Query 032190
Match_columns 145
No_of_seqs 110 out of 661
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:48:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032190.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032190hhsearch_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 3E-54 6.5E-59 332.2 16.0 145 1-145 1-145 (145)
2 PTZ00329 eukaryotic translatio 100.0 5.1E-54 1.1E-58 333.8 15.8 131 1-137 1-131 (155)
3 KOG3403 Translation initiation 100.0 1.6E-47 3.5E-52 289.0 6.7 145 1-145 1-145 (145)
4 TIGR00523 eIF-1A eukaryotic/ar 100.0 1.1E-36 2.3E-41 221.9 13.2 98 14-111 1-99 (99)
5 PRK04012 translation initiatio 100.0 2.3E-36 5E-41 220.6 13.3 95 17-111 6-100 (100)
6 smart00652 eIF1a eukaryotic tr 100.0 4.8E-36 1E-40 212.1 12.0 83 28-110 1-83 (83)
7 cd04456 S1_IF1A_like S1_IF1A_l 100.0 1.8E-33 3.9E-38 197.0 11.3 77 33-109 1-78 (78)
8 cd05792 S1_eIF1AD_like S1_eIF1 100.0 5.9E-33 1.3E-37 194.8 10.8 77 33-109 1-78 (78)
9 cd05793 S1_IF1A S1_IF1A: Trans 100.0 7.6E-33 1.6E-37 193.4 11.2 77 33-109 1-77 (77)
10 COG0361 InfA Translation initi 100.0 1.4E-28 3E-33 171.5 9.1 72 28-99 3-75 (75)
11 PF01176 eIF-1a: Translation i 99.9 2.8E-27 6.1E-32 159.7 7.5 65 30-94 1-65 (65)
12 KOG2925 Predicted translation 99.9 2.7E-27 5.9E-32 183.7 2.9 98 18-115 8-109 (167)
13 TIGR00008 infA translation ini 99.9 1.2E-24 2.7E-29 149.2 9.4 62 33-94 6-68 (68)
14 PRK12442 translation initiatio 99.9 8.8E-24 1.9E-28 150.9 9.9 64 33-96 8-72 (87)
15 CHL00010 infA translation init 99.8 2E-18 4.4E-23 120.6 9.0 66 33-98 8-74 (78)
16 PRK00276 infA translation init 99.8 6.2E-18 1.3E-22 116.1 9.1 64 33-96 8-72 (72)
17 cd04451 S1_IF1 S1_IF1: Transla 99.5 7.1E-14 1.5E-18 93.2 8.4 62 33-94 2-64 (64)
18 cd04466 S1_YloQ_GTPase S1_YloQ 98.3 4.6E-06 1E-10 54.9 7.3 60 35-97 2-62 (68)
19 PRK00098 GTPase RsgA; Reviewed 97.1 0.002 4.4E-08 54.1 7.6 58 35-95 2-60 (298)
20 PRK12289 GTPase RsgA; Reviewed 97.1 0.0022 4.7E-08 55.8 7.5 66 29-95 4-76 (352)
21 PRK12288 GTPase RsgA; Reviewed 96.7 0.0072 1.6E-07 52.3 7.8 60 34-97 40-101 (347)
22 cd01854 YjeQ_engC YjeQ/EngC. 96.6 0.0076 1.6E-07 50.4 6.9 59 36-98 1-60 (287)
23 PRK01889 GTPase RsgA; Reviewed 95.3 0.059 1.3E-06 46.6 6.9 63 31-99 26-93 (356)
24 cd00164 S1_like S1_like: Ribos 94.6 0.16 3.5E-06 31.2 5.7 57 35-92 2-63 (65)
25 cd05685 S1_Tex S1_Tex: The C-t 90.7 1.5 3.2E-05 27.4 6.2 59 32-92 2-66 (68)
26 TIGR00638 Mop molybdenum-pteri 89.9 1.7 3.7E-05 27.9 6.1 55 30-84 5-62 (69)
27 PF03459 TOBE: TOBE domain; I 89.2 0.83 1.8E-05 29.2 4.1 55 29-83 2-59 (64)
28 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 88.4 1.7 3.8E-05 29.3 5.5 65 29-95 4-78 (86)
29 PHA02945 interferon resistance 87.7 6 0.00013 28.6 8.0 66 26-93 6-79 (88)
30 COG1162 Predicted GTPases [Gen 85.5 2.4 5.1E-05 36.7 5.9 61 34-98 5-69 (301)
31 cd04454 S1_Rrp4_like S1_Rrp4_l 85.2 5.6 0.00012 26.6 6.6 63 28-92 3-71 (82)
32 PF02736 Myosin_N: Myosin N-te 84.2 3.7 8E-05 25.1 4.9 33 27-60 7-39 (42)
33 COG1093 SUI2 Translation initi 80.2 3.2 7E-05 35.5 4.6 76 27-102 7-92 (269)
34 PF15057 DUF4537: Domain of un 80.0 7.1 0.00015 29.2 6.0 49 34-83 15-67 (124)
35 cd05790 S1_Rrp40 S1_Rrp40: Rrp 79.7 5.3 0.00012 28.4 4.9 55 29-86 4-65 (86)
36 PF01455 HupF_HypC: HupF/HypC 77.9 13 0.00029 25.1 6.3 56 35-103 6-63 (68)
37 TIGR00074 hypC_hupF hydrogenas 77.5 11 0.00023 26.3 5.9 56 35-103 6-61 (76)
38 PF11948 DUF3465: Protein of u 76.6 13 0.00028 28.7 6.6 62 34-95 41-111 (131)
39 TIGR03689 pup_AAA proteasome A 76.5 4.8 0.0001 37.1 4.9 52 29-82 104-155 (512)
40 PTZ00248 eukaryotic translatio 76.4 11 0.00024 32.9 6.9 78 27-105 13-101 (319)
41 COG0048 RpsL Ribosomal protein 76.1 5.2 0.00011 30.8 4.2 36 46-84 58-93 (129)
42 PF04076 BOF: Bacterial OB fol 75.3 11 0.00023 27.6 5.6 48 33-81 38-85 (103)
43 PRK11642 exoribonuclease R; Pr 74.9 28 0.0006 33.8 9.8 45 71-115 186-239 (813)
44 PRK10413 hydrogenase 2 accesso 74.7 9.9 0.00022 26.9 5.1 59 35-102 6-67 (82)
45 cd05705 S1_Rrp5_repeat_hs14 S1 74.0 23 0.00051 23.6 7.5 60 32-92 5-72 (74)
46 cd05707 S1_Rrp5_repeat_sc11 S1 72.6 21 0.00045 22.8 6.0 59 33-92 3-66 (68)
47 cd04479 RPA3 RPA3: A subfamily 72.1 11 0.00024 27.0 5.0 30 33-63 19-48 (101)
48 cd05791 S1_CSL4 S1_CSL4: CSL4, 71.5 9.1 0.0002 26.9 4.4 58 28-86 3-76 (92)
49 CHL00051 rps12 ribosomal prote 71.4 6.9 0.00015 29.9 3.9 33 46-81 52-84 (123)
50 PTZ00454 26S protease regulato 70.7 13 0.00028 32.9 6.1 54 30-84 64-117 (398)
51 PRK03987 translation initiatio 70.5 22 0.00048 29.9 7.2 65 28-93 5-77 (262)
52 cd00319 Ribosomal_S12_like Rib 69.6 8 0.00017 28.3 3.8 33 46-81 37-69 (95)
53 PRK10409 hydrogenase assembly 69.5 20 0.00042 25.9 5.8 54 35-102 6-66 (90)
54 PF00717 Peptidase_S24: Peptid 68.8 2.3 5.1E-05 27.2 0.8 25 71-96 11-35 (70)
55 smart00316 S1 Ribosomal protei 68.4 24 0.00052 21.5 7.6 62 32-94 4-70 (72)
56 cd04452 S1_IF2_alpha S1_IF2_al 68.4 29 0.00063 22.3 7.0 63 30-94 2-73 (76)
57 cd05689 S1_RPS1_repeat_ec4 S1_ 68.1 29 0.00063 22.3 7.0 62 29-92 2-70 (72)
58 PRK05163 rpsL 30S ribosomal pr 66.5 10 0.00022 29.1 3.9 33 46-81 52-84 (124)
59 TIGR00981 rpsL_bact ribosomal 66.4 9.6 0.00021 29.2 3.8 33 46-81 52-84 (124)
60 COG0298 HypC Hydrogenase matur 66.2 13 0.00027 26.6 4.1 55 35-102 6-63 (82)
61 KOG2107 Uncharacterized conser 66.0 10 0.00022 30.7 4.0 48 41-106 100-147 (179)
62 cd03368 Ribosomal_S12 S12-like 64.8 11 0.00023 28.2 3.8 33 46-81 50-82 (108)
63 cd04482 RPA2_OBF_like RPA2_OBF 64.6 12 0.00025 26.3 3.8 39 44-82 18-59 (91)
64 PRK04163 exosome complex RNA-b 64.5 22 0.00047 29.2 5.9 78 27-105 59-161 (235)
65 PF08661 Rep_fac-A_3: Replicat 64.5 22 0.00047 25.5 5.3 33 34-66 23-56 (109)
66 cd05696 S1_Rrp5_repeat_hs4 S1_ 64.3 37 0.00079 22.3 6.0 57 36-92 7-68 (71)
67 PF03749 SfsA: Sugar fermentat 64.0 59 0.0013 26.6 8.3 78 45-124 5-104 (215)
68 PF09038 53-BP1_Tudor: Tumour 63.6 20 0.00044 27.3 5.1 37 36-84 22-58 (122)
69 PF04717 Phage_base_V: Phage-r 62.4 32 0.00069 23.0 5.5 56 44-99 10-72 (79)
70 cd04721 BAH_plant_1 BAH, or Br 62.2 13 0.00027 28.0 3.8 42 66-107 3-59 (130)
71 PLN00207 polyribonucleotide nu 62.0 27 0.00058 34.5 6.8 65 28-95 750-822 (891)
72 PF00164 Ribosom_S12_S23: Ribo 61.6 12 0.00026 28.5 3.5 49 32-83 27-85 (122)
73 PRK08059 general stress protei 60.0 56 0.0012 23.9 6.9 65 31-96 8-77 (123)
74 TIGR02063 RNase_R ribonuclease 59.6 1.2E+02 0.0027 28.6 10.6 84 32-115 121-225 (709)
75 cd06530 S26_SPase_I The S26 Ty 59.1 11 0.00025 25.1 2.8 25 71-95 14-41 (85)
76 TIGR00156 conserved hypothetic 58.6 34 0.00073 26.1 5.6 54 28-82 54-109 (126)
77 COG0509 GcvH Glycine cleavage 58.5 6.9 0.00015 30.1 1.8 40 59-98 3-48 (131)
78 CHL00141 rpl24 ribosomal prote 58.3 14 0.0003 26.0 3.2 32 68-99 6-37 (83)
79 cd05692 S1_RPS1_repeat_hs4 S1_ 57.4 42 0.00092 20.6 7.0 59 33-93 3-66 (69)
80 PRK07899 rpsA 30S ribosomal pr 57.4 56 0.0012 29.9 7.7 65 31-96 294-363 (486)
81 PF12857 TOBE_3: TOBE-like dom 57.4 48 0.001 21.2 5.9 53 29-82 2-58 (58)
82 PRK10676 DNA-binding transcrip 56.8 30 0.00064 28.8 5.5 53 31-83 199-254 (263)
83 TIGR02754 sod_Ni_protease nick 56.0 16 0.00034 24.8 3.1 27 71-97 12-41 (90)
84 smart00318 SNc Staphylococcal 55.9 33 0.00071 24.8 5.0 75 33-108 2-103 (138)
85 cd05704 S1_Rrp5_repeat_hs13 S1 54.7 59 0.0013 21.3 6.4 57 32-91 5-67 (72)
86 TIGR00358 3_prime_RNase VacB a 54.3 1.2E+02 0.0025 28.6 9.5 45 71-115 120-173 (654)
87 PRK01191 rpl24p 50S ribosomal 54.1 19 0.00042 27.3 3.6 32 68-99 43-74 (120)
88 PRK05054 exoribonuclease II; P 53.6 1.3E+02 0.0028 28.4 9.6 46 71-116 122-177 (644)
89 PF11302 DUF3104: Protein of u 53.4 18 0.00039 25.4 3.0 28 69-96 4-38 (75)
90 cd04508 TUDOR Tudor domains ar 53.2 26 0.00056 20.8 3.5 31 30-60 10-42 (48)
91 PRK12281 rplX 50S ribosomal pr 52.4 19 0.00041 24.9 3.1 31 69-99 5-35 (76)
92 TIGR02696 pppGpp_PNP guanosine 51.8 38 0.00083 32.7 5.9 62 29-92 645-716 (719)
93 PF08402 TOBE_2: TOBE domain; 51.7 57 0.0012 20.3 5.6 52 31-83 15-69 (75)
94 PRK10053 hypothetical protein; 51.6 48 0.001 25.4 5.4 48 33-81 65-112 (130)
95 cd05698 S1_Rrp5_repeat_hs6_sc5 51.5 60 0.0013 20.5 7.1 59 33-93 3-67 (70)
96 PTZ00361 26 proteosome regulat 50.8 45 0.00097 30.1 6.0 51 31-82 103-153 (438)
97 cd04472 S1_PNPase S1_PNPase: P 49.8 60 0.0013 20.0 6.7 58 33-92 3-65 (68)
98 cd04471 S1_RNase_R S1_RNase_R: 49.8 69 0.0015 20.7 6.4 62 33-95 4-82 (83)
99 PF04014 Antitoxin-MazE: Antid 49.4 4.4 9.5E-05 25.0 -0.5 30 54-83 4-33 (47)
100 PRK07252 hypothetical protein; 49.1 1.1E+02 0.0023 22.7 7.4 63 32-95 5-72 (120)
101 TIGR01439 lp_hng_hel_AbrB loop 48.8 11 0.00025 21.9 1.3 25 58-82 8-32 (43)
102 PTZ00115 40S ribosomal protein 48.6 26 0.00056 30.2 3.8 33 46-81 148-180 (290)
103 TIGR00230 sfsA sugar fermentat 47.5 71 0.0015 26.5 6.3 85 35-123 11-115 (232)
104 PTZ00194 60S ribosomal protein 47.4 26 0.00056 27.4 3.4 31 68-98 44-74 (143)
105 cd06462 Peptidase_S24_S26 The 47.4 23 0.0005 22.8 2.8 28 71-98 14-41 (84)
106 PF10017 Methyltransf_33: Hist 47.0 1E+02 0.0022 22.7 6.5 68 33-113 47-115 (127)
107 cd05693 S1_Rrp5_repeat_hs1_sc1 46.8 1E+02 0.0022 21.8 6.7 66 32-98 5-97 (100)
108 PRK13806 rpsA 30S ribosomal pr 44.6 82 0.0018 28.5 6.7 66 30-96 292-363 (491)
109 COG1098 VacB Predicted RNA bin 44.4 43 0.00093 25.8 4.1 61 32-94 7-72 (129)
110 PF08605 Rad9_Rad53_bind: Fung 44.0 73 0.0016 24.3 5.4 45 35-82 26-71 (131)
111 KOG1999 RNA polymerase II tran 43.8 60 0.0013 32.6 6.0 76 19-96 520-607 (1024)
112 PF07039 DUF1325: SGF29 tudor- 43.6 42 0.00092 25.3 4.0 60 34-94 20-96 (130)
113 cd04719 BAH_Orc1p_animal BAH, 43.6 23 0.00051 26.8 2.6 25 69-93 2-27 (128)
114 smart00743 Agenet Tudor-like d 43.0 57 0.0012 20.5 4.1 23 31-53 16-39 (61)
115 PRK09521 exosome complex RNA-b 42.9 71 0.0015 25.0 5.4 58 27-85 60-133 (189)
116 TIGR01080 rplX_A_E ribosomal p 42.6 37 0.00081 25.4 3.5 33 67-99 38-70 (114)
117 PRK00347 putative DNA-binding 42.0 1.5E+02 0.0032 24.6 7.3 87 33-123 7-115 (234)
118 PRK00004 rplX 50S ribosomal pr 41.0 33 0.00071 25.0 3.0 31 69-99 3-33 (105)
119 smart00333 TUDOR Tudor domain. 39.7 72 0.0016 19.5 4.1 30 31-60 15-46 (57)
120 TIGR02062 RNase_B exoribonucle 39.4 2.6E+02 0.0056 26.4 9.3 45 71-115 119-173 (639)
121 cd05708 S1_Rrp5_repeat_sc12 S1 39.4 99 0.0022 19.6 7.3 63 32-95 4-72 (77)
122 PF00575 S1: S1 RNA binding do 39.2 1E+02 0.0022 19.6 6.7 60 33-93 7-71 (74)
123 cd04453 S1_RNase_E S1_RNase_E: 38.9 1.3E+02 0.0028 20.8 6.6 54 32-85 9-71 (88)
124 PRK08582 hypothetical protein; 38.4 1.7E+02 0.0038 22.0 8.4 64 32-97 7-75 (139)
125 cd04487 RecJ_OBF2_like RecJ_OB 38.2 1.1E+02 0.0023 20.6 5.0 37 46-82 18-55 (73)
126 COG0198 RplX Ribosomal protein 38.1 48 0.001 24.5 3.5 31 68-98 2-32 (104)
127 PRK10676 DNA-binding transcrip 38.0 70 0.0015 26.6 4.9 50 31-80 127-190 (263)
128 cd05691 S1_RPS1_repeat_ec6 S1_ 37.9 1E+02 0.0022 19.3 6.2 60 33-93 3-67 (73)
129 smart00739 KOW KOW (Kyprides, 37.6 64 0.0014 16.8 3.3 24 71-94 2-25 (28)
130 TIGR01079 rplX_bact ribosomal 37.5 38 0.00082 24.8 2.8 30 70-99 3-32 (104)
131 TIGR00717 rpsA ribosomal prote 36.8 1.4E+02 0.0031 26.5 7.0 66 31-97 360-431 (516)
132 COG1222 RPT1 ATP-dependent 26S 36.6 2.1E+02 0.0046 26.0 7.8 80 30-110 70-170 (406)
133 cd05795 Ribosomal_P0_L10e Ribo 36.5 51 0.0011 25.7 3.6 41 59-110 134-175 (175)
134 PF01287 eIF-5a: Eukaryotic el 35.9 82 0.0018 21.4 4.1 47 35-83 6-58 (69)
135 cd06529 S24_LexA-like Peptidas 35.8 28 0.00061 22.5 1.8 12 71-82 14-25 (81)
136 cd05695 S1_Rrp5_repeat_hs3 S1_ 35.1 1.2E+02 0.0027 19.4 6.2 58 33-91 3-63 (66)
137 TIGR00982 S23_S12_E_A ribosoma 34.9 81 0.0018 24.6 4.4 35 46-81 64-99 (139)
138 cd05706 S1_Rrp5_repeat_sc10 S1 34.9 1.2E+02 0.0026 19.3 8.2 61 32-93 5-70 (73)
139 PF10447 EXOSC1: Exosome compo 34.9 72 0.0016 22.4 3.8 24 29-52 2-27 (82)
140 PF08922 DUF1905: Domain of un 34.8 46 0.00099 22.9 2.8 46 36-81 33-80 (80)
141 PF13533 Biotin_lipoyl_2: Biot 34.5 63 0.0014 20.0 3.2 35 57-101 5-39 (50)
142 PF03079 ARD: ARD/ARD' family; 34.4 64 0.0014 25.2 3.8 30 42-81 100-129 (157)
143 PF09902 DUF2129: Uncharacteri 33.9 40 0.00087 23.2 2.3 22 88-109 2-23 (71)
144 PRK04211 rps12P 30S ribosomal 33.3 88 0.0019 24.6 4.4 48 33-81 47-105 (145)
145 PRK08577 hypothetical protein; 33.0 37 0.00081 25.1 2.2 24 59-82 15-38 (136)
146 PRK06299 rpsA 30S ribosomal pr 32.4 1.7E+02 0.0037 26.6 6.8 65 31-96 374-444 (565)
147 PF00166 Cpn10: Chaperonin 10 31.6 56 0.0012 22.9 2.9 44 26-83 24-70 (93)
148 PF13986 DUF4224: Domain of un 31.1 27 0.00058 22.0 1.0 17 93-110 14-30 (47)
149 PRK06676 rpsA 30S ribosomal pr 30.8 2.5E+02 0.0055 24.1 7.3 64 31-95 278-346 (390)
150 PF08206 OB_RNB: Ribonuclease 30.7 66 0.0014 20.5 2.9 23 71-93 32-57 (58)
151 PRK05807 hypothetical protein; 30.7 2.3E+02 0.005 21.2 7.5 62 31-95 6-72 (136)
152 TIGR03591 polynuc_phos polyrib 30.6 1.3E+02 0.0028 28.6 5.9 60 29-91 616-682 (684)
153 cd03367 Ribosomal_S23 S12-like 30.4 60 0.0013 24.6 2.9 35 46-81 44-79 (115)
154 PRK13806 rpsA 30S ribosomal pr 30.1 2.4E+02 0.0051 25.6 7.3 65 31-96 380-449 (491)
155 PF08940 DUF1918: Domain of un 29.5 1.5E+02 0.0033 19.8 4.5 30 31-60 18-51 (58)
156 PF12859 Apc1: Anaphase-promot 29.4 87 0.0019 22.4 3.6 38 42-80 6-43 (105)
157 COG2996 Predicted RNA-bindinin 29.4 52 0.0011 28.5 2.8 63 35-101 78-143 (287)
158 cd05687 S1_RPS1_repeat_ec1_hs1 29.0 1.5E+02 0.0033 18.6 6.0 57 33-92 3-66 (70)
159 COG0511 AccB Biotin carboxyl c 28.8 39 0.00085 25.5 1.8 25 53-78 69-93 (140)
160 PRK06299 rpsA 30S ribosomal pr 28.6 2.9E+02 0.0062 25.1 7.6 66 31-97 461-531 (565)
161 PRK12269 bifunctional cytidyla 28.5 2.6E+02 0.0055 27.7 7.6 66 30-96 752-825 (863)
162 COG1489 SfsA DNA-binding prote 28.3 1.7E+02 0.0037 24.6 5.6 84 36-122 10-112 (235)
163 cd04461 S1_Rrp5_repeat_hs8_sc7 27.4 1.9E+02 0.0041 19.1 7.0 67 25-93 8-81 (83)
164 COG2002 AbrB Regulators of sta 27.3 77 0.0017 22.0 2.9 37 60-98 17-53 (89)
165 TIGR02609 doc_partner putative 27.2 46 0.001 22.5 1.7 40 54-97 7-46 (74)
166 TIGR03027 pepcterm_export puta 26.7 51 0.0011 25.1 2.1 21 63-83 144-164 (165)
167 PF01426 BAH: BAH domain; Int 26.5 74 0.0016 22.0 2.8 14 70-83 2-15 (119)
168 PRK02302 hypothetical protein; 26.4 60 0.0013 23.4 2.3 24 86-109 6-29 (89)
169 PRK02886 hypothetical protein; 26.3 62 0.0013 23.3 2.3 24 86-109 4-27 (87)
170 PF09866 DUF2093: Uncharacteri 26.0 52 0.0011 20.7 1.6 14 71-84 2-15 (42)
171 PRK11824 polynucleotide phosph 25.9 4.1E+02 0.0088 25.4 8.3 62 29-93 619-687 (693)
172 COG0539 RpsA Ribosomal protein 25.7 2.1E+02 0.0046 26.9 6.2 67 28-95 275-346 (541)
173 TIGR02227 sigpep_I_bact signal 25.7 61 0.0013 24.7 2.4 31 50-82 33-63 (163)
174 cd05702 S1_Rrp5_repeat_hs11_sc 25.7 1.9E+02 0.004 18.5 6.1 54 33-87 3-63 (70)
175 PF00467 KOW: KOW motif; Inte 25.4 82 0.0018 17.8 2.3 26 73-98 1-26 (32)
176 PF01551 Peptidase_M23: Peptid 25.4 2.2E+02 0.0047 19.2 5.3 53 25-77 15-69 (96)
177 cd06251 M14_ASTE_ASPA_like_1 A 25.3 2.1E+02 0.0047 23.7 5.8 43 31-78 242-284 (287)
178 PRK00087 4-hydroxy-3-methylbut 25.2 2.8E+02 0.0062 26.0 7.1 64 31-95 563-631 (647)
179 PTZ00067 40S ribosomal S23; Pr 25.1 84 0.0018 24.6 3.0 49 32-81 45-104 (143)
180 COG2063 FlgH Flagellar basal b 25.0 1.8E+02 0.0039 24.4 5.2 35 32-66 147-186 (230)
181 TIGR00358 3_prime_RNase VacB a 24.9 3.1E+02 0.0067 25.8 7.3 63 32-95 574-653 (654)
182 PRK08225 acetyl-CoA carboxylas 24.8 46 0.001 21.6 1.4 21 56-77 3-23 (70)
183 PRK02693 apocytochrome f; Revi 24.6 4.5E+02 0.0097 23.1 7.5 52 28-81 201-252 (312)
184 PF07732 Cu-oxidase_3: Multico 23.5 2E+02 0.0043 20.8 4.7 35 49-83 7-42 (117)
185 cd05690 S1_RPS1_repeat_ec5 S1_ 23.4 1.9E+02 0.0042 17.9 5.7 59 33-92 3-67 (69)
186 PF01336 tRNA_anti-codon: OB-f 23.4 1.3E+02 0.0029 18.6 3.4 49 34-82 3-56 (75)
187 cd06472 ACD_ScHsp26_like Alpha 23.1 1.9E+02 0.004 19.6 4.3 31 50-81 6-39 (92)
188 TIGR03406 FeS_long_SufT probab 23.0 1.2E+02 0.0026 24.0 3.7 29 34-66 24-52 (174)
189 PRK00215 LexA repressor; Valid 22.9 1.1E+02 0.0025 23.7 3.5 44 54-98 116-159 (205)
190 TIGR03032 conserved hypothetic 22.6 2.3E+02 0.0049 25.2 5.5 61 19-83 195-261 (335)
191 PF01957 NfeD: NfeD-like C-ter 22.6 2.9E+02 0.0063 19.6 6.0 37 40-83 98-134 (144)
192 PRK10276 DNA polymerase V subu 22.5 1.3E+02 0.0028 22.2 3.6 36 56-92 51-86 (139)
193 cd05703 S1_Rrp5_repeat_hs12_sc 22.5 2.4E+02 0.0051 18.5 6.5 60 33-93 3-69 (73)
194 TIGR02228 sigpep_I_arch signal 22.5 78 0.0017 24.5 2.4 20 72-91 46-66 (158)
195 PRK05889 putative acetyl-CoA c 22.3 57 0.0012 21.3 1.4 22 55-77 3-24 (71)
196 PF08541 ACP_syn_III_C: 3-Oxoa 22.1 85 0.0018 21.0 2.3 26 70-95 65-90 (90)
197 TIGR00717 rpsA ribosomal prote 21.7 3.6E+02 0.0077 24.1 6.8 62 31-93 447-513 (516)
198 PF02643 DUF192: Uncharacteriz 21.6 94 0.002 22.3 2.6 52 30-81 57-108 (108)
199 COG1791 Uncharacterized conser 21.6 1.6E+02 0.0035 23.9 4.1 31 42-82 103-133 (181)
200 cd05686 S1_pNO40 S1_pNO40: pNO 21.5 2.4E+02 0.0052 18.2 7.9 57 33-92 6-69 (73)
201 cd06555 ASCH_PF0470_like ASC-1 21.4 3E+02 0.0065 20.3 5.2 52 43-106 16-68 (109)
202 cd06253 M14_ASTE_ASPA_like_3 A 21.3 2.5E+02 0.0054 23.6 5.4 43 31-78 252-295 (298)
203 PF12843 DUF3820: Protein of u 21.2 56 0.0012 22.5 1.2 28 83-111 15-42 (67)
204 PTZ00240 60S ribosomal protein 21.2 1.1E+02 0.0024 26.7 3.3 47 60-117 149-196 (323)
205 PRK03992 proteasome-activating 21.0 2.9E+02 0.0062 24.1 5.9 50 31-81 51-100 (389)
206 PRK11642 exoribonuclease R; Pr 20.9 4.9E+02 0.011 25.5 7.9 68 32-100 645-729 (813)
207 PRK11144 modC molybdate transp 20.8 2.5E+02 0.0054 24.0 5.4 49 33-81 295-345 (352)
208 PRK07051 hypothetical protein; 20.7 49 0.0011 22.3 0.9 24 55-78 4-33 (80)
209 cd04714 BAH_BAHCC1 BAH, or Bro 20.6 1.1E+02 0.0025 22.3 2.9 25 89-113 39-63 (121)
210 PF06251 Caps_synth_GfcC: Caps 20.5 2.3E+02 0.0051 22.7 4.9 38 45-82 167-204 (229)
211 PF13742 tRNA_anti_2: OB-fold 20.4 1.2E+02 0.0026 21.3 2.9 47 33-82 25-80 (99)
212 PTZ00135 60S acidic ribosomal 20.2 1.2E+02 0.0026 26.1 3.4 46 60-116 142-188 (310)
213 PRK12701 flgH flagellar basal 20.2 2E+02 0.0044 23.9 4.6 34 32-65 143-181 (230)
214 TIGR03265 PhnT2 putative 2-ami 20.1 4.6E+02 0.0099 22.5 6.9 51 32-82 290-345 (353)
No 1
>PLN00208 translation initiation factor (eIF); Provisional
Probab=100.00 E-value=3e-54 Score=332.20 Aligned_cols=145 Identities=94% Similarity=1.473 Sum_probs=135.6
Q ss_pred CCCCCCCCCcccccCCCcccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEE
Q 032190 1 MPKNKGKGGKNRKRGKNEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVG 80 (145)
Q Consensus 1 m~~~~~~g~kn~r~~k~~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~ 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 032190 81 LRDYQDDKADVILKYMPDEARLLKAYGELPESTRLNEGIAGGLDEEDDGADNDYIEFEDEDIDKI 145 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~devk~L~k~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 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 99999999999999999999999999999999999999984422111245888999999999875
No 2
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=100.00 E-value=5.1e-54 Score=333.85 Aligned_cols=131 Identities=73% Similarity=1.157 Sum_probs=126.3
Q ss_pred CCCCCCCCCcccccCCCcccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEE
Q 032190 1 MPKNKGKGGKNRKRGKNEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVG 80 (145)
Q Consensus 1 m~~~~~~g~kn~r~~k~~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~ 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 032190 81 LRDYQDDKADVILKYMPDEARLLKAYGELPESTRLNEGIAGGLDEEDDGADNDYIEF 137 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~devk~L~k~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~e~ 137 (145)
+|+|+++||+|||||+++|+++|+++|+||+.|.++++++||.+ ++++|||
T Consensus 81 l~~yd~~KgdIi~Ry~~devr~Lk~~g~~P~~~~~~~~~~~~~~------~~~~~~f 131 (155)
T PTZ00329 81 LRDFQDSKADVILKYTPDEARALKQHGELPETAKINETDIFDDE------GDDGIEF 131 (155)
T ss_pred ccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccccCcC------cCCCeEE
Confidence 99999999999999999999999999999999999999999855 3345777
No 3
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-47 Score=289.00 Aligned_cols=145 Identities=77% Similarity=1.213 Sum_probs=140.4
Q ss_pred CCCCCCCCCcccccCCCcccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEE
Q 032190 1 MPKNKGKGGKNRKRGKNEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVG 80 (145)
Q Consensus 1 m~~~~~~g~kn~r~~k~~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~ 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 032190 81 LRDYQDDKADVILKYMPDEARLLKAYGELPESTRLNEGIAGGLDEEDDGADNDYIEFEDEDIDKI 145 (145)
Q Consensus 81 ~~~~~~~Kg~Ii~ry~~devk~L~k~g~wP~~f~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 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 99999999999999999999999999999999999999999999777777777788899999876
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=1.1e-36 Score=221.89 Aligned_cols=98 Identities=37% Similarity=0.716 Sum_probs=93.9
Q ss_pred cCCCcccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCC-CCceEEE
Q 032190 14 RGKNEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQ-DDKADVI 92 (145)
Q Consensus 14 ~~k~~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~-~~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 457888888999999999999999999999999999999999999999999999999999999999999998 7899999
Q ss_pred EEcChhHHHHHHHcCCCCc
Q 032190 93 LKYMPDEARLLKAYGELPE 111 (145)
Q Consensus 93 ~ry~~devk~L~k~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=2.3e-36 Score=220.55 Aligned_cols=95 Identities=35% Similarity=0.712 Sum_probs=91.5
Q ss_pred CcccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 17 NEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 17 ~~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~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 44667789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHcCCCCc
Q 032190 97 PDEARLLKAYGELPE 111 (145)
Q Consensus 97 ~devk~L~k~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=4.8e-36 Score=212.10 Aligned_cols=83 Identities=66% Similarity=1.042 Sum_probs=81.7
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcC
Q 032190 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYG 107 (145)
Q Consensus 28 ~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~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 032190 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 999
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=1.8e-33 Score=197.02 Aligned_cols=77 Identities=47% Similarity=0.771 Sum_probs=75.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccC-CCCceEEEEEcChhHHHHHHHcCCC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY-QDDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~-~~~Kg~Ii~ry~~devk~L~k~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
>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=5.9e-33 Score=194.79 Aligned_cols=77 Identities=29% Similarity=0.436 Sum_probs=75.2
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCC-CceEEEEEcChhHHHHHHHcCCC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQD-DKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~-~Kg~Ii~ry~~devk~L~k~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 689999999999999999999999999999999999999999999999999996 69999999999999999999998
No 9
>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=7.6e-33 Score=193.36 Aligned_cols=77 Identities=66% Similarity=1.122 Sum_probs=75.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~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 10
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.4e-28 Score=171.48 Aligned_cols=72 Identities=36% Similarity=0.596 Sum_probs=69.3
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 28 ~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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=2.8e-27 Score=159.69 Aligned_cols=65 Identities=40% Similarity=0.743 Sum_probs=59.5
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~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
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=2.7e-27 Score=183.73 Aligned_cols=98 Identities=27% Similarity=0.371 Sum_probs=91.3
Q ss_pred cccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccC---C-CCceEEEE
Q 032190 18 EADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY---Q-DDKADVIL 93 (145)
Q Consensus 18 ~~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~---~-~~Kg~Ii~ 93 (145)
-.+.+..+...|++.|+||+|++++|||+|+|+.++|...|++||.|||++|||++|+||+|+|+.+ + ..+|.|.|
T Consensus 8 ~~q~v~de~~~le~~q~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVkgeI~y 87 (167)
T KOG2925|consen 8 LKQAVSDEDFTLEECQSIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVKGEICY 87 (167)
T ss_pred hcccccCCCcchhhhhhHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccceEEEE
Confidence 3445667788999999999999999999999999999999999999999999999999999999988 3 35999999
Q ss_pred EcChhHHHHHHHcCCCCccccc
Q 032190 94 KYMPDEARLLKAYGELPESTRL 115 (145)
Q Consensus 94 ry~~devk~L~k~g~wP~~f~~ 115 (145)
++..+|++.|+|+|+||+.|..
T Consensus 88 Vl~~d~vr~lqk~g~WPe~F~d 109 (167)
T KOG2925|consen 88 VLFFDQVRLLQKSGEWPEIFKD 109 (167)
T ss_pred EEccHHHHHHHHcCCcchhhhh
Confidence 9999999999999999999976
No 13
>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=1.2e-24 Score=149.22 Aligned_cols=62 Identities=24% Similarity=0.342 Sum_probs=60.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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 14
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.90 E-value=8.8e-24 Score=150.89 Aligned_cols=64 Identities=22% Similarity=0.276 Sum_probs=63.0
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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 68999999999999999999999999999999999 99999999999999999999999999997
No 15
>CHL00010 infA translation initiation factor 1
Probab=99.77 E-value=2e-18 Score=120.56 Aligned_cols=66 Identities=26% Similarity=0.324 Sum_probs=62.9
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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 7999999999999999999999999999754
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.75 E-value=6.2e-18 Score=116.12 Aligned_cols=64 Identities=28% Similarity=0.364 Sum_probs=61.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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=99.52 E-value=7.1e-14 Score=93.24 Aligned_cols=62 Identities=27% Similarity=0.360 Sum_probs=58.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~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=98.29 E-value=4.6e-06 Score=54.86 Aligned_cols=60 Identities=25% Similarity=0.285 Sum_probs=48.5
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcCh
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~ 97 (145)
.|+|++..| +.|.|.+++|..+.|.++|++++ ..++..||+|++++++ ...+.|+.++.+
T Consensus 2 ~grVv~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~--~~~~~I~~vl~R 62 (68)
T cd04466 2 EGLIIKAIG-GFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPED--DGEGVIEEILPR 62 (68)
T ss_pred CEEEEEEEC-CEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEECC--CCcEEEEEEecc
Confidence 478998887 67899998788999999999986 6889999999999754 345667666543
No 19
>PRK00098 GTPase RsgA; Reviewed
Probab=97.12 E-value=0.002 Score=54.05 Aligned_cols=58 Identities=24% Similarity=0.324 Sum_probs=44.8
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
.|+|++..| +.|.|.+.+|..+.|.++|+|++ ...+..||+|+|++. ++..|-|..++
T Consensus 2 ~g~v~~~~~-~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~--~~~~g~i~~i~ 60 (298)
T PRK00098 2 EGLIIKALG-GFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAE--NNDEGVILEIH 60 (298)
T ss_pred eEEEEEEEC-CEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEEC--CCCcEEEEEEe
Confidence 589999886 57889988899999999999986 666889999999874 22344444333
No 20
>PRK12289 GTPase RsgA; Reviewed
Probab=97.07 E-value=0.0022 Score=55.77 Aligned_cols=66 Identities=18% Similarity=0.246 Sum_probs=49.3
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCC------CEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 29 KEDGQEYAQVLRMLGNGRCEAMCIDG------TKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 29 p~e~q~ig~V~~~lG~~~~~V~~~dG------~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
+...++.|+|++..++ .|.|.+.+| ...+|..+|++|+ ...+..||+|++++.++....|-|..++
T Consensus 4 ~~~~~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I~~vl 76 (352)
T PRK12289 4 TTTSQLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAIAEVL 76 (352)
T ss_pred cccCcccEEEEEEECC-EEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCCCCceEEEEEe
Confidence 3456778999998885 678888654 4789999999986 5559999999999765544556444333
No 21
>PRK12288 GTPase RsgA; Reviewed
Probab=96.72 E-value=0.0072 Score=52.34 Aligned_cols=60 Identities=17% Similarity=0.199 Sum_probs=46.9
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCC--CceEEEEEcCh
Q 032190 34 EYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQD--DKADVILKYMP 97 (145)
Q Consensus 34 ~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~--~Kg~Ii~ry~~ 97 (145)
+.|+|++..|+ .|.|.+.+|..+.|.++|+++. +..||+|.+++.+.+. ..|.|..++.+
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~~~~~~~~~I~~il~R 101 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKEALEGVSGVVEAVHPR 101 (347)
T ss_pred cceEEEEEECC-EEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCCcccccceEEEEEecc
Confidence 67999998885 7889999999999999999975 8899999998653221 24666655543
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=96.58 E-value=0.0076 Score=50.36 Aligned_cols=59 Identities=24% Similarity=0.356 Sum_probs=45.0
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 36 AQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 36 g~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~d 98 (145)
|+|++..| +.|.|.++ +..+.|.++|+|++ ..-+..||+|++++.+ ...|.|..++.+.
T Consensus 1 g~v~~~~~-~~~~v~~~-~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~--~~~~~i~~i~~R~ 60 (287)
T cd01854 1 GRVIAVHG-GFYDVETE-GGELRCRARGKLRKKGIKPVVGDWVEVEPDD--DGEGVIVRVLPRK 60 (287)
T ss_pred CEEEEEEC-CEEEEEEC-CeEEEEEeccccccCCCCccCCCEEEEEecC--CCcEEEEEEECCC
Confidence 57888887 67888875 77999999999986 4669999999998754 3456665555443
No 23
>PRK01889 GTPase RsgA; Reviewed
Probab=95.33 E-value=0.059 Score=46.59 Aligned_cols=63 Identities=19% Similarity=0.219 Sum_probs=46.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 3456799999887 5778887666 567999999984 23368899999985 24566766665544
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=94.58 E-value=0.16 Score=31.15 Aligned_cols=57 Identities=21% Similarity=0.240 Sum_probs=42.7
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEE
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 5888888865554 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=90.74 E-value=1.5 Score=27.45 Aligned_cols=59 Identities=20% Similarity=0.170 Sum_probs=43.0
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEecCCEEEEEeccCCCCceEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KV-----WIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~I-----wIk~GD~VlV~~~~~~~~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 3578999999888777 78888877777654 3332 12 47999999999887776666664
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=89.86 E-value=1.7 Score=27.91 Aligned_cols=55 Identities=16% Similarity=0.108 Sum_probs=41.4
Q ss_pred CCCeEEEEEEEeC-CCceEEEE--eCCCCEEEEEecccccceEEEecCCEEEEEeccC
Q 032190 30 EDGQEYAQVLRML-GNGRCEAM--CIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY 84 (145)
Q Consensus 30 ~e~q~ig~V~~~l-G~~~~~V~--~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~ 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 3578999999983 44456666 4566689999998766788889999998877543
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=89.17 E-value=0.83 Score=29.21 Aligned_cols=55 Identities=11% Similarity=0.048 Sum_probs=39.6
Q ss_pred CCCCeEEEEEEEeCCC---ceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 29 KEDGQEYAQVLRMLGN---GRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 29 p~e~q~ig~V~~~lG~---~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 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 4567788888766533 345566677777999999988889999999999988754
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=88.40 E-value=1.7 Score=29.31 Aligned_cols=65 Identities=15% Similarity=0.172 Sum_probs=43.5
Q ss_pred CCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEeccccc----ce-----EEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 29 KEDGQ-EYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH----KK-----VWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 29 p~e~q-~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR----k~-----IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
|..|+ +.|+|+++... -+.|....+.+=+++++-=.. .. =+++.||.|.+.....+.. +.|..-.
T Consensus 4 p~~GdiV~g~V~~i~~~-g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~ 78 (86)
T cd05789 4 PEVGDVVIGRVTEVGFK-RWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHT 78 (86)
T ss_pred CCCCCEEEEEEEEECCC-EEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEe
Confidence 55554 79999997654 477777777666666553221 11 1589999999999877654 6654433
No 29
>PHA02945 interferon resistance protein; Provisional
Probab=87.69 E-value=6 Score=28.58 Aligned_cols=66 Identities=9% Similarity=0.011 Sum_probs=47.0
Q ss_pred eecCCCCe-EEEEEEEeCCCceEEEEeCC-CCEEEEEec------ccccceEEEecCCEEEEEeccCCCCceEEEE
Q 032190 26 LVFKEDGQ-EYAQVLRMLGNGRCEAMCID-GTKRLCHIR------GKMHKKVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 26 l~~p~e~q-~ig~V~~~lG~~~~~V~~~d-G~~~La~Ip------GKfRk~IwIk~GD~VlV~~~~~~~~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 46799998 6899998 666655444443 788888777 333444445 888888888888888888743
No 30
>COG1162 Predicted GTPases [General function prediction only]
Probab=85.49 E-value=2.4 Score=36.70 Aligned_cols=61 Identities=15% Similarity=0.192 Sum_probs=46.7
Q ss_pred EEEEEEEeCCCceEEEEeCC---CCEEEEEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 34 EYAQVLRMLGNGRCEAMCID---GTKRLCHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 34 ~ig~V~~~lG~~~~~V~~~d---G~~~La~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~d 98 (145)
..|+|++.. .|.|.|.+.+ ++...|..+|+||+ ..-...||+|.++..... |-|..++.+.
T Consensus 5 ~~g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~---g~I~~i~~Rk 69 (301)
T COG1162 5 KRGRVVKVD-AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENNN---GVIEKILPRK 69 (301)
T ss_pred cCcEEEEee-CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCCc---ceEEEEeccc
Confidence 345666655 4788888874 78899999999999 588999999999987533 7776666543
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=85.17 E-value=5.6 Score=26.65 Aligned_cols=63 Identities=16% Similarity=0.172 Sum_probs=40.1
Q ss_pred cCCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEec---cc-ccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 28 FKEDGQ-EYAQVLRMLGNGRCEAMCIDGTKRLCHIR---GK-MHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 28 ~p~e~q-~ig~V~~~lG~~~~~V~~~dG~~~La~Ip---GK-fRk-~IwIk~GD~VlV~~~~~~~~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 LPDVGDIVIGIVTEVNS-RFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVL 71 (82)
T ss_pred CCCCCCEEEEEEEEEcC-CEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEE
Confidence 467665 6999999855 445588855433333332 22 122 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=84.21 E-value=3.7 Score=25.09 Aligned_cols=33 Identities=9% Similarity=0.107 Sum_probs=26.0
Q ss_pred ecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEE
Q 032190 27 VFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCH 60 (145)
Q Consensus 27 ~~p~e~q~ig~V~~~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 34567779999995 5666799999999988653
No 33
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=80.25 E-value=3.2 Score=35.46 Aligned_cols=76 Identities=13% Similarity=0.295 Sum_probs=61.5
Q ss_pred ecCCCCe-EEEEEEEeCCCceEEEEeC-CCCEEEEEec----ccccc-eEEEecCCEEEEEeccCCCCceEE---EEEcC
Q 032190 27 VFKEDGQ-EYAQVLRMLGNGRCEAMCI-DGTKRLCHIR----GKMHK-KVWIAAGDIILVGLRDYQDDKADV---ILKYM 96 (145)
Q Consensus 27 ~~p~e~q-~ig~V~~~lG~~~~~V~~~-dG~~~La~Ip----GKfRk-~IwIk~GD~VlV~~~~~~~~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 3689987 7999999998888877665 5688888875 66776 788999999999999999999988 55666
Q ss_pred hhHHHH
Q 032190 97 PDEARL 102 (145)
Q Consensus 97 ~devk~ 102 (145)
.+|.+.
T Consensus 87 ~~q~~~ 92 (269)
T COG1093 87 EHQRRK 92 (269)
T ss_pred HHHHHH
Confidence 666543
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=79.99 E-value=7.1 Score=29.18 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=37.0
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEe----cccccceEEEecCCEEEEEecc
Q 032190 34 EYAQVLRMLGNGRCEAMCIDGTKRLCHI----RGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 34 ~ig~V~~~lG~~~~~V~~~dG~~~La~I----pGKfRk~IwIk~GD~VlV~~~~ 83 (145)
--|+|.+.+.++.|.|+..++.+..... +...-.+--++.||+||+- |+
T Consensus 15 Y~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~-~~ 67 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP-WE 67 (124)
T ss_pred EeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe-cC
Confidence 4689999999999999998877665432 2233336678999999998 54
No 35
>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=79.67 E-value=5.3 Score=28.36 Aligned_cols=55 Identities=7% Similarity=0.088 Sum_probs=39.0
Q ss_pred CCC-CeEEEEEEEeCCCceEEEEeCCCCEEEEEe-----cccccc-eEEEecCCEEEEEeccCCC
Q 032190 29 KED-GQEYAQVLRMLGNGRCEAMCIDGTKRLCHI-----RGKMHK-KVWIAAGDIILVGLRDYQD 86 (145)
Q Consensus 29 p~e-~q~ig~V~~~lG~~~~~V~~~dG~~~La~I-----pGKfRk-~IwIk~GD~VlV~~~~~~~ 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 45899999975 57888887542 33443 444444 6789999999999877654
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=77.86 E-value=13 Score=25.11 Aligned_cols=56 Identities=23% Similarity=0.188 Sum_probs=34.5
Q ss_pred EEEEEEe-CCCceEEEEeCCCCEEEEEecccccceEE-EecCCEEEEEeccCCCCceEEEEEcChhHHHHH
Q 032190 35 YAQVLRM-LGNGRCEAMCIDGTKRLCHIRGKMHKKVW-IAAGDIILVGLRDYQDDKADVILKYMPDEARLL 103 (145)
Q Consensus 35 ig~V~~~-lG~~~~~V~~~dG~~~La~IpGKfRk~Iw-Ik~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L 103 (145)
-++|+++ .+++.-.|... |.++-+++. -+. +.+||||||.. |-.+.++++++.+..
T Consensus 6 P~~Vv~v~~~~~~A~v~~~-G~~~~V~~~-----lv~~v~~Gd~VLVHa-------G~Ai~~ideeeA~e~ 63 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFG-GVRREVSLA-----LVPDVKVGDYVLVHA-------GFAIEKIDEEEAEET 63 (68)
T ss_dssp EEEEEEEETTTTEEEEEET-TEEEEEEGT-----TCTSB-TT-EEEEET-------TEEEEEE-HHHHHHH
T ss_pred cEEEEEEeCCCCEEEEEcC-CcEEEEEEE-----EeCCCCCCCEEEEec-------ChhheeCCHHHHHHH
Confidence 4778888 34555555544 655555432 111 89999999985 467888888887764
No 37
>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=77.45 E-value=11 Score=26.28 Aligned_cols=56 Identities=25% Similarity=0.130 Sum_probs=33.3
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHH
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLL 103 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~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 3678887764 333333 355443332100 0378999999986 455667777776654
No 38
>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=76.59 E-value=13 Score=28.66 Aligned_cols=62 Identities=13% Similarity=0.165 Sum_probs=42.7
Q ss_pred EEEEEEEeCCC-------ceEEEEeCCCCEEEEEecccc-cceEEEecCCEEEEEec-cCCCCceEEEEEc
Q 032190 34 EYAQVLRMLGN-------GRCEAMCIDGTKRLCHIRGKM-HKKVWIAAGDIILVGLR-DYQDDKADVILKY 95 (145)
Q Consensus 34 ~ig~V~~~lG~-------~~~~V~~~dG~~~La~IpGKf-Rk~IwIk~GD~VlV~~~-~~~~~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 37888888876 579999999999876522222 22347999999998754 4455455555544
No 39
>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=76.54 E-value=4.8 Score=37.05 Aligned_cols=52 Identities=29% Similarity=0.505 Sum_probs=43.5
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 29 KEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 29 p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
+.-|++ ++|.+.++.+++.|....|..++.++.+.+... -+++||.|+|++.
T Consensus 104 ~~~g~~-~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~g~~~~~~~~ 155 (512)
T TIGR03689 104 ETVGEI-ATLKEVLGDGRALVVDHSGEERVVKLAGALADE-LIRAGDSLLVDPK 155 (512)
T ss_pred CCCCce-EEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHh-hCCCCCEEEEccc
Confidence 334554 599999999999999999999999999998763 2689999999874
No 40
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=76.44 E-value=11 Score=32.88 Aligned_cols=78 Identities=14% Similarity=0.238 Sum_probs=56.5
Q ss_pred ecCCCCe-EEEEEEEeCCCceEEEEeC--CCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEE---EEEc
Q 032190 27 VFKEDGQ-EYAQVLRMLGNGRCEAMCI--DGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADV---ILKY 95 (145)
Q Consensus 27 ~~p~e~q-~ig~V~~~lG~~~~~V~~~--dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 4676665 78999998887766 4443 57788887753 3333 445899999999999888888998 4477
Q ss_pred ChhHHHHHHH
Q 032190 96 MPDEARLLKA 105 (145)
Q Consensus 96 ~~devk~L~k 105 (145)
+++++..+.+
T Consensus 92 ~~~pw~~~~e 101 (319)
T PTZ00248 92 SPEDIEACEE 101 (319)
T ss_pred ccchHHHHHH
Confidence 7776666543
No 41
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=76.11 E-value=5.2 Score=30.78 Aligned_cols=36 Identities=17% Similarity=0.192 Sum_probs=31.0
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccC
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY 84 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~ 84 (145)
-.+|++.||.++.|.|||==.. |.+.|.|+|+-..-
T Consensus 58 ~~RVrL~NG~~VtAyiPg~Gh~---lqEH~~Vli~G~~v 93 (129)
T COG0048 58 VARVRLINGKEVTAYIPGEGHN---LQEHSEVLIRGGRV 93 (129)
T ss_pred eEEEEeeCCcEEEEEcCCCCcc---ccccCEEEEecCcc
Confidence 4689999999999999997665 99999999986643
No 42
>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=75.32 E-value=11 Score=27.64 Aligned_cols=48 Identities=10% Similarity=0.127 Sum_probs=37.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 3789999999999999999999 88999999977788899999887754
No 43
>PRK11642 exoribonuclease R; Provisional
Probab=74.87 E-value=28 Score=33.85 Aligned_cols=45 Identities=11% Similarity=0.045 Sum_probs=32.4
Q ss_pred EecCCEEEEEeccCCC----CceEEEEEcCh-----hHHHHHHHcCCCCccccc
Q 032190 71 IAAGDIILVGLRDYQD----DKADVILKYMP-----DEARLLKAYGELPESTRL 115 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~----~Kg~Ii~ry~~-----devk~L~k~g~wP~~f~~ 115 (145)
.+.||+|+|++..|.. -.|.|+.++-. -++..+....-+|.+|..
T Consensus 186 ~~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~Fp~ 239 (813)
T PRK11642 186 ARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQ 239 (813)
T ss_pred CCCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCCCCH
Confidence 4568999999976642 37999999943 456666666667777754
No 44
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=74.66 E-value=9.9 Score=26.86 Aligned_cols=59 Identities=24% Similarity=0.105 Sum_probs=34.8
Q ss_pred EEEEEEeCCCceEEEEe-CCCCEEEEEecccccc--eEEEecCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032190 35 YAQVLRMLGNGRCEAMC-IDGTKRLCHIRGKMHK--KVWIAAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~-~dG~~~La~IpGKfRk--~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~ 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 47888888875333333 34655554421 000 02467899999986 44566666666654
No 45
>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=74.04 E-value=23 Score=23.63 Aligned_cols=60 Identities=8% Similarity=0.008 Sum_probs=45.7
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEE---ecccccce-----EEEecCCEEEEEeccCCCCceEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCH---IRGKMHKK-----VWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~---IpGKfRk~-----IwIk~GD~VlV~~~~~~~~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 4589999999988888 888888887777 55544121 357999999999888777776653
No 46
>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=72.65 E-value=21 Score=22.82 Aligned_cols=59 Identities=12% Similarity=0.116 Sum_probs=42.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIR----GKMHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~Ip----GKfRk-~IwIk~GD~VlV~~~~~~~~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 4789999988766 5588888766666664 12222 2337999999999988887777774
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=72.15 E-value=11 Score=27.00 Aligned_cols=30 Identities=13% Similarity=0.207 Sum_probs=26.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecc
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG 63 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG 63 (145)
-++|+|++..|+ .+.+.|+||..+.+.++.
T Consensus 19 ~ivGkV~~~~~~-~~~~~~~Dg~~v~v~l~~ 48 (101)
T cd04479 19 RIVGKVEKVDGD-SLTLISSDGVNVTVELNR 48 (101)
T ss_pred EEEEEEEEecCC-eEEEEcCCCCEEEEEeCC
Confidence 379999999987 899999999888888765
No 48
>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=71.54 E-value=9.1 Score=26.94 Aligned_cols=58 Identities=19% Similarity=0.203 Sum_probs=34.3
Q ss_pred cCCCC-eEEEEEEEeCCCceEEEEe--CCCCEEEEEeccccc---------c----eEEEecCCEEEEEeccCCC
Q 032190 28 FKEDG-QEYAQVLRMLGNGRCEAMC--IDGTKRLCHIRGKMH---------K----KVWIAAGDIILVGLRDYQD 86 (145)
Q Consensus 28 ~p~e~-q~ig~V~~~lG~~~~~V~~--~dG~~~La~IpGKfR---------k----~IwIk~GD~VlV~~~~~~~ 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 LPKVGSIVIARVTRIN-PRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD 76 (92)
T ss_pred CCCCCCEEEEEEEEEc-CCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC
Confidence 46665 4899999976 44455544 333322222223222 1 2345999999999887664
No 49
>CHL00051 rps12 ribosomal protein S12
Probab=71.37 E-value=6.9 Score=29.92 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=28.3
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
..+|.+.||.+++|+|||==. .+.+.+.|||.=
T Consensus 52 varVrLsngk~v~AyIPGeGh---nlqehs~VLvrG 84 (123)
T CHL00051 52 VARVRLTSGFEITAYIPGIGH---NLQEHSVVLVRG 84 (123)
T ss_pred EEEEEccCCCEEEEEcCCCCc---cccccCEEEEeC
Confidence 467889999999999999765 788889999883
No 50
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=70.65 E-value=13 Score=32.90 Aligned_cols=54 Identities=9% Similarity=0.123 Sum_probs=46.4
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccC
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY 84 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~ 84 (145)
.....+|.|+++++.+++-|....|.++++.+.+.+.+.. +++|+.|.+....+
T Consensus 64 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~ 117 (398)
T PTZ00454 64 SVPLVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNREL-LKPNASVALHRHSH 117 (398)
T ss_pred CCCceEEEEEEEEcCCEEEEEcCCCCEEEEecccccCHhh-CCCCCEEEeeccch
Confidence 3467999999999999999999999999999999886633 68999999887544
No 51
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=70.50 E-value=22 Score=29.90 Aligned_cols=65 Identities=15% Similarity=0.247 Sum_probs=45.0
Q ss_pred cCCCCe-EEEEEEEeCCCceEEEEeCC--CCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 28 FKEDGQ-EYAQVLRMLGNGRCEAMCID--GTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 28 ~p~e~q-~ig~V~~~lG~~~~~V~~~d--G~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 456554 78999998766655 55653 7777777652 2222 23479999999999988888887743
No 52
>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=69.62 E-value=8 Score=28.30 Aligned_cols=33 Identities=12% Similarity=0.091 Sum_probs=26.9
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 35688899999999999876 5577888888875
No 53
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=69.49 E-value=20 Score=25.87 Aligned_cols=54 Identities=22% Similarity=0.193 Sum_probs=31.0
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEEEEecccccceE-------EEecCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKV-------WIAAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~I-------wIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~ 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 33555444332 12 368999999986 33455666666554
No 54
>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=68.82 E-value=2.3 Score=27.21 Aligned_cols=25 Identities=28% Similarity=0.549 Sum_probs=11.7
Q ss_pred EecCCEEEEEeccCCCCceEEEEEcC
Q 032190 71 IAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~~Kg~Ii~ry~ 96 (145)
|..||+|+|++.. ....|+|+....
T Consensus 11 i~~Gd~v~v~~~~-~~~~gdivv~~~ 35 (70)
T PF00717_consen 11 IKDGDIVLVDPSS-EPKDGDIVVVKI 35 (70)
T ss_dssp SSTTEEEEEEETS----TTSEEEEEE
T ss_pred eeCCCEEEEEEcC-CCccCeEEEEEE
Confidence 4466666666544 334555544433
No 55
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=68.44 E-value=24 Score=21.47 Aligned_cols=62 Identities=18% Similarity=0.137 Sum_probs=41.7
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 4666777665555543311111 356899999999998887766776543
No 56
>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=68.39 E-value=29 Score=22.33 Aligned_cols=63 Identities=13% Similarity=0.194 Sum_probs=41.1
Q ss_pred CCC-eEEEEEEEeCCCceEEEEeC--CCCEEEEEecccccc------eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 30 EDG-QEYAQVLRMLGNGRCEAMCI--DGTKRLCHIRGKMHK------KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 30 ~e~-q~ig~V~~~lG~~~~~V~~~--dG~~~La~IpGKfRk------~IwIk~GD~VlV~~~~~~~~Kg~Ii~r 94 (145)
+.| .+.|+|+++...+.| |.+. +|..=+++++- ++. .=.++.||.|.|.....+..++.|...
T Consensus 2 ~~G~~~~g~V~~v~~~g~~-v~l~~~~~~~gll~~s~-l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls 73 (76)
T cd04452 2 EEGELVVVTVKSIADMGAY-VSLLEYGNIEGMILLSE-LSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLS 73 (76)
T ss_pred CCCCEEEEEEEEEEccEEE-EEEcCCCCeEEEEEhHH-cCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEE
Confidence 344 578999998865554 5554 35666666653 222 123699999999988777666766543
No 57
>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=68.10 E-value=29 Score=22.25 Aligned_cols=62 Identities=18% Similarity=0.299 Sum_probs=42.3
Q ss_pred CCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc------c-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 29 KEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH------K-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 29 p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR------k-~IwIk~GD~VlV~~~~~~~~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 4456788999998776655 566666776766542 21 1 2347899999999887777666663
No 58
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=66.49 E-value=10 Score=29.08 Aligned_cols=33 Identities=12% Similarity=0.097 Sum_probs=27.7
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
..+|++.||.+++|.|||== -.+.+.|.|||.=
T Consensus 52 varVrL~ngk~v~AyIPGeG---hnlqehs~VLvrG 84 (124)
T PRK05163 52 VARVRLTNGFEVTAYIPGEG---HNLQEHSVVLIRG 84 (124)
T ss_pred EEEEEeCCCCEEEEEcCCCC---CCccccCEEEEeC
Confidence 46788999999999999876 5578888888883
No 59
>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=66.41 E-value=9.6 Score=29.16 Aligned_cols=33 Identities=12% Similarity=0.097 Sum_probs=27.8
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
..+|++.||..++|+|||== -.+.+.|.|||.=
T Consensus 52 varVrL~ngk~v~AyIPG~G---hnlqehs~VLvrG 84 (124)
T TIGR00981 52 VARVRLTNGFEVTAYIPGEG---HNLQEHSVVLIRG 84 (124)
T ss_pred eEEEEeCCCCEEEEEcCCCC---CCccccCEEEEeC
Confidence 46788999999999999976 5578888888883
No 60
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=66.18 E-value=13 Score=26.62 Aligned_cols=55 Identities=24% Similarity=0.286 Sum_probs=35.2
Q ss_pred EEEEEEeCCCceEEEEeCCCCEE---EEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHH
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKR---LCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARL 102 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~---La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~ 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 36788888877544444445444 444444 578899999985 44456666666654
No 61
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=66.05 E-value=10 Score=30.65 Aligned_cols=48 Identities=17% Similarity=0.360 Sum_probs=36.0
Q ss_pred eCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHc
Q 032190 41 MLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY 106 (145)
Q Consensus 41 ~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~ 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 6677765544444333
No 62
>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=64.85 E-value=11 Score=28.24 Aligned_cols=33 Identities=15% Similarity=0.111 Sum_probs=27.3
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
..+|++.||..++|+|||== -.+.+.+.|||.=
T Consensus 50 varV~L~ngk~v~AyIPG~G---hnlqehs~VLvrG 82 (108)
T cd03368 50 VARVRLSNGKEVTAYIPGEG---HNLQEHSVVLVRG 82 (108)
T ss_pred eEEEEecCCCEEEEEcCCCC---CCccccCEEEEeC
Confidence 46788999999999999876 4577888888875
No 63
>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=64.61 E-value=12 Score=26.33 Aligned_cols=39 Identities=10% Similarity=-0.070 Sum_probs=27.8
Q ss_pred CceEEEEeCCCCEEEEEeccc--ccc-eEEEecCCEEEEEec
Q 032190 44 NGRCEAMCIDGTKRLCHIRGK--MHK-KVWIAAGDIILVGLR 82 (145)
Q Consensus 44 ~~~~~V~~~dG~~~La~IpGK--fRk-~IwIk~GD~VlV~~~ 82 (145)
.-.|++...++....+..... +++ ...++.||.|+|.=.
T Consensus 18 H~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 18 HVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred CEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 345556555666677777665 776 788999999998744
No 64
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=64.51 E-value=22 Score=29.16 Aligned_cols=78 Identities=13% Similarity=0.153 Sum_probs=48.7
Q ss_pred ecCCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc-----cc-eEEEecCCEEEEEeccCCCC---------
Q 032190 27 VFKEDG-QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG---KM-----HK-KVWIAAGDIILVGLRDYQDD--------- 87 (145)
Q Consensus 27 ~~p~e~-q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG---Kf-----Rk-~IwIk~GD~VlV~~~~~~~~--------- 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 5588888765544444332 21 22 44689999999887644321
Q ss_pred ------ceEEEEEcChhHHHHHHH
Q 032190 88 ------KADVILKYMPDEARLLKA 105 (145)
Q Consensus 88 ------Kg~Ii~ry~~devk~L~k 105 (145)
.+=++....+.-++.|.-
T Consensus 138 ~~lG~L~~G~~~~V~~~~i~~lig 161 (235)
T PRK04163 138 KGLGKIEGGTIVEIKPVKVPRVIG 161 (235)
T ss_pred CCCCccCCCEEEEECHHHHHhhcC
Confidence 122456667777776643
No 65
>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=64.51 E-value=22 Score=25.51 Aligned_cols=33 Identities=12% Similarity=0.070 Sum_probs=24.5
Q ss_pred EEEEEEEeC-CCceEEEEeCCCCEEEEEeccccc
Q 032190 34 EYAQVLRML-GNGRCEAMCIDGTKRLCHIRGKMH 66 (145)
Q Consensus 34 ~ig~V~~~l-G~~~~~V~~~dG~~~La~IpGKfR 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 678999999999999999986543
No 66
>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=64.28 E-value=37 Score=22.28 Aligned_cols=57 Identities=16% Similarity=0.058 Sum_probs=39.5
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 36 AQVLRMLGNGRCEAMCIDGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 36 g~V~~~lG~~~~~V~~~dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 6888875333366888888777777641 1111 2238899999999998887776664
No 67
>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=64.04 E-value=59 Score=26.61 Aligned_cols=78 Identities=17% Similarity=0.181 Sum_probs=48.6
Q ss_pred ceEE--EEeCCCCEEEEEec--ccccceEEEecCCEEEEEeccCC--CCceEEEEEcCh-------------hHHHHHHH
Q 032190 45 GRCE--AMCIDGTKRLCHIR--GKMHKKVWIAAGDIILVGLRDYQ--DDKADVILKYMP-------------DEARLLKA 105 (145)
Q Consensus 45 ~~~~--V~~~dG~~~La~Ip--GKfRk~IwIk~GD~VlV~~~~~~--~~Kg~Ii~ry~~-------------devk~L~k 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 4444 45567999999997 5666544 39999999998654 223333333222 34667777
Q ss_pred cCCCCccc---cccccccCCCC
Q 032190 106 YGELPEST---RLNEGIAGGLD 124 (145)
Q Consensus 106 ~g~wP~~f---~~~~~~~~~~~ 124 (145)
.|.+|.-- ....+.++|..
T Consensus 83 ~~~i~~l~~~~~i~rEv~~g~s 104 (215)
T PF03749_consen 83 NGLIPELSGYSEIRREVKYGNS 104 (215)
T ss_pred cCCCccccCcceEeeceeeCCc
Confidence 88888432 23445666654
No 68
>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=63.61 E-value=20 Score=27.31 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=27.4
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccC
Q 032190 36 AQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDY 84 (145)
Q Consensus 36 g~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~ 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 89999999999999999997642 34456777666543
No 69
>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=62.42 E-value=32 Score=23.01 Aligned_cols=56 Identities=18% Similarity=0.089 Sum_probs=30.6
Q ss_pred CceEEEEeCC-CCEEE------EEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 44 NGRCEAMCID-GTKRL------CHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 44 ~~~~~V~~~d-G~~~L------a~IpGKfRk~IwIk~GD~VlV~~~~~~~~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 22334334466678999999999877788999988776543
No 70
>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=62.17 E-value=13 Score=28.03 Aligned_cols=42 Identities=19% Similarity=0.087 Sum_probs=28.3
Q ss_pred cceEEEecCCEEEEEeccCC-----------CC----ceEEEEEcChhHHHHHHHcC
Q 032190 66 HKKVWIAAGDIILVGLRDYQ-----------DD----KADVILKYMPDEARLLKAYG 107 (145)
Q Consensus 66 Rk~IwIk~GD~VlV~~~~~~-----------~~----Kg~Ii~ry~~devk~L~k~g 107 (145)
|..+.|+.||+|+|.+.+.. +. ...+.|=+.++|+..++...
T Consensus 3 r~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~ 59 (130)
T cd04721 3 RNGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPD 59 (130)
T ss_pred cCCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCC
Confidence 45788999999999875411 11 33457777888887754433
No 71
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=62.01 E-value=27 Score=34.54 Aligned_cols=65 Identities=25% Similarity=0.328 Sum_probs=49.7
Q ss_pred cCCCCeEE--EEEEEeCCCceEEEEeCCCCEEEEEecccccc-e-----EEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 28 FKEDGQEY--AQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-K-----VWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 28 ~p~e~q~i--g~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~-----IwIk~GD~VlV~~~~~~~~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 36789998 599999987776 66778899999988 4422 1 247889999999988876 78875554
No 72
>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=61.56 E-value=12 Score=28.53 Aligned_cols=49 Identities=18% Similarity=0.162 Sum_probs=35.5
Q ss_pred CeEEEEEEEeCC------Cc----eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 32 GQEYAQVLRMLG------NG----RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 32 ~q~ig~V~~~lG------~~----~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 83 (145)
-|.-|.|++..+ |+ ..+|.+.||..++|+|||== -.+.+-|.|||.=-.
T Consensus 27 Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL~n~k~v~AyIPg~G---hnlqehs~VLVrGgr 85 (122)
T PF00164_consen 27 PQKKGICLKVVTVKPKKPNSAIRKVARVRLSNGKKVTAYIPGEG---HNLQEHSVVLVRGGR 85 (122)
T ss_dssp SEEEEEEEEEEEEEESTTTCSEEEEEEEEETTSEEEEEEC-SSS---CCSTTTSEEEEEEES
T ss_pred CccCcEEeecccccccCccchhhhcceeeeccCceEEEEecCCc---ccccccceEEEeccc
Confidence 366666666542 32 46789999999999999866 558899999998643
No 73
>PRK08059 general stress protein 13; Validated
Probab=60.03 E-value=56 Score=23.91 Aligned_cols=65 Identities=18% Similarity=0.221 Sum_probs=44.6
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cccc--eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG---KMHK--KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG---KfRk--~IwIk~GD~VlV~~~~~~~~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 346889999988644 55677777776666542 1111 22578999999999887777777766543
No 74
>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=59.63 E-value=1.2e+02 Score=28.61 Aligned_cols=84 Identities=14% Similarity=0.161 Sum_probs=47.1
Q ss_pred CeEEEEEEEeCCCceEEEEe----CCCCEEEEEecccccceEEE--------ecCCEEEEEeccCC----CCceEEEEEc
Q 032190 32 GQEYAQVLRMLGNGRCEAMC----IDGTKRLCHIRGKMHKKVWI--------AAGDIILVGLRDYQ----DDKADVILKY 95 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~----~dG~~~La~IpGKfRk~IwI--------k~GD~VlV~~~~~~----~~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 34466666666554322222 33333443333444433444 56899999996553 2378999988
Q ss_pred C-----hhHHHHHHHcCCCCccccc
Q 032190 96 M-----PDEARLLKAYGELPESTRL 115 (145)
Q Consensus 96 ~-----~devk~L~k~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 3455555555556666644
No 75
>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=59.07 E-value=11 Score=25.06 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=13.8
Q ss_pred EecCCEEEEEeccC---CCCceEEEEEc
Q 032190 71 IAAGDIILVGLRDY---QDDKADVILKY 95 (145)
Q Consensus 71 Ik~GD~VlV~~~~~---~~~Kg~Ii~ry 95 (145)
+..||+|+|.+... ....|+|+.-.
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~~ 41 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVFK 41 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEEe
Confidence 46666666666554 24455554333
No 76
>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=58.62 E-value=34 Score=26.08 Aligned_cols=54 Identities=9% Similarity=0.104 Sum_probs=43.8
Q ss_pred cCCCC--eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 28 FKEDG--QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 28 ~p~e~--q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
.+++. .+.|.|++.+|+..|......|. +.+.|+-+.=+-.-|.++|.|.+.=.
T Consensus 54 ~~Ddt~V~L~G~Iv~~l~~d~Y~F~D~TG~-I~VeId~~~w~G~~v~p~d~V~I~Ge 109 (126)
T TIGR00156 54 MHDGASVTLRGNIISHIGDDRYVFRDKSGE-INVVIPAAVWNGREVQPKDMVNISGS 109 (126)
T ss_pred CCCCCEEEEEEEEEEEeCCceEEEECCCCC-EEEEECHHHcCCCcCCCCCEEEEEEE
Confidence 34444 37899999999999999999995 77888887767777889999887643
No 77
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=58.52 E-value=6.9 Score=30.14 Aligned_cols=40 Identities=28% Similarity=0.731 Sum_probs=30.9
Q ss_pred EEecccccc---eEEEec-C-CEEEEEeccCC-CCceEEEEEcChh
Q 032190 59 CHIRGKMHK---KVWIAA-G-DIILVGLRDYQ-DDKADVILKYMPD 98 (145)
Q Consensus 59 a~IpGKfRk---~IwIk~-G-D~VlV~~~~~~-~~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 78
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=58.27 E-value=14 Score=26.00 Aligned_cols=32 Identities=13% Similarity=0.155 Sum_probs=26.1
Q ss_pred eEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 68 ~IwIk~GD~VlV~~~~~~~~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 67899999999987766667888888876655
No 79
>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=57.45 E-value=42 Score=20.55 Aligned_cols=59 Identities=22% Similarity=0.160 Sum_probs=39.4
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 VVEGTVTRLKP-FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISL 66 (69)
T ss_pred EEEEEEEEEEe-eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEE
Confidence 57889999775 45556777777777765521111 1347999999999876665 566643
No 80
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=57.43 E-value=56 Score=29.91 Aligned_cols=65 Identities=17% Similarity=0.244 Sum_probs=49.5
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEec----ccccc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIR----GKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~Ip----GKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~ 96 (145)
...+.|+|+++...+.| |++.+|..-|+|++ .++.. .-.++.||.|.|.....+..+++|..-+.
T Consensus 294 G~vv~G~V~~I~~fGvF-VeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK 363 (486)
T PRK07899 294 GQIVPGKVTKLVPFGAF-VRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363 (486)
T ss_pred CCEEEEEEEEEeccEEE-EEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 45689999999887766 67778888888875 22222 34689999999999888888888876653
No 81
>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=57.42 E-value=48 Score=21.16 Aligned_cols=53 Identities=21% Similarity=0.236 Sum_probs=38.1
Q ss_pred CCCCeEEEEEEEeCC---CceEEEEeC-CCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 29 KEDGQEYAQVLRMLG---NGRCEAMCI-DGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 29 p~e~q~ig~V~~~lG---~~~~~V~~~-dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 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 455667777777663 334455445 7899999999777 7777788999988763
No 82
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=56.80 E-value=30 Score=28.81 Aligned_cols=53 Identities=15% Similarity=0.224 Sum_probs=41.1
Q ss_pred CCeEEEEEEEeC-CCceEEEE--eCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 31 DGQEYAQVLRML-GNGRCEAM--CIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 31 e~q~ig~V~~~l-G~~~~~V~--~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 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 55545555 568899999999866667888999998887654
No 83
>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=55.99 E-value=16 Score=24.83 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=15.7
Q ss_pred EecCCEEEEEeccC--C-CCceEEEEEcCh
Q 032190 71 IAAGDIILVGLRDY--Q-DDKADVILKYMP 97 (145)
Q Consensus 71 Ik~GD~VlV~~~~~--~-~~Kg~Ii~ry~~ 97 (145)
++.||+|+|.+... . ...|+|+....+
T Consensus 12 l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~ 41 (90)
T TIGR02754 12 LPPGDRIIVVPWLKIFRVPPIGNVVVVRHP 41 (90)
T ss_pred cCCCCEEEEEEccccCCCCCCCeEEEEecC
Confidence 46788888886422 1 234777654443
No 84
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=55.94 E-value=33 Score=24.81 Aligned_cols=75 Identities=13% Similarity=0.030 Sum_probs=44.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----cc------------------c-eEEEecCCEEEEEeccCCCCce
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGK----MH------------------K-KVWIAAGDIILVGLRDYQDDKA 89 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGK----fR------------------k-~IwIk~GD~VlV~~~~~~~~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 35789999999999999999876555555320 00 0 001225777888775533 334
Q ss_pred EE-EEEcChh---HHHHHHHcCC
Q 032190 90 DV-ILKYMPD---EARLLKAYGE 108 (145)
Q Consensus 90 ~I-i~ry~~d---evk~L~k~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 33 3444432 2356777776
No 85
>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=54.66 E-value=59 Score=21.33 Aligned_cols=57 Identities=12% Similarity=0.116 Sum_probs=41.2
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEecCCEEEEEeccCCCCceEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KV-----WIAAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~I-----wIk~GD~VlV~~~~~~~~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 4578999998875556888999999999987 4422 21 25779999998876542 544
No 86
>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=54.34 E-value=1.2e+02 Score=28.64 Aligned_cols=45 Identities=20% Similarity=0.098 Sum_probs=30.3
Q ss_pred EecCCEEEEEeccCCC----CceEEEEEcC-----hhHHHHHHHcCCCCccccc
Q 032190 71 IAAGDIILVGLRDYQD----DKADVILKYM-----PDEARLLKAYGELPESTRL 115 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~----~Kg~Ii~ry~-----~devk~L~k~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 4569999999876642 3789999983 3345555555556777744
No 87
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=54.09 E-value=19 Score=27.25 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=26.6
Q ss_pred eEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 68 ~IwIk~GD~VlV~~~~~~~~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 68899999999988777677899988876655
No 88
>PRK05054 exoribonuclease II; Provisional
Probab=53.56 E-value=1.3e+02 Score=28.43 Aligned_cols=46 Identities=15% Similarity=0.023 Sum_probs=33.0
Q ss_pred EecCCEEEEEeccCCC-----CceEEEEEcC-----hhHHHHHHHcCCCCcccccc
Q 032190 71 IAAGDIILVGLRDYQD-----DKADVILKYM-----PDEARLLKAYGELPESTRLN 116 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~-----~Kg~Ii~ry~-----~devk~L~k~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 4579999999986632 3789999993 34566666666678888653
No 89
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=53.37 E-value=18 Score=25.43 Aligned_cols=28 Identities=18% Similarity=0.129 Sum_probs=19.8
Q ss_pred EEEecCCEEEEEeccCCC----C---ceEEEEEcC
Q 032190 69 VWIAAGDIILVGLRDYQD----D---KADVILKYM 96 (145)
Q Consensus 69 IwIk~GD~VlV~~~~~~~----~---Kg~Ii~ry~ 96 (145)
+-+++||+|+|...+... . =|.|++.--
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEG 38 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEec
Confidence 458999999999876321 1 577777643
No 90
>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=53.18 E-value=26 Score=20.81 Aligned_cols=31 Identities=26% Similarity=0.597 Sum_probs=24.3
Q ss_pred CCCe-EEEEEEEeCCCceEEEEeCC-CCEEEEE
Q 032190 30 EDGQ-EYAQVLRMLGNGRCEAMCID-GTKRLCH 60 (145)
Q Consensus 30 ~e~q-~ig~V~~~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 3354 56899999999999999988 8876554
No 91
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=52.36 E-value=19 Score=24.94 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=24.6
Q ss_pred EEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 69 VWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 69 IwIk~GD~VlV~~~~~~~~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 5799999999987665566888888876655
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=51.83 E-value=38 Score=32.71 Aligned_cols=62 Identities=21% Similarity=0.332 Sum_probs=46.2
Q ss_pred CCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEec--------ccccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 29 KEDGQ-EYAQVLRMLGNGRCEAMCIDGTKRLCHIR--------GKMHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 29 p~e~q-~ig~V~~~lG~~~~~V~~~dG~~~La~Ip--------GKfRk-~IwIk~GD~VlV~~~~~~~~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 78999999987766 66778899999998 23333 3358899999999887763 66653
No 93
>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=51.68 E-value=57 Score=20.31 Aligned_cols=52 Identities=12% Similarity=0.166 Sum_probs=36.2
Q ss_pred CCeEEEEEEEeC--C-CceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 31 DGQEYAQVLRML--G-NGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 31 e~q~ig~V~~~l--G-~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 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 468888887765 3 45678888999998888877654 3556788888887654
No 94
>PRK10053 hypothetical protein; Provisional
Probab=51.57 E-value=48 Score=25.36 Aligned_cols=48 Identities=10% Similarity=0.027 Sum_probs=42.0
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 47899999999999999999994 7889998877777889999988764
No 95
>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=51.50 E-value=60 Score=20.53 Aligned_cols=59 Identities=10% Similarity=0.261 Sum_probs=41.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc------eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK------KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk------~IwIk~GD~VlV~~~~~~~~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 KTHGTIVKVKPN-GCIVSFYNNVKGFLPKS-ELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLL 67 (70)
T ss_pred EEEEEEEEEecC-cEEEEECCCCEEEEEHH-HcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEE
Confidence 467888888754 45577777777666664 2221 22378899999999988887777754
No 96
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=50.78 E-value=45 Score=30.06 Aligned_cols=51 Identities=10% Similarity=0.115 Sum_probs=42.3
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
.-..+|+|++++..+++.|....|..+++++.+..-+. -+++|+.|.+...
T Consensus 103 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~l~~~~~v~l~~~ 153 (438)
T PTZ00361 103 SPLSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVDKE-QLEPGCSVLLHNK 153 (438)
T ss_pred CCcEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCCHh-hCCCCCEEEEcCC
Confidence 45689999999999999999999999999999877542 2578888877654
No 97
>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=49.81 E-value=60 Score=20.03 Aligned_cols=58 Identities=17% Similarity=0.208 Sum_probs=37.9
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGK----MHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGK----fRk-~IwIk~GD~VlV~~~~~~~~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 44557777776666665321 111 1135899999999887666 66664
No 98
>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=49.79 E-value=69 Score=20.72 Aligned_cols=62 Identities=11% Similarity=0.095 Sum_probs=37.9
Q ss_pred eEEEEEEEeCCCceEEEEeCC-CCEEEEEec---cc-cc-----------c-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 33 QEYAQVLRMLGNGRCEAMCID-GTKRLCHIR---GK-MH-----------K-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~d-G~~~La~Ip---GK-fR-----------k-~IwIk~GD~VlV~~~~~~~~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 356777777655544 44443 444444443 21 11 1 2467889999999988777788886653
No 99
>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=49.37 E-value=4.4 Score=24.96 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=24.2
Q ss_pred CCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 54 GTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 54 G~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 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 100
>PRK07252 hypothetical protein; Provisional
Probab=49.12 E-value=1.1e+02 Score=22.67 Aligned_cols=63 Identities=17% Similarity=0.263 Sum_probs=44.8
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 4588999998875554 677777666666542 1111 1237899999999998888888887664
No 101
>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=48.79 E-value=11 Score=21.93 Aligned_cols=25 Identities=20% Similarity=0.133 Sum_probs=22.2
Q ss_pred EEEecccccceEEEecCCEEEEEec
Q 032190 58 LCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 58 La~IpGKfRk~IwIk~GD~VlV~~~ 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 102
>PTZ00115 40S ribosomal protein S12; Provisional
Probab=48.58 E-value=26 Score=30.19 Aligned_cols=33 Identities=18% Similarity=0.122 Sum_probs=26.7
Q ss_pred eEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
..+|++.+|.+++|+|||==. -+.+.+.|||.-
T Consensus 148 varVrLsNGk~VtAyIPGeGH---nLQEHs~VLVRG 180 (290)
T PTZ00115 148 VARVRLSTGRTVTVYIPGIGH---NLNTHSVVLVRG 180 (290)
T ss_pred eEEEEecCCCEEEEEcCCCCc---ccccCCEEEEeC
Confidence 457889999999999999765 677778887743
No 103
>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=47.46 E-value=71 Score=26.52 Aligned_cols=85 Identities=13% Similarity=0.114 Sum_probs=51.9
Q ss_pred EEEEEEeCCCceEEEEeC-CCCEEEEEec--ccccceEEEecCCEEEEEeccCCCC--ceEE---------EEEc---Ch
Q 032190 35 YAQVLRMLGNGRCEAMCI-DGTKRLCHIR--GKMHKKVWIAAGDIILVGLRDYQDD--KADV---------ILKY---MP 97 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~-dG~~~La~Ip--GKfRk~IwIk~GD~VlV~~~~~~~~--Kg~I---------i~ry---~~ 97 (145)
.|+.++=. |+|.+.+. ||++.+||+| |||.-- +.+|..|++.+++.... +-++ |..- ..
T Consensus 11 ~~~fi~R~--nRF~~~V~~~G~~~~aH~pNtGrl~el--l~pG~~vll~~~~~p~rK~~y~l~~v~~~g~~V~int~~~N 86 (232)
T TIGR00230 11 RGRLIGRY--NRFLVDVEVDGRRETAHCPNTGRLTEL--IFPGNDVGLSKSDNGGRKLSYTWEAVQCDGGWVLVNTQLQN 86 (232)
T ss_pred EEEEEeec--CCEEEEEEECCeEEEEEcCCCCCChhh--cCCCCEEEEEECCCCCCCCCEEEEEEEECCeEEEEcCccHH
Confidence 46666644 67777764 8999999997 666664 34999999998865321 2222 1111 12
Q ss_pred hHHHHHHHcCCCCcc--c-cccccccCCC
Q 032190 98 DEARLLKAYGELPES--T-RLNEGIAGGL 123 (145)
Q Consensus 98 devk~L~k~g~wP~~--f-~~~~~~~~~~ 123 (145)
.=+.+..++|.+|.- + ....+..+|.
T Consensus 87 ~l~~~~l~~~~i~~l~~~~~ikrEv~~g~ 115 (232)
T TIGR00230 87 RLFKVAIPSSKISELDGYEVRKREVKYGN 115 (232)
T ss_pred HHHHHHHHcCCCccccCcceEeeccccCC
Confidence 235566677888852 2 2244566665
No 104
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=47.43 E-value=26 Score=27.40 Aligned_cols=31 Identities=13% Similarity=0.124 Sum_probs=22.4
Q ss_pred eEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 68 ~IwIk~GD~VlV~~~~~~~~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 6778888888887766656677777766544
No 105
>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=47.37 E-value=23 Score=22.77 Aligned_cols=28 Identities=29% Similarity=0.685 Sum_probs=18.7
Q ss_pred EecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 71 IAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~~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 7788888888876545667665444433
No 106
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=47.00 E-value=1e+02 Score=22.72 Aligned_cols=68 Identities=21% Similarity=0.219 Sum_probs=39.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHc-CCCCc
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAY-GELPE 111 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~-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 34444433332 33333333333444444 34446667777766655 4699999999998876 66554
Q ss_pred cc
Q 032190 112 ST 113 (145)
Q Consensus 112 ~f 113 (145)
..
T Consensus 114 ~~ 115 (127)
T PF10017_consen 114 KR 115 (127)
T ss_pred EE
Confidence 43
No 107
>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=46.81 E-value=1e+02 Score=21.85 Aligned_cols=66 Identities=12% Similarity=0.086 Sum_probs=47.3
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc------------------------ceEEEecCCEEEEEeccCCCC
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH------------------------KKVWIAAGDIILVGLRDYQDD 87 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR------------------------k~IwIk~GD~VlV~~~~~~~~ 87 (145)
..+.|+|+.+...+. .|.+++|.+=++++.-=-. -.=+++.||.|.+.....+..
T Consensus 5 ~vV~G~V~~v~~~gl-~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~ 83 (100)
T cd05693 5 MLVLGQVKEITKLDL-VISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS 83 (100)
T ss_pred CEEEEEEEEEcCCCE-EEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCC
Confidence 568999999876654 4688888777776642211 124579999999999988875
Q ss_pred ---ceEEEEEcChh
Q 032190 88 ---KADVILKYMPD 98 (145)
Q Consensus 88 ---Kg~Ii~ry~~d 98 (145)
+.+|..-+.++
T Consensus 84 ~~~~~~i~LSlr~~ 97 (100)
T cd05693 84 KSGKKRIELSLEPE 97 (100)
T ss_pred cCCCcEEEEEecHH
Confidence 67777666554
No 108
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=44.63 E-value=82 Score=28.51 Aligned_cols=66 Identities=21% Similarity=0.353 Sum_probs=49.1
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG-----KMHK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG-----KfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~ 96 (145)
....+.|+|+.+...+.| |.+..|..-++|++- +..+ .-+++.||.|.|.....+..+++|..-+.
T Consensus 292 ~G~~v~G~V~~v~~~G~f-V~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K 363 (491)
T PRK13806 292 AGDKVTGKVVRLAPFGAF-VEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363 (491)
T ss_pred CCCEEEEEEEEEeCceEE-EEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEe
Confidence 345689999999876666 577778888888753 2222 45799999999999888877888865543
No 109
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=44.40 E-value=43 Score=25.82 Aligned_cols=61 Identities=15% Similarity=0.190 Sum_probs=49.2
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 8999999999999965443 3368999999999998877 8887554
No 110
>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=43.96 E-value=73 Score=24.30 Aligned_cols=45 Identities=22% Similarity=0.108 Sum_probs=32.0
Q ss_pred EEEEEEeCC-CceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 35 YAQVLRMLG-NGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 35 ig~V~~~lG-~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 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 366666633 235999999999 344433346889999999999874
No 111
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=43.84 E-value=60 Score=32.60 Aligned_cols=76 Identities=17% Similarity=0.172 Sum_probs=53.2
Q ss_pred ccccceeeecCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccce------------EEEecCCEEEEEeccCCC
Q 032190 19 ADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKK------------VWIAAGDIILVGLRDYQD 86 (145)
Q Consensus 19 ~~~~~~el~~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~------------IwIk~GD~VlV~~~~~~~ 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 45567777777665 6776666 889999999999966655544444432 248889999987765544
Q ss_pred CceEEEEEcC
Q 032190 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 4578877764
No 112
>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=43.63 E-value=42 Score=25.29 Aligned_cols=60 Identities=20% Similarity=0.137 Sum_probs=35.8
Q ss_pred EEEEEEEeCCCc-eEEEEeCCCC----------EEEEEeccccc----ceEEEecCCEEEEEeccCCCC--ceEEEEE
Q 032190 34 EYAQVLRMLGNG-RCEAMCIDGT----------KRLCHIRGKMH----KKVWIAAGDIILVGLRDYQDD--KADVILK 94 (145)
Q Consensus 34 ~ig~V~~~lG~~-~~~V~~~dG~----------~~La~IpGKfR----k~IwIk~GD~VlV~~~~~~~~--Kg~Ii~r 94 (145)
+.|+|++..+++ .|+|+.+|-. ..+..||.+.. ...-...|..||.- +|..+. +|.|+..
T Consensus 20 Ila~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~~~~~~~~~f~~g~~VLAl-YP~TT~FY~A~V~~~ 96 (130)
T PF07039_consen 20 ILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAPPDTDPLAEFPKGTKVLAL-YPDTTCFYPATVVSP 96 (130)
T ss_dssp EEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-SB--TTT-GGGS--TT-EEEEE--TTSSEEEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCCccCCCCCchhhCCCCCEEEEE-CCCCceEEEEEEEeC
Confidence 899999999888 9999998754 33455665222 24445677777654 443332 6666655
No 113
>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=43.60 E-value=23 Score=26.81 Aligned_cols=25 Identities=28% Similarity=0.401 Sum_probs=16.8
Q ss_pred EEEecCCEEEEEeccC-CCCceEEEE
Q 032190 69 VWIAAGDIILVGLRDY-QDDKADVIL 93 (145)
Q Consensus 69 IwIk~GD~VlV~~~~~-~~~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 5689999999998763 223444433
No 114
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=42.99 E-value=57 Score=20.49 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=19.6
Q ss_pred CCe-EEEEEEEeCCCceEEEEeCC
Q 032190 31 DGQ-EYAQVLRMLGNGRCEAMCID 53 (145)
Q Consensus 31 e~q-~ig~V~~~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 455 45999999999999999987
No 115
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=42.93 E-value=71 Score=25.04 Aligned_cols=58 Identities=16% Similarity=0.164 Sum_probs=36.2
Q ss_pred ecCCCC-eEEEEEEEeCCCceEEEEe----------CCCCEEEEEecccccc-----eEEEecCCEEEEEeccCC
Q 032190 27 VFKEDG-QEYAQVLRMLGNGRCEAMC----------IDGTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQ 85 (145)
Q Consensus 27 ~~p~e~-q~ig~V~~~lG~~~~~V~~----------~dG~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~ 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 345556 479999999776554 443 2344444444432211 234799999999988765
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=42.63 E-value=37 Score=25.39 Aligned_cols=33 Identities=12% Similarity=0.163 Sum_probs=26.2
Q ss_pred ceEEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 67 KKVWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 67 k~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~de 99 (145)
+.+.|+.||.|.|---.+....|.|+.++....
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~ 70 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRY 70 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcCCC
Confidence 367899999999988777777899988874443
No 117
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=41.96 E-value=1.5e+02 Score=24.58 Aligned_cols=87 Identities=17% Similarity=0.182 Sum_probs=54.0
Q ss_pred eEEEEEEEeCCCceEEEEeC--CCCEEEEEec--ccccceEEEecCCEEEEEeccCCCCce----EEEEE------c---
Q 032190 33 QEYAQVLRMLGNGRCEAMCI--DGTKRLCHIR--GKMHKKVWIAAGDIILVGLRDYQDDKA----DVILK------Y--- 95 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~--dG~~~La~Ip--GKfRk~IwIk~GD~VlV~~~~~~~~Kg----~Ii~r------y--- 95 (145)
-+.|+.++=. |+|.|.+. ||+..+||+| |||+--+ .+|-.|++.+.+-...|- +++.. .
T Consensus 7 l~~g~fi~R~--nRF~~~V~~~~g~~~~aH~pntGRl~ell--~pG~~v~l~~~~~pkrK~~~~~~l~~~~~~~~V~int 82 (234)
T PRK00347 7 LQEATLIKRY--KRFLADVELDDGEELTAHCPNTGRMTGLL--TPGNTVWLSTSDNPKRKYPHTWELTETPNGRLIGINT 82 (234)
T ss_pred ceEEEEEEec--CCEEEEEEECCCCEEEEEcCCCCCChhhc--cCCCEEEEEECCCCCCccceEEEEEEeCCCeEEEECc
Confidence 3567777755 78887764 6999999997 6777643 399999999875432221 12221 1
Q ss_pred --ChhHHHHHHHcCCCCcc--c-cccccccCCC
Q 032190 96 --MPDEARLLKAYGELPES--T-RLNEGIAGGL 123 (145)
Q Consensus 96 --~~devk~L~k~g~wP~~--f-~~~~~~~~~~ 123 (145)
...=+.++.++|.+|.- + ....+.++|.
T Consensus 83 ~~~N~l~~~~l~~~~i~~l~~~~~ikrEv~~g~ 115 (234)
T PRK00347 83 ALPNKLVEEALEAGLIPELAGYSTIKREVKYGE 115 (234)
T ss_pred ccHHHHHHHHHHcCCCccccCcceEeeecccCC
Confidence 12235666777888742 2 2355677773
No 118
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=41.02 E-value=33 Score=25.02 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=23.4
Q ss_pred EEEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 69 VWIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 69 IwIk~GD~VlV~~~~~~~~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 3689999999987665566788887776554
No 119
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=39.73 E-value=72 Score=19.46 Aligned_cols=30 Identities=27% Similarity=0.501 Sum_probs=23.1
Q ss_pred CCe-EEEEEEEeCCCceEEEEeCC-CCEEEEE
Q 032190 31 DGQ-EYAQVLRMLGNGRCEAMCID-GTKRLCH 60 (145)
Q Consensus 31 e~q-~ig~V~~~lG~~~~~V~~~d-G~~~La~ 60 (145)
++. --|+|++..+++.+.|.+.| |.+..+.
T Consensus 15 d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~ 46 (57)
T smart00333 15 DGEWYRARIIKVDGEQLYEVFFIDYGNEEVVP 46 (57)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCCccEEEe
Confidence 444 57899999988999999988 8765443
No 120
>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=39.44 E-value=2.6e+02 Score=26.42 Aligned_cols=45 Identities=16% Similarity=-0.023 Sum_probs=31.3
Q ss_pred EecCCEEEEEeccCCC-----CceEEEEEcC-----hhHHHHHHHcCCCCccccc
Q 032190 71 IAAGDIILVGLRDYQD-----DKADVILKYM-----PDEARLLKAYGELPESTRL 115 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~-----~Kg~Ii~ry~-----~devk~L~k~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 4579999999986643 2589999993 3455555555557777754
No 121
>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=39.43 E-value=99 Score=19.57 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=40.9
Q ss_pred CeEEEEEEEeCCCceEEEEeCC-CCEEEEEecccccc-----eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 32 GQEYAQVLRMLGNGRCEAMCID-GTKRLCHIRGKMHK-----KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~d-G~~~La~IpGKfRk-----~IwIk~GD~VlV~~~~~~~~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 3578999999765555 56653 55555554321111 1236999999999888777777776543
No 122
>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=39.17 E-value=1e+02 Score=19.60 Aligned_cols=60 Identities=12% Similarity=0.000 Sum_probs=45.1
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc-----ceEEEecCCEEEEEeccCCCCceEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH-----KKVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR-----k~IwIk~GD~VlV~~~~~~~~Kg~Ii~ 93 (145)
-+.|+|+++-. +-+-|.+.+|..-+++++-=-. ..-.++.||.|.|.....+..++.|+.
T Consensus 7 iv~g~V~~v~~-~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 7 IVEGKVTSVED-FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRL 71 (74)
T ss_dssp EEEEEEEEEET-TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred EEEEEEEEEEC-CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence 47888888877 5556777788887777653332 246789999999999988888887764
No 123
>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=38.88 E-value=1.3e+02 Score=20.76 Aligned_cols=54 Identities=15% Similarity=0.099 Sum_probs=39.3
Q ss_pred CeEEEEEEEeCCC-ceEEEEeCCCCEEEEEeccc-------ccc-eEEEecCCEEEEEeccCC
Q 032190 32 GQEYAQVLRMLGN-GRCEAMCIDGTKRLCHIRGK-------MHK-KVWIAAGDIILVGLRDYQ 85 (145)
Q Consensus 32 ~q~ig~V~~~lG~-~~~~V~~~dG~~~La~IpGK-------fRk-~IwIk~GD~VlV~~~~~~ 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 3478999999986 45667888888888888632 111 234889999999987543
No 124
>PRK08582 hypothetical protein; Provisional
Probab=38.38 E-value=1.7e+02 Score=22.04 Aligned_cols=64 Identities=17% Similarity=0.199 Sum_probs=44.7
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccc----cc-eEEEecCCEEEEEeccCCCCceEEEEEcCh
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKM----HK-KVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKf----Rk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~ 97 (145)
..+.|+|+.+...+.| |.+.++.+=|+|++-=- +. .-.++.||.|.|.....+. .|.|...+.+
T Consensus 7 ~iv~G~V~~I~~fG~f-V~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~ 75 (139)
T PRK08582 7 SKLQGKVTGITNFGAF-VELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK 75 (139)
T ss_pred CEEEEEEEEEECCeEE-EEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence 4589999998877654 67788888888876321 11 2347899999999887665 4777655533
No 125
>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=38.24 E-value=1.1e+02 Score=20.63 Aligned_cols=37 Identities=16% Similarity=-0.010 Sum_probs=22.3
Q ss_pred eEEEEeCCCCEEEEEecccc-cceEEEecCCEEEEEec
Q 032190 46 RCEAMCIDGTKRLCHIRGKM-HKKVWIAAGDIILVGLR 82 (145)
Q Consensus 46 ~~~V~~~dG~~~La~IpGKf-Rk~IwIk~GD~VlV~~~ 82 (145)
.|.+...++....+..++.. +-...+++||.|+|.=.
T Consensus 18 yfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 18 IFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred EEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 33444444444455555443 33678999999998765
No 126
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=38.06 E-value=48 Score=24.51 Aligned_cols=31 Identities=16% Similarity=0.152 Sum_probs=23.7
Q ss_pred eEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 68 ~IwIk~GD~VlV~~~~~~~~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 4568999999998766656788888777654
No 127
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=38.00 E-value=70 Score=26.58 Aligned_cols=50 Identities=14% Similarity=0.108 Sum_probs=34.6
Q ss_pred CCeEEEEEEEeCC---CceEEEEeCCCC-EEEEEecccccc----------eEEEecCCEEEEE
Q 032190 31 DGQEYAQVLRMLG---NGRCEAMCIDGT-KRLCHIRGKMHK----------KVWIAAGDIILVG 80 (145)
Q Consensus 31 e~q~ig~V~~~lG---~~~~~V~~~dG~-~~La~IpGKfRk----------~IwIk~GD~VlV~ 80 (145)
-|++-|+|+++.+ +...+|.+..|. ...|.|...=-+ .+.|+.-|+.+..
T Consensus 127 rN~l~g~V~~i~~~~~~~~v~v~l~~g~~~l~a~IT~~s~~~L~l~~G~~v~~~Ika~~V~l~~ 190 (263)
T PRK10676 127 RNQWFGTITARDHQQVQQHVDVLLADGKTRLKVAITAQSAERLGLDEGKEVLVLIKAPWVGITQ 190 (263)
T ss_pred hhcceeEEEEEEeCCcccEEEEEEcCCCcEEEEEeCHHHHhhcCCCCCCeEEEEEECCEEEEEc
Confidence 4799999999975 467788888775 688888764433 4555555555553
No 128
>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=37.94 E-value=1e+02 Score=19.33 Aligned_cols=60 Identities=10% Similarity=0.084 Sum_probs=39.6
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGK----MHK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGK----fRk-~IwIk~GD~VlV~~~~~~~~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 46788999875 45557777777767666421 221 22368999999998877766565543
No 129
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=37.56 E-value=64 Score=16.83 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=19.1
Q ss_pred EecCCEEEEEeccCCCCceEEEEE
Q 032190 71 IAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~~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 468999999988877778887654
No 130
>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=37.47 E-value=38 Score=24.78 Aligned_cols=30 Identities=17% Similarity=0.124 Sum_probs=23.2
Q ss_pred EEecCCEEEEEeccCCCCceEEEEEcChhH
Q 032190 70 WIAAGDIILVGLRDYQDDKADVILKYMPDE 99 (145)
Q Consensus 70 wIk~GD~VlV~~~~~~~~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 589999999987665556888888876655
No 131
>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=36.80 E-value=1.4e+02 Score=26.53 Aligned_cols=66 Identities=14% Similarity=0.145 Sum_probs=49.1
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc--cc-eEEEecCCEEEEEeccCCCCceEEEEEcCh
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG---KM--HK-KVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG---Kf--Rk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~ 97 (145)
...+.|+|+.+...+.| |.+..|..-+++++- .. .. .-+++.||.|.|.....+..+++|..-+..
T Consensus 360 G~~v~g~V~~v~~~G~f-V~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~ 431 (516)
T TIGR00717 360 GDRVTGKIKKITDFGAF-VELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ 431 (516)
T ss_pred CCEEEEEEEEEecceEE-EECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence 44578999999887776 888888888877542 11 11 467899999999988888888888655543
No 132
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=36.59 E-value=2.1e+02 Score=26.00 Aligned_cols=80 Identities=20% Similarity=0.295 Sum_probs=55.5
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEE--------ec--cCCC--------CceEE
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVG--------LR--DYQD--------DKADV 91 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~--------~~--~~~~--------~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 45679999999999999999999999999998765543 224555555444 32 2222 13444
Q ss_pred EEEc---ChhHHHHHHHcCCCC
Q 032190 92 ILKY---MPDEARLLKAYGELP 110 (145)
Q Consensus 92 i~ry---~~devk~L~k~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 578999988887666
No 133
>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=36.50 E-value=51 Score=25.71 Aligned_cols=41 Identities=32% Similarity=0.370 Sum_probs=29.7
Q ss_pred EEecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCCC
Q 032190 59 CHIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGELP 110 (145)
Q Consensus 59 a~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~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 4888887542 46889999998888655
No 134
>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=35.85 E-value=82 Score=21.36 Aligned_cols=47 Identities=23% Similarity=0.314 Sum_probs=36.0
Q ss_pred EEEEEEeCCCceEEEEeCCCCEEE-EEec-----ccccceEEEecCCEEEEEecc
Q 032190 35 YAQVLRMLGNGRCEAMCIDGTKRL-CHIR-----GKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 35 ig~V~~~lG~~~~~V~~~dG~~~L-a~Ip-----GKfRk~IwIk~GD~VlV~~~~ 83 (145)
..+|+.+-|.+....+..+|.++- ..+| ..++.. +..|.-|+|..+.
T Consensus 6 eyqli~I~~Dg~lsLMde~get~eDl~lP~~el~~ei~~~--~~~g~~~~Vtv~~ 58 (69)
T PF01287_consen 6 EYQLIDIDGDGFLSLMDEDGETREDLKLPDGELGEEIKAK--FEEGKEVLVTVLS 58 (69)
T ss_dssp EEEEEEEETTTEEEEEETTS-EEEEEECCSHHHHHHHHHH--HHTTCEEEEEEEE
T ss_pred EEEEEEEccCcEEEEEcCCCCeeccEEecccchhHHHHhh--ccCCCeEEEEEEe
Confidence 468888889999999999999999 9999 333333 3788887777664
No 135
>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=35.76 E-value=28 Score=22.49 Aligned_cols=12 Identities=42% Similarity=0.728 Sum_probs=6.4
Q ss_pred EecCCEEEEEec
Q 032190 71 IAAGDIILVGLR 82 (145)
Q Consensus 71 Ik~GD~VlV~~~ 82 (145)
|..||+|+|++.
T Consensus 14 i~~gd~lii~~~ 25 (81)
T cd06529 14 IPDGDLVLVDPS 25 (81)
T ss_pred cCCCCEEEEcCC
Confidence 555555555543
No 136
>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=35.10 E-value=1.2e+02 Score=19.42 Aligned_cols=58 Identities=14% Similarity=0.037 Sum_probs=36.7
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecc--ccc-ceEEEecCCEEEEEeccCCCCceEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG--KMH-KKVWIAAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG--KfR-k~IwIk~GD~VlV~~~~~~~~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 4678999998666 55787776444433321 000 0233788999998888777665554
No 137
>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=34.94 E-value=81 Score=24.60 Aligned_cols=35 Identities=11% Similarity=0.061 Sum_probs=28.2
Q ss_pred eEEEEe-CCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMC-IDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~-~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 799999999998542 23689999999985
No 138
>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=34.93 E-value=1.2e+02 Score=19.28 Aligned_cols=61 Identities=8% Similarity=-0.023 Sum_probs=41.6
Q ss_pred CeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cc-cc-eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG---KM-HK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG---Kf-Rk-~IwIk~GD~VlV~~~~~~~~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 4578999997554 566888888777777642 22 11 22368999999998887766666643
No 139
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=34.92 E-value=72 Score=22.36 Aligned_cols=24 Identities=25% Similarity=0.434 Sum_probs=13.6
Q ss_pred CCCC-eEEEEEEEeCCC-ceEEEEeC
Q 032190 29 KEDG-QEYAQVLRMLGN-GRCEAMCI 52 (145)
Q Consensus 29 p~e~-q~ig~V~~~lG~-~~~~V~~~ 52 (145)
|..| -++|+|+++-.. ..+++.|-
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v 27 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCV 27 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEE
Confidence 5555 478999987543 34555666
No 140
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=34.83 E-value=46 Score=22.85 Aligned_cols=46 Identities=17% Similarity=0.207 Sum_probs=30.1
Q ss_pred EEEEEeCCCceEEEEeCC-C-CEEEEEecccccceEEEecCCEEEEEe
Q 032190 36 AQVLRMLGNGRCEAMCID-G-TKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 36 g~V~~~lG~~~~~V~~~d-G-~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
.+|....++..|+-.+.- | -..+-.|...+|+.+-+..||.|.|++
T Consensus 33 v~V~~tI~g~~~~~sl~p~g~G~~~Lpv~~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 33 VPVRGTIDGHPWRTSLFPMGNGGYILPVKAAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEEEEEETTEEEEEEEEESSTT-EEEEE-HHHHHHHT--TTSEEEEEE
T ss_pred eEEEEEECCEEEEEEEEECCCCCEEEEEcHHHHHHcCCCCCCEEEEEC
Confidence 455556666666665532 3 467778888889989999999999874
No 141
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=34.51 E-value=63 Score=19.99 Aligned_cols=35 Identities=20% Similarity=0.436 Sum_probs=23.7
Q ss_pred EEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChhHHH
Q 032190 57 RLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEAR 101 (145)
Q Consensus 57 ~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk 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 688999998777655
No 142
>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=34.41 E-value=64 Score=25.17 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=22.5
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 42 LGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 42 lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
-|.+.|-|...++.-+ +|.+.+||++.|-+
T Consensus 100 ~G~g~Fdvr~~~~~wi----------ri~~e~GDli~vP~ 129 (157)
T PF03079_consen 100 DGSGYFDVRDGDDVWI----------RILCEKGDLIVVPA 129 (157)
T ss_dssp ECEEEEEEE-TTCEEE----------EEEEETTCEEEE-T
T ss_pred CcEEEEEEEcCCCEEE----------EEEEcCCCEEecCC
Confidence 6889999998877644 67788999988755
No 143
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=33.93 E-value=40 Score=23.23 Aligned_cols=22 Identities=23% Similarity=0.582 Sum_probs=19.3
Q ss_pred ceEEEEEcChhHHHHHHHcCCC
Q 032190 88 KADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 88 Kg~Ii~ry~~devk~L~k~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
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed
Probab=33.29 E-value=88 Score=24.56 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=34.9
Q ss_pred eEEEEEEEeCC------C----ceEEEEe-CCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 33 QEYAQVLRMLG------N----GRCEAMC-IDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 33 q~ig~V~~~lG------~----~~~~V~~-~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
|.-|.|++..+ | -..+|++ .||.+++|.|||==. .-.|.+.|.|||.-
T Consensus 47 q~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~-~~~lqEh~~VLV~G 105 (145)
T PRK04211 47 MARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGA-INFIDEHDEVVIEG 105 (145)
T ss_pred ccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCcc-ccccccCCEEEEee
Confidence 55555555543 2 2467889 699999999998542 22689999999986
No 145
>PRK08577 hypothetical protein; Provisional
Probab=32.97 E-value=37 Score=25.11 Aligned_cols=24 Identities=17% Similarity=0.133 Sum_probs=20.7
Q ss_pred EEecccccceEEEecCCEEEEEec
Q 032190 59 CHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 59 a~IpGKfRk~IwIk~GD~VlV~~~ 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 146
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=32.39 E-value=1.7e+02 Score=26.59 Aligned_cols=65 Identities=14% Similarity=0.077 Sum_probs=46.8
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccc-----cc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKM-----HK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKf-----Rk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~ 96 (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~k 444 (565)
T PRK06299 374 GDVVEGKVKNITDFGAF-VGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444 (565)
T ss_pred CCEEEEEEEEEecceEE-EECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 34688999998766655 77777777777775322 22 46789999999998887777777755543
No 147
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=31.60 E-value=56 Score=22.90 Aligned_cols=44 Identities=20% Similarity=0.375 Sum_probs=26.8
Q ss_pred eecCCC---CeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 26 LVFKED---GQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 26 l~~p~e---~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 83 (145)
+.+|+. -...|+|+++ |.+.+. .+|... ...++.||.|+.....
T Consensus 24 iiLp~~~~~~~~~G~VvaV-G~G~~~---~~g~~~----------~~~vk~GD~Vl~~~~~ 70 (93)
T PF00166_consen 24 IILPESAKEKPNQGKVVAV-GPGRYN---ENGEEV----------PMDVKVGDKVLFPKYA 70 (93)
T ss_dssp CCE-CCSSSSEEEEEEEEE--SEEET---TTSSEE----------ETSS-TTSEEEEETTT
T ss_pred EEeccccccccceeEEEEc-CCcccc---CCCcEe----------eeeeeeccEEeccccC
Confidence 555643 3478888884 445444 666633 3458889999998764
No 148
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=31.08 E-value=27 Score=21.98 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.2
Q ss_pred EEcChhHHHHHHHcCCCC
Q 032190 93 LKYMPDEARLLKAYGELP 110 (145)
Q Consensus 93 ~ry~~devk~L~k~g~wP 110 (145)
|+....|++||+++| ||
T Consensus 14 ~k~~~~Q~~~L~~~G-i~ 30 (47)
T PF13986_consen 14 YKRPSKQIRWLRRNG-IP 30 (47)
T ss_pred CCCHHHHHHHHHHCC-Ce
Confidence 567889999999998 44
No 149
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=30.82 E-value=2.5e+02 Score=24.07 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=44.7
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccce-----EEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKK-----VWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~-----IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
...+.|.|+.+...+. -|++.+|..=|++++---..+ --++.||.|.|.....+..+++|...+
T Consensus 278 G~~v~g~V~~i~~~G~-fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~ 346 (390)
T PRK06676 278 GDVIEGTVKRLTDFGA-FVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346 (390)
T ss_pred CcEEEEEEEEEeCceE-EEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEE
Confidence 3468899998765444 467778887788766421111 236999999999988887777775444
No 150
>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=30.69 E-value=66 Score=20.54 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=14.3
Q ss_pred EecCCEEEEEeccCCC---CceEEEE
Q 032190 71 IAAGDIILVGLRDYQD---DKADVIL 93 (145)
Q Consensus 71 Ik~GD~VlV~~~~~~~---~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 151
>PRK05807 hypothetical protein; Provisional
Probab=30.65 E-value=2.3e+02 Score=21.21 Aligned_cols=62 Identities=16% Similarity=0.226 Sum_probs=42.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
...+.|+|+.+...+.| |.+ +|.+-|+|++- ..+. .-.++.||.|.|.....+. .+.|...+
T Consensus 6 G~vv~G~Vt~i~~~Gaf-V~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSl 72 (136)
T PRK05807 6 GSILEGTVVNITNFGAF-VEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSI 72 (136)
T ss_pred CCEEEEEEEEEECCeEE-EEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEE
Confidence 34689999998876655 555 67777777652 1222 3347999999999876665 57764444
No 152
>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=30.64 E-value=1.3e+02 Score=28.65 Aligned_cols=60 Identities=22% Similarity=0.393 Sum_probs=42.9
Q ss_pred CCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEecCCEEEEEeccCCCCceEE
Q 032190 29 KEDGQ-EYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KV-----WIAAGDIILVGLRDYQDDKADV 91 (145)
Q Consensus 29 p~e~q-~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~I-----wIk~GD~VlV~~~~~~~~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 45554 78999999876555 66677888899987 3332 22 26889999999887665 5554
No 153
>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=30.43 E-value=60 Score=24.56 Aligned_cols=35 Identities=20% Similarity=0.183 Sum_probs=27.6
Q ss_pred eEEEEe-CCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 46 RCEAMC-IDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 46 ~~~V~~-~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 599999999998542 23578899999985
No 154
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=30.08 E-value=2.4e+02 Score=25.57 Aligned_cols=65 Identities=12% Similarity=0.014 Sum_probs=49.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccc----cc-eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKM----HK-KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKf----Rk-~IwIk~GD~VlV~~~~~~~~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 45689999999988876 68888999999986322 11 22359999999998888877777766655
No 155
>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=29.47 E-value=1.5e+02 Score=19.78 Aligned_cols=30 Identities=13% Similarity=0.165 Sum_probs=20.0
Q ss_pred CCeEEEEEEEeCCC---ceEEEEeCC-CCEEEEE
Q 032190 31 DGQEYAQVLRMLGN---GRCEAMCID-GTKRLCH 60 (145)
Q Consensus 31 e~q~ig~V~~~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 44577888888854 489999999 9988764
No 156
>PF12859 Apc1: Anaphase-promoting complex subunit 1
Probab=29.40 E-value=87 Score=22.38 Aligned_cols=38 Identities=5% Similarity=0.010 Sum_probs=27.2
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEE
Q 032190 42 LGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVG 80 (145)
Q Consensus 42 lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~ 80 (145)
+-.....|.+.+|+.+.+++|=.+.+-.+. +..++|-.
T Consensus 6 ~l~~~~~vy~~~G~~~~v~LPF~V~~~~~~-~~GlLLqR 43 (105)
T PF12859_consen 6 VLKDQAHVYFPSGESYTVPLPFEVSSAWPL-PRGLLLQR 43 (105)
T ss_pred EECCEEEEEeCCCCEEEEEeceEeeEEecc-CCEEEEEE
Confidence 336888999999999999999776654444 44444433
No 157
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=29.39 E-value=52 Score=28.50 Aligned_cols=63 Identities=19% Similarity=0.185 Sum_probs=38.1
Q ss_pred EEEEEEeC-CCceE-EEEeCCCCEEEEEeccccc-ceEEEecCCEEEEEeccCCCCceEEEEEcChhHHH
Q 032190 35 YAQVLRML-GNGRC-EAMCIDGTKRLCHIRGKMH-KKVWIAAGDIILVGLRDYQDDKADVILKYMPDEAR 101 (145)
Q Consensus 35 ig~V~~~l-G~~~~-~V~~~dG~~~La~IpGKfR-k~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk 101 (145)
.++|++.. .-+.| .+=++ +..+.++.-.=. +.+|.++||.++|.+.- +.+++|.=.+..+++-
T Consensus 78 ~~~Vv~v~~~lGaFlD~Gl~--KDl~vp~~elp~~~~~wpq~Gd~l~v~l~~--Dkk~Ri~g~~a~~~~l 143 (287)
T COG2996 78 WLKVVEVNKDLGAFLDWGLP--KDLLVPLDELPTLKSLWPQKGDKLLVYLYV--DKKGRIWGTLAIEKIL 143 (287)
T ss_pred EEEEEEEcCCcceEEecCCC--cceeeehhhcccccccCCCCCCEEEEEEEE--ccCCcEEEEecchhHH
Confidence 45566655 32322 11122 445555544333 48999999999999863 6778887666555543
No 158
>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=28.95 E-value=1.5e+02 Score=18.61 Aligned_cols=57 Identities=12% Similarity=0.011 Sum_probs=34.9
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEeccc-c-cce-----EEEecCCEEEEEeccCCCCceEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGK-M-HKK-----VWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGK-f-Rk~-----IwIk~GD~VlV~~~~~~~~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-EVLVDIGYKS--EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVV 66 (70)
T ss_pred EEEEEEEEEeCC-EEEEEeCCCc--eEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEE
Confidence 367888887654 4556665443 4444422 1 111 127899999999887776666664
No 159
>COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism]
Probab=28.78 E-value=39 Score=25.54 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=20.7
Q ss_pred CCCEEEEEecccccceEEEecCCEEE
Q 032190 53 DGTKRLCHIRGKMHKKVWIAAGDIIL 78 (145)
Q Consensus 53 dG~~~La~IpGKfRk~IwIk~GD~Vl 78 (145)
++..+.+-|+|.|-+ +.++.||.|-
T Consensus 69 ~~~~V~SPm~Gtv~~-~~V~vGd~V~ 93 (140)
T COG0511 69 GGTQVTSPMVGTVYK-PFVEVGDTVK 93 (140)
T ss_pred cCceEecCcceEEEE-EeeccCCEEc
Confidence 678899999999988 8888888773
No 160
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=28.58 E-value=2.9e+02 Score=25.10 Aligned_cols=66 Identities=12% Similarity=0.115 Sum_probs=48.8
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccc----ccc-eEEEecCCEEEEEeccCCCCceEEEEEcCh
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGK----MHK-KVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGK----fRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~ 97 (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~ 531 (565)
T PRK06299 461 GSIVTGTVTEVKDKGAF-VELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531 (565)
T ss_pred CCEEEEEEEEEecCceE-EecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeee
Confidence 34689999999988776 8888888888876432 222 234599999999999888888888655543
No 161
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=28.45 E-value=2.6e+02 Score=27.69 Aligned_cols=66 Identities=14% Similarity=0.045 Sum_probs=48.3
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc---cccc-----eEEEecCCEEEEEeccCCCCceEEEEEcC
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG---KMHK-----KVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG---KfRk-----~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~ 96 (145)
-...+.|+|+++...+.| |++++|.+-+++++- .+.. .-+++.||.|-|.....+..+..|..-+.
T Consensus 752 vG~iV~GkV~~v~~~GvF-VeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk 825 (863)
T PRK12269 752 VGSTVEGEVSSVTDFGIF-VRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825 (863)
T ss_pred CCCEEEEEEEEEecCeEE-EEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence 345789999998877754 788888888887652 1111 23589999999999888877778866665
No 162
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=28.30 E-value=1.7e+02 Score=24.61 Aligned_cols=84 Identities=18% Similarity=0.316 Sum_probs=47.3
Q ss_pred EEEEEeCCCceEEEEeCCCCEEEEEec--ccccceEEEecCCEEEEEeccCCCCceEEEEEc-------------ChhH-
Q 032190 36 AQVLRMLGNGRCEAMCIDGTKRLCHIR--GKMHKKVWIAAGDIILVGLRDYQDDKADVILKY-------------MPDE- 99 (145)
Q Consensus 36 g~V~~~lG~~~~~V~~~dG~~~La~Ip--GKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry-------------~~de- 99 (145)
|+.++=.--=+..|.++ |+.++||+| |+|+- -+.+|+.|.+.-++-...|=.+.+-+ .+++
T Consensus 10 a~li~R~nRFl~dv~l~-G~~~~~H~~ntGrm~~--l~~pG~~v~l~~sd~~~rK~~~~~~~~~~~~~~v~VnT~l~N~l 86 (235)
T COG1489 10 ATLIKRYNRFLADVELD-GEEVTAHCPNTGRMTE--LLTPGNTVWLSRSDNPKRKYRYTLELVEADNTLVCVNTGLPNRL 86 (235)
T ss_pred eEEEeeecceEEEEEEC-CeEEEEEcCCCCcccc--ccCCCCEEEEEEecCCCccceEEEEEEEcCCeEEEEeCCccHHH
Confidence 44444332223456666 999999997 56654 36789999998887653322222211 2333
Q ss_pred HHHHHHcCCCCc--ccc-ccccccCC
Q 032190 100 ARLLKAYGELPE--STR-LNEGIAGG 122 (145)
Q Consensus 100 vk~L~k~g~wP~--~f~-~~~~~~~~ 122 (145)
+.+...++.+|+ .+. ...+.+||
T Consensus 87 ~~eai~~~~~~~L~gy~~~k~EvkyG 112 (235)
T COG1489 87 AEEAIPNGQIPELAGYSTIKREVKYG 112 (235)
T ss_pred HHHHHhhCcccccccchheeeecccc
Confidence 344455566654 222 25567788
No 163
>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=27.41 E-value=1.9e+02 Score=19.09 Aligned_cols=67 Identities=12% Similarity=0.125 Sum_probs=44.0
Q ss_pred eeecCCCCe-EEEEEEEeCCCceEEEEeCCCCEEEEEecccccc------eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 25 ELVFKEDGQ-EYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK------KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 25 el~~p~e~q-~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk------~IwIk~GD~VlV~~~~~~~~Kg~Ii~ 93 (145)
.+..+..|+ +.|+|+.+...+ +-|.+.+|..-+++++ .+.. .--++.||.|.|.....+..+++|..
T Consensus 8 ~~~~~~~G~i~~g~V~~v~~~G-~fv~l~~~~~g~v~~~-el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~l 81 (83)
T cd04461 8 NFSDLKPGMVVHGYVRNITPYG-VFVEFLGGLTGLAPKS-YISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeece-EEEEcCCCCEEEEEHH-HCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence 344456665 677888777544 4467777766666654 2221 22478899999998887777777754
No 164
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=27.33 E-value=77 Score=22.02 Aligned_cols=37 Identities=22% Similarity=0.310 Sum_probs=28.4
Q ss_pred EecccccceEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 60 HIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 60 ~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~d 98 (145)
-||-..|+++=|++||.|.+.....+.. -|+.+|...
T Consensus 17 vIPkeiR~~lgi~~Gd~lei~~~~~~~~--ivl~k~~~~ 53 (89)
T COG2002 17 VIPKEIREALGIKEGDVLEIIVDGDGGR--IVLKKYKPA 53 (89)
T ss_pred EecHHHHHHhCCCCCCEEEEEEeCCCCE--EEEEECCcc
Confidence 4899999999999999999998653211 456677665
No 165
>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=27.21 E-value=46 Score=22.49 Aligned_cols=40 Identities=10% Similarity=0.216 Sum_probs=30.6
Q ss_pred CCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcCh
Q 032190 54 GTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
Q Consensus 54 G~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~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 3445555554
No 166
>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=26.69 E-value=51 Score=25.12 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=16.1
Q ss_pred ccccceEEEecCCEEEEEecc
Q 032190 63 GKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 63 GKfRk~IwIk~GD~VlV~~~~ 83 (145)
|.+...+++++||.|.|..+.
T Consensus 144 g~~~~n~~L~~gD~I~Vp~~~ 164 (165)
T TIGR03027 144 GDVTANVELKPGDVLIIPESW 164 (165)
T ss_pred CCccCCceeCCCCEEEEeccc
Confidence 456678889999999887653
No 167
>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=26.51 E-value=74 Score=22.02 Aligned_cols=14 Identities=29% Similarity=0.366 Sum_probs=11.9
Q ss_pred EEecCCEEEEEecc
Q 032190 70 WIAAGDIILVGLRD 83 (145)
Q Consensus 70 wIk~GD~VlV~~~~ 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 47889999999876
No 168
>PRK02302 hypothetical protein; Provisional
Probab=26.36 E-value=60 Score=23.43 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=21.0
Q ss_pred CCceEEEEEcChhHHHHHHHcCCC
Q 032190 86 DDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 86 ~~Kg~Ii~ry~~devk~L~k~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 457899999999999999999864
No 169
>PRK02886 hypothetical protein; Provisional
Probab=26.31 E-value=62 Score=23.28 Aligned_cols=24 Identities=13% Similarity=0.335 Sum_probs=20.8
Q ss_pred CCceEEEEEcChhHHHHHHHcCCC
Q 032190 86 DDKADVILKYMPDEARLLKAYGEL 109 (145)
Q Consensus 86 ~~Kg~Ii~ry~~devk~L~k~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 347889999999999999999864
No 170
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=25.96 E-value=52 Score=20.72 Aligned_cols=14 Identities=7% Similarity=0.328 Sum_probs=11.7
Q ss_pred EecCCEEEEEeccC
Q 032190 71 IAAGDIILVGLRDY 84 (145)
Q Consensus 71 Ik~GD~VlV~~~~~ 84 (145)
+++|+||++..+..
T Consensus 2 l~pG~~V~CAVTg~ 15 (42)
T PF09866_consen 2 LSPGSFVRCAVTGQ 15 (42)
T ss_pred ccCCCEEEEEeeCC
Confidence 67999999998753
No 171
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=25.94 E-value=4.1e+02 Score=25.40 Aligned_cols=62 Identities=23% Similarity=0.355 Sum_probs=44.6
Q ss_pred CCCC-eEEEEEEEeCCCceEEEEeCCCCEEEEEecccccc-eE-----EEecCCEEEEEeccCCCCceEEEE
Q 032190 29 KEDG-QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHK-KV-----WIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 29 p~e~-q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk-~I-----wIk~GD~VlV~~~~~~~~Kg~Ii~ 93 (145)
+..| .+.|+|+.+...+.| |++..|..=|.|++ .+.. ++ -++.||.|.|.....+.. ++|..
T Consensus 619 ~~vG~v~~G~V~~I~~fGaf-Vei~~~~~GllhiS-els~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~L 687 (693)
T PRK11824 619 PEVGEIYEGKVVRIVDFGAF-VEILPGKDGLVHIS-EIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRL 687 (693)
T ss_pred CcCCeEEEEEEEEEECCeEE-EEECCCCEEEEEee-eccCccccCccceeCCCCEEEEEEEEECCC-CcEEE
Confidence 4445 478999999866555 67777888888887 4432 22 479999999998877655 77654
No 172
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=25.75 E-value=2.1e+02 Score=26.87 Aligned_cols=67 Identities=15% Similarity=0.226 Sum_probs=53.9
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 28 ~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 45567899999999887766 899999999999993 2222 3457999999999999999999986554
No 173
>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=25.69 E-value=61 Score=24.71 Aligned_cols=31 Identities=16% Similarity=0.080 Sum_probs=16.8
Q ss_pred EeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 50 MCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 50 ~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
.+.+|..+++.--.. ..--+++||+|++...
T Consensus 33 tl~~Gd~vlv~k~~~--~~~~~~rGDiVvf~~~ 63 (163)
T TIGR02227 33 TLKEGDRILVNKFAY--GTSDPKRGDIVVFKDP 63 (163)
T ss_pred chhCCCEEEEEEeEc--CCCCCCCCcEEEEecC
Confidence 345666666542111 0123678888888753
No 174
>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=25.68 E-value=1.9e+02 Score=18.48 Aligned_cols=54 Identities=13% Similarity=0.046 Sum_probs=35.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecccc------cc-eEEEecCCEEEEEeccCCCC
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKM------HK-KVWIAAGDIILVGLRDYQDD 87 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKf------Rk-~IwIk~GD~VlV~~~~~~~~ 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 46688887766666554211 11 12268999999988766543
No 175
>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=25.44 E-value=82 Score=17.77 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=20.3
Q ss_pred cCCEEEEEeccCCCCceEEEEEcChh
Q 032190 73 AGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 73 ~GD~VlV~~~~~~~~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 58999998878877888888776543
No 176
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=25.36 E-value=2.2e+02 Score=19.15 Aligned_cols=53 Identities=13% Similarity=0.019 Sum_probs=31.6
Q ss_pred eeecCCCCeEEEEEEEeCCCceEEEEeCCC-CEEEEEecc-cccceEEEecCCEE
Q 032190 25 ELVFKEDGQEYAQVLRMLGNGRCEAMCIDG-TKRLCHIRG-KMHKKVWIAAGDII 77 (145)
Q Consensus 25 el~~p~e~q~ig~V~~~lG~~~~~V~~~dG-~~~La~IpG-KfRk~IwIk~GD~V 77 (145)
++..|.+|.++..-.....++...+++.+| .++.+++.. ..+.-=||++|+.+
T Consensus 15 ~V~A~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~v~~G~~V~~G~~I 69 (96)
T PF01551_consen 15 PVYAPADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVSVKVGDRVKAGQVI 69 (96)
T ss_dssp EEEESSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEESS-TTSEE-TTCEE
T ss_pred EEEeCccEEEEEEEeccCCccEEEEEeCCcCCEEEeccccccceecccccCCCEE
Confidence 456677777755555435577888888887 566677654 22334555555553
No 177
>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=25.28 E-value=2.1e+02 Score=23.74 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=28.2
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEE
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIIL 78 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~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 588888888888877766666533333332 3355677787765
No 178
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=25.24 E-value=2.8e+02 Score=25.97 Aligned_cols=64 Identities=16% Similarity=0.196 Sum_probs=46.6
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEeccccc----c-eEEEecCCEEEEEeccCCCCceEEEEEc
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH----K-KVWIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR----k-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry 95 (145)
...+.|.|+.+...+.| |++.+|..-|++++-=.. + .--++.||.|.|.....+..+++|...+
T Consensus 563 G~~v~g~V~~i~~~G~f-V~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lsl 631 (647)
T PRK00087 563 GSIVLGKVVRIAPFGAF-VELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631 (647)
T ss_pred CeEEEEEEEEEECCeEE-EEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 44688999998876665 577888888888754221 1 2247999999999888877788875554
No 179
>PTZ00067 40S ribosomal S23; Provisional
Probab=25.11 E-value=84 Score=24.62 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=35.0
Q ss_pred CeEEEEEEEeCC------Cc----eEEEEeC-CCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 32 GQEYAQVLRMLG------NG----RCEAMCI-DGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 32 ~q~ig~V~~~lG------~~----~~~V~~~-dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 355666665553 22 4678887 99999999998531 23588999999986
No 180
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=24.96 E-value=1.8e+02 Score=24.39 Aligned_cols=35 Identities=26% Similarity=0.433 Sum_probs=27.0
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEeccccc
Q 032190 32 GQEYAQVLRMLGNGRCEAMC-----IDGTKRLCHIRGKMH 66 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~-----~dG~~~La~IpGKfR 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 466667667776544
No 181
>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=24.89 E-value=3.1e+02 Score=25.83 Aligned_cols=63 Identities=16% Similarity=0.167 Sum_probs=43.9
Q ss_pred CeEEEEEEEeCCCceEEEEeC-CCCEEEEEec---ccc------------cc-eEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCI-DGTKRLCHIR---GKM------------HK-KVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~-dG~~~La~Ip---GKf------------Rk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~r 94 (145)
....|+|+.+...+ +-|+++ .|.+-++++. ..+ ++ .-.++.||.|.|.....+..++.|.+.
T Consensus 574 ~~~~g~I~~v~~~G-ifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~ 652 (654)
T TIGR00358 574 TEFSGEISSVTRFG-MFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFE 652 (654)
T ss_pred cEEEEEEEeEEcCc-EEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEE
Confidence 45789999988877 456665 4555555553 322 11 245889999999999888888888765
Q ss_pred c
Q 032190 95 Y 95 (145)
Q Consensus 95 y 95 (145)
+
T Consensus 653 l 653 (654)
T TIGR00358 653 L 653 (654)
T ss_pred E
Confidence 4
No 182
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=24.75 E-value=46 Score=21.55 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=13.1
Q ss_pred EEEEEecccccceEEEecCCEE
Q 032190 56 KRLCHIRGKMHKKVWIAAGDII 77 (145)
Q Consensus 56 ~~La~IpGKfRk~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 445556665
No 183
>PRK02693 apocytochrome f; Reviewed
Probab=24.57 E-value=4.5e+02 Score=23.08 Aligned_cols=52 Identities=15% Similarity=0.057 Sum_probs=39.3
Q ss_pred cCCCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 28 FKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 28 ~p~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
.+..|.+-.....--|+....+..+||.++.-.||.= -.+-|++||.|.++-
T Consensus 201 as~~G~i~~I~~~e~Gg~~vtI~~~dG~~v~~~iP~G--peliV~eG~~v~~dq 252 (312)
T PRK02693 201 ASAAGTITSIETGEDGGYVVTITTEDGEAVTETIPAG--PELIVKEGDTVEAGD 252 (312)
T ss_pred ccCCcEEEEEEecCCCceEEEEEcCCCCEEEEecCCC--CeEEEecCcEEecCC
Confidence 3455666665555567778888889999999999852 267799999998874
No 184
>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=23.53 E-value=2e+02 Score=20.80 Aligned_cols=35 Identities=14% Similarity=0.340 Sum_probs=24.6
Q ss_pred EEeCCCCEEEEEecccccc-eEEEecCCEEEEEecc
Q 032190 49 AMCIDGTKRLCHIRGKMHK-KVWIAAGDIILVGLRD 83 (145)
Q Consensus 49 V~~~dG~~~La~IpGKfRk-~IwIk~GD~VlV~~~~ 83 (145)
+....+...+..+-|.+=- .|++++||.|.|....
T Consensus 7 ~~~~~~~~~~~~~ng~~pGPtI~v~~Gd~v~i~~~N 42 (117)
T PF07732_consen 7 VSPDGGTRKVWTYNGQFPGPTIRVREGDTVRITVTN 42 (117)
T ss_dssp EETTSTEEEEEEETTBSSEEEEEEETTEEEEEEEEE
T ss_pred EEeCCcEEEEEEECCCCCCCEEEEEcCCeeEEEEEe
Confidence 3344445555556666654 8999999999999874
No 185
>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=23.41 E-value=1.9e+02 Score=17.90 Aligned_cols=59 Identities=10% Similarity=0.092 Sum_probs=39.8
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEecc-----cccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG-----KMHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG-----KfRk-~IwIk~GD~VlV~~~~~~~~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 VVSGKIKSITDFG-IFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred EEEEEEEEEEeee-EEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEe
Confidence 4678888887655 44677778777777652 1111 2247999999999877766666653
No 186
>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=23.41 E-value=1.3e+02 Score=18.65 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=26.1
Q ss_pred EEEEEEEe--CCCceEEEEeCCCC--EEEEEecccccc-eEEEecCCEEEEEec
Q 032190 34 EYAQVLRM--LGNGRCEAMCIDGT--KRLCHIRGKMHK-KVWIAAGDIILVGLR 82 (145)
Q Consensus 34 ~ig~V~~~--lG~~~~~V~~~dG~--~~La~IpGKfRk-~IwIk~GD~VlV~~~ 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 34555555555544 333333313332 455789999988743
No 187
>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=23.12 E-value=1.9e+02 Score=19.65 Aligned_cols=31 Identities=16% Similarity=0.218 Sum_probs=20.0
Q ss_pred EeCCCCEEEEEecccccc---eEEEecCCEEEEEe
Q 032190 50 MCIDGTKRLCHIRGKMHK---KVWIAAGDIILVGL 81 (145)
Q Consensus 50 ~~~dG~~~La~IpGKfRk---~IwIk~GD~VlV~~ 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 45667788899999 554 56665444555543
No 188
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=22.97 E-value=1.2e+02 Score=24.01 Aligned_cols=29 Identities=21% Similarity=0.347 Sum_probs=20.0
Q ss_pred EEEEEEEeCCCceEEEEeCCCCEEEEEeccccc
Q 032190 34 EYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMH 66 (145)
Q Consensus 34 ~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfR 66 (145)
..+.|+++||++ |.|... |. |++|.|+=-
T Consensus 24 ~~~~~~q~lgg~-~t~~~~-g~--~~r~~~~~~ 52 (174)
T TIGR03406 24 TEVTITQALGGN-FTVVVE-GN--MARIDGKDA 52 (174)
T ss_pred CEEEEEEccCCe-EEEEEc-Ce--EEEecCcCh
Confidence 467899999865 666443 43 778877653
No 189
>PRK00215 LexA repressor; Validated
Probab=22.88 E-value=1.1e+02 Score=23.68 Aligned_cols=44 Identities=20% Similarity=0.414 Sum_probs=27.9
Q ss_pred CCEEEEEecccccceEEEecCCEEEEEeccCCCCceEEEEEcChh
Q 032190 54 GTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
Q Consensus 54 G~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~d 98 (145)
+..+..++.|-=.-.--|..||+|+|+++. +...|+|+..+..+
T Consensus 116 ~~~~~~~V~GdSM~~~~i~~Gd~v~v~~~~-~~~~G~ivv~~~~~ 159 (205)
T PRK00215 116 GEDFLLRVRGDSMIDAGILDGDLVIVRKQQ-TARNGQIVVALIDD 159 (205)
T ss_pred CCeEEEEEccCCCCCCCcCCCCEEEEeCCC-CCCCCCEEEEEECC
Confidence 456666666654333358899999999753 34567776555444
No 190
>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=22.62 E-value=2.3e+02 Score=25.16 Aligned_cols=61 Identities=16% Similarity=0.208 Sum_probs=40.4
Q ss_pred ccccceeeecCC-----CCeEEEEEEEeCCCceEEEEeCCCC-EEEEEecccccceEEEecCCEEEEEecc
Q 032190 19 ADDEKRELVFKE-----DGQEYAQVLRMLGNGRCEAMCIDGT-KRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 19 ~~~~~~el~~p~-----e~q~ig~V~~~lG~~~~~V~~~dG~-~~La~IpGKfRk~IwIk~GD~VlV~~~~ 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 444455555554 34443 445555555555554354 8899999999886666 9999999984
No 191
>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=22.59 E-value=2.9e+02 Score=19.59 Aligned_cols=37 Identities=22% Similarity=0.224 Sum_probs=21.7
Q ss_pred EeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEecc
Q 032190 40 RMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRD 83 (145)
Q Consensus 40 ~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~ 83 (145)
....++.-+|.. +|+..-|+-.+. |.+||.|.|.-.+
T Consensus 98 ~~~~~~~G~V~~-~G~~w~A~s~~~------i~~G~~V~Vv~v~ 134 (144)
T PF01957_consen 98 EIPLNGSGRVKV-DGERWRARSEDE------IPKGDRVRVVGVE 134 (144)
T ss_dssp EEBSSS-EEEEE-TTEEEEEEESST------B-TT-EEEEEEEE
T ss_pred EeecCCcEEEEE-CCeEEEEEeCCC------CCCCCEEEEEEEE
Confidence 334444555555 578887777766 7888887776543
No 192
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=22.54 E-value=1.3e+02 Score=22.24 Aligned_cols=36 Identities=17% Similarity=0.302 Sum_probs=19.1
Q ss_pred EEEEEecccccceEEEecCCEEEEEeccCCCCceEEE
Q 032190 56 KRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 56 ~~La~IpGKfRk~IwIk~GD~VlV~~~~~~~~Kg~Ii 92 (145)
.+..+++|-=..---|..||+|+|++.. ....|+|+
T Consensus 51 ~f~l~V~GdSM~~~~I~~GD~liVd~~~-~~~~Gdiv 86 (139)
T PRK10276 51 TYFVKASGDSMIDAGISDGDLLIVDSAI-TASHGDIV 86 (139)
T ss_pred EEEEEEecCCCCCCCCCCCCEEEEECCC-CCCCCCEE
Confidence 4444444432221237778888888653 23455554
No 193
>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=22.46 E-value=2.4e+02 Score=18.50 Aligned_cols=60 Identities=7% Similarity=-0.068 Sum_probs=41.2
Q ss_pred eEEEEEEEeCCCceEEEEeCCCCEEEEEec------ccccc-eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDGTKRLCHIR------GKMHK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG~~~La~Ip------GKfRk-~IwIk~GD~VlV~~~~~~~~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 EVTGFVNNVSKEF-VWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRL 69 (73)
T ss_pred EEEEEEEEEeCCE-EEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEE
Confidence 4778999986544 4577887765555542 11332 34489999999999988877766654
No 194
>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=22.46 E-value=78 Score=24.51 Aligned_cols=20 Identities=40% Similarity=0.438 Sum_probs=10.7
Q ss_pred ecCCEEEEEeccC-CCCceEE
Q 032190 72 AAGDIILVGLRDY-QDDKADV 91 (145)
Q Consensus 72 k~GD~VlV~~~~~-~~~Kg~I 91 (145)
.+||+|+|.+..+ +...|+|
T Consensus 46 ~~GD~vlv~~~~~~~~~~GDI 66 (158)
T TIGR02228 46 NTGDLILVTGADPNDIQVGDV 66 (158)
T ss_pred cCCCEEEEEecccCCCCCCCE
Confidence 4666666665332 2345555
No 195
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=22.32 E-value=57 Score=21.32 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=12.4
Q ss_pred CEEEEEecccccceEEEecCCEE
Q 032190 55 TKRLCHIRGKMHKKVWIAAGDII 77 (145)
Q Consensus 55 ~~~La~IpGKfRk~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 3466777777755 334445444
No 196
>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=22.06 E-value=85 Score=20.98 Aligned_cols=26 Identities=19% Similarity=0.166 Sum_probs=19.4
Q ss_pred EEecCCEEEEEeccCCCCceEEEEEc
Q 032190 70 WIAAGDIILVGLRDYQDDKADVILKY 95 (145)
Q Consensus 70 wIk~GD~VlV~~~~~~~~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 47789999998777676777777765
No 197
>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=21.71 E-value=3.6e+02 Score=24.07 Aligned_cols=62 Identities=16% Similarity=0.109 Sum_probs=43.8
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecc----cccc-eEEEecCCEEEEEeccCCCCceEEEE
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRG----KMHK-KVWIAAGDIILVGLRDYQDDKADVIL 93 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpG----KfRk-~IwIk~GD~VlV~~~~~~~~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 34588999997765554 677888777777753 1111 34579999999999888777777754
No 198
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=21.63 E-value=94 Score=22.32 Aligned_cols=52 Identities=12% Similarity=0.056 Sum_probs=26.5
Q ss_pred CCCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 30 EDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 30 ~e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 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 4566666665554666655444444556666666655666789999998765
No 199
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=21.60 E-value=1.6e+02 Score=23.93 Aligned_cols=31 Identities=26% Similarity=0.352 Sum_probs=25.4
Q ss_pred CCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 42 LGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 42 lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
-|++.|-|.-+||..+ .|...+||++.|-+-
T Consensus 103 aG~GiF~v~~~d~~~~----------~i~c~~gDLI~vP~g 133 (181)
T COG1791 103 AGEGIFDVHSPDGKVY----------QIRCEKGDLISVPPG 133 (181)
T ss_pred ecceEEEEECCCCcEE----------EEEEccCCEEecCCC
Confidence 5999999999999887 566777998888664
No 200
>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=21.45 E-value=2.4e+02 Score=18.22 Aligned_cols=57 Identities=12% Similarity=0.113 Sum_probs=36.5
Q ss_pred eEEEEEEEeCCCceEEEEeCCC--CEEEEEeccc----ccc-eEEEecCCEEEEEeccCCCCceEEE
Q 032190 33 QEYAQVLRMLGNGRCEAMCIDG--TKRLCHIRGK----MHK-KVWIAAGDIILVGLRDYQDDKADVI 92 (145)
Q Consensus 33 q~ig~V~~~lG~~~~~V~~~dG--~~~La~IpGK----fRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii 92 (145)
.+.|+|+++...+.| |++ +| ..-|+|++-= +.+ .-.++.||.|.|.....+..+ .|.
T Consensus 6 ~~~g~V~~i~~fG~f-v~l-~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ 69 (73)
T cd05686 6 IFKGEVASVTEYGAF-VKI-PGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMK 69 (73)
T ss_pred EEEEEEEEEEeeeEE-EEE-CCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEE
Confidence 468889888876665 444 34 4677776621 111 224689999999987766544 554
No 201
>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=21.43 E-value=3e+02 Score=20.28 Aligned_cols=52 Identities=25% Similarity=0.095 Sum_probs=36.0
Q ss_pred CCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEeccCC-CCceEEEEEcChhHHHHHHHc
Q 032190 43 GNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQ-DDKADVILKYMPDEARLLKAY 106 (145)
Q Consensus 43 G~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~~~~-~~Kg~Ii~ry~~devk~L~k~ 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 347788777766666666554
No 202
>cd06253 M14_ASTE_ASPA_like_3 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=21.30 E-value=2.5e+02 Score=23.65 Aligned_cols=43 Identities=9% Similarity=0.128 Sum_probs=28.8
Q ss_pred CCeEEEEEEEeCCCc-eEEEEeCCCCEEEEEecccccceEEEecCCEEE
Q 032190 31 DGQEYAQVLRMLGNG-RCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIIL 78 (145)
Q Consensus 31 e~q~ig~V~~~lG~~-~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~Vl 78 (145)
.||++|.|+..+++. .-+|.-+..-.+++ .+..-.|.+||.|.
T Consensus 252 ~Gq~lg~i~dp~~g~~~~~v~Ap~dGiv~~-----~~~~p~v~~G~~l~ 295 (298)
T cd06253 252 RGDVIGEIVDPLEGEVIEEVIAPCDGILFT-----LREYPLVYEGSLVA 295 (298)
T ss_pred CCCEEEEEeCCCCCCeeEEEEcCCCeEEEE-----eecCCeecCCceEE
Confidence 688999999988665 55555554444444 34466788888765
No 203
>PF12843 DUF3820: Protein of unknown function (DUF3820); InterPro: IPR024530 This protein family is mostly found in bacteria and is currently functionally uncharacterised.
Probab=21.25 E-value=56 Score=22.46 Aligned_cols=28 Identities=11% Similarity=0.146 Sum_probs=25.3
Q ss_pred cCCCCceEEEEEcChhHHHHHHHcCCCCc
Q 032190 83 DYQDDKADVILKYMPDEARLLKAYGELPE 111 (145)
Q Consensus 83 ~~~~~Kg~Ii~ry~~devk~L~k~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 7777899999999999999999999 775
No 204
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=21.21 E-value=1.1e+02 Score=26.70 Aligned_cols=47 Identities=23% Similarity=0.200 Sum_probs=33.8
Q ss_pred Eecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCCCccccccc
Q 032190 60 HIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGELPESTRLNE 117 (145)
Q Consensus 60 ~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~g~wP~~f~~~~ 117 (145)
-||.|+.+ .|+|. .|+++|..-+ +.+++|..-|++.|.=|-+|...=
T Consensus 149 GIpTkI~kGkIeI~-~d~~v~k~Ge----------~V~~~~A~LL~~L~IkP~~~gl~l 196 (323)
T PTZ00240 149 NIATKIAKGMVEIV-TEKKVLSVGD----------KVDNSTATLLQKLNISPFYYQVEV 196 (323)
T ss_pred CCCeEecCcEEEEe-cCeEEecCCC----------CcCHHHHHHHHHcCCCeEEEEEEE
Confidence 46666666 66664 3666665432 468999999999999999886543
No 205
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=20.97 E-value=2.9e+02 Score=24.06 Aligned_cols=50 Identities=18% Similarity=0.231 Sum_probs=39.0
Q ss_pred CCeEEEEEEEeCCCceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 31 DGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 31 e~q~ig~V~~~lG~~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
....+|.|.+.+..+...|....|..+++.++..+-. --+++|+.|.+..
T Consensus 51 ~~~~~~~i~~~~~~~~~~v~~~~g~~~~~~~~~~~~~-~~l~~g~~v~~~~ 100 (389)
T PRK03992 51 PPLIVATVLEVLDDGRVVVKSSGGPQFLVNVSPFIDR-EKLKPGARVALNQ 100 (389)
T ss_pred CCceEEEEEEEeCCCeEEEEECCCCEEEEeccccCCH-hHCCCCCEEEEcC
Confidence 3579999999999999999999999998888865433 2256777776654
No 206
>PRK11642 exoribonuclease R; Provisional
Probab=20.91 E-value=4.9e+02 Score=25.50 Aligned_cols=68 Identities=15% Similarity=0.112 Sum_probs=46.8
Q ss_pred CeEEEEEEEeCCCceEEEEeCCC-CEEEEEec---cc---cc----------ceEEEecCCEEEEEeccCCCCceEEEEE
Q 032190 32 GQEYAQVLRMLGNGRCEAMCIDG-TKRLCHIR---GK---MH----------KKVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~~dG-~~~La~Ip---GK---fR----------k~IwIk~GD~VlV~~~~~~~~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 3468999998877776 666553 44444443 21 11 1245778999999999888888999888
Q ss_pred cChhHH
Q 032190 95 YMPDEA 100 (145)
Q Consensus 95 y~~dev 100 (145)
+...+.
T Consensus 724 l~~~~~ 729 (813)
T PRK11642 724 LISSER 729 (813)
T ss_pred Eecccc
Confidence 765444
No 207
>PRK11144 modC molybdate transporter ATP-binding protein; Provisional
Probab=20.81 E-value=2.5e+02 Score=23.99 Aligned_cols=49 Identities=16% Similarity=0.222 Sum_probs=26.6
Q ss_pred eEEEEEEEeCC-CceEEEEeC-CCCEEEEEecccccceEEEecCCEEEEEe
Q 032190 33 QEYAQVLRMLG-NGRCEAMCI-DGTKRLCHIRGKMHKKVWIAAGDIILVGL 81 (145)
Q Consensus 33 q~ig~V~~~lG-~~~~~V~~~-dG~~~La~IpGKfRk~IwIk~GD~VlV~~ 81 (145)
.+-|+|+.+.- +..+.|.+. .|...+++++..--....+.+|+.|.+..
T Consensus 295 ~~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~v~~~~ 345 (352)
T PRK11144 295 ILRAKVVEIYDDNGQVEVKLEVGGKTLWARITPWARDELALKPGQWLYAQI 345 (352)
T ss_pred eeEEEEEEEEcCCCEEEEEEEeCCcEEEEEecHHHHHhcCCCCCCEEEEEE
Confidence 35666766642 223444332 45566677764332334567787777664
No 208
>PRK07051 hypothetical protein; Validated
Probab=20.74 E-value=49 Score=22.34 Aligned_cols=24 Identities=13% Similarity=0.380 Sum_probs=16.9
Q ss_pred CEEEEEecccccc------eEEEecCCEEE
Q 032190 55 TKRLCHIRGKMHK------KVWIAAGDIIL 78 (145)
Q Consensus 55 ~~~La~IpGKfRk------~IwIk~GD~Vl 78 (145)
+++.|.++|+|.+ .+++..||.|-
T Consensus 4 ~~~~ap~~g~~~~~~~~~~~~~v~~Gd~V~ 33 (80)
T PRK07051 4 HEIVSPLPGTFYRRPSPDAPPYVEVGDAVA 33 (80)
T ss_pred cEEeCCCceEEEecCCCCCCCccCCCCEEC
Confidence 4667888888865 37777777654
No 209
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=20.64 E-value=1.1e+02 Score=22.30 Aligned_cols=25 Identities=16% Similarity=0.109 Sum_probs=14.2
Q ss_pred eEEEEEcChhHHHHHHHcCCCCccc
Q 032190 89 ADVILKYMPDEARLLKAYGELPEST 113 (145)
Q Consensus 89 g~Ii~ry~~devk~L~k~g~wP~~f 113 (145)
..+.|=|.++|....++..+.|.+.
T Consensus 39 ~~v~WfyrPeEt~~~~~~~~~~~Ev 63 (121)
T cd04714 39 VRVKWYYRPEETKGGRKPNHGEKEL 63 (121)
T ss_pred EEEEEEEcHHHccCcccccCCCCce
Confidence 3456667777776544444444443
No 210
>PF06251 Caps_synth_GfcC: Capsule biosynthesis GfcC; InterPro: IPR010425 This entry represents uncharacterised bacterial proteins that contain a central beta-grasp like domain related to the SLBB domain [].; PDB: 3P42_B.
Probab=20.50 E-value=2.3e+02 Score=22.70 Aligned_cols=38 Identities=18% Similarity=0.164 Sum_probs=22.8
Q ss_pred ceEEEEeCCCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 45 GRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 45 ~~~~V~~~dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
+..-|.-+||+...+.+.-=+++..-+.+||.|.|-..
T Consensus 167 s~v~VI~pdG~v~~~~~a~Wn~~~~~l~PG~~I~Vp~~ 204 (229)
T PF06251_consen 167 SRVYVIQPDGSVQKVPVAYWNNQHQELAPGATIYVPFD 204 (229)
T ss_dssp SEEEEE-TTS-EEEEE-STTT--EEE--TT-EEEE-B-
T ss_pred ccEEEEeCCCcEEEcceehhccCCCCCCCCCEEEEcCC
Confidence 45567779999998888876667888999999999873
No 211
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=20.39 E-value=1.2e+02 Score=21.34 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=29.9
Q ss_pred eEEEEEEEeCC--CceEEEEeCCCCEEEEEecccc-----cc-e-EEEecCCEEEEEec
Q 032190 33 QEYAQVLRMLG--NGRCEAMCIDGTKRLCHIRGKM-----HK-K-VWIAAGDIILVGLR 82 (145)
Q Consensus 33 q~ig~V~~~lG--~~~~~V~~~dG~~~La~IpGKf-----Rk-~-IwIk~GD~VlV~~~ 82 (145)
-+.|.|..... ++++-..+-|+. |+|+.-| ++ . ..++.|+.|+|.-.
T Consensus 25 wV~GEIs~~~~~~~gh~YftLkD~~---a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~ 80 (99)
T PF13742_consen 25 WVEGEISNLKRHSSGHVYFTLKDEE---ASISCVIFRSRARRIRGFDLKDGDKVLVRGR 80 (99)
T ss_pred EEEEEEeecEECCCceEEEEEEcCC---cEEEEEEEHHHHhhCCCCCCCCCCEEEEEEE
Confidence 36677766554 666666666655 4444443 33 3 67999999998765
No 212
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=20.21 E-value=1.2e+02 Score=26.11 Aligned_cols=46 Identities=26% Similarity=0.247 Sum_probs=32.5
Q ss_pred Eecccccc-eEEEecCCEEEEEeccCCCCceEEEEEcChhHHHHHHHcCCCCcccccc
Q 032190 60 HIRGKMHK-KVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYGELPESTRLN 116 (145)
Q Consensus 60 ~IpGKfRk-~IwIk~GD~VlV~~~~~~~~Kg~Ii~ry~~devk~L~k~g~wP~~f~~~ 116 (145)
-||.|+.+ .|+|. .|+++|..- + +.+++|..-|++.|.=|-+|...
T Consensus 142 gipTkI~kG~I~I~-~d~~v~k~G-------e---~v~~~~A~LL~~L~I~p~~~~l~ 188 (310)
T PTZ00135 142 GIATKIVKGQIEIT-NEVHLIKEG-------Q---KVGASQAVLLQKLNIKPFSYGLE 188 (310)
T ss_pred CCceEecCCeEEEe-cCeEEecCC-------C---CcCHHHHHHHHHcCCCeEEEEEE
Confidence 35666666 66664 366666543 2 46899999999999999888654
No 213
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=20.16 E-value=2e+02 Score=23.86 Aligned_cols=34 Identities=21% Similarity=0.343 Sum_probs=24.5
Q ss_pred CeEEEEEEEeCCCceEEEEe-----CCCCEEEEEecccc
Q 032190 32 GQEYAQVLRMLGNGRCEAMC-----IDGTKRLCHIRGKM 65 (145)
Q Consensus 32 ~q~ig~V~~~lG~~~~~V~~-----~dG~~~La~IpGKf 65 (145)
+.+-++|+++|+|+.+.|+= -|+.....+|+|-.
T Consensus 143 ~tItv~V~~VlpNGnL~I~GeK~v~vN~e~e~i~lsGvV 181 (230)
T PRK12701 143 GSISVTVAKVLANGNMVVQGEKWVRINQGNEFVRLSGIV 181 (230)
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEEECCCeEEEEEEEEE
Confidence 56889999999999998864 34555555555543
No 214
>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=20.05 E-value=4.6e+02 Score=22.55 Aligned_cols=51 Identities=22% Similarity=0.179 Sum_probs=31.4
Q ss_pred CeEEEEEEEeC--CC-ceEEEEeC--CCCEEEEEecccccceEEEecCCEEEEEec
Q 032190 32 GQEYAQVLRML--GN-GRCEAMCI--DGTKRLCHIRGKMHKKVWIAAGDIILVGLR 82 (145)
Q Consensus 32 ~q~ig~V~~~l--G~-~~~~V~~~--dG~~~La~IpGKfRk~IwIk~GD~VlV~~~ 82 (145)
+.+-|+|+.+. |+ ..+.|.+. +|....+.++...-....+..|+.|.+...
T Consensus 290 ~~~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~ 345 (353)
T TIGR03265 290 NLLLARVEDMEFLGAFYRLRLRLEGLPGQALVADVSASEVERLGIRAGQPIWIELP 345 (353)
T ss_pred ceEEEEEEEEEEcCCeEEEEEEECCCCCcEEEEEeccccccccCCCCCCEEEEEEe
Confidence 44567776664 43 23344454 356777888865545566788888877653
Done!