.0013 24.5 2.7 35 46-81 44-79 (115)
166 COG0511 AccB Biotin carboxyl c 28.2 41 0.00088 25.5 1.8 24 53-77 69-92 (140)
167 cd05702 S1_Rrp5_repeat_hs11_sc 28.2 1.7E+02 0.0036 18.7 6.2 54 33-87 3-63 (70)
168 PF01336 tRNA_anti-codon: OB-f 27.6 94 0.002 19.4 3.2 49 34-82 3-56 (75)
169 PF01287 eIF-5a: Eukaryotic el 27.5 2E+02 0.0044 19.5 5.2 48 35-84 6-59 (69)
170 TIGR02609 doc_partner putative 27.3 48 0.001 22.4 1.8 40 54-97 7-46 (74)
171 PF08206 OB_RNB: Ribonuclease 27.3 83 0.0018 20.1 2.9 23 71-93 32-57 (58)
172 cd05686 S1_pNO40 S1_pNO40: pNO 26.6 1.9E+02 0.004 18.8 8.0 56 33-92 6-69 (73)
173 PF00467 KOW: KOW motif; Inte 26.2 79 0.0017 17.9 2.4 26 73-98 1-26 (32)
174 PRK02302 hypothetical protein; 25.8 63 0.0014 23.4 2.3 24 86-109 6-29 (89)
175 COG2002 AbrB Regulators of sta 25.5 74 0.0016 22.2 2.6 36 60-98 17-53 (89)
176 cd05703 S1_Rrp5_repeat_hs12_sc 25.4 2E+02 0.0044 18.8 6.5 60 33-93 3-69 (73)
177 PF01200 Ribosomal_S28e: Ribos 25.4 2.4E+02 0.0051 19.6 6.1 45 32-82 7-61 (69)
178 TIGR02227 sigpep_I_bact signal 25.2 63 0.0014 24.6 2.4 30 51-82 34-63 (163)
179 PF10844 DUF2577: Protein of u 25.2 2.6E+02 0.0055 19.9 5.8 17 34-53 20-36 (100)
180 PF01426 BAH: BAH domain; Int 24.7 81 0.0018 21.8 2.7 14 70-83 2-15 (119)
181 PRK00249 flgH flagellar basal 24.6 1.4E+02 0.0031 24.6 4.4 35 32-66 136-175 (222)
182 PRK02886 hypothetical protein; 24.6 82 0.0018 22.7 2.7 24 86-109 4-27 (87)
183 PRK08225 acetyl-CoA carboxylas 24.3 48 0.001 21.5 1.4 21 56-77 3-23 (70)
184 TIGR00717 rpsA ribosomal prote 24.0 3.1E+02 0.0067 24.5 6.8 62 31-93 447-513 (516)
185 PF07732 Cu-oxidase_3: Multico 23.9 1.8E+02 0.0039 21.1 4.5 36 49-84 7-43 (117)
186 COG1791 Uncharacterized conser 23.9 1.4E+02 0.003 24.4 4.1 32 41-82 102-133 (181)
187 PF09565 RE_NgoFVII: NgoFVII r 23.5 1.4E+02 0.0031 25.7 4.5 28 43-70 236-263 (296)
188 TIGR02228 sigpep_I_arch signal 23.5 72 0.0016 24.7 2.4 31 60-92 36-67 (158)
189 PRK12696 flgH flagellar basal 23.4 1.5E+02 0.0032 24.8 4.4 35 32-66 150-189 (236)
190 PF00575 S1: S1 RNA binding do 23.3 2.1E+02 0.0045 18.1 6.2 61 32-93 6-71 (74)
191 PRK11642 exoribonuclease R; Pr 23.0 4.2E+02 0.0092 25.9 7.9 68 32-100 645-729 (813)
192 PF12843 DUF3820: Protein of u 23.0 49 0.0011 22.8 1.2 28 83-111 15-42 (67)
193 PTZ00067 40S ribosomal S23; Pr 22.9 99 0.0021 24.3 3.0 49 32-81 45-104 (143)
194 PF01957 NfeD: NfeD-like C-ter 22.8 2.9E+02 0.0062 19.6 5.9 41 36-83 94-134 (144)
195 PRK11824 polynucleotide phosph 22.5 4.9E+02 0.011 24.9 8.1 63 29-94 619-688 (693)
196 PF02107 FlgH: Flagellar L-rin 22.4 1.8E+02 0.0039 23.0 4.5 35 32-66 94-133 (179)
197 PRK00215 LexA repressor; Valid 22.2 1.2E+02 0.0026 23.6 3.5 45 54-99 116-160 (205)
198 PRK05889 putative acetyl-CoA c 22.1 59 0.0013 21.3 1.5 22 55-77 3-24 (71)
199 cd06251 M14_ASTE_ASPA_like_1 A 22.0 2.8E+02 0.006 23.1 5.8 43 31-78 242-284 (287)
200 PF08541 ACP_syn_III_C: 3-Oxoa 22.0 88 0.0019 20.9 2.4 26 70-95 65-90 (90)
201 PRK10276 DNA polymerase V subu 21.6 1.4E+02 0.0031 22.1 3.6 37 56-93 51-87 (139)
202 PF03123 CAT_RBD: CAT RNA bind 21.5 1.9E+02 0.004 19.1 3.8 37 37-77 2-39 (59)
203 TIGR03032 conserved hypothetic 21.2 2.5E+02 0.0055 24.9 5.5 61 19-83 195-261 (335)
204 PF02643 DUF192: Uncharacteriz 21.1 97 0.0021 22.3 2.6 52 30-81 57-108 (108)
205 cd05684 S1_DHX8_helicase S1_DH 20.7 2.5E+02 0.0055 18.2 7.5 59 33-94 3-70 (79)
206 TIGR02142 modC_ABC molybdenum 20.6 2.5E+02 0.0054 24.0 5.4 50 32-81 296-348 (354)
207 cd06555 ASCH_PF0470_like ASC-1 20.4 3.3E+02 0.0072 20.1 5.3 52 43-106 16-68 (109)
208 PRK11144 modC molybdate transp 20.4 2.7E+02 0.0058 23.8 5.5 50 33-82 295-346 (352)
209 cd06472 ACD_ScHsp26_like Alpha 20.2 2.2E+02 0.0048 19.3 4.1 31 50-81 6-39 (92)
210 TIGR03265 PhnT2 putative 2-ami 20.2 4.7E+02 0.01 22.5 7.0 51 32-82 290-345 (353)
211 PRK12698 flgH flagellar basal 20.1 1.9E+02 0.0042 23.9 4.4 35 32-66 137-176 (224)
212 PF09866 DUF2093: Uncharacteri 20.1 82 0.0018 19.9 1.7 14 71-84 2-15 (42)
No 1
>PLN00208 translation initiation factor (eIF); Provisional
Probab=100.00 E-value=7.8e-54 Score=330.39 Aligned_cols=145 Identities=88% Similarity=1.419 Sum_probs=133.9
Q ss_pred CCCCCCCCCcccccCCCcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEE
Q 032228 1 MPKNKGKGGKNRKRGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVG 80 (145)
Q Consensus 1 mp~~~~~g~kn~rr~~~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe 80 (145)
||+||+|||||+||+|++++...++|++|+++|+||+|+++|||++|+|+|+||+++||||||||||+|||++||+|+|+
T Consensus 1 m~k~k~kggk~~~~~k~~~~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVe 80 (145)
T PLN00208 1 MPKNKGKGGKNRKRGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVG 80 (145)
T ss_pred CCCCCCCCccccccccccCccceeecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCCCceEEEEEcChhHHHHHHHcCCCCcccccccccccCCCCCCCCCCCCCccccCccccCC
Q 032228 81 LRDYQDDKADVILKYMPDEARLLKAYGELPETTRLNEGIAAGIDDDDEAGPDNYIEFEDEDIDRI 145 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~deik~Lrk~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (145)
+|+|+++||+|+|||+++|++||+++|+||+.|.++++++.+.....++++|++|||+|++++-+
T Consensus 81 l~~~d~~KgdIv~ry~~dqvr~Lkk~G~~P~~f~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~ 145 (145)
T PLN00208 81 LRDYQDDKADVILKYMPDEARLLKAYGELPENTRLNEGIAGDLDEEEDGEGDDYIEFEDEDIDKI 145 (145)
T ss_pred ccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccccccccccCcccCcceeecccccccC
Confidence 99999999999999999999999999999999999999973322111222567999999998754
No 2
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=100.00 E-value=1.3e-53 Score=332.09 Aligned_cols=131 Identities=74% Similarity=1.205 Sum_probs=126.5
Q ss_pred CCCCCCCCCcccccCCCcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEE
Q 032228 1 MPKNKGKGGKNRKRGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVG 80 (145)
Q Consensus 1 mp~~~~~g~kn~rr~~~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe 80 (145)
|||||||||||+||+||+++...++|++|+++|+||+|+++|||++|+|+|+||+++||||||||||+|||++||+|+|+
T Consensus 1 mpk~kgkggk~~~rgk~~~~~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVe 80 (155)
T PTZ00329 1 MPKNKGKGGKNRRRGKNDNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVS 80 (155)
T ss_pred CCCCCCCCCcccccccccCccceeeeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCCCceEEEEEcChhHHHHHHHcCCCCcccccccccccCCCCCCCCCCCCCccc
Q 032228 81 LRDYQDDKADVILKYMPDEARLLKAYGELPETTRLNEGIAAGIDDDDEAGPDNYIEF 137 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~deik~Lrk~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~~~ 137 (145)
+|+|+++||+|||||+++|++||+++|+||+.|.++++++ ||++.+ ++|+|
T Consensus 81 l~~yd~~KgdIi~Ry~~devr~Lk~~g~~P~~~~~~~~~~--~~~~~~----~~~~f 131 (155)
T PTZ00329 81 LRDFQDSKADVILKYTPDEARALKQHGELPETAKINETDI--FDDEGD----DGIEF 131 (155)
T ss_pred ccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccc--cCcCcC----CCeEE
Confidence 9999999999999999999999999999999999999999 885533 47777
No 3
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-47 Score=287.13 Aligned_cols=145 Identities=75% Similarity=1.195 Sum_probs=135.4
Q ss_pred CCCCCCCCCcccccCCCcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEE
Q 032228 1 MPKNKGKGGKNRKRGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVG 80 (145)
Q Consensus 1 mp~~~~~g~kn~rr~~~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe 80 (145)
|||||||||||+||++|+++...|+|++.++||+||+|+++|||++++|.|.||..|||||+||+||+|||.+||+|||.
T Consensus 1 mpknkgkggknrRrGknend~~kReLvfkEegqeYaQv~kmLGnGr~e~~CfDGvkR~~hiRGklrkkVwi~~GDIiLv~ 80 (145)
T KOG3403|consen 1 MPKNKGKGGKNRRRGKNENDFEKRELVFKEEGQEYAQVIKMLGNGRLEASCFDGVKRLCHIRGKLRKKVWINQGDIILVG 80 (145)
T ss_pred CCCCCCCCccccccCcccccchhhheeehhcchhHHHHHhhhcCCcEEEEEecchhhhhhhhccceeeEeecCCCEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCCCceEEEEEcChhHHHHHHHcCCCCcccccccccccCCCCCCCCCCCCCccccCccccCC
Q 032228 81 LRDYQDDKADVILKYMPDEARLLKAYGELPETTRLNEGIAAGIDDDDEAGPDNYIEFEDEDIDRI 145 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~deik~Lrk~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (145)
+++|++.||+|+.+|+++|++.|+..|.+|+.|.+|++++.++.+++++.+++.++++++|+|+|
T Consensus 81 lRD~qd~kaDvilKY~~dEar~LK~~Gelpe~~k~Ne~~~~~~e~~d~~~~~~~~~~~~ed~d~~ 145 (145)
T KOG3403|consen 81 LRDYQDDKADVILKYMPDEARILKAYGELPENAKINETDTFGVEDDDDDIDFDDIEDDDEDIDDI 145 (145)
T ss_pred eecccccccceehhhChHHHHHHHhcCcCCcccccccccccCccCCccccccccccccccccccC
Confidence 99999999999999999999999999999999999999993333344555666677788898876
No 4
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=100.00 E-value=1.2e-36 Score=222.03 Aligned_cols=98 Identities=37% Similarity=0.710 Sum_probs=94.3
Q ss_pred cCCCcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCC-CCceEEE
Q 032228 14 RGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQ-DDKADVI 92 (145)
Q Consensus 14 r~~~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~-~~Kg~Ii 92 (145)
|+|++++....++|.++++|++|+|++++||++|+|+|+||+++||+||||||++|||++||+|+|+||+++ +.||+|+
T Consensus 1 ~~~~~~~~~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d~~~~~kg~Iv 80 (99)
T TIGR00523 1 RGQQQEQQIRVRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIV 80 (99)
T ss_pred CCcCccCcceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEccCCCCccEEEE
Confidence 468888888999999999999999999999999999999999999999999999999999999999999998 7899999
Q ss_pred EEcChhHHHHHHHcCCCCc
Q 032228 93 LKYMPDEARLLKAYGELPE 111 (145)
Q Consensus 93 ~ry~~deik~Lrk~g~wP~ 111 (145)
|||+++|+++|+++|+||+
T Consensus 81 ~r~~~~qv~~L~~~g~~p~ 99 (99)
T TIGR00523 81 WRYTKTQVEWLKRKGYLKE 99 (99)
T ss_pred EEcCHHHHHHHHHcCCCCC
Confidence 9999999999999999994
No 5
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=100.00 E-value=3.7e-36 Score=219.79 Aligned_cols=95 Identities=35% Similarity=0.708 Sum_probs=91.2
Q ss_pred CcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 17 NEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 17 ~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
...+...+++++|+++|++|+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|++|+|+++||+|+|||+
T Consensus 6 ~~~~~~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 85 (100)
T PRK04012 6 DDEEVTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWRYT 85 (100)
T ss_pred cCCCceeEEccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEEcC
Confidence 34566789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHcCCCCc
Q 032228 97 PDEARLLKAYGELPE 111 (145)
Q Consensus 97 ~deik~Lrk~g~wP~ 111 (145)
++|++||+++|++|+
T Consensus 86 ~~qv~~L~~~g~~~~ 100 (100)
T PRK04012 86 KPQVDWLRRKGYISE 100 (100)
T ss_pred HHHHHHHHHcCCCCC
Confidence 999999999999984
No 6
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=100.00 E-value=6.4e-36 Score=211.73 Aligned_cols=83 Identities=66% Similarity=1.038 Sum_probs=81.7
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcC
Q 032228 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYG 107 (145)
Q Consensus 28 ~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~Lrk~g 107 (145)
.|+++|++|+|++++||++|+|+|+||+++||+||||||++|||++||+|+|++|+|+++||+|+|||+++|+++|+++|
T Consensus 1 ~p~e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~~vk~L~k~g 80 (83)
T smart00652 1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEVRWLKKEG 80 (83)
T ss_pred CCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecCCCCCEEEEEEEeCHHHHHHHHHcC
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q 032228 108 ELP 110 (145)
Q Consensus 108 ~wP 110 (145)
+||
T Consensus 81 ~wp 83 (83)
T smart00652 81 ELP 83 (83)
T ss_pred CCC
Confidence 998
No 7
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=100.00 E-value=2.2e-33 Score=196.88 Aligned_cols=77 Identities=47% Similarity=0.767 Sum_probs=75.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccC-CCCceEEEEEcChhHHHHHHHcCCC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDY-QDDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~-~~~Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
|++|+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|++|+| +++||+|+|||+++|+++|+++|+|
T Consensus 1 q~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~~vk~L~k~g~w 78 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFVYCKDHVRSLKKEGFL 78 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEecccCCCceEEEEEEeCHHHHHHHHHcCcC
Confidence 6899999999999999999999999999999999999999999999999999 6899999999999999999999998
No 8
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=100.00 E-value=8.6e-33 Score=193.33 Aligned_cols=77 Identities=66% Similarity=1.123 Sum_probs=75.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
|++|+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|++|+|+++||+|+|||+++|+++|+++|++
T Consensus 1 e~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~~v~~L~~~g~i 77 (77)
T cd05793 1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEVRWLKRKGEL 77 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEEEcCHHHHHHHHHcCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999975
No 9
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=100.00 E-value=1.1e-32 Score=193.73 Aligned_cols=77 Identities=29% Similarity=0.431 Sum_probs=75.3
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCC-CceEEEEEcChhHHHHHHHcCCC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQD-DKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~-~Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
|.+|+|++++|||+|+|+|+||.++||+||||||++|||++||||||+||++++ .||+|+|+|+++|+++|+++|+|
T Consensus 1 q~i~rV~~~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~qvk~L~k~g~W 78 (78)
T cd05792 1 QQIVRVLGSKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78 (78)
T ss_pred CeEEEEEEcCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEEecccCCceEEEEEEEECHHHHHHHHHcCCC
Confidence 689999999999999999999999999999999999999999999999999995 79999999999999999999998
No 10
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.2e-28 Score=172.10 Aligned_cols=72 Identities=36% Similarity=0.579 Sum_probs=69.3
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 28 ~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
.|+++++.|+|+++|||++|+|+|+||++++||||||||+ +|||.+||+|+|++|||+++||+|+|||.++|
T Consensus 3 ~~d~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~~~ 75 (75)
T COG0361 3 KPDEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYKKDE 75 (75)
T ss_pred cccccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEEecCCC
Confidence 3578999999999999999999999999999999999999 99999999999999999999999999999875
No 11
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=99.94 E-value=3.6e-27 Score=159.37 Aligned_cols=65 Identities=40% Similarity=0.740 Sum_probs=59.5
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 30 EDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 30 ~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
+++|++|+|++++||++|+|+|+||+++||+||||||++|||++||+|+|++|+|+.+||+|+||
T Consensus 1 ee~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 1 EEGEVIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp STTEEEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred CCcEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 57999999999999999999999999999999999999999999999999999999999999997
No 12
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=99.92 E-value=7.4e-25 Score=150.56 Aligned_cols=62 Identities=24% Similarity=0.322 Sum_probs=60.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
++.|+|+++|||+.|+|+|+||++++||||||||+ +|||.+||.|+|++|||+++||+|+||
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~R 68 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEeC
Confidence 68999999999999999999999999999999997 999999999999999999999999997
No 13
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.91 E-value=5.4e-24 Score=152.25 Aligned_cols=64 Identities=22% Similarity=0.260 Sum_probs=63.0
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
++.|+|+++|||+.|.|+|+||+++|||||||||+ +|||.+||.|+|++|+||++||+|+|||.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 78999999999999999999999999999999999 99999999999999999999999999996
No 14
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.5e-25 Score=174.38 Aligned_cols=100 Identities=26% Similarity=0.366 Sum_probs=92.6
Q ss_pred CcccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccC---C-CCceEEE
Q 032228 17 NEADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDY---Q-DDKADVI 92 (145)
Q Consensus 17 ~~~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~---~-~~Kg~Ii 92 (145)
...+.+..+...+++.|+||+|++++|+|+|+|+.++|+..|++||.|||++|||++|+||+|.|+.+ + ..+|.|.
T Consensus 7 y~~q~v~de~~~le~~q~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVkgeI~ 86 (167)
T KOG2925|consen 7 YLKQAVSDEDFTLEECQSIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVKGEIC 86 (167)
T ss_pred hhcccccCCCcchhhhhhHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccceEEE
Confidence 33456677888999999999999999999999999999999999999999999999999999999988 3 3699999
Q ss_pred EEcChhHHHHHHHcCCCCcccccc
Q 032228 93 LKYMPDEARLLKAYGELPETTRLN 116 (145)
Q Consensus 93 ~ry~~deik~Lrk~g~wP~~f~~~ 116 (145)
|++..+|++.|+|+|+||+.|...
T Consensus 87 yVl~~d~vr~lqk~g~WPe~F~d~ 110 (167)
T KOG2925|consen 87 YVLFFDQVRLLQKSGEWPEIFKDT 110 (167)
T ss_pred EEEccHHHHHHHHcCCcchhhhhc
Confidence 999999999999999999999763
No 15
>CHL00010 infA translation initiation factor 1
Probab=99.78 E-value=1.5e-18 Score=121.39 Aligned_cols=66 Identities=26% Similarity=0.313 Sum_probs=62.9
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcChh
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
++.|+|++++|++.|.|.|++|+.++|+++||||+ ++|+..||+|.|++|++++.+|+|||||...
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 47899999999999999999999999999999998 7999999999999999999999999999753
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.76 E-value=3.9e-18 Score=117.23 Aligned_cols=64 Identities=28% Similarity=0.345 Sum_probs=61.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
++.|+|+++++++.|.|.|+||..++|+++||||+ .+|+..||+|+|++|++++++|+|||||.
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 67899999999999999999999999999999996 99999999999999999999999999983
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=99.53 E-value=5.2e-14 Score=93.98 Aligned_cols=62 Identities=27% Similarity=0.340 Sum_probs=58.2
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
++.|+|++++|++.|.|.|++|..++|+++||||+ ++|+..||+|+++++++++.+|.||||
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecCCCEEEEEEC
Confidence 46799999999999999999999999999999996 999999999999999988889999996
No 18
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=98.26 E-value=5.9e-06 Score=54.37 Aligned_cols=59 Identities=24% Similarity=0.282 Sum_probs=48.1
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
.|+|+...+ +.|.|.+++|..+.|.++|++++ ..++..||+|++++++ ...+.|+..+.
T Consensus 2 ~grVv~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~--~~~~~I~~vl~ 61 (68)
T cd04466 2 EGLIIKAIG-GFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPED--DGEGVIEEILP 61 (68)
T ss_pred CEEEEEEEC-CEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEECC--CCcEEEEEEec
Confidence 478998887 67899998788999999999986 7889999999999754 34566766654
No 19
>PRK00098 GTPase RsgA; Reviewed
Probab=97.10 E-value=0.0023 Score=53.81 Aligned_cols=47 Identities=26% Similarity=0.348 Sum_probs=40.6
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEec
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLR 82 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~ 82 (145)
.|+|++..| +.|.|.+.+|..+.|.++|+|++ ...+..||+|+|++.
T Consensus 2 ~g~v~~~~~-~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~ 49 (298)
T PRK00098 2 EGLIIKALG-GFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAE 49 (298)
T ss_pred eEEEEEEEC-CEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEEC
Confidence 589999886 57889888899999999999986 667889999999874
No 20
>PRK12289 GTPase RsgA; Reviewed
Probab=97.05 E-value=0.0023 Score=55.61 Aligned_cols=62 Identities=19% Similarity=0.273 Sum_probs=47.2
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCC------CEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEE
Q 032228 29 KEDGQEYAQVLRMLGNGRCEAMCIDG------AKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 29 p~e~q~ig~Vv~~lG~~~~~V~~~dG------~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~I 91 (145)
+...++.|+|++..++ .|.|.+.+| ...+|..++++|+ ...+..||+|++++.++....|-|
T Consensus 4 ~~~~~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I 72 (352)
T PRK12289 4 TTTSQLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAI 72 (352)
T ss_pred cccCcccEEEEEEECC-EEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCCCCceEE
Confidence 3446678999998885 678888654 4799999999986 556999999999976554445533
No 21
>PRK12288 GTPase RsgA; Reviewed
Probab=96.67 E-value=0.0084 Score=51.97 Aligned_cols=58 Identities=17% Similarity=0.206 Sum_probs=45.3
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCC--CceEEEEEc
Q 032228 34 EYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQD--DKADVILKY 95 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~--~Kg~Ii~ry 95 (145)
+.|+|++..++ .|.|.+.+|..+.|.++|+++. +..||+|.+++.+... ..|.|..++
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~~~~~~~~~I~~il 99 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKEALEGVSGVVEAVH 99 (347)
T ss_pred cceEEEEEECC-EEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCCcccccceEEEEEe
Confidence 67999999885 7889999999999999999975 8899999998653221 236665444
No 22
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=96.55 E-value=0.0084 Score=50.11 Aligned_cols=57 Identities=25% Similarity=0.360 Sum_probs=43.1
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 36 AQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 36 g~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
|+|++..| +.|.|..+ +..+.|.++|+|++ ..-+..||+|++++.+ ...|.|..++.
T Consensus 1 g~v~~~~~-~~~~v~~~-~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~--~~~~~i~~i~~ 58 (287)
T cd01854 1 GRVIAVHG-GFYDVETE-GGELRCRARGKLRKKGIKPVVGDWVEVEPDD--DGEGVIVRVLP 58 (287)
T ss_pred CEEEEEEC-CEEEEEEC-CeEEEEEeccccccCCCCccCCCEEEEEecC--CCcEEEEEEEC
Confidence 57888887 67888775 77999999999986 4669999999998754 33455544443
No 23
>PRK01889 GTPase RsgA; Reviewed
Probab=95.20 E-value=0.069 Score=46.19 Aligned_cols=63 Identities=17% Similarity=0.209 Sum_probs=45.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
++-..|+|++..| +.|.|.+.+| .+.|.++||++. .--...||+|++++ ...|-|..+|.+..
T Consensus 26 ~~~~~g~v~~~~~-~~~~v~~~~~-~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~----~~~g~I~~i~pR~~ 93 (356)
T PRK01889 26 EGLEPGRVVEEHR-SGYVVATEEG-EVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN----EKKARIVRLLPRRS 93 (356)
T ss_pred cCCccEEEEEEEC-CEEEEEECCc-EEEEEecchhhccccccCCCCccCcEEEEec----CCceEEEEEECCCc
Confidence 3456799999987 5778887665 567999999984 23378899999985 23466665554443
No 24
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=94.69 E-value=0.15 Score=31.29 Aligned_cols=57 Identities=21% Similarity=0.236 Sum_probs=43.0
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEE
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
.|+|+++..++.| |.+.++.+-+++++.--.. .-+++.||.|.|.....+..++.|.
T Consensus 2 ~g~V~~v~~~g~~-v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ 63 (65)
T cd00164 2 TGKVVSITKFGVF-VELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63 (65)
T ss_pred EEEEEEEEeeeEE-EEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEe
Confidence 5888888866554 8888888888887654321 4679999999999998776666653
No 25
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=91.17 E-value=1.3 Score=27.69 Aligned_cols=59 Identities=20% Similarity=0.165 Sum_probs=43.5
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEccCCEEEEEeccCCCCceEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KV-----WIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~I-----wIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
..+.|+|+++...+.| |.+.++..-+++++ .+.. .+ +++.||.|.|.....+..++.|.
T Consensus 2 ~~~~g~V~~i~~~G~f-v~l~~~~~g~~~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 2 MVLEGVVTNVTDFGAF-VDIGVKQDGLIHIS-KMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred CEEEEEEEEEecccEE-EEcCCCCEEEEEHH-HCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 3578999999988877 78888877777765 3332 12 47999999999887776667664
No 26
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=89.29 E-value=2.1 Score=27.49 Aligned_cols=55 Identities=15% Similarity=0.093 Sum_probs=41.7
Q ss_pred CCCeEEEEEEEeC-CCceEEEEe--CCCCEEEEEecccccceEEEccCCEEEEEeccC
Q 032228 30 EDGQEYAQVLRML-GNGRCEAMC--IDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDY 84 (145)
Q Consensus 30 ~e~q~ig~Vv~~l-G~~~~~V~~--~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~ 84 (145)
..|++.|+|.++. ++...+|.+ .++.+..|.++.+--..+-+.+|+.|.+...+.
T Consensus 5 ~~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 5 ARNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKAP 62 (69)
T ss_pred cccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEECc
Confidence 3588999999984 344566664 566689999998766788889999998877553
No 27
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=88.74 E-value=0.94 Score=28.99 Aligned_cols=55 Identities=11% Similarity=0.045 Sum_probs=39.2
Q ss_pred CCCCeEEEEEEEeCCC---ceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEecc
Q 032228 29 KEDGQEYAQVLRMLGN---GRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 29 p~e~q~ig~Vv~~lG~---~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
+..|++-|+|..+... ....+.+.++....|+++..-...+-+++||-|.+...+
T Consensus 2 s~~N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 2 SARNQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIKA 59 (64)
T ss_dssp STSEEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-G
T ss_pred CCCcEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEeh
Confidence 4567888888766533 244555567777999999988889999999999988754
No 28
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=87.88 E-value=2 Score=29.06 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=43.2
Q ss_pred CCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc----ce-----EEEccCCEEEEEeccCCCCceEEEEE
Q 032228 29 KEDG-QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMH----KK-----VWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 29 p~e~-q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~R----k~-----IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
|..| .+.|+|+++...+ +.|....+.+=+++++-=.. .. =+++.||.|.+.....+.. +.|..-
T Consensus 4 p~~GdiV~g~V~~i~~~g-~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS 77 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKR-WKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLH 77 (86)
T ss_pred CCCCCEEEEEEEEECCCE-EEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEE
Confidence 5555 4799999976544 67777777666666653221 11 1589999999999887654 555443
No 29
>PHA02945 interferon resistance protein; Provisional
Probab=87.15 E-value=5.9 Score=28.69 Aligned_cols=66 Identities=9% Similarity=0.022 Sum_probs=47.4
Q ss_pred eccCCCCe-EEEEEEEeCCCceEEEEeC-CCCEEEEEeccc------ccceEEEccCCEEEEEeccCCCCceEEEE
Q 032228 26 LIFKEDGQ-EYAQVLRMLGNGRCEAMCI-DGAKRLCHIRGK------MHKKVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 26 l~~p~e~q-~ig~Vv~~lG~~~~~V~~~-dG~~~la~IpGK------~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
+.+|++|+ ++|+|.+ ...+.|--..+ .|.+-+.+++-- +|.+=.+ .|..|.|...--+..||.|=.
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~~kg~IDl 79 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 56899988 6889988 66666544444 488888888733 3334445 888888888888888888843
No 30
>COG1162 Predicted GTPases [General function prediction only]
Probab=85.47 E-value=2.1 Score=37.10 Aligned_cols=60 Identities=17% Similarity=0.185 Sum_probs=45.8
Q ss_pred EEEEEEEeCCCceEEEEeC---CCCEEEEEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcCh
Q 032228 34 EYAQVLRMLGNGRCEAMCI---DGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~---dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~ 97 (145)
..++|++.. .+.|.|.+. +++...|..+|+||+ ..-...||+|.++..... |-|..++.+
T Consensus 5 ~~g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~---g~I~~i~~R 68 (301)
T COG1162 5 KRGRVVKVD-AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENNN---GVIEKILPR 68 (301)
T ss_pred cCcEEEEee-CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCCc---ceEEEEecc
Confidence 345666655 477888886 478899999999999 688999999999987533 666666544
No 31
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=84.70 E-value=6.2 Score=26.47 Aligned_cols=63 Identities=16% Similarity=0.189 Sum_probs=40.3
Q ss_pred cCCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEecc---c-ccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 28 FKEDGQ-EYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---K-MHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 28 ~p~e~q-~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K-~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
+|..|+ ++|+|+++..+ .+.|.+..+..-+.+++. . .+. .=+++.||.|.+.....+.. +.|.
T Consensus 3 ~p~~GdiV~G~V~~v~~~-~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~ 71 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSR-FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVL 71 (82)
T ss_pred CCCCCCEEEEEEEEEcCC-EEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEE
Confidence 466665 69999998554 455877555433333322 2 122 45589999999999877664 5554
No 32
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=82.81 E-value=4 Score=24.98 Aligned_cols=33 Identities=9% Similarity=0.094 Sum_probs=26.2
Q ss_pred ccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEE
Q 032228 27 IFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCH 60 (145)
Q Consensus 27 ~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~ 60 (145)
|-|.++=+.|.|++ ..++.+.|.+.||+++.+.
T Consensus 7 pD~~egfv~g~I~~-~~g~~vtV~~~~G~~~tv~ 39 (42)
T PF02736_consen 7 PDPKEGFVKGEIIE-EEGDKVTVKTEDGKEVTVK 39 (42)
T ss_dssp EESSSSEEEEEEEE-EESSEEEEEETTTEEEEEE
T ss_pred eCCcccEEEEEEEE-EcCCEEEEEECCCCEEEeC
Confidence 44667889999995 5666799999999988764
No 33
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=81.49 E-value=2.8 Score=35.88 Aligned_cols=75 Identities=13% Similarity=0.299 Sum_probs=61.5
Q ss_pred ccCCCCe-EEEEEEEeCCCceEEEEeC-CCCEEEEEec----ccccc-eEEEccCCEEEEEeccCCCCceEE---EEEcC
Q 032228 27 IFKEDGQ-EYAQVLRMLGNGRCEAMCI-DGAKRLCHIR----GKMHK-KVWIGAGDIILVGLRDYQDDKADV---ILKYM 96 (145)
Q Consensus 27 ~~p~e~q-~ig~Vv~~lG~~~~~V~~~-dG~~~la~Ip----GK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~I---i~ry~ 96 (145)
.+|++|+ ++|+|.++..-+-|-...+ +|..=+.||+ |.+|. +=.+++|..|++-...-++.+|-| ..|.+
T Consensus 7 ~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~ 86 (269)
T COG1093 7 EYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT 86 (269)
T ss_pred CCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence 4689887 7999999999888877775 6788888885 66776 788999999999999999999998 45556
Q ss_pred hhHHH
Q 032228 97 PDEAR 101 (145)
Q Consensus 97 ~deik 101 (145)
.+|.+
T Consensus 87 ~~q~~ 91 (269)
T COG1093 87 EHQRR 91 (269)
T ss_pred HHHHH
Confidence 66654
No 34
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=81.21 E-value=7.7 Score=29.97 Aligned_cols=62 Identities=13% Similarity=0.162 Sum_probs=42.7
Q ss_pred EEEEEEEeCCC-------ceEEEEeCCCCEEEEEeccccc-ceEEEccCCEEEEEec-cCCCCceEEEEEc
Q 032228 34 EYAQVLRMLGN-------GRCEAMCIDGAKRLCHIRGKMH-KKVWIGAGDIILVGLR-DYQDDKADVILKY 95 (145)
Q Consensus 34 ~ig~Vv~~lG~-------~~~~V~~~dG~~~la~IpGK~R-k~IwIk~GD~VlVe~~-~~~~~Kg~Ii~ry 95 (145)
-.|+|+++|+. .+|-|.+++|.++++-=-=-+. +-=|+++||.|.+--. .|+...|-|.|-.
T Consensus 41 g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe~n~kggvIHWTH 111 (131)
T PF11948_consen 41 GCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWNPKGGVIHWTH 111 (131)
T ss_pred ccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEEECCCCCEEEeec
Confidence 37899999875 5799999999998765222222 2347999999998764 3345445554444
No 35
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=80.32 E-value=7 Score=29.22 Aligned_cols=50 Identities=16% Similarity=0.093 Sum_probs=38.0
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEe----cccccceEEEccCCEEEEEeccC
Q 032228 34 EYAQVLRMLGNGRCEAMCIDGAKRLCHI----RGKMHKKVWIGAGDIILVGLRDY 84 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~dG~~~la~I----pGK~Rk~IwIk~GD~VlVe~~~~ 84 (145)
-.|+|.+.+....|.|+..++.+..... +...-.+--++.||+||+- |+-
T Consensus 15 Y~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~-~~~ 68 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP-WEP 68 (124)
T ss_pred EeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe-cCc
Confidence 5689999999999999998877665532 3333336779999999998 543
No 36
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=77.90 E-value=19 Score=24.42 Aligned_cols=56 Identities=23% Similarity=0.170 Sum_probs=34.4
Q ss_pred EEEEEEe-CCCceEEEEeCCCCEEEEEecccccceEE-EccCCEEEEEeccCCCCceEEEEEcChhHHHHH
Q 032228 35 YAQVLRM-LGNGRCEAMCIDGAKRLCHIRGKMHKKVW-IGAGDIILVGLRDYQDDKADVILKYMPDEARLL 103 (145)
Q Consensus 35 ig~Vv~~-lG~~~~~V~~~dG~~~la~IpGK~Rk~Iw-Ik~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~L 103 (145)
-++|+++ .+++.-.|... |.++-+++.- +. +.+||||||.. |-.+.++++++.+..
T Consensus 6 P~~Vv~v~~~~~~A~v~~~-G~~~~V~~~l-----v~~v~~Gd~VLVHa-------G~Ai~~ideeeA~e~ 63 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFG-GVRREVSLAL-----VPDVKVGDYVLVHA-------GFAIEKIDEEEAEET 63 (68)
T ss_dssp EEEEEEEETTTTEEEEEET-TEEEEEEGTT-----CTSB-TT-EEEEET-------TEEEEEE-HHHHHHH
T ss_pred cEEEEEEeCCCCEEEEEcC-CcEEEEEEEE-----eCCCCCCCEEEEec-------ChhheeCCHHHHHHH
Confidence 4778887 34555555543 6655554321 11 88999999985 467888888887764
No 37
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=77.57 E-value=19 Score=24.17 Aligned_cols=60 Identities=8% Similarity=-0.004 Sum_probs=46.0
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEE---ecccccce-----EEEccCCEEEEEeccCCCCceEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCH---IRGKMHKK-----VWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~---IpGK~Rk~-----IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
..+.|+|.++...+.| |.+..|..=+.+ |+-.+-+. =.++.||.|.+.....+..+++|.
T Consensus 5 ~~V~g~V~~i~~~G~f-V~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~ 72 (74)
T cd05705 5 QLLRGYVSSVTKQGVF-FRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVE 72 (74)
T ss_pred CEEEEEEEEEeCCcEE-EEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEe
Confidence 5689999999988888 888888888888 55544121 357999999999888877777653
No 38
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=76.67 E-value=5 Score=36.95 Aligned_cols=54 Identities=30% Similarity=0.505 Sum_probs=44.4
Q ss_pred ccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 27 IFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 27 ~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..+.-|++ ++|.+.++.+++.|....+..++.++.+.+... -+++||.|+|++.
T Consensus 102 ~~~~~g~~-~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~g~~~~~~~~ 155 (512)
T TIGR03689 102 DFETVGEI-ATLKEVLGDGRALVVDHSGEERVVKLAGALADE-LIRAGDSLLVDPK 155 (512)
T ss_pred CCCCCCce-EEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHh-hCCCCCEEEEccc
Confidence 33344554 499999999999999999999999999998763 2689999998864
No 39
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=76.54 E-value=5 Score=30.90 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=35.1
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCC---CceEEEE
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQD---DKADVIL 93 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~---~Kg~Ii~ 93 (145)
-.+|++.||.++.|.|||-=.. |.+.|.|+|+-.--.+ ++-.||.
T Consensus 58 ~~RVrL~NG~~VtAyiPg~Gh~---lqEH~~Vli~G~~v~DlPGVRy~vvr 105 (129)
T COG0048 58 VARVRLINGKEVTAYIPGEGHN---LQEHSEVLIRGGRVKDLPGVRYKVVR 105 (129)
T ss_pred eEEEEeeCCcEEEEEcCCCCcc---ccccCEEEEecCccCCCCCceEEEEE
Confidence 4689999999999999997766 9999999999765433 3444443
No 40
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=76.10 E-value=8.4 Score=27.27 Aligned_cols=59 Identities=24% Similarity=0.086 Sum_probs=35.9
Q ss_pred EEEEEEeCCCceEEEEe-CCCCEEEEEecccccc--eEEEccCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032228 35 YAQVLRMLGNGRCEAMC-IDGAKRLCHIRGKMHK--KVWIGAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~-~dG~~~la~IpGK~Rk--~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~ 102 (145)
-++|+++.|+......+ ..|.++-+++. +=- ...+++||||||.. |-.+.++.+++.+.
T Consensus 6 P~kVi~i~~~~~~~A~vd~~Gv~r~V~l~--Lv~~~~~~~~vGDyVLVHa-------GfAi~~ideeeA~e 67 (82)
T PRK10413 6 PGQVLAVGEDIHQLAQVEVCGIKRDVNIA--LICEGNPADLLGQWVLVHV-------GFAMSIIDEDEAKA 67 (82)
T ss_pred ceEEEEECCCCCcEEEEEcCCeEEEEEee--eeccCCcccccCCEEEEec-------chhhhhCCHHHHHH
Confidence 47888888875344444 34666655432 100 12467899999986 44566667766654
No 41
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=75.83 E-value=13 Score=25.99 Aligned_cols=56 Identities=25% Similarity=0.125 Sum_probs=33.8
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHH
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLL 103 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~L 103 (145)
-++|+++.|+ .-.|.. .|.++-+++.== =-+++||||||.. |-.+.+..+++.+..
T Consensus 6 P~~V~~i~~~-~A~v~~-~G~~~~v~l~lv----~~~~vGD~VLVH~-------G~Ai~~ide~eA~e~ 61 (76)
T TIGR00074 6 PGQVVEIDEN-IALVEF-CGIKRDVSLDLV----GEVKVGDYVLVHV-------GFAISVLDEEEARET 61 (76)
T ss_pred ceEEEEEcCC-EEEEEc-CCeEEEEEEEee----CCCCCCCEEEEec-------ChhhhhCCHHHHHHH
Confidence 3678888774 333333 455554432100 0378999999986 455667777776654
No 42
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=74.17 E-value=16 Score=31.93 Aligned_cols=78 Identities=14% Similarity=0.234 Sum_probs=56.4
Q ss_pred ccCCCCe-EEEEEEEeCCCceEEEEeC--CCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEE---EEEc
Q 032228 27 IFKEDGQ-EYAQVLRMLGNGRCEAMCI--DGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADV---ILKY 95 (145)
Q Consensus 27 ~~p~e~q-~ig~Vv~~lG~~~~~V~~~--dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~I---i~ry 95 (145)
.+|..|+ +.|+|+++...+.| |.+. +|..=|.|++- +.+. +=.++.||.|.|.....+..+|.| +.+.
T Consensus 13 ~~P~~GdvV~g~V~~I~d~Gaf-V~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v 91 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAY-VSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRV 91 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEE-EEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence 4676554 78999999887776 4443 58888888753 3333 445899999999999888888998 4466
Q ss_pred ChhHHHHHHH
Q 032228 96 MPDEARLLKA 105 (145)
Q Consensus 96 ~~deik~Lrk 105 (145)
++++++.+.+
T Consensus 92 ~~~pw~~~~e 101 (319)
T PTZ00248 92 SPEDIEACEE 101 (319)
T ss_pred ccchHHHHHH
Confidence 7776666543
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=73.24 E-value=21 Score=22.85 Aligned_cols=59 Identities=12% Similarity=0.112 Sum_probs=42.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIR----GKMHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~Ip----GK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
.+.|+|+++...+ .-|++.++..=+++++ ..+++ .=-++.||.|.|.....+..+++|.
T Consensus 3 ~v~g~V~~v~~~G-v~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ 66 (68)
T cd05707 3 VVRGFVKNIANNG-VFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIE 66 (68)
T ss_pred EEEEEEEEEECcc-EEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEe
Confidence 4789999998766 4578887777777664 12222 2337999999999888887777774
No 44
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=72.72 E-value=13 Score=27.18 Aligned_cols=48 Identities=10% Similarity=0.115 Sum_probs=37.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
.+.|.+++.+|+..|......| ++.+.|+-+.-.-.-|.+.|.|.+.-
T Consensus 38 ~L~G~Iv~~l~~d~Y~F~D~TG-~I~VeId~~~w~g~~vt~~~~Vri~G 85 (103)
T PF04076_consen 38 TLEGNIVKQLGDDKYLFRDATG-EIEVEIDDDVWRGQTVTPDDKVRISG 85 (103)
T ss_dssp EEEEEEEEEEETTEEEEEETTE-EEEEE--GGGSTT----TTSEEEEEE
T ss_pred EEEEEEEEEecCCEEEEECCCC-cEEEEEChhhcCCcccCCCCEEEEEE
Confidence 4899999999999999999999 88999999977788889999887754
No 45
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=72.56 E-value=8.8 Score=27.05 Aligned_cols=58 Identities=21% Similarity=0.210 Sum_probs=34.4
Q ss_pred cCCCC-eEEEEEEEeCCCceEEEEe--CCCCEEEEEecccccc-------------eEEEccCCEEEEEeccCCC
Q 032228 28 FKEDG-QEYAQVLRMLGNGRCEAMC--IDGAKRLCHIRGKMHK-------------KVWIGAGDIILVGLRDYQD 86 (145)
Q Consensus 28 ~p~e~-q~ig~Vv~~lG~~~~~V~~--~dG~~~la~IpGK~Rk-------------~IwIk~GD~VlVe~~~~~~ 86 (145)
.|..| -++|+|+.+.. ....|.. .++...-....|-+|. +=.+++||+|......+++
T Consensus 3 ~P~~GDiVig~V~~v~~-~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~ 76 (92)
T cd05791 3 LPKVGSIVIARVTRINP-RFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD 76 (92)
T ss_pred CCCCCCEEEEEEEEEcC-CEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC
Confidence 46655 58999999764 4444443 3333322222333331 2345999999999887764
No 46
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=72.16 E-value=8.5 Score=31.12 Aligned_cols=48 Identities=17% Similarity=0.353 Sum_probs=36.5
Q ss_pred eCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHHHHc
Q 032228 41 MLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY 106 (145)
Q Consensus 41 ~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~Lrk~ 106 (145)
+-|++-|.|+..|+.=+ |||+..||.|++-+- |-||++-+--...+.+
T Consensus 100 l~GtgYfDVrd~dd~WI----------Ri~vekGDlivlPaG--------iyHRFTtt~~n~vkam 147 (179)
T KOG2107|consen 100 LEGTGYFDVRDKDDQWI----------RIFVEKGDLIVLPAG--------IYHRFTTTPSNYVKAM 147 (179)
T ss_pred eecceEEeeccCCCCEE----------EEEEecCCEEEecCc--------ceeeeecCchHHHHHH
Confidence 35999999999997765 899999999998653 6778866555444443
No 47
>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=71.48 E-value=12 Score=26.90 Aligned_cols=31 Identities=13% Similarity=0.195 Sum_probs=26.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK 64 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK 64 (145)
-++|+|++..|+ .+.+.|+||..+.+.++.-
T Consensus 19 ~ivGkV~~~~~~-~~~~~~~Dg~~v~v~l~~~ 49 (101)
T cd04479 19 RIVGKVEKVDGD-SLTLISSDGVNVTVELNRP 49 (101)
T ss_pred EEEEEEEEecCC-eEEEEcCCCCEEEEEeCCC
Confidence 379999999987 8999999998888887653
No 48
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=71.29 E-value=21 Score=30.02 Aligned_cols=65 Identities=15% Similarity=0.224 Sum_probs=45.4
Q ss_pred cCCCC-eEEEEEEEeCCCceEEEEeCC--CCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 28 FKEDG-QEYAQVLRMLGNGRCEAMCID--GAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 28 ~p~e~-q~ig~Vv~~lG~~~~~V~~~d--G~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
+|..| .+.|+|+.+...+.| |.+.+ |..=+++++- +++. +=.++.||.|.|.....+..++.|..
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~f-V~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~L 77 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAF-VTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDL 77 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEE-EEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEE
Confidence 45555 578999998776665 55543 7777777652 2222 23479999999999988888887743
No 49
>PRK11642 exoribonuclease R; Provisional
Probab=71.13 E-value=39 Score=32.88 Aligned_cols=46 Identities=11% Similarity=0.047 Sum_probs=33.6
Q ss_pred EccCCEEEEEeccCCC----CceEEEEEcCh-----hHHHHHHHcCCCCcccccc
Q 032228 71 IGAGDIILVGLRDYQD----DKADVILKYMP-----DEARLLKAYGELPETTRLN 116 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~----~Kg~Ii~ry~~-----deik~Lrk~g~wP~~f~~~ 116 (145)
.+.||+|+|++..|.. -.|.|+.++.. -++..+....-+|.+|...
T Consensus 186 ~~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~Fp~~ 240 (813)
T PRK11642 186 ARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240 (813)
T ss_pred CCCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCCCCHH
Confidence 4568999999976643 37999999943 4666666666678888653
No 50
>CHL00051 rps12 ribosomal protein S12
Probab=71.07 E-value=7.2 Score=29.87 Aligned_cols=34 Identities=18% Similarity=0.104 Sum_probs=29.0
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..+|.+.||.+++|+|||-=+ .+.+.+.|||.--
T Consensus 52 varVrLsngk~v~AyIPGeGh---nlqehs~VLvrGG 85 (123)
T CHL00051 52 VARVRLTSGFEITAYIPGIGH---NLQEHSVVLVRGG 85 (123)
T ss_pred EEEEEccCCCEEEEEcCCCCc---cccccCEEEEeCC
Confidence 467889999999999999875 7888999999843
No 51
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=70.80 E-value=25 Score=22.58 Aligned_cols=62 Identities=18% Similarity=0.296 Sum_probs=42.8
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc------c-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 29 KEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMH------K-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 29 p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~R------k-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
|......|+|+.+...+.| |++.+|..-|++++- +. + .--++.||.|.|.....+..+.+|.
T Consensus 2 ~~g~~~~g~V~~i~~~G~f-v~l~~~~~Gl~~~~~-l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~ 70 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCF-VELEEGVEGLVHVSE-MDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRIS 70 (72)
T ss_pred cCCCEEEEEEEEEEeeEEE-EEcCCCCEEEEEEEe-ccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEe
Confidence 4456788999998876665 556666777777652 22 1 2247899999999887777776663
No 52
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=70.66 E-value=18 Score=26.09 Aligned_cols=54 Identities=22% Similarity=0.190 Sum_probs=31.5
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccceE-------EEccCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKV-------WIGAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~I-------wIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~ 102 (145)
-++|+++.|+ .-.|. ..|.++-+++. -+ .++.||||||.. |--+.++.+++++.
T Consensus 6 P~kVv~i~~~-~A~vd-~~Gv~reV~l~-----Lv~~~~~~~~~~vGDyVLVHa-------GfAi~~ideeeA~e 66 (90)
T PRK10409 6 PGQIRTIDGN-QAKVD-VCGIQRDVDLT-----LVGSCDENGQPRVGQWVLVHV-------GFAMSVINEAEARD 66 (90)
T ss_pred ceEEEEEcCC-eEEEE-cCCeEEEEEEe-----eecccCCCCccCCCCEEEEec-------ChHHhhCCHHHHHH
Confidence 3678887664 22222 33555544432 12 368999999986 34456666666654
No 53
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=70.47 E-value=26 Score=22.58 Aligned_cols=61 Identities=10% Similarity=0.121 Sum_probs=40.9
Q ss_pred CeEEEEEEEeCCCceEEEEeC--CCCEEEEEecccccc------eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCI--DGAKRLCHIRGKMHK------KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~--dG~~~la~IpGK~Rk------~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
..+.|+|+++...+.| |.+. +|..-+++++- +.. .=.++.||.|.|.....+..++.|...
T Consensus 5 ~~~~g~V~~v~~~g~~-v~l~~~~~~~gll~~s~-l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls 73 (76)
T cd04452 5 ELVVVTVKSIADMGAY-VSLLEYGNIEGMILLSE-LSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLS 73 (76)
T ss_pred CEEEEEEEEEEccEEE-EEEcCCCCeEEEEEhHH-cCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEE
Confidence 3578999998876655 4454 35677777663 322 122699999999988777666776543
No 54
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=70.33 E-value=14 Score=32.75 Aligned_cols=54 Identities=9% Similarity=0.116 Sum_probs=46.6
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccC
Q 032228 30 EDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDY 84 (145)
Q Consensus 30 ~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~ 84 (145)
.....+|.|+++++.+++-|....|.++++.+.+.+.+.. +++|+.|.+....+
T Consensus 64 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~ 117 (398)
T PTZ00454 64 SVPLVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNREL-LKPNASVALHRHSH 117 (398)
T ss_pred CCCceEEEEEEEEcCCEEEEEcCCCCEEEEecccccCHhh-CCCCCEEEeeccch
Confidence 3467999999999999999999999999999999887633 68999999887544
No 55
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=69.49 E-value=8.3 Score=28.28 Aligned_cols=33 Identities=12% Similarity=0.080 Sum_probs=27.2
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
..+|++.||.+++|+|||-= -.+.+.|.|||.-
T Consensus 37 ~arV~L~ngk~v~ayIPg~G---h~lqeh~~VLvrG 69 (95)
T cd00319 37 VAKVRLTSGYEVTAYIPGEG---HNLQEHSVVLIRG 69 (95)
T ss_pred EEEEEccCCCEEEEECCCCC---cccccccEEEEeC
Confidence 45678899999999999876 5578888888875
No 56
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=68.65 E-value=44 Score=27.41 Aligned_cols=65 Identities=20% Similarity=0.187 Sum_probs=43.2
Q ss_pred ceEEEEe--CCCCEEEEEec--ccccceEEEccCCEEEEEeccCC--CCceEEEEEcCh-------------hHHHHHHH
Q 032228 45 GRCEAMC--IDGAKRLCHIR--GKMHKKVWIGAGDIILVGLRDYQ--DDKADVILKYMP-------------DEARLLKA 105 (145)
Q Consensus 45 ~~~~V~~--~dG~~~la~Ip--GK~Rk~IwIk~GD~VlVe~~~~~--~~Kg~Ii~ry~~-------------deik~Lrk 105 (145)
|+|.|.+ .||++.+||+| |||+--+ .+|-.|++.+++-. ..+.+++-.+.. .=+.++.+
T Consensus 5 nRF~~~v~l~~g~~~~~H~pntGRl~ell--~pG~~v~l~~~~~~~RKt~y~l~av~~~~~~~V~int~~~N~lv~~~l~ 82 (215)
T PF03749_consen 5 NRFLADVELDDGEEVTAHCPNTGRLKELL--VPGARVLLSKSDNPKRKTKYTLEAVEKDNGVWVGINTQLPNRLVEEALE 82 (215)
T ss_pred CcEEEEEEECCCCEEEEEcCCCCcchhhc--cCCCEEEEEECCCCCCCCcEEEEEEEcCCCeEEEEccchHHHHHHHHHH
Confidence 4555544 66999999997 5555433 49999999998755 234454433333 34667777
Q ss_pred cCCCCc
Q 032228 106 YGELPE 111 (145)
Q Consensus 106 ~g~wP~ 111 (145)
.|.+|.
T Consensus 83 ~~~i~~ 88 (215)
T PF03749_consen 83 NGLIPE 88 (215)
T ss_pred cCCCcc
Confidence 888874
No 57
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=68.15 E-value=25 Score=21.44 Aligned_cols=62 Identities=18% Similarity=0.134 Sum_probs=42.0
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
..+.|+|+++..+ -+.|.+..+..-+++..--... .-+++.||.|.|.....+..++.|...
T Consensus 4 ~~v~g~V~~v~~~-g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 4 DVVEGTVTEITPF-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred CEEEEEEEEEEcc-EEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 3578999998774 4666777666655554321111 356899999999998887766776543
No 58
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=67.75 E-value=2.5 Score=27.09 Aligned_cols=24 Identities=29% Similarity=0.527 Sum_probs=11.3
Q ss_pred EccCCEEEEEeccCCCCceEEEEEc
Q 032228 71 IGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
|..||+|+|.+.. ....|+|+...
T Consensus 11 i~~Gd~v~v~~~~-~~~~gdivv~~ 34 (70)
T PF00717_consen 11 IKDGDIVLVDPSS-EPKDGDIVVVK 34 (70)
T ss_dssp SSTTEEEEEEETS----TTSEEEEE
T ss_pred eeCCCEEEEEEcC-CCccCeEEEEE
Confidence 4466666666544 33445554443
No 59
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=67.75 E-value=30 Score=22.75 Aligned_cols=57 Identities=16% Similarity=0.054 Sum_probs=39.8
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 36 AQVLRMLGNGRCEAMCIDGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 36 g~Vv~~lG~~~~~V~~~dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
|+|+++.-..-.-|.+++|..-++|++- +... .=.++.||.|.+....++..++.|.
T Consensus 7 g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~ 68 (71)
T cd05696 7 VKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQ 68 (71)
T ss_pred eEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEE
Confidence 6888875333356888888887777641 1111 2238899999999998887776664
No 60
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=65.92 E-value=10 Score=29.08 Aligned_cols=34 Identities=12% Similarity=0.076 Sum_probs=28.5
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..+|.+.||..++|+|||-= -.+.+.|.|||.--
T Consensus 52 varVrL~ngk~v~AyIPG~G---hnlqehs~VLvrGG 85 (124)
T TIGR00981 52 VARVRLTNGFEVTAYIPGEG---HNLQEHSVVLIRGG 85 (124)
T ss_pred eEEEEeCCCCEEEEEcCCCC---CCccccCEEEEeCC
Confidence 46788999999999999976 55788899998843
No 61
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=65.50 E-value=11 Score=28.92 Aligned_cols=34 Identities=12% Similarity=0.076 Sum_probs=28.3
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..+|.+.||..++|.|||-= -.+.+.|.|||.--
T Consensus 52 varVrL~ngk~v~AyIPGeG---hnlqehs~VLvrGG 85 (124)
T PRK05163 52 VARVRLTNGFEVTAYIPGEG---HNLQEHSVVLIRGG 85 (124)
T ss_pred EEEEEeCCCCEEEEEcCCCC---CCccccCEEEEeCC
Confidence 46788999999999999976 55788889998843
No 62
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=65.37 E-value=22 Score=25.23 Aligned_cols=55 Identities=7% Similarity=0.092 Sum_probs=38.7
Q ss_pred CCC-CeEEEEEEEeCCCceEEEEeCCCCEEEEEe-----cccccc-eEEEccCCEEEEEeccCCC
Q 032228 29 KED-GQEYAQVLRMLGNGRCEAMCIDGAKRLCHI-----RGKMHK-KVWIGAGDIILVGLRDYQD 86 (145)
Q Consensus 29 p~e-~q~ig~Vv~~lG~~~~~V~~~dG~~~la~I-----pGK~Rk-~IwIk~GD~VlVe~~~~~~ 86 (145)
|.. +-++|+|+... +..|.|....- ..|.| +|.-|+ +=.++.||.|.......+.
T Consensus 4 P~~gD~VIG~V~~~~-~~~~~VdI~s~--~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~ 65 (86)
T cd05790 4 PAKGDHVIGIVVAKA-GDFFKVDIGGS--EPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANR 65 (86)
T ss_pred CCCCCEEEEEEEEEc-CCeEEEEcCCC--cceEechHHcccccccccccCCCCCEEEEEEEecCC
Confidence 554 56899999975 57888887542 33443 344444 6789999999999877654
No 63
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=64.96 E-value=18 Score=27.70 Aligned_cols=37 Identities=14% Similarity=0.187 Sum_probs=27.8
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccC
Q 032228 36 AQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDY 84 (145)
Q Consensus 36 g~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~ 84 (145)
|+|+.-.|+++|.|.+.||...- ++.-|+|++.|.|.
T Consensus 22 G~I~~~~~~~kykv~FdDG~~~~------------v~~~div~~dplpl 58 (122)
T PF09038_consen 22 GKITSDKGKNKYKVLFDDGYECR------------VLGKDIVVCDPLPL 58 (122)
T ss_dssp EEEEEEETTTEEEEEETTS-EEE------------EECCCEEEESSS-T
T ss_pred ceEeecCCCCeEEEEecCCccce------------eccCcEEEEcceec
Confidence 99999999999999999998642 34457777766654
No 64
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=64.26 E-value=23 Score=35.01 Aligned_cols=65 Identities=25% Similarity=0.323 Sum_probs=50.0
Q ss_pred cCCCCeEE--EEEEEeCCCceEEEEeCCCCEEEEEecccccc-e-----EEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 28 FKEDGQEY--AQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-K-----VWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 28 ~p~e~q~i--g~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~-----IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
.|..|+++ |+|+++...+.| |++..|..=|+||+ .+.. + =-++.||.|.|.....+. +++|...+
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaF-VeL~~g~EGLVHIS-eLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSl 822 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAF-VEIAPGREGLCHIS-ELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSR 822 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEE-EEeCCCCEEEEEhh-hcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEE
Confidence 46789998 599999987777 56677899999988 4422 1 247899999999998876 78886554
No 65
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=63.89 E-value=12 Score=28.09 Aligned_cols=34 Identities=15% Similarity=0.086 Sum_probs=28.1
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..+|.+.||..++|+|||-= -.+.+.+.|||.--
T Consensus 50 varV~L~ngk~v~AyIPG~G---hnlqehs~VLvrGG 83 (108)
T cd03368 50 VARVRLSNGKEVTAYIPGEG---HNLQEHSVVLVRGG 83 (108)
T ss_pred eEEEEecCCCEEEEEcCCCC---CCccccCEEEEeCC
Confidence 46788999999999999976 45788888888754
No 66
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=62.62 E-value=26 Score=28.77 Aligned_cols=78 Identities=13% Similarity=0.155 Sum_probs=48.9
Q ss_pred ccCCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc-----cc-eEEEccCCEEEEEeccCCCC---------
Q 032228 27 IFKEDG-QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---KM-----HK-KVWIGAGDIILVGLRDYQDD--------- 87 (145)
Q Consensus 27 ~~p~e~-q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K~-----Rk-~IwIk~GD~VlVe~~~~~~~--------- 87 (145)
..|..| -++|+|+++.+ ..+.|.+..+..-+.|+.. +. ++ +=++++||+|.+.....+..
T Consensus 59 y~P~vGDiViG~V~~i~~-~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~ 137 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTF-SGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG 137 (235)
T ss_pred ccCCCCCEEEEEEEEEeC-ceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence 456665 58999999765 4578888766554555442 21 22 45689999999887654432
Q ss_pred ------ceEEEEEcChhHHHHHHH
Q 032228 88 ------KADVILKYMPDEARLLKA 105 (145)
Q Consensus 88 ------Kg~Ii~ry~~deik~Lrk 105 (145)
.+=++....+.-++.|.-
T Consensus 138 ~~lG~L~~G~~~~V~~~~i~~lig 161 (235)
T PRK04163 138 KGLGKIEGGTIVEIKPVKVPRVIG 161 (235)
T ss_pred CCCCccCCCEEEEECHHHHHhhcC
Confidence 122456666776766643
No 67
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=62.56 E-value=25 Score=25.24 Aligned_cols=33 Identities=12% Similarity=0.086 Sum_probs=24.5
Q ss_pred EEEEEEEeC-CCceEEEEeCCCCEEEEEeccccc
Q 032228 34 EYAQVLRML-GNGRCEAMCIDGAKRLCHIRGKMH 66 (145)
Q Consensus 34 ~ig~Vv~~l-G~~~~~V~~~dG~~~la~IpGK~R 66 (145)
++|+|++.- +++.+.+.|.||..+.++++.-..
T Consensus 23 ivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~~ 56 (109)
T PF08661_consen 23 IVGKVESVDPDGGSATLSTSDGGQVTVSLNPPSD 56 (109)
T ss_dssp EEEEEEEE-TTSSEEEEE-TTS-EEEEEESS--S
T ss_pred EEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCCC
Confidence 789999877 578999999999999999986543
No 68
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=62.37 E-value=14 Score=26.00 Aligned_cols=38 Identities=11% Similarity=-0.114 Sum_probs=26.4
Q ss_pred ceEEEEeCCCCEEEEEeccc--ccc-eEEEccCCEEEEEec
Q 032228 45 GRCEAMCIDGAKRLCHIRGK--MHK-KVWIGAGDIILVGLR 82 (145)
Q Consensus 45 ~~~~V~~~dG~~~la~IpGK--~Rk-~IwIk~GD~VlVe~~ 82 (145)
-.|++...++....+..... +++ ...++.||.|+|.-.
T Consensus 19 ~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 19 VFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred EEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 44555555556666666655 776 788999999998754
No 69
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=61.42 E-value=38 Score=21.31 Aligned_cols=59 Identities=10% Similarity=0.053 Sum_probs=40.3
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc-----ccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK-----MHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK-----~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
.+.|+|+.+...+. -|++.++..-|++++-- .+. .--++.||.|.|....-+..+++|.
T Consensus 3 ~~~g~V~~i~~~G~-fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~ 67 (69)
T cd05690 3 VVSGKIKSITDFGI-FVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred EEEEEEEEEEeeeE-EEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEe
Confidence 46788888876554 46777788888876531 111 2247999999999887776666663
No 70
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=60.99 E-value=13 Score=28.38 Aligned_cols=51 Identities=18% Similarity=0.133 Sum_probs=37.2
Q ss_pred CeEEEEEEEeCC------Cc----eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCC
Q 032228 32 GQEYAQVLRMLG------NG----RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQ 85 (145)
Q Consensus 32 ~q~ig~Vv~~lG------~~----~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~ 85 (145)
-|.-|.|++.++ |+ ..+|.+.||..++|+|||== -.+.+-|.|||.---..
T Consensus 27 Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL~n~k~v~AyIPg~G---hnlqehs~VLVrGgrv~ 87 (122)
T PF00164_consen 27 PQKKGICLKVVTVKPKKPNSAIRKVARVRLSNGKKVTAYIPGEG---HNLQEHSVVLVRGGRVG 87 (122)
T ss_dssp SEEEEEEEEEEEEEESTTTCSEEEEEEEEETTSEEEEEEC-SSS---CCSTTTSEEEEEEESBT
T ss_pred CccCcEEeecccccccCccchhhhcceeeeccCceEEEEecCCc---ccccccceEEEeccccC
Confidence 466666666553 22 46789999999999999876 55889999999865433
No 71
>PRK08059 general stress protein 13; Validated
Probab=60.85 E-value=56 Score=23.96 Aligned_cols=65 Identities=17% Similarity=0.208 Sum_probs=45.0
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cccc--eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---KMHK--KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K~Rk--~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
...+.|+|+.+...+ +.|.+.++..-+++++- .+-. .=.++.||.|.|.....+..++.|.....
T Consensus 8 G~iv~G~V~~i~~~G-~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 8 GSVVTGKVTGIQPYG-AFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred CCEEEEEEEEEecce-EEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 356889999988755 45677777777776552 1111 22578999999999887777788766553
No 72
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=60.38 E-value=37 Score=20.83 Aligned_cols=59 Identities=22% Similarity=0.167 Sum_probs=39.6
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+.|+|+.+... -+.|.+.++..-+.+++---.. .=+++.||.|.|.....+. .++|..
T Consensus 3 ~~~g~V~~i~~~-g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~l 66 (69)
T cd05692 3 VVEGTVTRLKPF-GAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISL 66 (69)
T ss_pred EEEEEEEEEEee-eEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEE
Confidence 578999998764 4556777777777776521111 1347999999999876665 566643
No 73
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=60.25 E-value=48 Score=30.37 Aligned_cols=64 Identities=17% Similarity=0.250 Sum_probs=49.3
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIR----GKMHK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~Ip----GK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
...+.|+|+++...+.| |.+.+|..-|+|++ .++.. .-.++.||.|.|.....+..+++|..-+
T Consensus 294 G~vv~G~V~~I~~fGvF-VeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSl 362 (486)
T PRK07899 294 GQIVPGKVTKLVPFGAF-VRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362 (486)
T ss_pred CCEEEEEEEEEeccEEE-EEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 45689999999887776 66777888888875 22222 3468999999999988888888887664
No 74
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=59.68 E-value=47 Score=21.81 Aligned_cols=57 Identities=12% Similarity=0.109 Sum_probs=41.3
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEccCCEEEEEeccCCCCceEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KV-----WIGAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~I-----wIk~GD~VlVe~~~~~~~Kg~I 91 (145)
..+.|+|+++....-.-|.++.|.+=++|++ .+.. ++ -++.||.|.|.....+. ++|
T Consensus 5 ~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis-~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i 67 (72)
T cd05704 5 AVTLGMVTKVIPHSGLTVQLPFGKTGLVSIF-HLSDSYTENPLEGFKPGKIVRCCILSKKD--GKY 67 (72)
T ss_pred CEEEEEEEEeeCCcEEEEECCCCCEEEEEHH-HhcCcccCCHHHhCCCCCEEEEEEEEecC--CEE
Confidence 4578999998875556788999999999987 4422 21 25779999998876542 444
No 75
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=59.64 E-value=14 Score=26.01 Aligned_cols=32 Identities=13% Similarity=0.148 Sum_probs=26.0
Q ss_pred eEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 68 KVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 68 ~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
++-|++||.|.|---++-...|.|+..+...+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~ 37 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSN 37 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 67899999999988776667888888876655
No 76
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=59.21 E-value=27 Score=25.28 Aligned_cols=75 Identities=13% Similarity=0.014 Sum_probs=45.0
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----cc------------------c-eEEEccCCEEEEEeccCCCCce
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK----MH------------------K-KVWIGAGDIILVGLRDYQDDKA 89 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK----~R------------------k-~IwIk~GD~VlVe~~~~~~~Kg 89 (145)
++.|+|++++-+..|.|.+.+|.....+|.|= +. . ---+..|-.|.+.+...+ .-|
T Consensus 2 ~~~~~V~~V~DGDT~~v~~~~~~~~~vrL~gIdaPe~~~~~~~~~~~~~~~g~~A~~~l~~~l~g~~V~~~~~~~D-~~g 80 (138)
T smart00318 2 EIRGVVERVLDGDTIRVRLPKNKLITIRLSGIDAPETARPNKGDGTTDEPFGEEAKEFLKKLLLGKKVQVEVDSKD-RYG 80 (138)
T ss_pred ceeEEEEEEecCCEEEEEeCCCCEEEEEEEeccCCccCCCCCCCccccCcHHHHHHHHHHHHhCCCEEEEEEeccC-CCC
Confidence 35789999999999999999876655555330 00 0 001225777888775533 334
Q ss_pred EE-EEEcChh---HHHHHHHcCC
Q 032228 90 DV-ILKYMPD---EARLLKAYGE 108 (145)
Q Consensus 90 ~I-i~ry~~d---eik~Lrk~g~ 108 (145)
++ -+.|..+ =-.+|.+.|+
T Consensus 81 r~~a~v~~~~~~~l~~~Lv~~G~ 103 (138)
T smart00318 81 RFLGTVYLNGGNNIAEELVKEGL 103 (138)
T ss_pred CEEEEEEECCCCcHHHHHHhcCC
Confidence 43 3333322 3356777786
No 77
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=59.15 E-value=11 Score=25.08 Aligned_cols=24 Identities=29% Similarity=0.632 Sum_probs=13.1
Q ss_pred EccCCEEEEEeccC---CCCceEEEEE
Q 032228 71 IGAGDIILVGLRDY---QDDKADVILK 94 (145)
Q Consensus 71 Ik~GD~VlVe~~~~---~~~Kg~Ii~r 94 (145)
+..||+|+|.++.. ....|+|+.-
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~ 40 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVF 40 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEE
Confidence 45666666666554 2445555433
No 78
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=58.18 E-value=44 Score=22.35 Aligned_cols=56 Identities=18% Similarity=0.083 Sum_probs=30.5
Q ss_pred CceEEEEeCC-CCEEE------EEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 44 NGRCEAMCID-GAKRL------CHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 44 ~~~~~V~~~d-G~~~l------a~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
.++++|++.+ +.... +.-.|..+-...-..||-|+|....-+..++-|+-.++.++
T Consensus 10 ~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~~~Gd~~~~~vlg~l~~~~ 72 (79)
T PF04717_consen 10 KGRVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLFPGGDPERPVVLGSLYSDA 72 (79)
T ss_dssp TTEEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEEGGCTTTSEEEEEEE--SS
T ss_pred CCEEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEccCCcCCCCEEEEEECCCC
Confidence 4889999743 33322 22334344466778999999999777788999987776543
No 79
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=58.10 E-value=1.1e+02 Score=28.84 Aligned_cols=84 Identities=15% Similarity=0.182 Sum_probs=48.3
Q ss_pred CeEEEEEEEeCCCceEEEE--e--CCCCEEEEEecccccceEEE--------ccCCEEEEEeccCCC----CceEEEEEc
Q 032228 32 GQEYAQVLRMLGNGRCEAM--C--IDGAKRLCHIRGKMHKKVWI--------GAGDIILVGLRDYQD----DKADVILKY 95 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~--~--~dG~~~la~IpGK~Rk~IwI--------k~GD~VlVe~~~~~~----~Kg~Ii~ry 95 (145)
+...|+|+++++...=.+. + ..+..++.-.-.++...|.| +.||+|+|++..|.. -.|.|+.++
T Consensus 121 ~~~eg~Vv~Il~r~~~~~VG~~~~~~~~~~v~p~d~~~~~~I~i~~~~~~~~~~g~~v~v~i~~~p~~~~~~~g~i~~~l 200 (709)
T TIGR02063 121 DRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYLDIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEIL 200 (709)
T ss_pred CCceEEEEEEEeeCCCEEEEEEEEcCcEEEEEECCCCCCCCEEECCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEe
Confidence 3456677776654322222 1 23333333333444433444 568999999965532 479999998
Q ss_pred C-----hhHHHHHHHcCCCCccccc
Q 032228 96 M-----PDEARLLKAYGELPETTRL 115 (145)
Q Consensus 96 ~-----~deik~Lrk~g~wP~~f~~ 115 (145)
. .-++..+....-+|.+|..
T Consensus 201 g~~~d~~~~~~~il~~~~i~~~f~~ 225 (709)
T TIGR02063 201 GHADDPGIDILIIIRKHGIPYEFPE 225 (709)
T ss_pred CCCCcccchHHHHHHHcCcCCCCCH
Confidence 3 4456665555557777755
No 80
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=57.95 E-value=34 Score=24.52 Aligned_cols=55 Identities=22% Similarity=0.260 Sum_probs=35.4
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEE---EecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRLC---HIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~la---~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~ 102 (145)
-|+|+++-+++.+-+...-|.+|-+ .++. -++.||||||.. |--+.+...++++.
T Consensus 6 PgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~------~v~~GdyVLVHv-------GfAi~~idEeeAke 63 (82)
T COG0298 6 PGQIVEIDDNNHLAIVDVGGVKREVNLDLVGE------EVKVGDYVLVHV-------GFAMSKIDEEEAKE 63 (82)
T ss_pred ccEEEEEeCCCceEEEEeccEeEEEEeeeecC------ccccCCEEEEEe-------eEEEeecCHHHHHH
Confidence 3678888887754444444554433 3343 578899999985 44566677777664
No 81
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=57.85 E-value=46 Score=21.11 Aligned_cols=59 Identities=12% Similarity=0.302 Sum_probs=41.9
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc------eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK------KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk------~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+.|+|+.+...+ .-|.+.++..-+++++ .+.. .=.++.||.|.|.....+..+++|..
T Consensus 3 ~~~g~V~~v~~~G-~~V~l~~~~~gli~~s-~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~l 67 (70)
T cd05698 3 KTHGTIVKVKPNG-CIVSFYNNVKGFLPKS-ELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLL 67 (70)
T ss_pred EEEEEEEEEecCc-EEEEECCCCEEEEEHH-HcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEE
Confidence 4678899887544 4577777777777764 2221 22378899999999988887777754
No 82
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=57.57 E-value=14 Score=25.96 Aligned_cols=45 Identities=13% Similarity=0.066 Sum_probs=28.7
Q ss_pred EEEccCCEEEEEeccCCC----C---ceEEEEEcChhHHHHHHHcCCCCccccccccc
Q 032228 69 VWIGAGDIILVGLRDYQD----D---KADVILKYMPDEARLLKAYGELPETTRLNEGI 119 (145)
Q Consensus 69 IwIk~GD~VlVe~~~~~~----~---Kg~Ii~ry~~deik~Lrk~g~wP~~f~~~~~~ 119 (145)
+-+++||+|+|...+... . -|.|++.--. -+.+..|.-|...+=|
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg------aR~P~~~tlFQVadVD 55 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG------ARDPKVPTLFQVADVD 55 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEecc------ccCCCCCceEEEEEcc
Confidence 458999999999887321 1 5888887543 2345555556554433
No 83
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=57.10 E-value=49 Score=21.15 Aligned_cols=53 Identities=21% Similarity=0.239 Sum_probs=38.7
Q ss_pred CCCCeEEEEEEEeCC-Cc--eEEEEeC-CCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 29 KEDGQEYAQVLRMLG-NG--RCEAMCI-DGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 29 p~e~q~ig~Vv~~lG-~~--~~~V~~~-dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
|.++-+-|+|..++. +. +.++... +|+.+-+.||..= ...-+..||.|-+.|.
T Consensus 2 ~~~~~l~a~V~~v~~~G~~vRlEl~~~~~~~~iEvel~~~~-~~l~l~~G~~V~l~Pr 58 (58)
T PF12857_consen 2 PGEGGLPARVRRVRPVGPEVRLELKRLDDGEPIEVELPRER-RQLGLQPGDRVYLRPR 58 (58)
T ss_pred CCCCcEeEEEEEEEecCCeEEEEEEECCCCCEEEEEeCHhH-HhcCCCCCCEEEEEeC
Confidence 456677788877764 33 3444445 7899999999777 7777888999988763
No 84
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=56.78 E-value=7 Score=30.15 Aligned_cols=40 Identities=28% Similarity=0.728 Sum_probs=30.7
Q ss_pred EEecccccc---eEEEcc-C-CEEEEEeccCC-CCceEEEEEcChh
Q 032228 59 CHIRGKMHK---KVWIGA-G-DIILVGLRDYQ-DDKADVILKYMPD 98 (145)
Q Consensus 59 a~IpGK~Rk---~IwIk~-G-D~VlVe~~~~~-~~Kg~Ii~ry~~d 98 (145)
|.+|..++. ..||+. | +.+.|.+++|. ..-|+|+|.=.++
T Consensus 3 ~~~p~~l~Y~~~heWvr~e~d~~~tvGiT~~aq~~lGdiv~Velpe 48 (131)
T COG0509 3 CNIPDDLKYTAEHEWVRVEGDGTATVGITDYAQDQLGDIVFVELPE 48 (131)
T ss_pred ccccccceeccceEEEEecCCCEEEEeCCHHHHHhcCCEEEEEcCC
Confidence 456777775 899998 5 89999999884 5688998876554
No 85
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=56.37 E-value=18 Score=27.28 Aligned_cols=48 Identities=19% Similarity=0.088 Sum_probs=31.2
Q ss_pred cceEEEccCCEEEEEeccCC-----------C----CceEEEEEcChhHHHHHHHcC-CCCccc
Q 032228 66 HKKVWIGAGDIILVGLRDYQ-----------D----DKADVILKYMPDEARLLKAYG-ELPETT 113 (145)
Q Consensus 66 Rk~IwIk~GD~VlVe~~~~~-----------~----~Kg~Ii~ry~~deik~Lrk~g-~wP~~f 113 (145)
|+.+.|+.||.|+|.+.+-. + ....+.|=|.++|+..+++.. ..|.|.
T Consensus 3 r~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~Ev 66 (130)
T cd04721 3 RNGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREI 66 (130)
T ss_pred cCCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeE
Confidence 45788999999999875411 1 134456777888887754444 444443
No 86
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=55.61 E-value=33 Score=28.54 Aligned_cols=53 Identities=15% Similarity=0.218 Sum_probs=41.4
Q ss_pred CCeEEEEEEEeC-CCceEEEE--eCCCCEEEEEecccccceEEEccCCEEEEEecc
Q 032228 31 DGQEYAQVLRML-GNGRCEAM--CIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 31 e~q~ig~Vv~~l-G~~~~~V~--~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
.|.+-|+|+++. ++...+|. |++|.+..|.|+..=-..+-+.+|+-|.+....
T Consensus 199 rN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~~L~L~~G~~V~a~iKa 254 (263)
T PRK10676 199 DNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAARLSLQQGDAVTAYFNA 254 (263)
T ss_pred hheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHHhcCCCCCCEEEEEEEc
Confidence 478999999996 45545555 568899999999866667888999999887654
No 87
>PRK07252 hypothetical protein; Provisional
Probab=55.39 E-value=83 Score=23.28 Aligned_cols=63 Identities=16% Similarity=0.249 Sum_probs=45.2
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
..+.|+|+.+...+.| |.+..+..-+++++- ++.. .=.++.||.|.|.....+..+++|...+
T Consensus 5 ~iv~G~V~~V~~~G~f-Vei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSl 72 (120)
T PRK07252 5 DKLKGTITGIKPYGAF-VALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72 (120)
T ss_pred CEEEEEEEEEeCcEEE-EEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 4588999999876555 577777777777652 1111 1237999999999998888888887664
No 88
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=54.83 E-value=43 Score=25.56 Aligned_cols=49 Identities=10% Similarity=0.072 Sum_probs=41.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
.+.|.|++.+|+.+|......|. +.+.|+-+.=+-.-|.++|.|-+.-.
T Consensus 61 ~L~G~Iv~~l~~d~Y~F~D~TG~-I~VeId~~~w~G~~v~p~d~V~I~Ge 109 (126)
T TIGR00156 61 TLRGNIISHIGDDRYVFRDKSGE-INVVIPAAVWNGREVQPKDMVNISGS 109 (126)
T ss_pred EEEEEEEEEeCCceEEEECCCCC-EEEEECHHHcCCCcCCCCCEEEEEEE
Confidence 47999999999999999999995 77888877767777889999887654
No 89
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=54.34 E-value=19 Score=27.36 Aligned_cols=32 Identities=16% Similarity=0.248 Sum_probs=26.7
Q ss_pred eEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 68 KVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 68 ~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
++.|+.||.|.|---.+-...|.|+..+...+
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~ 74 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG 74 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCC
Confidence 68899999999998777777899988876554
No 90
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=53.62 E-value=18 Score=24.48 Aligned_cols=26 Identities=19% Similarity=0.149 Sum_probs=15.0
Q ss_pred EccCCEEEEEeccC--C-CCceEEEEEcC
Q 032228 71 IGAGDIILVGLRDY--Q-DDKADVILKYM 96 (145)
Q Consensus 71 Ik~GD~VlVe~~~~--~-~~Kg~Ii~ry~ 96 (145)
++.||+|+|.+... . ...|+|+..+.
T Consensus 12 l~~GD~vlv~~~~~~~~~~~~Gdivv~~~ 40 (90)
T TIGR02754 12 LPPGDRIIVVPWLKIFRVPPIGNVVVVRH 40 (90)
T ss_pred cCCCCEEEEEEccccCCCCCCCeEEEEec
Confidence 46788888886422 1 23477654443
No 91
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=53.50 E-value=25 Score=20.86 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=24.4
Q ss_pred CCCe-EEEEEEEeCCCceEEEEeCC-CCEEEEE
Q 032228 30 EDGQ-EYAQVLRMLGNGRCEAMCID-GAKRLCH 60 (145)
Q Consensus 30 ~e~q-~ig~Vv~~lG~~~~~V~~~d-G~~~la~ 60 (145)
+++. --|+|+++.+++.+.|.+.| |.+..+.
T Consensus 10 ~d~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~ 42 (48)
T cd04508 10 DDGKWYRAKITSILSDGKVEVFFVDYGNTEVVP 42 (48)
T ss_pred CCCeEEEEEEEEECCCCcEEEEEEcCCCcEEEe
Confidence 3344 57899999999999999988 8876654
No 92
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=53.18 E-value=36 Score=32.95 Aligned_cols=62 Identities=21% Similarity=0.325 Sum_probs=46.2
Q ss_pred CCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEec--------ccccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 29 KEDGQ-EYAQVLRMLGNGRCEAMCIDGAKRLCHIR--------GKMHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 29 p~e~q-~ig~Vv~~lG~~~~~V~~~dG~~~la~Ip--------GK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
|..|+ +.|+|+++...+.| |.+..|..=|+|++ .+.++ .=.++.||.|.|.....+. +|+|.
T Consensus 645 ~~vG~i~~GkV~~I~dfGaF-Vel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~ 716 (719)
T TIGR02696 645 PEVGERFLGTVVKTTAFGAF-VSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLS 716 (719)
T ss_pred CCCCCEEEEEEEEEECceEE-EEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCee
Confidence 56665 78999999987776 56678899999998 23333 3358999999999887773 66663
No 93
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=51.99 E-value=56 Score=27.20 Aligned_cols=74 Identities=12% Similarity=0.064 Sum_probs=47.4
Q ss_pred EEEEEEEeCCCceEEEEeC-CCCEEEEEec--ccccceEEEccCCEEEEEeccCCC--CceEEEEEc------------C
Q 032228 34 EYAQVLRMLGNGRCEAMCI-DGAKRLCHIR--GKMHKKVWIGAGDIILVGLRDYQD--DKADVILKY------------M 96 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~-dG~~~la~Ip--GK~Rk~IwIk~GD~VlVe~~~~~~--~Kg~Ii~ry------------~ 96 (145)
+.|+.++=. |+|.+.+. ||++.+||+| |||.-- +.+|-.|++.+++... .+.+++-.+ .
T Consensus 10 ~~~~fi~R~--nRF~~~V~~~G~~~~aH~pNtGrl~el--l~pG~~vll~~~~~p~rK~~y~l~~v~~~g~~V~int~~~ 85 (232)
T TIGR00230 10 VRGRLIGRY--NRFLVDVEVDGRRETAHCPNTGRLTEL--IFPGNDVGLSKSDNGGRKLSYTWEAVQCDGGWVLVNTQLQ 85 (232)
T ss_pred eEEEEEeec--CCEEEEEEECCeEEEEEcCCCCCChhh--cCCCCEEEEEECCCCCCCCCEEEEEEEECCeEEEEcCccH
Confidence 346666655 67877764 8999999997 566653 4599999999886532 223332222 1
Q ss_pred hhHHHHHHHcCCCCc
Q 032228 97 PDEARLLKAYGELPE 111 (145)
Q Consensus 97 ~deik~Lrk~g~wP~ 111 (145)
..=+.++.++|.+|.
T Consensus 86 N~l~~~~l~~~~i~~ 100 (232)
T TIGR00230 86 NRLFKVAIPSSKISE 100 (232)
T ss_pred HHHHHHHHHcCCCcc
Confidence 223556667788875
No 94
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=51.70 E-value=56 Score=20.21 Aligned_cols=58 Identities=17% Similarity=0.201 Sum_probs=38.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEccCCEEEEEeccCCCCceEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK----MHK-KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK----~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
...|+|+.+.. .-+.|.+.++..-+++++-- ++. .-.++.||.|.|.....+. .+.|.
T Consensus 3 ~~~g~V~~v~~-~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ 65 (68)
T cd04472 3 IYEGKVVKIKD-FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRIS 65 (68)
T ss_pred EEEEEEEEEEE-eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEE
Confidence 56788888886 44556777776666665321 111 1136899999999887766 66664
No 95
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=51.35 E-value=21 Score=24.81 Aligned_cols=31 Identities=16% Similarity=0.198 Sum_probs=24.4
Q ss_pred EEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 69 VWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 69 IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
+.|++||.|.|---.+-...|.|+..+...+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~ 35 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKN 35 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 5799999999987665566788888876655
No 96
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=50.98 E-value=63 Score=20.58 Aligned_cols=60 Identities=10% Similarity=0.066 Sum_probs=41.6
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEec---cc-ccc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIR---GK-MHK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~Ip---GK-~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+.|+|+++...+ ..|++.+|.+-+++++ .. ++. .-.++.||.+.|.....+..+++|..
T Consensus 3 ~v~g~V~~v~~~G-v~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~l 67 (69)
T cd05697 3 VVKGTIRKLRPSG-IFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67 (69)
T ss_pred EEEEEEEEEeccE-EEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEE
Confidence 4678999987554 4577778877777532 21 222 23588999999999988877777754
No 97
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=50.23 E-value=4.4 Score=25.00 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=24.3
Q ss_pred CCEEEEEecccccceEEEccCCEEEEEecc
Q 032228 54 GAKRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 54 G~~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
|...-.+||-.+++..-|.+||.|.+...+
T Consensus 4 g~s~~v~iPk~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 4 GNSGQVTIPKEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp TTCSEEEE-HHHHHHTTSSTTTEEEEEEET
T ss_pred CCCceEECCHHHHHHcCCCCCCEEEEEEeC
Confidence 344567899999999999999999999864
No 98
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=50.00 E-value=1.5e+02 Score=27.88 Aligned_cols=45 Identities=18% Similarity=0.082 Sum_probs=31.6
Q ss_pred EccCCEEEEEeccCCC----CceEEEEEcC-----hhHHHHHHHcCCCCccccc
Q 032228 71 IGAGDIILVGLRDYQD----DKADVILKYM-----PDEARLLKAYGELPETTRL 115 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~----~Kg~Ii~ry~-----~deik~Lrk~g~wP~~f~~ 115 (145)
.+.||.|.|+...|.. -.|.|+.++. .-++..+....-+|.+|..
T Consensus 120 ~~~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~~f~~ 173 (654)
T TIGR00358 120 LAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFEFPD 173 (654)
T ss_pred CCCCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCCCCCH
Confidence 4579999999876642 3799999983 3346666666556777754
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=49.54 E-value=50 Score=29.78 Aligned_cols=51 Identities=10% Similarity=0.111 Sum_probs=42.4
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
.-..+|+|++++..+++.|....|..+++++.+..-+. -+++|+.|.+...
T Consensus 103 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~l~~~~~v~l~~~ 153 (438)
T PTZ00361 103 SPLSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVDKE-QLEPGCSVLLHNK 153 (438)
T ss_pred CCcEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCCHh-hCCCCCEEEEcCC
Confidence 45689999999999999999999999999999877552 2578888877654
No 100
>PRK05054 exoribonuclease II; Provisional
Probab=48.74 E-value=1.7e+02 Score=27.63 Aligned_cols=46 Identities=15% Similarity=0.016 Sum_probs=33.7
Q ss_pred EccCCEEEEEeccCCC-----CceEEEEEcC-----hhHHHHHHHcCCCCcccccc
Q 032228 71 IGAGDIILVGLRDYQD-----DKADVILKYM-----PDEARLLKAYGELPETTRLN 116 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~-----~Kg~Ii~ry~-----~deik~Lrk~g~wP~~f~~~ 116 (145)
.+.||+|.|+...|.. -.|.|+.++- .-++..+..+--+|.+|...
T Consensus 122 ~~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~f~~~ 177 (644)
T PRK05054 122 FKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLEREAPAG 177 (644)
T ss_pred CCCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCCCCch
Confidence 5679999999986642 3799999993 34566666666678888763
No 101
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=48.73 E-value=69 Score=20.38 Aligned_cols=63 Identities=16% Similarity=0.140 Sum_probs=41.5
Q ss_pred CeEEEEEEEeCCCceEEEEeCC-CCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 32 GQEYAQVLRMLGNGRCEAMCID-GAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~d-G~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
..+.|+|+.+...+.| |.+.+ +..=+++++---.. .=.++.||.|.|.....+..+++|...+
T Consensus 4 ~~v~g~V~~i~~~g~~-v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~ 72 (77)
T cd05708 4 QKIDGTVRRVEDYGVF-IDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGL 72 (77)
T ss_pred CEEEEEEEEEEcceEE-EEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEE
Confidence 4578999999866655 45553 55555554321111 1236999999999888887778876543
No 102
>PRK10053 hypothetical protein; Provisional
Probab=48.57 E-value=57 Score=24.99 Aligned_cols=48 Identities=10% Similarity=0.023 Sum_probs=42.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
.+.|.+++.+|+..|......|. +.+.|+-+.-.-.-|.+.|.|.+.-
T Consensus 65 ~L~G~Iv~~lg~d~Y~F~D~tG~-I~VeID~~~w~G~~v~p~~kV~I~G 112 (130)
T PRK10053 65 SLRGNLIDHKGDDRYVFRDKSGE-INVIIPAAVFDGREVQPDQMINING 112 (130)
T ss_pred EEEEEEEEEeCCceEEEECCCCc-EEEEeCHHHcCCCcCCCCCEEEEEE
Confidence 48999999999999999999994 7889998877777889999998764
No 103
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=48.51 E-value=65 Score=20.05 Aligned_cols=52 Identities=12% Similarity=0.162 Sum_probs=36.4
Q ss_pred CCeEEEEEEEeC--C-CceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEecc
Q 032228 31 DGQEYAQVLRML--G-NGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 31 e~q~ig~Vv~~l--G-~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
++.+-|+|+.+. | ...+.|.+.++...++..+..-. ..-+..|+.|-+...+
T Consensus 15 ~~~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~-~~~~~~G~~v~l~~~~ 69 (75)
T PF08402_consen 15 ENRLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQR-DSPLEPGDEVRLSWDP 69 (75)
T ss_dssp TTEEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG--TTT--TTSEEEEEEEG
T ss_pred CCeEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccc-cCCCCCCCEEEEEECc
Confidence 468888888765 4 45677888999998888877654 3556788888887654
No 104
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=48.23 E-value=27 Score=30.15 Aligned_cols=33 Identities=18% Similarity=0.125 Sum_probs=27.3
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 46 RCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
..+|.+.+|.+++|.|||-=+ -+.+.+.|||.-
T Consensus 148 varVrLsNGk~VtAyIPGeGH---nLQEHs~VLVRG 180 (290)
T PTZ00115 148 VARVRLSTGRTVTVYIPGIGH---NLNTHSVVLVRG 180 (290)
T ss_pred eEEEEecCCCEEEEEcCCCCc---ccccCCEEEEeC
Confidence 467889999999999999776 677888888854
No 105
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=48.23 E-value=34 Score=26.40 Aligned_cols=61 Identities=15% Similarity=0.183 Sum_probs=49.4
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
+-+.|+|+.+-.-+-| |.+++|.+=|+||+-=... .=.++.||-|.|...+.+. .|.|.--
T Consensus 7 ~~l~GkItgI~~yGAF-V~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLS 72 (129)
T COG1098 7 SKLKGKITGITPYGAF-VELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLS 72 (129)
T ss_pred ceEEEEEEeeEecceE-EEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCccee
Confidence 4578999998877777 8999999999999865543 3468999999999998887 8888554
No 106
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=47.87 E-value=80 Score=28.59 Aligned_cols=65 Identities=20% Similarity=0.356 Sum_probs=48.9
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 30 EDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG-----KMHK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 30 ~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG-----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
....+.|+|+.+...+.| |.+..|..-++|++- +..+ .-+++.||.|.|.....+..+++|..-+
T Consensus 292 ~G~~v~G~V~~v~~~G~f-V~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~ 362 (491)
T PRK13806 292 AGDKVTGKVVRLAPFGAF-VEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSL 362 (491)
T ss_pred CCCEEEEEEEEEeCceEE-EEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEE
Confidence 345689999999877766 577778888888763 2222 4579999999999988887788875554
No 107
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=47.63 E-value=13 Score=21.76 Aligned_cols=25 Identities=20% Similarity=0.123 Sum_probs=22.3
Q ss_pred EEEecccccceEEEccCCEEEEEec
Q 032228 58 LCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 58 la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
-..||..+|+.+-+..||.|.+...
T Consensus 8 ri~iP~~~r~~l~~~~gd~~~i~~~ 32 (43)
T TIGR01439 8 QIVIPKEIREKLGLKEGDRLEVIRV 32 (43)
T ss_pred eEEecHHHHHHcCcCCCCEEEEEEe
Confidence 4579999999999999999999964
No 108
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=47.08 E-value=24 Score=22.72 Aligned_cols=28 Identities=29% Similarity=0.662 Sum_probs=19.0
Q ss_pred EccCCEEEEEeccCCCCceEEEEEcChh
Q 032228 71 IGAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
|..||+|+|.+.......|+|+......
T Consensus 14 i~~gd~v~i~~~~~~~~~G~iv~~~~~~ 41 (84)
T cd06462 14 IPDGDLVLVDKSSYEPKRGDIVVFRLPG 41 (84)
T ss_pred ccCCCEEEEEecCCCCcCCEEEEEEcCC
Confidence 7888888888876546677765444433
No 109
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=46.34 E-value=1.2e+02 Score=25.22 Aligned_cols=49 Identities=20% Similarity=0.288 Sum_probs=36.7
Q ss_pred eEEEEEEEeCCCceEEEEeC--CCCEEEEEec--ccccceEEEccCCEEEEEeccCC
Q 032228 33 QEYAQVLRMLGNGRCEAMCI--DGAKRLCHIR--GKMHKKVWIGAGDIILVGLRDYQ 85 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~--dG~~~la~Ip--GK~Rk~IwIk~GD~VlVe~~~~~ 85 (145)
-+.|+.++=. |+|.|.+. ||+..+||+| |||+-- +.+|-.|++.+++-.
T Consensus 7 l~~g~fi~R~--nRF~~~V~~~~g~~~~aH~pntGRl~el--l~pG~~v~l~~~~~p 59 (234)
T PRK00347 7 LQEATLIKRY--KRFLADVELDDGEELTAHCPNTGRMTGL--LTPGNTVWLSTSDNP 59 (234)
T ss_pred ceEEEEEEec--CCEEEEEEECCCCEEEEEcCCCCCChhh--ccCCCEEEEEECCCC
Confidence 4567777755 78888875 6999999997 566653 349999999987643
No 110
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=46.11 E-value=98 Score=21.42 Aligned_cols=54 Identities=15% Similarity=0.092 Sum_probs=39.5
Q ss_pred CeEEEEEEEeCCC-ceEEEEeCCCCEEEEEeccc-------ccc-eEEEccCCEEEEEeccCC
Q 032228 32 GQEYAQVLRMLGN-GRCEAMCIDGAKRLCHIRGK-------MHK-KVWIGAGDIILVGLRDYQ 85 (145)
Q Consensus 32 ~q~ig~Vv~~lG~-~~~~V~~~dG~~~la~IpGK-------~Rk-~IwIk~GD~VlVe~~~~~ 85 (145)
+-..|+|+++... +-.-|.+.+|..-++|++-= ..+ .=-++.||.|+|......
T Consensus 9 ~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~ 71 (88)
T cd04453 9 NIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEP 71 (88)
T ss_pred CEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEec
Confidence 4578999999986 45567778889989888632 111 234889999999987654
No 111
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=45.96 E-value=28 Score=27.28 Aligned_cols=31 Identities=13% Similarity=0.119 Sum_probs=23.1
Q ss_pred eEEEccCCEEEEEeccCCCCceEEEEEcChh
Q 032228 68 KVWIGAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 68 ~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
++.|+.||.|.|-.-.+-...|.|+.++...
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~ 74 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKK 74 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCC
Confidence 6788888888888776666678887776544
No 112
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=44.53 E-value=52 Score=20.73 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=19.5
Q ss_pred CCe-EEEEEEEeCCCceEEEEeCC
Q 032228 31 DGQ-EYAQVLRMLGNGRCEAMCID 53 (145)
Q Consensus 31 e~q-~ig~Vv~~lG~~~~~V~~~d 53 (145)
++. -.|+|++.++++.|.|.+.+
T Consensus 16 ~~~W~~a~V~~~~~~~~~~V~~~~ 39 (61)
T smart00743 16 EDSWWEAVVTKVLGDGKYLVRYLT 39 (61)
T ss_pred CCEEEEEEEEEECCCCEEEEEECC
Confidence 444 56999999999999999987
No 113
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=43.17 E-value=75 Score=24.26 Aligned_cols=45 Identities=20% Similarity=0.091 Sum_probs=32.1
Q ss_pred EEEEEEeCC-CceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 35 YAQVLRMLG-NGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 35 ig~Vv~~lG-~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
-|+++..-. ...+.|.++||. ..|.-.==+.+=|+.||.|.|...
T Consensus 26 Pa~~~~~~~~~~~~~V~Fedg~---~~i~~~dv~~LDlRIGD~Vkv~~~ 71 (131)
T PF08605_consen 26 PATCVGSGVDRDRSLVRFEDGT---YEIKNEDVKYLDLRIGDTVKVDGP 71 (131)
T ss_pred eEEEEeecCCCCeEEEEEecCc---eEeCcccEeeeeeecCCEEEECCC
Confidence 466666633 235999999999 344433346889999999999874
No 114
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=42.88 E-value=24 Score=26.82 Aligned_cols=25 Identities=28% Similarity=0.391 Sum_probs=16.9
Q ss_pred EEEccCCEEEEEeccC-CCCceEEEE
Q 032228 69 VWIGAGDIILVGLRDY-QDDKADVIL 93 (145)
Q Consensus 69 IwIk~GD~VlVe~~~~-~~~Kg~Ii~ 93 (145)
+-|+.||+|+|.+.+- ..-=|+|.+
T Consensus 2 ~~i~vGd~VlI~~~d~~~~yVAkI~~ 27 (128)
T cd04719 2 LTIEVGDFVLIEGEDADGPDVARILH 27 (128)
T ss_pred eEEecCCEEEEECCCCCCCcEeeehh
Confidence 5689999999998773 223444433
No 115
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=41.98 E-value=1.2e+02 Score=21.44 Aligned_cols=67 Identities=12% Similarity=0.082 Sum_probs=47.5
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc------------------------ceEEEccCCEEEEEeccCCC
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMH------------------------KKVWIGAGDIILVGLRDYQD 86 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~R------------------------k~IwIk~GD~VlVe~~~~~~ 86 (145)
...+.|+|+++...+. .|.+++|.+=++++.-=-. -.=+++.||.|.+.....+.
T Consensus 4 G~vV~G~V~~v~~~gl-~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~ 82 (100)
T cd05693 4 GMLVLGQVKEITKLDL-VISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDK 82 (100)
T ss_pred CCEEEEEEEEEcCCCE-EEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccC
Confidence 3568999999876654 4688888877777642211 12457999999999998887
Q ss_pred C---ceEEEEEcChh
Q 032228 87 D---KADVILKYMPD 98 (145)
Q Consensus 87 ~---Kg~Ii~ry~~d 98 (145)
. +.+|..-+.++
T Consensus 83 ~~~~~~~i~LSlr~~ 97 (100)
T cd05693 83 SKSGKKRIELSLEPE 97 (100)
T ss_pred CcCCCcEEEEEecHH
Confidence 5 67776655544
No 116
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=41.46 E-value=39 Score=25.32 Aligned_cols=31 Identities=13% Similarity=0.169 Sum_probs=25.7
Q ss_pred eEEEccCCEEEEEeccCCCCceEEEEEcChh
Q 032228 68 KVWIGAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 68 ~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
.+.|+.||.|.|---.+....|.|+.++...
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~ 69 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKR 69 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCC
Confidence 6789999999999877777889998887444
No 117
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=40.58 E-value=33 Score=23.58 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=31.2
Q ss_pred EEEEEEeCCCceEEEEeCC-C-CEEEEEecccccceEEEccCCEEEEEe
Q 032228 35 YAQVLRMLGNGRCEAMCID-G-AKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~d-G-~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
-.+|....++..|+-.+.- | -..+-.|...+||.+-+..||.|.|++
T Consensus 32 ~v~V~~tI~g~~~~~sl~p~g~G~~~Lpv~~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 32 RVPVRGTIDGHPWRTSLFPMGNGGYILPVKAAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp -EEEEEEETTEEEEEEEEESSTT-EEEEE-HHHHHHHT--TTSEEEEEE
T ss_pred ceEEEEEECCEEEEEEEEECCCCCEEEEEcHHHHHHcCCCCCCEEEEEC
Confidence 3456666777777766632 3 467788888899999999999999874
No 118
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=40.16 E-value=36 Score=24.87 Aligned_cols=31 Identities=16% Similarity=0.198 Sum_probs=23.5
Q ss_pred EEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 69 VWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 69 IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
+.|++||.|.|---.+-...|.|+..+...+
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~ 33 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKN 33 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 3689999999987666566788887775554
No 119
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=39.93 E-value=1.5e+02 Score=21.82 Aligned_cols=67 Identities=21% Similarity=0.218 Sum_probs=40.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHHHHc-CCCCc
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY-GELPE 111 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~Lrk~-g~wP~ 111 (145)
+..++.-...| +++..+.--....++|+ .....|-+++|..|.++ ..|+|+++++.+|-.+ |+-|.
T Consensus 47 ~~~a~~~~~~~--r~e~~l~~~~~~~v~i~-~~~~~i~~~~GE~I~~e----------~S~Ky~~~~~~~l~~~aGl~~~ 113 (127)
T PF10017_consen 47 EHVARYNPEEG--RHEMYLVAKRDQTVRIG-GLDLTIHFKEGERIHTE----------NSYKYSPEEFEALAEQAGLEVE 113 (127)
T ss_pred EEEEEEcCCcC--EEEEEEEeCCcEEEEEc-CCCceeEECCCCEEEEE----------EeeCcCHHHHHHHHHHCCCeeE
Confidence 44455444333 34444433344445555 34456777777777765 4599999999998876 55443
Q ss_pred c
Q 032228 112 T 112 (145)
Q Consensus 112 ~ 112 (145)
.
T Consensus 114 ~ 114 (127)
T PF10017_consen 114 K 114 (127)
T ss_pred E
Confidence 3
No 120
>PRK08582 hypothetical protein; Provisional
Probab=39.82 E-value=1.6e+02 Score=22.20 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=44.7
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccc----cc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKM----HK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~----Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
..+.|+|+.+...+.| |.+.++.+=|+|++-=- +. .-.++.||.|.|.....+. .+.|...+.
T Consensus 7 ~iv~G~V~~I~~fG~f-V~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk 74 (139)
T PRK08582 7 SKLQGKVTGITNFGAF-VELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIK 74 (139)
T ss_pred CEEEEEEEEEECCeEE-EEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEE
Confidence 4689999998887655 67778888888876321 11 2347899999999887665 477765553
No 121
>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=38.77 E-value=76 Score=19.37 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=21.8
Q ss_pred EEEEEEEeCCCceEEEEeCC-CCEEEEE
Q 032228 34 EYAQVLRMLGNGRCEAMCID-GAKRLCH 60 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~d-G~~~la~ 60 (145)
.-|+|++..+++.+.|.+.| |.+..+.
T Consensus 19 yra~I~~~~~~~~~~V~f~D~G~~~~v~ 46 (57)
T smart00333 19 YRARIIKVDGEQLYEVFFIDYGNEEVVP 46 (57)
T ss_pred EEEEEEEECCCCEEEEEEECCCccEEEe
Confidence 67899999988899999988 8775443
No 122
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=38.19 E-value=54 Score=24.76 Aligned_cols=61 Identities=21% Similarity=0.156 Sum_probs=35.0
Q ss_pred eEEEEEEEeCCCc-eEEEEeCCCC----------EEEEEeccccc----ceEEEccCCEEEEEeccCCCC--ceEEEEE
Q 032228 33 QEYAQVLRMLGNG-RCEAMCIDGA----------KRLCHIRGKMH----KKVWIGAGDIILVGLRDYQDD--KADVILK 94 (145)
Q Consensus 33 q~ig~Vv~~lG~~-~~~V~~~dG~----------~~la~IpGK~R----k~IwIk~GD~VlVe~~~~~~~--Kg~Ii~r 94 (145)
=+.|+|++..+++ .|+|...|-. ..+.-||.+.. ..--...|..||. ++|..+. +|.|+..
T Consensus 19 WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~~~~~~~~~f~~g~~VLA-lYP~TT~FY~A~V~~~ 96 (130)
T PF07039_consen 19 WILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAPPDTDPLAEFPKGTKVLA-LYPDTTCFYPATVVSP 96 (130)
T ss_dssp EEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-SB--TTT-GGGS--TT-EEEE-E-TTSSEEEEEEEEEE
T ss_pred EEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCCccCCCCCchhhCCCCCEEEE-ECCCCceEEEEEEEeC
Confidence 3899999999987 9999997654 23445555221 2344466777664 3554332 6666655
No 123
>PRK02693 apocytochrome f; Reviewed
Probab=38.16 E-value=1.8e+02 Score=25.45 Aligned_cols=70 Identities=17% Similarity=0.147 Sum_probs=46.0
Q ss_pred cccccCC--Cccccc-ceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 10 KNRKRGK--NEADDE-KRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 10 kn~rr~~--~~~~~~-~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
-||.|+- -.++.. ..-+-.+..|.+......--|+....+..+||.++.-.||.= -.+-|++||.|.+.-
T Consensus 180 gNRGRGQvYP~G~kSNN~v~~as~~G~i~~I~~~e~Gg~~vtI~~~dG~~v~~~iP~G--peliV~eG~~v~~dq 252 (312)
T PRK02693 180 GNRGRGQVYPTGEKSNNNVFTASAAGTITSIETGEDGGYVVTITTEDGEAVTETIPAG--PELIVKEGDTVEAGD 252 (312)
T ss_pred ccCCccccCCCCccccCceecccCCcEEEEEEecCCCceEEEEEcCCCCEEEEecCCC--CeEEEecCcEEecCC
Confidence 3566652 122222 233334556666666665567778888889999999999842 267799999998764
No 124
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.91 E-value=1.1e+02 Score=19.55 Aligned_cols=61 Identities=8% Similarity=-0.026 Sum_probs=42.0
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc-cc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---KM-HK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K~-Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
..+.|+|+++... -.-|+++++.+-+++++- .+ .+ .=.++.||.|.+.....+..++.|..
T Consensus 5 ~iv~g~V~~v~~~-gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~l 70 (73)
T cd05706 5 DILPGRVTKVNDR-YVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIAL 70 (73)
T ss_pred CEEEEEEEEEeCC-eEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEE
Confidence 4578999997654 566788888777777642 21 11 22368999999998887776666643
No 125
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=37.79 E-value=1.6e+02 Score=24.85 Aligned_cols=55 Identities=11% Similarity=0.095 Sum_probs=34.7
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCCCCceEE
Q 032228 36 AQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 36 g~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~I 91 (145)
|+.++=.--=+..|.++ |..++||+|--=|.+=-+.+|+.|.+.-++-...|-.+
T Consensus 10 a~li~R~nRFl~dv~l~-G~~~~~H~~ntGrm~~l~~pG~~v~l~~sd~~~rK~~~ 64 (235)
T COG1489 10 ATLIKRYNRFLADVELD-GEEVTAHCPNTGRMTELLTPGNTVWLSRSDNPKRKYRY 64 (235)
T ss_pred eEEEeeecceEEEEEEC-CeEEEEEcCCCCccccccCCCCEEEEEEecCCCccceE
Confidence 44454442223455556 99999999744444444678999999988766444333
No 126
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=37.65 E-value=48 Score=24.57 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=23.7
Q ss_pred eEEEccCCEEEEEeccCCCCceEEEEEcChh
Q 032228 68 KVWIGAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 68 ~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
.+.|+.||.|+|---.+--..|.|+..+.+.
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe
Confidence 4568999999998766666788887777653
No 127
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=37.63 E-value=1.4e+02 Score=26.61 Aligned_cols=65 Identities=14% Similarity=0.143 Sum_probs=48.7
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc--cc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---KM--HK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K~--Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
...+.|+|+.+...+.| |.+..|..-+++++- .+ .. .-+++.||.|.|.....+..+++|..-+.
T Consensus 360 G~~v~g~V~~v~~~G~f-V~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K 430 (516)
T TIGR00717 360 GDRVTGKIKKITDFGAF-VELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVK 430 (516)
T ss_pred CCEEEEEEEEEecceEE-EECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeec
Confidence 45678999999888777 888888888887542 11 11 46789999999998888887888765553
No 128
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=37.60 E-value=81 Score=31.76 Aligned_cols=76 Identities=16% Similarity=0.167 Sum_probs=52.2
Q ss_pred ccccceeeccCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccce------------EEEccCCEEEEEeccCCC
Q 032228 19 ADDEKRELIFKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKK------------VWIGAGDIILVGLRDYQD 86 (145)
Q Consensus 19 ~~~~~~el~~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~------------IwIk~GD~VlVe~~~~~~ 86 (145)
++-..++++..+.. -+|++++ ++.-.|.|.-.+|..+.+.-..=+++. =-|+.+|+|.|---+-..
T Consensus 520 ge~e~hdlVqLd~~-~vgvI~r-le~e~~~vl~~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g 597 (1024)
T KOG1999|consen 520 GEYELHDLVQLDNQ-NVGVIVR-LERETFQVLGMNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKG 597 (1024)
T ss_pred ccccccceeecCCC-cEEEEEE-ecchheeeecCcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCC
Confidence 45556677766555 6666666 889999999999976666555544432 247889999988766544
Q ss_pred CceEEEEEcC
Q 032228 87 DKADVILKYM 96 (145)
Q Consensus 87 ~Kg~Ii~ry~ 96 (145)
.-|.|.|.|.
T Consensus 598 ~~G~v~~i~r 607 (1024)
T KOG1999|consen 598 REGEVLHIYR 607 (1024)
T ss_pred ccCccceeec
Confidence 4478876663
No 129
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=37.37 E-value=3e+02 Score=26.02 Aligned_cols=45 Identities=16% Similarity=-0.031 Sum_probs=32.3
Q ss_pred EccCCEEEEEeccCCC-----CceEEEEEcC-----hhHHHHHHHcCCCCccccc
Q 032228 71 IGAGDIILVGLRDYQD-----DKADVILKYM-----PDEARLLKAYGELPETTRL 115 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~-----~Kg~Ii~ry~-----~deik~Lrk~g~wP~~f~~ 115 (145)
.+.||.|.|+...|.. -.|.|+.++. .-++..+..+.-+|.+|..
T Consensus 119 ~~~gd~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~~f~~ 173 (639)
T TIGR02062 119 FQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLEREEPD 173 (639)
T ss_pred CCCCCEEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCCCCCH
Confidence 4579999999987653 2589999994 3455566666667888865
No 130
>PRK05807 hypothetical protein; Provisional
Probab=36.90 E-value=1.8e+02 Score=21.84 Aligned_cols=62 Identities=16% Similarity=0.208 Sum_probs=42.5
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
...+.|+|+.+...+.|- .+ ++.+-|+|++- ..+. .-.++.||.|.|.....+. .+.|...+
T Consensus 6 G~vv~G~Vt~i~~~GafV-~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSl 72 (136)
T PRK05807 6 GSILEGTVVNITNFGAFV-EV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSI 72 (136)
T ss_pred CCEEEEEEEEEECCeEEE-EE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEE
Confidence 346899999988776664 55 67777887752 1222 3347999999999877665 56764444
No 131
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=36.11 E-value=69 Score=16.75 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=19.2
Q ss_pred EccCCEEEEEeccCCCCceEEEEE
Q 032228 71 IGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
+.+||.|.|---++....|.|+..
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 468999999988887778887654
No 132
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=35.69 E-value=43 Score=24.51 Aligned_cols=30 Identities=17% Similarity=0.117 Sum_probs=23.1
Q ss_pred EEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 70 WIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 70 wIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
.|+.||.|.|---.+-...|.|+..+...+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~ 32 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTN 32 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 589999999987665556788888776554
No 133
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=35.36 E-value=1.2e+02 Score=19.49 Aligned_cols=62 Identities=11% Similarity=0.087 Sum_probs=38.8
Q ss_pred eEEEEEEEeCCCceEEEEeCC-CCEEEEEecc---c-cc-----------c-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 33 QEYAQVLRMLGNGRCEAMCID-GAKRLCHIRG---K-MH-----------K-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~d-G~~~la~IpG---K-~R-----------k-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
...|.|+.+...+.| |.++. |..=++++.- . +. + .-.++.||.|.|.....+..+++|...+
T Consensus 4 ~~~g~V~~v~~~G~f-v~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~~l 82 (83)
T cd04471 4 EFDGVISGVTSFGLF-VELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDFEL 82 (83)
T ss_pred EEEEEEEeEEeeeEE-EEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEEEE
Confidence 356777777666554 44443 5444444442 1 11 1 2467889999999988877788887653
No 134
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=35.26 E-value=85 Score=26.12 Aligned_cols=46 Identities=11% Similarity=0.168 Sum_probs=31.1
Q ss_pred CCeEEEEEEEeCC---CceEEEEeCCCC-EEEEEecccccceEEEccCCE
Q 032228 31 DGQEYAQVLRMLG---NGRCEAMCIDGA-KRLCHIRGKMHKKVWIGAGDI 76 (145)
Q Consensus 31 e~q~ig~Vv~~lG---~~~~~V~~~dG~-~~la~IpGK~Rk~IwIk~GD~ 76 (145)
-|++-|+|+++.+ +...+|.+..|. ...|.|...=-+.+-+.+|+.
T Consensus 127 rN~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~~L~l~~G~~ 176 (263)
T PRK10676 127 RNQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAERLGLDEGKE 176 (263)
T ss_pred hhcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHhhcCCCCCCe
Confidence 4799999999975 467778888765 688888765433333344433
No 135
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=34.85 E-value=1.3e+02 Score=20.26 Aligned_cols=40 Identities=18% Similarity=0.071 Sum_probs=23.7
Q ss_pred CCceEEEEeCC--CCEEEEEecccc-cceEEEccCCEEEEEec
Q 032228 43 GNGRCEAMCID--GAKRLCHIRGKM-HKKVWIGAGDIILVGLR 82 (145)
Q Consensus 43 G~~~~~V~~~d--G~~~la~IpGK~-Rk~IwIk~GD~VlVe~~ 82 (145)
.+++.-+.+.| +....+.-++.. +-...+++||.|+|.-.
T Consensus 13 ~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 13 TSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred CCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 44444444433 334444444433 33678999999998766
No 136
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=34.72 E-value=2.4e+02 Score=25.67 Aligned_cols=80 Identities=20% Similarity=0.293 Sum_probs=56.0
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEE--------ec--cCCC--------CceEE
Q 032228 30 EDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVG--------LR--DYQD--------DKADV 91 (145)
Q Consensus 30 ~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe--------~~--~~~~--------~Kg~I 91 (145)
+...++|+|++++..+++-|....|-.+++.+..-.-+ =-+++|..|.+. +- ..++ .+-++
T Consensus 70 ~~pl~vg~v~e~id~~~~iVks~~g~~~vV~i~~~vd~-~~L~pG~rVal~~~s~~Iv~vLp~~~Dp~V~~M~v~e~Pdv 148 (406)
T COG1222 70 EPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDR-DLLEPGMRVALNRDSYSIVRVLPPEVDPRVSVMEVEEKPDV 148 (406)
T ss_pred CCCceEEEEEEEcCCceEEEEeCCCCeEEEeccCCcCH-HHcCCCCEEEEcCCcceeeeeCCCccCchhheeeeccCCCC
Confidence 45679999999999999999999999999998865543 224555555544 32 2222 13444
Q ss_pred EEEc---ChhHHHHHHHcCCCC
Q 032228 92 ILKY---MPDEARLLKAYGELP 110 (145)
Q Consensus 92 i~ry---~~deik~Lrk~g~wP 110 (145)
.|-- ..+|++.|++-=.+|
T Consensus 149 tY~dIGGL~~Qi~EirE~VELP 170 (406)
T COG1222 149 TYEDIGGLDEQIQEIREVVELP 170 (406)
T ss_pred ChhhccCHHHHHHHHHHHhccc
Confidence 4433 578999998887766
No 137
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=33.96 E-value=1.3e+02 Score=19.34 Aligned_cols=58 Identities=14% Similarity=0.032 Sum_probs=37.0
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecc--ccc-ceEEEccCCEEEEEeccCCCCceEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG--KMH-KKVWIGAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG--K~R-k~IwIk~GD~VlVe~~~~~~~Kg~I 91 (145)
.+.|+|+++..++ ..|.+.+|..-+++++- .-+ ..=.++.||.|.+.....+..+.+|
T Consensus 3 ~V~g~V~~i~~~G-~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i 63 (66)
T cd05695 3 LVNARVKKVLSNG-LILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVV 63 (66)
T ss_pred EEEEEEEEEeCCc-EEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEE
Confidence 4679999998666 45777776444443321 000 0233788999988888777665555
No 138
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12). This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.
Probab=33.95 E-value=88 Score=24.47 Aligned_cols=35 Identities=11% Similarity=0.060 Sum_probs=28.4
Q ss_pred eEEEEe-CCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 46 RCEAMC-IDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~-~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
..+|++ .||.+++|.|||==. .-.|.+.|.|||.-
T Consensus 64 ~~rV~L~~ngk~vtAyiPg~G~-~~~lqeh~~VLV~G 99 (139)
T TIGR00982 64 CVRVQLIKNGKVVTAFCPGDGA-INFIDEHDEVIIEG 99 (139)
T ss_pred EEEEEEccCCeEEEEEeCCCcc-ccccccCCEEEEEe
Confidence 467888 699999999998543 23589999999986
No 139
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=33.89 E-value=2.3e+02 Score=22.15 Aligned_cols=58 Identities=16% Similarity=0.152 Sum_probs=36.8
Q ss_pred ccCCCC-eEEEEEEEeCCCceEEEEe----------CCCCEEEEEecccccc-----eEEEccCCEEEEEeccCC
Q 032228 27 IFKEDG-QEYAQVLRMLGNGRCEAMC----------IDGAKRLCHIRGKMHK-----KVWIGAGDIILVGLRDYQ 85 (145)
Q Consensus 27 ~~p~e~-q~ig~Vv~~lG~~~~~V~~----------~dG~~~la~IpGK~Rk-----~IwIk~GD~VlVe~~~~~ 85 (145)
..|..| -++|+|+++...+.| |.+ .++.+-+.+++..... +=.+++||.|.+.....+
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~-V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRAL-VRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEE-EEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 345555 579999999776554 333 2344555555432211 344799999999988766
No 140
>PRK08577 hypothetical protein; Provisional
Probab=33.87 E-value=36 Score=25.19 Aligned_cols=24 Identities=17% Similarity=0.127 Sum_probs=20.7
Q ss_pred EEecccccceEEEccCCEEEEEec
Q 032228 59 CHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 59 a~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
..||-.+|+.+-|++||.|.+...
T Consensus 15 i~ip~~~r~~l~~~~g~~~~~~~~ 38 (136)
T PRK08577 15 ITIPLEIREALGIREGMYVLLIAD 38 (136)
T ss_pred EEecHHHHHHcCcCCCCEEEEEEE
Confidence 358999999999999999998764
No 141
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=33.70 E-value=66 Score=19.95 Aligned_cols=35 Identities=20% Similarity=0.430 Sum_probs=23.6
Q ss_pred EEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhHHH
Q 032228 57 RLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDEAR 101 (145)
Q Consensus 57 ~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik 101 (145)
+-+.++|+.. .+.+++||.| .+|++++++...+..
T Consensus 5 I~~~~~G~V~-~v~V~~G~~V---------kkGd~L~~ld~~~~~ 39 (50)
T PF13533_consen 5 IQAPVSGRVE-SVYVKEGQQV---------KKGDVLLVLDSPDLQ 39 (50)
T ss_pred EeCCCCEEEE-EEEecCCCEE---------cCCCEEEEECcHHHH
Confidence 3344555332 5677788877 588999988777655
No 142
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=33.65 E-value=32 Score=22.21 Aligned_cols=12 Identities=42% Similarity=0.675 Sum_probs=6.2
Q ss_pred EccCCEEEEEec
Q 032228 71 IGAGDIILVGLR 82 (145)
Q Consensus 71 Ik~GD~VlVe~~ 82 (145)
|..||+|+|++.
T Consensus 14 i~~gd~lii~~~ 25 (81)
T cd06529 14 IPDGDLVLVDPS 25 (81)
T ss_pred cCCCCEEEEcCC
Confidence 455555555543
No 143
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=33.27 E-value=42 Score=23.18 Aligned_cols=22 Identities=23% Similarity=0.582 Sum_probs=19.0
Q ss_pred ceEEEEEcChhHHHHHHHcCCC
Q 032228 88 KADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 88 Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
.|-|||-|+--+++.|++-|.+
T Consensus 2 ~gliVyl~~~k~~r~L~kfG~i 23 (71)
T PF09902_consen 2 QGLIVYLYSLKDARQLRKFGDI 23 (71)
T ss_pred eEEEEEEechHhHHhHhhcccE
Confidence 4779999999999999998854
No 144
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.89 E-value=1.3e+02 Score=18.90 Aligned_cols=60 Identities=10% Similarity=0.081 Sum_probs=39.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK----MHK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK----~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+.|+|+++.. .-.-|.+..+.+-+++++-- +++ .=.++.||.|.+.....+..++.|..
T Consensus 3 ~v~g~V~~v~~-~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~l 67 (73)
T cd05691 3 IVTGKVTEVDA-KGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISL 67 (73)
T ss_pred EEEEEEEEEEC-CeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEE
Confidence 46789999875 44557777777777766521 211 22368999999988877766565543
No 145
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.83 E-value=1.3e+02 Score=18.99 Aligned_cols=59 Identities=12% Similarity=0.037 Sum_probs=35.2
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccce-----EEEccCCEEEEEeccCCCCceEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKK-----VWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~-----IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
-+.|+|+++... -..|.+..+.+-+.+++--.... =-++.||.|.+.....+...+.|.
T Consensus 3 iv~g~V~~i~~~-~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~ 66 (70)
T cd05687 3 IVKGTVVSVDDD-EVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVV 66 (70)
T ss_pred EEEEEEEEEeCC-EEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEE
Confidence 467889888654 44555554443333332111111 127899999999887776666664
No 146
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=32.42 E-value=2.4e+02 Score=24.28 Aligned_cols=64 Identities=19% Similarity=0.251 Sum_probs=44.9
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccce-----EEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKK-----VWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~-----IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
...+.|.|+.+...+.| |.+.+|..-+++++---..+ --++.||.|.|.....+..+++|...+
T Consensus 278 G~~v~g~V~~i~~~G~f-V~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~ 346 (390)
T PRK06676 278 GDVIEGTVKRLTDFGAF-VEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346 (390)
T ss_pred CcEEEEEEEEEeCceEE-EEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEE
Confidence 44688999987765544 67777888888876422112 236999999999988887777875444
No 147
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=32.24 E-value=2.1e+02 Score=25.87 Aligned_cols=65 Identities=12% Similarity=0.020 Sum_probs=49.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc----c-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMH----K-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~R----k-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
...+.|+|+++...+.| |.+.+|..-|||++---. + .=.++.||.|-|.....+..+.+|.-.+.
T Consensus 380 G~~v~G~V~~i~~~G~F-V~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~ 449 (491)
T PRK13806 380 GTTVTGTVEKRAQFGLF-VNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPA 449 (491)
T ss_pred CCEEEEEEEEEecCceE-EEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEee
Confidence 45789999999988877 588889999999863221 1 22359999999998888877777766555
No 148
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=32.20 E-value=64 Score=25.21 Aligned_cols=41 Identities=32% Similarity=0.340 Sum_probs=29.4
Q ss_pred EEecccccc-eEEEccCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCCC
Q 032228 59 CHIRGKMHK-KVWIGAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGELP 110 (145)
Q Consensus 59 a~IpGK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik~Lrk~g~wP 110 (145)
.-||.|+.+ .|+|. .|+++|..-+ .++++|++-|++.|.=|
T Consensus 134 lgiptki~~G~i~i~-~d~~v~k~G~----------~v~~~~A~lL~~l~i~P 175 (175)
T cd05795 134 LGIPTKIEKGKIEII-SDVVVVKKGE----------KVGASEATLLNKLNIKP 175 (175)
T ss_pred cCCceEEecCEEEEe-cCeEEecCCC----------CcCHHHHHHHHHcCCCC
Confidence 357777777 77774 4888876542 46888999998887655
No 149
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=32.17 E-value=25 Score=22.17 Aligned_cols=16 Identities=25% Similarity=0.281 Sum_probs=13.7
Q ss_pred EEcChhHHHHHHHcCC
Q 032228 93 LKYMPDEARLLKAYGE 108 (145)
Q Consensus 93 ~ry~~deik~Lrk~g~ 108 (145)
|+....|++||+++|.
T Consensus 14 ~k~~~~Q~~~L~~~Gi 29 (47)
T PF13986_consen 14 YKRPSKQIRWLRRNGI 29 (47)
T ss_pred CCCHHHHHHHHHHCCC
Confidence 5678899999999983
No 150
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=32.15 E-value=1.8e+02 Score=26.46 Aligned_cols=64 Identities=14% Similarity=0.080 Sum_probs=46.5
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccc-----cc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKM-----HK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~-----Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
...+.|+|+.+...+.| |.+..|..-+++++-=. +. .-+++.||.|.|-....+..+.+|..-+
T Consensus 374 G~~v~g~V~~v~~~G~f-V~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~ 443 (565)
T PRK06299 374 GDVVEGKVKNITDFGAF-VGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443 (565)
T ss_pred CCEEEEEEEEEecceEE-EECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 34688999998766655 77777787777775322 22 4678999999998888777777775544
No 151
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=31.97 E-value=97 Score=24.38 Aligned_cols=49 Identities=16% Similarity=0.138 Sum_probs=35.7
Q ss_pred CeEEEEEEEeCC------C----ceEEEEe-CCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 32 GQEYAQVLRMLG------N----GRCEAMC-IDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 32 ~q~ig~Vv~~lG------~----~~~~V~~-~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
-|.-|.|++..+ | -..+|++ .||..++|.|||==. .-.|.+.|.|||.-
T Consensus 46 Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~-~~~lqEh~~VLV~G 105 (145)
T PRK04211 46 PMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGA-INFIDEHDEVVIEG 105 (145)
T ss_pred CccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCcc-ccccccCCEEEEee
Confidence 355566665553 2 2467888 699999999998543 22689999999996
No 152
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=31.72 E-value=1.1e+02 Score=25.82 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=27.6
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032228 32 GQEYAQVLRMLGNGRCEAMC-----IDGAKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~-----~dG~~~la~IpGK~R 66 (145)
+.+-++|+++|+|+.+-|+= -|+..+.-+++|-.|
T Consensus 147 ~tIta~V~~VLpNGNL~I~G~Kev~vN~~~e~i~vsGvVR 186 (230)
T COG2063 147 GTITATVVQVLPNGNLVIEGEKEVRVNGEKEIIRVSGVVR 186 (230)
T ss_pred EEEEEEEEEEcCCCCEEEEEEEEEEECCceEEEEEeeeEc
Confidence 67899999999999998864 467777777777544
No 153
>PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 from SWISSPROT, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ []. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions []. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [, ]. This family also contains other proteins, whose functions are not well characterised.; GO: 0010309 acireductone dioxygenase [iron(II)-requiring] activity, 0055114 oxidation-reduction process; PDB: 1VR3_A 1ZRR_A 2HJI_A.
Probab=31.54 E-value=70 Score=24.98 Aligned_cols=31 Identities=23% Similarity=0.241 Sum_probs=22.7
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 42 LGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 42 lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
-|.+.|.|...++.-+ +|.+.+||++.|-+-
T Consensus 100 ~G~g~Fdvr~~~~~wi----------ri~~e~GDli~vP~g 130 (157)
T PF03079_consen 100 DGSGYFDVRDGDDVWI----------RILCEKGDLIVVPAG 130 (157)
T ss_dssp ECEEEEEEE-TTCEEE----------EEEEETTCEEEE-TT
T ss_pred CcEEEEEEEcCCCEEE----------EEEEcCCCEEecCCC
Confidence 6889999998876644 677889999887543
No 154
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=31.51 E-value=1.2e+02 Score=28.81 Aligned_cols=60 Identities=22% Similarity=0.368 Sum_probs=43.0
Q ss_pred CCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEccCCEEEEEeccCCCCceEE
Q 032228 29 KEDG-QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KV-----WIGAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 29 p~e~-q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~I-----wIk~GD~VlVe~~~~~~~Kg~I 91 (145)
|..| ...|+|+++...+.| |++..|..=|+|++ .+.. ++ .++.||.|.|.....+. +|+|
T Consensus 616 ~~~G~i~~G~V~~I~~~Gaf-Vei~~g~~GllHiS-ei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki 682 (684)
T TIGR03591 616 PEVGKIYEGKVVRIMDFGAF-VEILPGKDGLVHIS-EIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRI 682 (684)
T ss_pred cccCcEEEEEEEEEeCCEEE-EEECCCcEEEEEHH-HcCCCcccChhhccCCCCEEEEEEEEECC-CCCc
Confidence 4555 478999999876655 66667888899987 3332 22 26899999999887665 5554
No 155
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=30.01 E-value=19 Score=26.03 Aligned_cols=12 Identities=67% Similarity=0.916 Sum_probs=10.1
Q ss_pred CccccCccccCC
Q 032228 134 YIEFEDEDIDRI 145 (145)
Q Consensus 134 ~~~~~~~~~~~~ 145 (145)
-||+|||+.|+|
T Consensus 43 AFeYEDE~gDRI 54 (91)
T cd06395 43 AFEYEDEDGDRI 54 (91)
T ss_pred ceeeccccCCee
Confidence 578899999887
No 156
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=30.01 E-value=43 Score=25.60 Aligned_cols=22 Identities=18% Similarity=0.349 Sum_probs=17.1
Q ss_pred cccccceEEEccCCEEEEEecc
Q 032228 62 RGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 62 pGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
.|.+...+++++||.|.|..+.
T Consensus 143 ~g~~~~n~~L~~gD~I~Vp~~~ 164 (165)
T TIGR03027 143 DGDVTANVELKPGDVLIIPESW 164 (165)
T ss_pred cCCccCCceeCCCCEEEEeccc
Confidence 3556678999999999997654
No 157
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=29.87 E-value=2.7e+02 Score=25.25 Aligned_cols=65 Identities=12% Similarity=0.112 Sum_probs=48.6
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGK----MHK-KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK----~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
...+.|+|+.+...+.| |.+.+|..-+|+++-- ... .=-++.||.|.+.....+..+++|.-.+.
T Consensus 461 G~vV~G~V~~v~~~G~f-V~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k 530 (565)
T PRK06299 461 GSIVTGTVTEVKDKGAF-VELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530 (565)
T ss_pred CCEEEEEEEEEecCceE-EecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEee
Confidence 44689999999988777 7788888888886432 222 23459999999999988888888855554
No 158
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=29.71 E-value=1.7e+02 Score=27.59 Aligned_cols=67 Identities=15% Similarity=0.223 Sum_probs=53.9
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEEEEc
Q 032228 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 28 ~p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
.|-...+.|+|+.+...+-| |+...|..=|+|++- +... .=-++.||.|.|..-+.+..+-+|.--+
T Consensus 275 ~~~g~~v~G~Vt~i~~~Gaf-Vei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~i 346 (541)
T COG0539 275 YPVGDKVEGKVTNLTDYGAF-VEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGL 346 (541)
T ss_pred cCCCCEEEEEEEEeecCcEE-EEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeee
Confidence 45567899999999987766 889999999999993 2222 3357999999999999999999986554
No 159
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.61 E-value=1.7e+02 Score=19.32 Aligned_cols=68 Identities=12% Similarity=0.106 Sum_probs=44.8
Q ss_pred eeeccCCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEecccccc------eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 24 RELIFKEDGQ-EYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK------KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 24 ~el~~p~e~q-~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk------~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
..+..+..|+ +.|+|..+...+. -|.+.+|..-+++++ .+.. .--++.||.|.|.....+..+++|..
T Consensus 7 ~~~~~~~~G~i~~g~V~~v~~~G~-fv~l~~~~~g~v~~~-el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~l 81 (83)
T cd04461 7 TNFSDLKPGMVVHGYVRNITPYGV-FVEFLGGLTGLAPKS-YISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81 (83)
T ss_pred hhHHhCCCCCEEEEEEEEEeeceE-EEEcCCCCEEEEEHH-HCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence 3344455665 6788888776554 466677777776654 2221 22478899999998887777777754
No 160
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=29.52 E-value=2e+02 Score=25.07 Aligned_cols=64 Identities=19% Similarity=0.150 Sum_probs=39.9
Q ss_pred EEEEEEEeC-CCceEE-EEeCCCCEEEEEeccccc-ceEEEccCCEEEEEeccCCCCceEEEEEcChhHHH
Q 032228 34 EYAQVLRML-GNGRCE-AMCIDGAKRLCHIRGKMH-KKVWIGAGDIILVGLRDYQDDKADVILKYMPDEAR 101 (145)
Q Consensus 34 ~ig~Vv~~l-G~~~~~-V~~~dG~~~la~IpGK~R-k~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~deik 101 (145)
-.++|++.. .-+.|- +=++ +..+.++.-.=. +.+|.++||.++|.+. -+.+++|.=....+++-
T Consensus 77 g~~~Vv~v~~~lGaFlD~Gl~--KDl~vp~~elp~~~~~wpq~Gd~l~v~l~--~Dkk~Ri~g~~a~~~~l 143 (287)
T COG2996 77 GWLKVVEVNKDLGAFLDWGLP--KDLLVPLDELPTLKSLWPQKGDKLLVYLY--VDKKGRIWGTLAIEKIL 143 (287)
T ss_pred eEEEEEEEcCCcceEEecCCC--cceeeehhhcccccccCCCCCCEEEEEEE--EccCCcEEEEecchhHH
Confidence 355666665 333331 1122 455555554434 4899999999999986 36788887776655543
No 161
>PF12859 Apc1: Anaphase-promoting complex subunit 1
Probab=29.50 E-value=88 Score=22.40 Aligned_cols=36 Identities=6% Similarity=0.020 Sum_probs=26.5
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceEEEccCCEEE
Q 032228 42 LGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIIL 78 (145)
Q Consensus 42 lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~Vl 78 (145)
+-.....|.+.+|+.+.+++|=.+.+-.+... .++|
T Consensus 6 ~l~~~~~vy~~~G~~~~v~LPF~V~~~~~~~~-GlLL 41 (105)
T PF12859_consen 6 VLKDQAHVYFPSGESYTVPLPFEVSSAWPLPR-GLLL 41 (105)
T ss_pred EECCEEEEEeCCCCEEEEEeceEeeEEeccCC-EEEE
Confidence 34688899999999999999977765544444 3443
No 162
>CHL00037 petA cytochrome f
Probab=29.09 E-value=3e+02 Score=24.32 Aligned_cols=71 Identities=17% Similarity=0.207 Sum_probs=43.1
Q ss_pred CcccccCC--Ccccccceeec-cCCCCeEEEEEEEeCCCceEEE-EeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 9 GKNRKRGK--NEADDEKRELI-FKEDGQEYAQVLRMLGNGRCEA-MCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 9 ~kn~rr~~--~~~~~~~~el~-~p~e~q~ig~Vv~~lG~~~~~V-~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
|=||.|+- -.++.....+. .+..|++-..-..--|+....+ ..+||.++.-.||.= -.+-|++||.|.++-
T Consensus 186 GgNRGRGQvyP~G~KSNNnv~~as~~G~I~~I~~~ekGg~~vti~~t~~G~~v~~~iP~G--p~LiVs~G~~v~~~q 260 (320)
T CHL00037 186 GGNRGRGQIYPDGSKSNNTVYNATAAGIVSKILRKEKGGYEITIVDTSDGRQVVDIIPPG--PELLVSEGESIKLDQ 260 (320)
T ss_pred ccccCccccCCCCcccCCcccccccCcEEEEEEEcCCCcEEEEEEecCCCCEEEEeeCCC--CeEEEecCceEecCC
Confidence 44666763 22333333333 3445664433334455556666 568999999888842 278899999998853
No 163
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=29.08 E-value=2.5e+02 Score=27.77 Aligned_cols=67 Identities=12% Similarity=0.030 Sum_probs=48.9
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cccc-----eEEEccCCEEEEEeccCCCCceEEEEEcC
Q 032228 29 KEDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG---KMHK-----KVWIGAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 29 p~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG---K~Rk-----~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~ 96 (145)
+-...+.|+|+++...+.| |++++|.+-+++++- .+.. .-+++.||.|-|.....+..+..|..-+.
T Consensus 751 ~vG~iV~GkV~~v~~~GvF-VeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk 825 (863)
T PRK12269 751 GVGSTVEGEVSSVTDFGIF-VRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825 (863)
T ss_pred CCCCEEEEEEEEEecCeEE-EEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence 3345789999998877754 788888888887752 1111 23589999999999888877778866655
No 164
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=28.95 E-value=1.1e+02 Score=20.51 Aligned_cols=30 Identities=13% Similarity=0.180 Sum_probs=19.5
Q ss_pred CCeEEEEEEEeCC---CceEEEEeCC-CCEEEEE
Q 032228 31 DGQEYAQVLRMLG---NGRCEAMCID-GAKRLCH 60 (145)
Q Consensus 31 e~q~ig~Vv~~lG---~~~~~V~~~d-G~~~la~ 60 (145)
.-+-.|.|++++| +-.|.|...| |++.|+.
T Consensus 18 ~~~r~GeIveV~g~dG~PPY~VRw~D~Ghe~lv~ 51 (58)
T PF08940_consen 18 QPDRHGEIVEVRGPDGSPPYLVRWDDTGHESLVF 51 (58)
T ss_dssp --EEEEEEEE-S-SSS-S-EEEEETTTTEEEEE-
T ss_pred CCCcEeEEEEEECCCCCCCEEEEecCCCcEEEEe
Confidence 4457888888886 4489999999 9988764
No 165
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=28.36 E-value=62 Score=24.55 Aligned_cols=35 Identities=20% Similarity=0.182 Sum_probs=27.7
Q ss_pred eEEEEe-CCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 46 RCEAMC-IDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~-~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
..+|++ .||..++|.|||==. --.|.+.|.|||.-
T Consensus 44 ~~rV~L~~ngk~itAyIPG~G~-~~~lqeh~~VLV~G 79 (115)
T cd03367 44 CVRVQLIKNGKKITAFVPGDGC-LNFIDENDEVLVAG 79 (115)
T ss_pred EEEEEEccCCeEEEEEeCCCCc-ccccccCCEEEEEe
Confidence 467888 599999999998543 13478999999986
No 166
>COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism]
Probab=28.21 E-value=41 Score=25.49 Aligned_cols=24 Identities=21% Similarity=0.450 Sum_probs=20.2
Q ss_pred CCCEEEEEecccccceEEEccCCEE
Q 032228 53 DGAKRLCHIRGKMHKKVWIGAGDII 77 (145)
Q Consensus 53 dG~~~la~IpGK~Rk~IwIk~GD~V 77 (145)
++..+.+-|+|.|-+ +.++.||.|
T Consensus 69 ~~~~V~SPm~Gtv~~-~~V~vGd~V 92 (140)
T COG0511 69 GGTQVTSPMVGTVYK-PFVEVGDTV 92 (140)
T ss_pred cCceEecCcceEEEE-EeeccCCEE
Confidence 678889999999987 888888876
No 167
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.17 E-value=1.7e+02 Score=18.75 Aligned_cols=54 Identities=13% Similarity=0.042 Sum_probs=35.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccc------cc-eEEEccCCEEEEEeccCCCC
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKM------HK-KVWIGAGDIILVGLRDYQDD 87 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~------Rk-~IwIk~GD~VlVe~~~~~~~ 87 (145)
.+.|+|+++... ...|.+.+|.+-++++.-=. .. .=.++.||.|.+.....+..
T Consensus 3 iV~g~V~~i~~~-gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 3 LVKAKVKSVKPT-QLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred EEEEEEEEEECC-cEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCc
Confidence 478999998664 46678887876666654211 11 12268999999988776543
No 168
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=27.60 E-value=94 Score=19.42 Aligned_cols=49 Identities=16% Similarity=0.114 Sum_probs=26.8
Q ss_pred EEEEEEEe--CCCceEEEEeCCCC-EEEEEecc-cccc-eEEEccCCEEEEEec
Q 032228 34 EYAQVLRM--LGNGRCEAMCIDGA-KRLCHIRG-KMHK-KVWIGAGDIILVGLR 82 (145)
Q Consensus 34 ~ig~Vv~~--lG~~~~~V~~~dG~-~~la~IpG-K~Rk-~IwIk~GD~VlVe~~ 82 (145)
+.|+|... .++....+.+.|+. ..-|.+.. .+.. .=.+++||.|.|.-.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~ 56 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVRGK 56 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEEEE
Confidence 45666665 34555555555554 23333333 3332 455789999998744
No 169
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=27.46 E-value=2e+02 Score=19.47 Aligned_cols=48 Identities=23% Similarity=0.288 Sum_probs=36.5
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEE-EEec-----ccccceEEEccCCEEEEEeccC
Q 032228 35 YAQVLRMLGNGRCEAMCIDGAKRL-CHIR-----GKMHKKVWIGAGDIILVGLRDY 84 (145)
Q Consensus 35 ig~Vv~~lG~~~~~V~~~dG~~~l-a~Ip-----GK~Rk~IwIk~GD~VlVe~~~~ 84 (145)
..+|+.+-+++....+..+|.++- ..+| .+++.. +..|.-|+|..+..
T Consensus 6 eyqli~I~~Dg~lsLMde~get~eDl~lP~~el~~ei~~~--~~~g~~~~Vtv~~a 59 (69)
T PF01287_consen 6 EYQLIDIDGDGFLSLMDEDGETREDLKLPDGELGEEIKAK--FEEGKEVLVTVLSA 59 (69)
T ss_dssp EEEEEEEETTTEEEEEETTS-EEEEEECCSHHHHHHHHHH--HHTTCEEEEEEEEE
T ss_pred EEEEEEEccCcEEEEEcCCCCeeccEEecccchhHHHHhh--ccCCCeEEEEEEee
Confidence 467888889999999999999999 9999 334433 38888877777643
No 170
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=27.29 E-value=48 Score=22.45 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=30.5
Q ss_pred CCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcCh
Q 032228 54 GAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 54 G~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~ 97 (145)
|.....+||..++..+-+.+||.|.|...+ .+-|+..+.+
T Consensus 7 GNS~~vtIPk~i~~~lgl~~Gd~v~v~~~~----~~iii~~~~~ 46 (74)
T TIGR02609 7 GNSLVVTLPKEVLESLGLKEGDTLYVDEEE----GGLKLKRFDE 46 (74)
T ss_pred CCeeEEEECHHHHHHcCcCCCCEEEEEEEC----CEEEEEECCC
Confidence 566788999999999999999999887653 2344555544
No 171
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=27.25 E-value=83 Score=20.10 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=14.4
Q ss_pred EccCCEEEEEeccCCC---CceEEEE
Q 032228 71 IGAGDIILVGLRDYQD---DKADVIL 93 (145)
Q Consensus 71 Ik~GD~VlVe~~~~~~---~Kg~Ii~ 93 (145)
..-||.|+|.+...+. -.|+|+.
T Consensus 32 A~~gD~V~v~i~~~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 32 AMDGDKVLVRITPPSRGKRPEGEVVE 57 (58)
T ss_dssp S-TT-EEEEEEEESSSEEEEEEEEEE
T ss_pred CCCCCEEEEEEecCCCCCCCCEEEEe
Confidence 3579999999998322 2566664
No 172
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=26.63 E-value=1.9e+02 Score=18.79 Aligned_cols=56 Identities=14% Similarity=0.121 Sum_probs=37.2
Q ss_pred eEEEEEEEeCCCceEEEEeCCC--CEEEEEecccccc------eEEEccCCEEEEEeccCCCCceEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDG--AKRLCHIRGKMHK------KVWIGAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG--~~~la~IpGK~Rk------~IwIk~GD~VlVe~~~~~~~Kg~Ii 92 (145)
.+.|+|+++...+.|- .+ +| ..-|+|++- +.. .-.++.||.|.|.....+..+ +|.
T Consensus 6 ~~~g~V~~i~~fG~fv-~l-~~~~~eGlvh~se-l~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ 69 (73)
T cd05686 6 IFKGEVASVTEYGAFV-KI-PGCRKQGLVHKSH-MSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMK 69 (73)
T ss_pred EEEEEEEEEEeeeEEE-EE-CCCCeEEEEEchh-hCCCcccCHhhEECCCCEEEEEEEEECCCC-cEE
Confidence 4788999988766664 44 34 467777762 221 224799999999987766654 554
No 173
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=26.20 E-value=79 Score=17.87 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=20.6
Q ss_pred cCCEEEEEeccCCCCceEEEEEcChh
Q 032228 73 AGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 73 ~GD~VlVe~~~~~~~Kg~Ii~ry~~d 98 (145)
+||.|.|---+|....|.|+......
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 58999998888888888888776543
No 174
>PRK02302 hypothetical protein; Provisional
Probab=25.84 E-value=63 Score=23.38 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=20.6
Q ss_pred CCceEEEEEcChhHHHHHHHcCCC
Q 032228 86 DDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 86 ~~Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
...|-|||-|+-.+++.|++-|.+
T Consensus 6 ~R~glIVyl~~~k~~r~LrkfG~I 29 (89)
T PRK02302 6 ERIGLIVYLYYNRDARKLSKYGDI 29 (89)
T ss_pred ceeEEEEEEeecHhHHHHhhcCcE
Confidence 347889999999999999999864
No 175
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=25.50 E-value=74 Score=22.15 Aligned_cols=36 Identities=22% Similarity=0.318 Sum_probs=28.1
Q ss_pred EecccccceEEEccCCEEEEEeccCCCCce-EEEEEcChh
Q 032228 60 HIRGKMHKKVWIGAGDIILVGLRDYQDDKA-DVILKYMPD 98 (145)
Q Consensus 60 ~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg-~Ii~ry~~d 98 (145)
-||-.+|+++=|++||.|.+..... .+ -|+.+|...
T Consensus 17 vIPkeiR~~lgi~~Gd~lei~~~~~---~~~ivl~k~~~~ 53 (89)
T COG2002 17 VIPKEIREALGIKEGDVLEIIVDGD---GGRIVLKKYKPA 53 (89)
T ss_pred EecHHHHHHhCCCCCCEEEEEEeCC---CCEEEEEECCcc
Confidence 4899999999999999999988653 23 456666654
No 176
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.43 E-value=2e+02 Score=18.84 Aligned_cols=60 Identities=7% Similarity=-0.089 Sum_probs=41.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEec------ccccc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCIDGAKRLCHIR------GKMHK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~dG~~~la~Ip------GK~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+.|.|++....+. -|.++++.+=+++++ .+.+. .=.++.||.|.+.....+..+.+|.-
T Consensus 3 ~V~g~V~~i~~~g~-~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~L 69 (73)
T cd05703 3 EVTGFVNNVSKEFV-WLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRL 69 (73)
T ss_pred EEEEEEEEEeCCEE-EEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEE
Confidence 57889999865544 477877766666543 11332 34489999999999888877766654
No 177
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=25.37 E-value=2.4e+02 Score=19.56 Aligned_cols=45 Identities=22% Similarity=0.441 Sum_probs=27.5
Q ss_pred CeEEEEEEEeCC-----Cc--eEEEEeCC---CCEEEEEecccccceEEEccCCEEEEEec
Q 032228 32 GQEYAQVLRMLG-----NG--RCEAMCID---GAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 32 ~q~ig~Vv~~lG-----~~--~~~V~~~d---G~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
....|+|++++| +. ..+|++.+ |.+++-.+.|- |+.||++.+.-+
T Consensus 7 ~~~~A~V~kVlgRtGs~G~~tQVrv~~l~~~~gR~i~RNVkGP------Vr~GDil~LlEt 61 (69)
T PF01200_consen 7 PIKLARVIKVLGRTGSRGQVTQVRVEFLDGDKGRSIIRNVKGP------VREGDILTLLET 61 (69)
T ss_dssp SSEEEEEEEEECCCTSSSSEEEEEEEESSSSSS-EEEEEECST------TSTT-EEEESSS
T ss_pred CceeEEEEEEcccccCcccEEEEEEEEecCCcceEEeecccCC------cccCcEEEEeeh
Confidence 347899999997 23 34445544 46677677766 457888766443
No 178
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=25.24 E-value=63 Score=24.64 Aligned_cols=30 Identities=17% Similarity=0.078 Sum_probs=16.1
Q ss_pred eCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 51 CIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 51 ~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
+.+|..+++.--.. ..--+++||+|++...
T Consensus 34 l~~Gd~vlv~k~~~--~~~~~~rGDiVvf~~~ 63 (163)
T TIGR02227 34 LKEGDRILVNKFAY--GTSDPKRGDIVVFKDP 63 (163)
T ss_pred hhCCCEEEEEEeEc--CCCCCCCCcEEEEecC
Confidence 34666666542111 0123677888888753
No 179
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=25.17 E-value=2.6e+02 Score=19.89 Aligned_cols=17 Identities=6% Similarity=-0.113 Sum_probs=13.1
Q ss_pred EEEEEEEeCCCceEEEEeCC
Q 032228 34 EYAQVLRMLGNGRCEAMCID 53 (145)
Q Consensus 34 ~ig~Vv~~lG~~~~~V~~~d 53 (145)
++|+|+++.+ ++|...+
T Consensus 20 ~~G~V~s~~P---L~I~i~~ 36 (100)
T PF10844_consen 20 VIGTVVSVPP---LKIKIDQ 36 (100)
T ss_pred EEEEEEeccc---EEEEECC
Confidence 7899999887 6666655
No 180
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=24.68 E-value=81 Score=21.84 Aligned_cols=14 Identities=29% Similarity=0.349 Sum_probs=11.9
Q ss_pred EEccCCEEEEEecc
Q 032228 70 WIGAGDIILVGLRD 83 (145)
Q Consensus 70 wIk~GD~VlVe~~~ 83 (145)
-++.||+|+|.+.+
T Consensus 2 ~~~vGD~V~v~~~~ 15 (119)
T PF01426_consen 2 TYKVGDFVYVKPDD 15 (119)
T ss_dssp EEETTSEEEEECTS
T ss_pred EEeCCCEEEEeCCC
Confidence 47889999999887
No 181
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.59 E-value=1.4e+02 Score=24.58 Aligned_cols=35 Identities=17% Similarity=0.277 Sum_probs=27.4
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032228 32 GQEYAQVLRMLGNGRCEAMC-----IDGAKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~-----~dG~~~la~IpGK~R 66 (145)
+.+-++|+++|+|+.+.|+= -|+.....+|+|-.|
T Consensus 136 ~~Ita~V~~VlpNGnLvI~G~K~i~vN~e~~~i~lsGiVR 175 (222)
T PRK00249 136 GTITVTVTQVLPNGNLVIRGEKEVRVNQGTEFLRVSGVVR 175 (222)
T ss_pred EEEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEEC
Confidence 55889999999999998864 467777777777655
No 182
>PRK02886 hypothetical protein; Provisional
Probab=24.55 E-value=82 Score=22.72 Aligned_cols=24 Identities=13% Similarity=0.335 Sum_probs=20.3
Q ss_pred CCceEEEEEcChhHHHHHHHcCCC
Q 032228 86 DDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 86 ~~Kg~Ii~ry~~deik~Lrk~g~w 109 (145)
...|-|||-++--++++|++-|.+
T Consensus 4 ~R~glIVyl~~~k~~r~LrkyG~I 27 (87)
T PRK02886 4 NRQGIIVWLHSLKQAKQLRKFGNV 27 (87)
T ss_pred CeeEEEEEEeecHhHHHHhhcCcE
Confidence 346889999999999999998864
No 183
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=24.28 E-value=48 Score=21.49 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=12.9
Q ss_pred EEEEEecccccceEEEccCCEE
Q 032228 56 KRLCHIRGKMHKKVWIGAGDII 77 (145)
Q Consensus 56 ~~la~IpGK~Rk~IwIk~GD~V 77 (145)
.+.|.+||++.+ ++++.||.|
T Consensus 3 ~i~a~~~G~i~~-~~v~~G~~V 23 (70)
T PRK08225 3 KVYASMAGNVWK-IVVKVGDTV 23 (70)
T ss_pred eEeCCCCEEEEE-EEeCCCCEE
Confidence 355677777765 445556654
No 184
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=23.98 E-value=3.1e+02 Score=24.47 Aligned_cols=62 Identities=16% Similarity=0.106 Sum_probs=44.4
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEccCCEEEEEeccCCCCceEEEE
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRG----KMHK-KVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpG----K~Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
...+.|+|+++...+.| |.+.++..=+++++- +..+ .=.++.||.|.|.....+..+++|..
T Consensus 447 G~~v~g~V~~v~~~G~f-V~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~l 513 (516)
T TIGR00717 447 GSVVKGKVTEIKDFGAF-VELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513 (516)
T ss_pred ceEEEEEEEEEecceEE-EEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEE
Confidence 34688999998766655 677788777777754 1111 34579999999998888777777754
No 185
>PF07732 Cu-oxidase_3: Multicopper oxidase; InterPro: IPR011707 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 3 (or coupled binuclear) domains. ; GO: 0005507 copper ion binding; PDB: 2QT6_B 3KW7_B 2R7E_A 3CDZ_A 1SDD_A 3G5W_D 3UAC_A 2YXV_A 3OD3_A 3NSY_A ....
Probab=23.94 E-value=1.8e+02 Score=21.09 Aligned_cols=36 Identities=11% Similarity=0.296 Sum_probs=25.1
Q ss_pred EEeCCCCEEEEEecccccc-eEEEccCCEEEEEeccC
Q 032228 49 AMCIDGAKRLCHIRGKMHK-KVWIGAGDIILVGLRDY 84 (145)
Q Consensus 49 V~~~dG~~~la~IpGK~Rk-~IwIk~GD~VlVe~~~~ 84 (145)
+....+...+..+-|.+=- .|++++||.|.|.....
T Consensus 7 ~~~~~~~~~~~~~ng~~pGPtI~v~~Gd~v~i~~~N~ 43 (117)
T PF07732_consen 7 VSPDGGTRKVWTYNGQFPGPTIRVREGDTVRITVTNN 43 (117)
T ss_dssp EETTSTEEEEEEETTBSSEEEEEEETTEEEEEEEEEE
T ss_pred EEeCCcEEEEEEECCCCCCCEEEEEcCCeeEEEEEec
Confidence 3334445555556666655 89999999999998753
No 186
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=23.87 E-value=1.4e+02 Score=24.37 Aligned_cols=32 Identities=25% Similarity=0.344 Sum_probs=26.1
Q ss_pred eCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 41 MLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 41 ~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
+-|++.|.|.-+||..+ .|.+.+||++.|-+-
T Consensus 102 vaG~GiF~v~~~d~~~~----------~i~c~~gDLI~vP~g 133 (181)
T COG1791 102 VAGEGIFDVHSPDGKVY----------QIRCEKGDLISVPPG 133 (181)
T ss_pred EecceEEEEECCCCcEE----------EEEEccCCEEecCCC
Confidence 35999999999999887 566778999888664
No 187
>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This domain is found in NgoFVII restriction endonuclease, which recognises GCSGC but cleavage site is unknown. It is also found as the C-terminal domain of the res subunit of some type III restriction endonucleases.
Probab=23.54 E-value=1.4e+02 Score=25.68 Aligned_cols=28 Identities=11% Similarity=-0.042 Sum_probs=23.9
Q ss_pred CCceEEEEeCCCCEEEEEecccccceEE
Q 032228 43 GNGRCEAMCIDGAKRLCHIRGKMHKKVW 70 (145)
Q Consensus 43 G~~~~~V~~~dG~~~la~IpGK~Rk~Iw 70 (145)
.+..|.|.++||....|++.|--.|.+.
T Consensus 236 ~~~~f~~itddG~~~~~~~~~~~~K~l~ 263 (296)
T PF09565_consen 236 KKKPFTVITDDGWIFEAKVCQDNGKALM 263 (296)
T ss_pred CCCceEEEcCCCcEEEEEeccccCcccc
Confidence 3788999999999999999998766543
No 188
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=23.53 E-value=72 Score=24.73 Aligned_cols=31 Identities=35% Similarity=0.468 Sum_probs=16.0
Q ss_pred EecccccceEEEccCCEEEEEeccC-CCCceEEE
Q 032228 60 HIRGKMHKKVWIGAGDIILVGLRDY-QDDKADVI 92 (145)
Q Consensus 60 ~IpGK~Rk~IwIk~GD~VlVe~~~~-~~~Kg~Ii 92 (145)
-..+.|.-. +.+||+|+|.+..+ +...|+||
T Consensus 36 V~g~SM~Pt--l~~GD~vlv~~~~~~~~~~GDIV 67 (158)
T TIGR02228 36 VLSGSMEPT--FNTGDLILVTGADPNDIQVGDVI 67 (158)
T ss_pred EcCCCCcCC--ccCCCEEEEEecccCCCCCCCEE
Confidence 334444444 35677777766433 23456653
No 189
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=23.40 E-value=1.5e+02 Score=24.76 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=27.4
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032228 32 GQEYAQVLRMLGNGRCEAMC-----IDGAKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~-----~dG~~~la~IpGK~R 66 (145)
+.+-++|+++|+|+.+.|+= -|+.....+++|-.|
T Consensus 150 ~tIta~V~~VLPNGNLvI~G~k~v~vN~e~~~i~lsGvVR 189 (236)
T PRK12696 150 ATIAARVVRVLPGGLMQVEGARETRVNDETQYIVVSGLVR 189 (236)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEEC
Confidence 45889999999999998864 467777777777554
No 190
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=23.30 E-value=2.1e+02 Score=18.13 Aligned_cols=61 Identities=11% Similarity=-0.004 Sum_probs=45.9
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc-----ceEEEccCCEEEEEeccCCCCceEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMH-----KKVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~R-----k~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
..+.|+|+++-. .-+-|.+.+|..-+++++-=-. ..-.++.||.|.|.....+..+++|+.
T Consensus 6 ~iv~g~V~~v~~-~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 6 DIVEGKVTSVED-FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp SEEEEEEEEEET-TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred CEEEEEEEEEEC-CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 347888888887 5555777788888877764332 245789999999999998888887764
No 191
>PRK11642 exoribonuclease R; Provisional
Probab=23.02 E-value=4.2e+02 Score=25.94 Aligned_cols=68 Identities=15% Similarity=0.109 Sum_probs=47.3
Q ss_pred CeEEEEEEEeCCCceEEEEeCCC-CEEEEEec---cc---cc----------ceEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 32 GQEYAQVLRMLGNGRCEAMCIDG-AKRLCHIR---GK---MH----------KKVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~~dG-~~~la~Ip---GK---~R----------k~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
....|+|+.+...+.| |+++++ ..-++++. .- |. ..-.++.||.|.|.....+..++.|.+.
T Consensus 645 e~f~G~Is~V~~fGif-VeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~ 723 (813)
T PRK11642 645 NVFKGVISSVTGFGFF-VRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFS 723 (813)
T ss_pred cEEEEEEEEeecCceE-EEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEEE
Confidence 3468999998887776 666553 55555543 21 11 1245778999999999888889999888
Q ss_pred cChhHH
Q 032228 95 YMPDEA 100 (145)
Q Consensus 95 y~~dei 100 (145)
+...+.
T Consensus 724 l~~~~~ 729 (813)
T PRK11642 724 LISSER 729 (813)
T ss_pred Eecccc
Confidence 865544
No 192
>PF12843 DUF3820: Protein of unknown function (DUF3820); InterPro: IPR024530 This protein family is mostly found in bacteria and is currently functionally uncharacterised.
Probab=22.97 E-value=49 Score=22.81 Aligned_cols=28 Identities=11% Similarity=0.146 Sum_probs=25.3
Q ss_pred cCCCCceEEEEEcChhHHHHHHHcCCCCc
Q 032228 83 DYQDDKADVILKYMPDEARLLKAYGELPE 111 (145)
Q Consensus 83 ~~~~~Kg~Ii~ry~~deik~Lrk~g~wP~ 111 (145)
||+.-||+.+.-+..+-+.|+.++| +|+
T Consensus 15 PFGKyKG~~l~dLP~~YL~W~~~kG-fP~ 42 (67)
T PF12843_consen 15 PFGKYKGRPLADLPESYLVWFARKG-FPK 42 (67)
T ss_pred CCcccCCcCHhhCCHHHHHHHHHcC-CCc
Confidence 6777899999999999999999999 775
No 193
>PTZ00067 40S ribosomal S23; Provisional
Probab=22.90 E-value=99 Score=24.30 Aligned_cols=49 Identities=20% Similarity=0.229 Sum_probs=35.5
Q ss_pred CeEEEEEEEeCC------C----ceEEEEeC-CCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 32 GQEYAQVLRMLG------N----GRCEAMCI-DGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 32 ~q~ig~Vv~~lG------~----~~~~V~~~-dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
-|.-|.|++..+ | -..+|++. ||..++|.|||-=. --.|.+.|.|||.-
T Consensus 45 pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiPg~G~-lh~lqEh~~VLV~G 104 (143)
T PTZ00067 45 SHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGC-LNFINENDEVLVSG 104 (143)
T ss_pred CccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeCCCCc-ccccccCCEEEEEe
Confidence 356666666554 2 24678887 99999999998531 13588999999986
No 194
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=22.77 E-value=2.9e+02 Score=19.62 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=23.7
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEecc
Q 032228 36 AQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 36 g~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
|+|+....++.-+|.. +|...-|+-.+. |.+||.|.|.-.+
T Consensus 94 g~v~~~~~~~~G~V~~-~G~~w~A~s~~~------i~~G~~V~Vv~v~ 134 (144)
T PF01957_consen 94 GTVIEIPLNGSGRVKV-DGERWRARSEDE------IPKGDRVRVVGVE 134 (144)
T ss_dssp EEEEEEBSSS-EEEEE-TTEEEEEEESST------B-TT-EEEEEEEE
T ss_pred EEEEEeecCCcEEEEE-CCeEEEEEeCCC------CCCCCEEEEEEEE
Confidence 3443444445555655 577887877766 7888887776543
No 195
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=22.46 E-value=4.9e+02 Score=24.90 Aligned_cols=63 Identities=22% Similarity=0.343 Sum_probs=45.1
Q ss_pred CCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEccCCEEEEEeccCCCCceEEEEE
Q 032228 29 KEDG-QEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHK-KV-----WIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 29 p~e~-q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk-~I-----wIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
+..| .+.|+|+++...+.| |.+..|..=|+|++ ++.. ++ -++.||.|.|.....+.. ++|...
T Consensus 619 ~~vG~v~~G~V~~I~~fGaf-Vei~~~~~GllhiS-els~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS 688 (693)
T PRK11824 619 PEVGEIYEGKVVRIVDFGAF-VEILPGKDGLVHIS-EIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLS 688 (693)
T ss_pred CcCCeEEEEEEEEEECCeEE-EEECCCCEEEEEee-eccCccccCccceeCCCCEEEEEEEEECCC-CcEEEE
Confidence 3444 578999999876655 66677888888887 4432 22 479999999998877655 776543
No 196
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=22.43 E-value=1.8e+02 Score=22.96 Aligned_cols=35 Identities=23% Similarity=0.396 Sum_probs=26.7
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032228 32 GQEYAQVLRMLGNGRCEAMC-----IDGAKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~-----~dG~~~la~IpGK~R 66 (145)
+.+-|+|+++++|+.+.|+= -|+.+...+|+|-.|
T Consensus 94 ~~ita~Vv~VlpNGnL~I~G~k~i~vn~e~~~i~lsGiVR 133 (179)
T PF02107_consen 94 GTITARVVEVLPNGNLVIEGEKQIRVNGEEQYIRLSGIVR 133 (179)
T ss_pred EEEEEEEEEECCCCcEEEEEEEEEEECCCEEEEEEEEEEC
Confidence 45889999999999998864 466666667777554
No 197
>PRK00215 LexA repressor; Validated
Probab=22.23 E-value=1.2e+02 Score=23.56 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=28.7
Q ss_pred CCEEEEEecccccceEEEccCCEEEEEeccCCCCceEEEEEcChhH
Q 032228 54 GAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 54 G~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ry~~de 99 (145)
+..+..++.|-=.-.--|..||+|+|+++. +...|+|+..+..++
T Consensus 116 ~~~~~~~V~GdSM~~~~i~~Gd~v~v~~~~-~~~~G~ivv~~~~~~ 160 (205)
T PRK00215 116 GEDFLLRVRGDSMIDAGILDGDLVIVRKQQ-TARNGQIVVALIDDE 160 (205)
T ss_pred CCeEEEEEccCCCCCCCcCCCCEEEEeCCC-CCCCCCEEEEEECCE
Confidence 456666666654333458899999999753 345677765554443
No 198
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=22.07 E-value=59 Score=21.29 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=12.4
Q ss_pred CEEEEEecccccceEEEccCCEE
Q 032228 55 AKRLCHIRGKMHKKVWIGAGDII 77 (145)
Q Consensus 55 ~~~la~IpGK~Rk~IwIk~GD~V 77 (145)
..+.+.++|++-+ +++..||.|
T Consensus 3 ~~v~a~~~G~i~~-~~v~~Gd~V 24 (71)
T PRK05889 3 EDVRAEIVASVLE-VVVNEGDQI 24 (71)
T ss_pred cEEeCCCCEEEEE-EEeCCCCEE
Confidence 3466777777655 344445444
No 199
>cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=22.00 E-value=2.8e+02 Score=23.09 Aligned_cols=43 Identities=16% Similarity=0.218 Sum_probs=27.7
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEE
Q 032228 31 DGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIIL 78 (145)
Q Consensus 31 e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~Vl 78 (145)
.||++|+|....|....+|..+-.-.++++ +..-.+.+||.|.
T Consensus 242 ~G~~ig~i~d~~~~~~~~v~ap~~G~v~~~-----~~~~~v~~G~~l~ 284 (287)
T cd06251 242 KGQLLATITDPFGEEEAEVKAPFDGIVIGR-----NNLPLVNEGDALF 284 (287)
T ss_pred CCCEEEEEECCCCCceEEEECCCCeEEEEe-----cCCCccCCCCEEE
Confidence 578888888888877766666533333332 3355677787765
No 200
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=21.96 E-value=88 Score=20.92 Aligned_cols=26 Identities=19% Similarity=0.157 Sum_probs=19.5
Q ss_pred EEccCCEEEEEeccCCCCceEEEEEc
Q 032228 70 WIGAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 70 wIk~GD~VlVe~~~~~~~Kg~Ii~ry 95 (145)
.+++||.|++--...+..-|-++++|
T Consensus 65 ~~~~Gd~vl~~~~G~G~~~~~~~~~~ 90 (90)
T PF08541_consen 65 RIKPGDRVLLVGFGAGFSWGAAVLRW 90 (90)
T ss_dssp SSCTTEEEEEEEEETTTEEEEEEEE-
T ss_pred CCCCCCEEEEEEEEhhheeEEEEEEC
Confidence 47789999998777666777777765
No 201
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=21.58 E-value=1.4e+02 Score=22.07 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=19.6
Q ss_pred EEEEEecccccceEEEccCCEEEEEeccCCCCceEEEE
Q 032228 56 KRLCHIRGKMHKKVWIGAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 56 ~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~~~Kg~Ii~ 93 (145)
.+..+++|-=...--|..||+|+|++.. ....|+|+.
T Consensus 51 ~f~l~V~GdSM~~~~I~~GD~liVd~~~-~~~~Gdivv 87 (139)
T PRK10276 51 TYFVKASGDSMIDAGISDGDLLIVDSAI-TASHGDIVI 87 (139)
T ss_pred EEEEEEecCCCCCCCCCCCCEEEEECCC-CCCCCCEEE
Confidence 4444555432221237778888888653 234555543
No 202
>PF03123 CAT_RBD: CAT RNA binding domain; InterPro: IPR004341 The CAT RNA-binding domain is found at the amino terminus of a family of transcriptional antiterminator proteins, the Co-AntiTerminator (CAT) domain. This domain forms a dimer in the crystal structure []. Transcriptional antiterminators of the BglG/SacY family are regulatory proteins that mediate the induction of sugar metabolizing operons in Gram-positive and Gram-negative bacteria. Upon activation, these proteins bind to specific targets in nascent mRNAs, thereby preventing abortive dissociation of the RNA polymerase from the DNA template [].; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1AUU_B 1TLV_A 1L1C_A 1H99_A 3RIO_A.
Probab=21.51 E-value=1.9e+02 Score=19.08 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=25.3
Q ss_pred EEEEeCCCceEEEEeCCCCEEEEEeccc-ccceEEEccCCEE
Q 032228 37 QVLRMLGNGRCEAMCIDGAKRLCHIRGK-MHKKVWIGAGDII 77 (145)
Q Consensus 37 ~Vv~~lG~~~~~V~~~dG~~~la~IpGK-~Rk~IwIk~GD~V 77 (145)
+|.+++.||...+...+|.++++.=.|= |. -++||.|
T Consensus 2 ~I~KvlNNNvvl~~~~~~~E~Iv~GkGIGF~----kk~G~~i 39 (59)
T PF03123_consen 2 KIKKVLNNNVVLAKDDNGQEVIVMGKGIGFG----KKPGDEI 39 (59)
T ss_dssp EEEEEEETTEEEEE-CCSSEEEEE-TTSSTT------TTSEE
T ss_pred EEEEEccCeEEEEEeCCCCEEEEEeecceec----cCCCCcc
Confidence 6899999999999989998887764441 32 3567665
No 203
>TIGR03032 conserved hypothetical protein TIGR03032. This protein family is uncharacterized. A number of motifs are conserved perfectly among all member sequences. The function of this protein is unknown.
Probab=21.23 E-value=2.5e+02 Score=24.93 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=39.7
Q ss_pred ccccceeeccCC-----CCeEEEEEEEeCCCceEEEEeCCCC-EEEEEecccccceEEEccCCEEEEEecc
Q 032228 19 ADDEKRELIFKE-----DGQEYAQVLRMLGNGRCEAMCIDGA-KRLCHIRGKMHKKVWIGAGDIILVGLRD 83 (145)
Q Consensus 19 ~~~~~~el~~p~-----e~q~ig~Vv~~lG~~~~~V~~~dG~-~~la~IpGK~Rk~IwIk~GD~VlVe~~~ 83 (145)
++.+..-|..|. +|.+. |..+..+..+.|....|. +.+|.+||..|--=|. |++.+|.+|.
T Consensus 195 ~evl~~GLsmPhSPRWhdgrLw--vldsgtGev~~vD~~~G~~e~Va~vpG~~rGL~f~--G~llvVgmSk 261 (335)
T TIGR03032 195 GEVVASGLSMPHSPRWYQGKLW--LLNSGRGELGYVDPQAGKFQPVAFLPGFTRGLAFA--GDFAFVGLSK 261 (335)
T ss_pred CCEEEcCccCCcCCcEeCCeEE--EEECCCCEEEEEcCCCCcEEEEEECCCCCccccee--CCEEEEEecc
Confidence 344445555554 34443 445444555555554354 8899999999886666 9999999984
No 204
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=21.07 E-value=97 Score=22.27 Aligned_cols=52 Identities=13% Similarity=0.063 Sum_probs=26.0
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEe
Q 032228 30 EDGQEYAQVLRMLGNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 30 ~e~q~ig~Vv~~lG~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
+++.++....-..+.....+....+...+..++.=+=.+..|+.||.|.+.|
T Consensus 57 ~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd~v~~~~ 108 (108)
T PF02643_consen 57 SDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGDRVRIEP 108 (108)
T ss_dssp TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-EEE---
T ss_pred CCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCCEEEecC
Confidence 4566655555554666555434444556666666666667789999998765
No 205
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=20.69 E-value=2.5e+02 Score=18.21 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=38.0
Q ss_pred eEEEEEEEeCCCceEEEEeC---CCCEEEEEeccc----c-cc-eEEEccCCEEEEEeccCCCCceEEEEE
Q 032228 33 QEYAQVLRMLGNGRCEAMCI---DGAKRLCHIRGK----M-HK-KVWIGAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 33 q~ig~Vv~~lG~~~~~V~~~---dG~~~la~IpGK----~-Rk-~IwIk~GD~VlVe~~~~~~~Kg~Ii~r 94 (145)
...|+|+++...+.| |.+. +|..-+.+++-- + .. .-.++.||.|.|.....+ +++|...
T Consensus 3 ~~~g~V~~v~~~G~f-v~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s 70 (79)
T cd05684 3 IYKGKVTSIMDFGCF-VQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLS 70 (79)
T ss_pred EEEEEEEEEEeeeEE-EEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEE
Confidence 467888888876555 4444 356667666422 1 21 224799999999987766 6666544
No 206
>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein. This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.
Probab=20.61 E-value=2.5e+02 Score=24.00 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=32.8
Q ss_pred CeEEEEEEEeC--CCceEEEEeCC-CCEEEEEecccccceEEEccCCEEEEEe
Q 032228 32 GQEYAQVLRML--GNGRCEAMCID-GAKRLCHIRGKMHKKVWIGAGDIILVGL 81 (145)
Q Consensus 32 ~q~ig~Vv~~l--G~~~~~V~~~d-G~~~la~IpGK~Rk~IwIk~GD~VlVe~ 81 (145)
+.+.|+|..+. |...+.|.+.. +....|+++.+-....-+..|+.|.+..
T Consensus 296 n~~~~~v~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~g~~v~~~~ 348 (354)
T TIGR02142 296 NILPARVVEIEDSDIGRVGVVLESGGKTLWARITRWARDELGIAPGTPVFAQI 348 (354)
T ss_pred cEEEEEEEEEEecCCCeEEEEEEcCCcEEEEEecHHHHHhcCCCCCCEEEEEE
Confidence 55678888774 42455554432 6677888887655555577888888764
No 207
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.43 E-value=3.3e+02 Score=20.05 Aligned_cols=52 Identities=25% Similarity=0.088 Sum_probs=35.8
Q ss_pred CCceEEEEeCCCCEEEEEecccccceEEEccCCEEEEEeccCC-CCceEEEEEcChhHHHHHHHc
Q 032228 43 GNGRCEAMCIDGAKRLCHIRGKMHKKVWIGAGDIILVGLRDYQ-DDKADVILKYMPDEARLLKAY 106 (145)
Q Consensus 43 G~~~~~V~~~dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~~~~-~~Kg~Ii~ry~~deik~Lrk~ 106 (145)
|--.++++|.|... -.|++||.++..-|+.. ....+|++...=+.-++|-+.
T Consensus 16 G~KtiEiRlnD~kr------------~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y~sF~~ll~~ 68 (109)
T cd06555 16 GKKTIEIRLNDEKR------------QQIKVGDKILFNDLDTGQQLLVKVVDIRKYDSFRELLEE 68 (109)
T ss_pred CCCEEEEEecccch------------hcCCCCCEEEEEEcCCCcEEEEEEEEEEecCCHHHHHHh
Confidence 55567777776543 45899999999888643 347788777666666666554
No 208
>PRK11144 modC molybdate transporter ATP-binding protein; Provisional
Probab=20.36 E-value=2.7e+02 Score=23.84 Aligned_cols=50 Identities=16% Similarity=0.227 Sum_probs=28.0
Q ss_pred eEEEEEEEeCC-CceEEEEeC-CCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 33 QEYAQVLRMLG-NGRCEAMCI-DGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 33 q~ig~Vv~~lG-~~~~~V~~~-dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
.+.|+|..+.- +..+.|.+. .|...+++++..-.....+.+|+.|.+...
T Consensus 295 ~~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~v~~~~~ 346 (352)
T PRK11144 295 ILRAKVVEIYDDNGQVEVKLEVGGKTLWARITPWARDELALKPGQWLYAQIK 346 (352)
T ss_pred eeEEEEEEEEcCCCEEEEEEEeCCcEEEEEecHHHHHhcCCCCCCEEEEEEE
Confidence 46677776642 223444332 456667777643323345777887777643
No 209
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=20.19 E-value=2.2e+02 Score=19.29 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=19.9
Q ss_pred EeCCCCEEEEEecccccc---eEEEccCCEEEEEe
Q 032228 50 MCIDGAKRLCHIRGKMHK---KVWIGAGDIILVGL 81 (145)
Q Consensus 50 ~~~dG~~~la~IpGK~Rk---~IwIk~GD~VlVe~ 81 (145)
+..+.-.+.+.||| +++ .|++..+..+.|.-
T Consensus 6 E~~~~~~i~~~lPG-v~~edi~i~v~~~~~L~I~g 39 (92)
T cd06472 6 ETPEAHVFKADVPG-VKKEDVKVEVEDGRVLRISG 39 (92)
T ss_pred EcCCeEEEEEECCC-CChHhEEEEEeCCCEEEEEE
Confidence 44667788899999 554 56665444555544
No 210
>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=20.18 E-value=4.7e+02 Score=22.52 Aligned_cols=51 Identities=22% Similarity=0.175 Sum_probs=32.2
Q ss_pred CeEEEEEEEeC--CC-ceEEEEeC--CCCEEEEEecccccceEEEccCCEEEEEec
Q 032228 32 GQEYAQVLRML--GN-GRCEAMCI--DGAKRLCHIRGKMHKKVWIGAGDIILVGLR 82 (145)
Q Consensus 32 ~q~ig~Vv~~l--G~-~~~~V~~~--dG~~~la~IpGK~Rk~IwIk~GD~VlVe~~ 82 (145)
+.+-|+|+.+. |+ ..+.|.+. +|....+.++...-....+..|+.|.+...
T Consensus 290 ~~~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~ 345 (353)
T TIGR03265 290 NLLLARVEDMEFLGAFYRLRLRLEGLPGQALVADVSASEVERLGIRAGQPIWIELP 345 (353)
T ss_pred ceEEEEEEEEEEcCCeEEEEEEECCCCCcEEEEEeccccccccCCCCCCEEEEEEe
Confidence 44667777664 43 23344444 356778888865555566788988887653
No 211
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=20.14 E-value=1.9e+02 Score=23.88 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=25.6
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032228 32 GQEYAQVLRMLGNGRCEAMC-----IDGAKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~Vv~~lG~~~~~V~~-----~dG~~~la~IpGK~R 66 (145)
+.+-++|+++|+|+.+.|+= -|+.....+|+|-.|
T Consensus 137 ~tIta~V~~VlpNGnL~I~GeK~i~vN~~~e~I~lsGvVR 176 (224)
T PRK12698 137 GSISANVMQVLPNGNLVIRGEKWISINNGDEFIRLTGIVR 176 (224)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCEEEEEEEEEEC
Confidence 55889999999999998864 355566666666443
No 212
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.07 E-value=82 Score=19.90 Aligned_cols=14 Identities=7% Similarity=0.311 Sum_probs=11.5
Q ss_pred EccCCEEEEEeccC
Q 032228 71 IGAGDIILVGLRDY 84 (145)
Q Consensus 71 Ik~GD~VlVe~~~~ 84 (145)
+++|+||++..+..
T Consensus 2 l~pG~~V~CAVTg~ 15 (42)
T PF09866_consen 2 LSPGSFVRCAVTGQ 15 (42)
T ss_pred ccCCCEEEEEeeCC
Confidence 67999999998753
Done!