Query 033976
Match_columns 107
No_of_seqs 101 out of 186
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 08:24:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033976.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033976hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08661 Rep_fac-A_3: Replicat 100.0 5.2E-41 1.1E-45 226.4 12.5 103 1-106 1-109 (109)
2 cd04479 RPA3 RPA3: A subfamily 100.0 1.6E-40 3.4E-45 222.0 14.3 100 6-106 1-101 (101)
3 PF15490 Ten1_2: Telomere-capp 98.0 0.00014 3.1E-09 49.9 10.6 85 17-102 18-114 (118)
4 PF12658 Ten1: Telomere cappin 96.8 0.014 3E-07 40.3 8.5 90 6-96 10-124 (124)
5 COG1107 Archaea-specific RecJ- 96.3 0.027 5.9E-07 48.1 8.3 73 5-78 198-282 (715)
6 cd04317 EcAspRS_like_N EcAspRS 94.7 0.26 5.5E-06 33.6 7.4 55 16-70 10-76 (135)
7 cd04316 ND_PkAspRS_like_N ND_P 94.7 0.37 8E-06 31.7 7.9 68 16-83 8-95 (108)
8 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.4 0.78 1.7E-05 29.1 8.9 69 22-91 1-85 (95)
9 PRK05159 aspC aspartyl-tRNA sy 93.9 0.78 1.7E-05 37.5 9.8 77 8-84 3-99 (437)
10 PF04076 BOF: Bacterial OB fol 93.8 0.33 7.2E-06 32.5 6.2 57 15-72 29-91 (103)
11 PRK03932 asnC asparaginyl-tRNA 93.2 1.8 3.9E-05 35.5 10.8 69 16-84 12-99 (450)
12 PF02736 Myosin_N: Myosin N-te 93.1 0.28 6.1E-06 27.5 4.3 27 25-51 14-40 (42)
13 TIGR00457 asnS asparaginyl-tRN 92.8 1.1 2.4E-05 36.8 9.1 68 16-83 12-100 (453)
14 PRK13254 cytochrome c-type bio 92.6 2.7 5.8E-05 29.8 13.5 93 7-99 35-140 (148)
15 TIGR00458 aspS_arch aspartyl-t 91.2 1.9 4E-05 35.2 8.6 67 17-83 9-95 (428)
16 PRK10053 hypothetical protein; 91.0 2.8 6E-05 29.3 8.1 58 14-72 55-118 (130)
17 PRK00484 lysS lysyl-tRNA synth 90.4 2.5 5.4E-05 35.2 8.8 63 21-83 55-135 (491)
18 TIGR00156 conserved hypothetic 90.4 3.3 7.2E-05 28.7 8.1 57 15-72 52-114 (126)
19 PF12869 tRNA_anti-like: tRNA_ 90.4 0.77 1.7E-05 31.2 4.9 55 16-70 63-131 (144)
20 TIGR00459 aspS_bact aspartyl-t 90.1 3.1 6.8E-05 35.6 9.2 71 13-83 8-102 (583)
21 COG3111 Periplasmic protein wi 89.8 3.9 8.4E-05 28.5 7.9 56 15-71 52-113 (128)
22 TIGR00499 lysS_bact lysyl-tRNA 89.1 3.4 7.3E-05 34.5 8.6 64 20-83 53-135 (496)
23 PLN02221 asparaginyl-tRNA synt 88.9 2 4.4E-05 36.6 7.2 54 16-69 46-112 (572)
24 PLN02903 aminoacyl-tRNA ligase 88.5 4.4 9.5E-05 35.2 9.1 58 12-69 64-134 (652)
25 PRK14639 hypothetical protein; 88.2 2.1 4.6E-05 29.9 5.9 46 6-51 74-128 (140)
26 PRK02983 lysS lysyl-tRNA synth 88.2 4.4 9.5E-05 37.1 9.2 69 15-83 646-733 (1094)
27 PF10451 Stn1: Telomere regula 88.2 4.3 9.4E-05 31.2 8.0 78 20-98 66-164 (256)
28 PF03100 CcmE: CcmE; InterPro 88.1 6.6 0.00014 26.9 8.8 71 8-79 35-119 (131)
29 PRK14630 hypothetical protein; 87.8 1.4 3E-05 31.0 4.7 45 6-51 83-134 (143)
30 PLN02502 lysyl-tRNA synthetase 87.6 5.4 0.00012 33.9 9.0 67 18-84 106-193 (553)
31 PRK14633 hypothetical protein; 87.5 1.9 4E-05 30.5 5.3 46 6-51 80-137 (150)
32 PRK00476 aspS aspartyl-tRNA sy 87.4 3.9 8.4E-05 34.9 8.1 58 12-69 9-77 (588)
33 PRK12445 lysyl-tRNA synthetase 87.4 4.3 9.3E-05 34.0 8.2 65 20-84 65-148 (505)
34 PRK14638 hypothetical protein; 87.2 1.7 3.7E-05 30.8 5.0 45 7-52 87-139 (150)
35 PRK14631 hypothetical protein; 86.8 2 4.2E-05 31.3 5.2 46 6-51 103-162 (174)
36 PF14485 DUF4431: Domain of un 86.6 0.69 1.5E-05 26.9 2.2 21 12-32 11-31 (48)
37 cd01734 YlxS_C YxlS is a Bacil 86.4 3.5 7.7E-05 26.0 5.7 46 6-51 11-71 (83)
38 COG0779 Uncharacterized protei 86.4 2.5 5.3E-05 30.3 5.4 48 6-54 85-144 (153)
39 PRK14636 hypothetical protein; 86.2 2.3 5E-05 30.9 5.4 46 6-51 84-141 (176)
40 PRK14647 hypothetical protein; 86.2 2.3 5E-05 30.3 5.3 46 6-51 85-147 (159)
41 PLN02603 asparaginyl-tRNA synt 85.8 5.3 0.00011 34.1 8.0 67 17-83 104-191 (565)
42 PF13567 DUF4131: Domain of un 85.5 5.9 0.00013 26.3 6.8 75 13-93 66-160 (176)
43 TIGR00739 yajC preprotein tran 85.2 2.3 5E-05 27.3 4.4 33 19-51 40-76 (84)
44 cd04322 LysRS_N LysRS_N: N-ter 85.1 8.2 0.00018 25.1 7.9 62 22-83 1-81 (108)
45 PRK05585 yajC preprotein trans 84.7 2.3 4.9E-05 28.5 4.4 33 19-51 55-91 (106)
46 PRK14634 hypothetical protein; 84.6 2.6 5.6E-05 30.0 4.9 45 6-51 86-142 (155)
47 PRK12820 bifunctional aspartyl 84.1 6.3 0.00014 34.6 7.8 60 11-70 9-82 (706)
48 PF02576 DUF150: Uncharacteris 84.0 2.3 5E-05 29.3 4.3 47 6-52 73-134 (141)
49 PRK14646 hypothetical protein; 83.8 3.3 7.1E-05 29.4 5.1 44 7-51 87-142 (155)
50 PRK14637 hypothetical protein; 83.4 2.8 6E-05 29.8 4.6 45 6-51 84-137 (151)
51 cd04320 AspRS_cyto_N AspRS_cyt 83.2 9.8 0.00021 24.4 7.2 49 22-70 1-66 (102)
52 cd04319 PhAsnRS_like_N PhAsnRS 82.4 11 0.00023 24.4 7.5 63 22-84 1-82 (103)
53 PLN02850 aspartate-tRNA ligase 82.2 8 0.00017 32.6 7.6 61 9-69 69-146 (530)
54 PRK00092 ribosome maturation p 81.6 4.1 8.9E-05 28.6 4.9 45 6-51 84-142 (154)
55 cd04318 EcAsnRS_like_N EcAsnRS 80.2 11 0.00024 23.1 6.9 48 22-69 1-61 (82)
56 PTZ00401 aspartyl-tRNA synthet 80.1 13 0.00028 31.6 8.1 61 9-69 65-142 (550)
57 cd04321 ScAspRS_mt_like_N ScAs 79.9 12 0.00026 23.4 9.0 49 22-70 1-62 (86)
58 PRK05886 yajC preprotein trans 79.8 4.5 9.7E-05 27.4 4.4 33 19-51 41-77 (109)
59 PRK14640 hypothetical protein; 79.1 6.1 0.00013 27.9 5.1 45 6-51 83-139 (152)
60 PTZ00425 asparagine-tRNA ligas 79.1 9.2 0.0002 32.8 7.0 57 13-69 74-145 (586)
61 PTZ00417 lysine-tRNA ligase; P 79.0 16 0.00036 31.3 8.5 64 20-83 132-217 (585)
62 PF01336 tRNA_anti-codon: OB-f 77.2 12 0.00026 21.8 6.8 56 23-79 1-72 (75)
63 PF09696 Ctf8: Ctf8; InterPro 76.6 14 0.0003 25.2 6.1 50 18-70 61-111 (122)
64 PRK14645 hypothetical protein; 73.6 12 0.00026 26.6 5.4 45 6-51 88-139 (154)
65 PRK14643 hypothetical protein; 72.3 13 0.00029 26.6 5.4 46 6-51 90-152 (164)
66 PF07076 DUF1344: Protein of u 72.0 6.8 0.00015 24.0 3.3 25 25-49 5-29 (61)
67 COG2451 Ribosomal protein L35A 71.9 16 0.00034 24.4 5.2 42 16-65 42-94 (100)
68 COG1862 YajC Preprotein transl 71.5 9.6 0.00021 25.3 4.2 34 19-52 46-83 (97)
69 PF01176 eIF-1a: Translation i 70.8 13 0.00029 22.3 4.5 30 24-53 4-34 (65)
70 PRK13150 cytochrome c-type bio 68.4 42 0.00091 24.2 11.5 82 18-99 55-147 (159)
71 cd04456 S1_IF1A_like S1_IF1A_l 68.3 18 0.00039 22.8 4.8 40 25-64 2-47 (78)
72 COG1190 LysU Lysyl-tRNA synthe 68.1 45 0.00097 28.3 8.3 62 23-84 64-144 (502)
73 PRK02001 hypothetical protein; 67.7 24 0.00052 25.1 5.8 35 6-40 76-118 (152)
74 PRK14644 hypothetical protein; 66.0 32 0.0007 23.9 6.1 44 7-51 73-129 (136)
75 PTZ00385 lysyl-tRNA synthetase 65.9 47 0.001 29.0 8.3 64 20-84 107-191 (659)
76 COG0017 AsnS Aspartyl/asparagi 65.6 62 0.0013 27.0 8.6 62 9-70 4-79 (435)
77 PF02699 YajC: Preprotein tran 64.7 2.2 4.7E-05 27.2 0.0 33 19-51 39-75 (82)
78 PRK04337 50S ribosomal protein 64.5 16 0.00035 23.9 4.1 42 16-65 36-87 (87)
79 cd04100 Asp_Lys_Asn_RS_N Asp_L 63.9 32 0.00068 21.2 7.1 49 22-70 1-62 (85)
80 smart00652 eIF1a eukaryotic tr 62.6 27 0.00058 22.3 4.9 40 25-64 7-52 (83)
81 COG0090 RplB Ribosomal protein 62.5 30 0.00064 27.1 5.9 46 27-72 152-199 (275)
82 TIGR00752 slp outer membrane l 62.3 54 0.0012 24.0 7.0 55 16-70 44-118 (182)
83 PF04410 Gar1: Gar1/Naf1 RNA b 62.3 13 0.00029 26.1 3.7 53 19-71 19-75 (154)
84 PRK14632 hypothetical protein; 62.1 25 0.00055 25.3 5.2 21 6-26 84-104 (172)
85 smart00318 SNc Staphylococcal 60.0 48 0.001 22.0 8.9 29 25-53 3-32 (138)
86 PRK14635 hypothetical protein; 58.8 32 0.00069 24.5 5.2 46 6-51 85-133 (162)
87 CHL00052 rpl2 ribosomal protei 57.9 34 0.00075 26.7 5.6 53 19-71 135-196 (273)
88 PF03843 Slp: Outer membrane l 57.7 66 0.0014 22.8 7.4 55 16-70 30-105 (160)
89 COG1588 POP4 RNase P/RNase MRP 57.1 26 0.00057 23.2 4.1 42 8-50 3-57 (95)
90 PRK09612 rpl2p 50S ribosomal p 56.5 37 0.00079 26.0 5.4 53 19-71 102-163 (238)
91 PRK09374 rplB 50S ribosomal pr 56.1 32 0.00069 26.9 5.1 52 19-70 137-197 (276)
92 TIGR01171 rplB_bact ribosomal 56.1 38 0.00083 26.4 5.6 54 19-72 135-197 (273)
93 PRK04012 translation initiatio 55.1 40 0.00087 22.3 4.8 29 25-53 23-52 (100)
94 cd05793 S1_IF1A S1_IF1A: Trans 54.6 45 0.00098 20.9 4.8 41 25-65 2-48 (77)
95 COG0173 AspS Aspartyl-tRNA syn 53.6 51 0.0011 28.5 6.3 58 12-69 7-77 (585)
96 PF01938 TRAM: TRAM domain; I 52.2 45 0.00097 19.3 5.2 46 17-65 2-47 (61)
97 PF12701 LSM14: Scd6-like Sm d 50.6 12 0.00026 24.7 1.7 17 13-29 1-17 (96)
98 PTZ00031 ribosomal protein L2; 50.4 53 0.0011 26.3 5.6 53 19-71 168-229 (317)
99 PF09939 DUF2171: Uncharacteri 50.2 23 0.00049 22.0 2.8 19 25-43 15-33 (67)
100 PRK12366 replication factor A; 50.0 67 0.0015 27.7 6.6 59 8-66 278-355 (637)
101 TIGR00523 eIF-1A eukaryotic/ar 48.5 60 0.0013 21.4 4.9 40 25-64 21-66 (99)
102 TIGR00008 infA translation ini 47.8 66 0.0014 19.9 5.5 32 22-53 4-36 (68)
103 cd05792 S1_eIF1AD_like S1_eIF1 47.6 57 0.0012 20.7 4.5 55 25-80 2-62 (78)
104 KOG2411 Aspartyl-tRNA syntheta 47.5 71 0.0015 27.6 6.1 57 13-69 40-109 (628)
105 PTZ00180 60S ribosomal protein 47.0 80 0.0017 24.5 6.0 53 19-71 109-172 (260)
106 PF02237 BPL_C: Biotin protein 46.4 52 0.0011 18.4 4.6 26 19-44 2-35 (48)
107 PTZ00041 60S ribosomal protein 43.6 58 0.0012 22.5 4.3 32 25-64 80-113 (120)
108 PRK06009 flgD flagellar basal 42.7 46 0.001 23.5 3.8 11 16-26 93-103 (140)
109 PF11495 Regulator_TrmB: Archa 41.7 44 0.00095 24.7 3.8 32 19-51 179-216 (233)
110 PF10842 DUF2642: Protein of u 41.6 84 0.0018 19.3 5.5 38 13-51 14-58 (66)
111 KOG1783 Small nuclear ribonucl 41.1 20 0.00044 22.7 1.6 17 9-25 5-21 (77)
112 cd01717 Sm_B The eukaryotic Sm 41.1 33 0.00071 21.3 2.6 17 12-28 2-18 (79)
113 COG0361 InfA Translation initi 41.0 93 0.002 19.7 5.0 32 21-52 5-37 (75)
114 PRK06531 yajC preprotein trans 40.8 58 0.0013 22.1 4.0 32 19-51 39-76 (113)
115 PRK00276 infA translation init 40.0 87 0.0019 19.1 7.1 44 22-65 6-56 (72)
116 cd04466 S1_YloQ_GTPase S1_YloQ 39.7 76 0.0017 18.3 5.6 40 26-65 2-47 (68)
117 cd04323 AsnRS_cyto_like_N AsnR 39.3 91 0.002 19.1 7.4 48 22-69 1-60 (84)
118 cd06395 PB1_Map2k5 PB1 domain 38.9 1.8 4E-05 28.2 -3.4 47 38-84 4-52 (91)
119 PRK13165 cytochrome c-type bio 38.8 1.5E+02 0.0032 21.4 13.2 92 8-99 36-147 (160)
120 PRK14699 replication factor A; 38.7 2.1E+02 0.0045 24.1 7.7 50 20-69 67-137 (484)
121 PF08863 YolD: YolD-like prote 38.7 70 0.0015 19.7 3.9 33 19-51 52-86 (92)
122 cd04483 hOBFC1_like hOBFC1_lik 37.0 1.1E+02 0.0024 19.5 7.8 13 58-70 65-77 (92)
123 cd00175 SNc Staphylococcal nuc 36.9 49 0.0011 21.6 3.1 22 32-53 3-24 (129)
124 PF11213 DUF3006: Protein of u 36.7 1E+02 0.0022 18.8 6.6 37 28-64 3-42 (71)
125 PF13457 SH3_8: SH3-like domai 36.5 96 0.0021 18.5 4.7 37 10-47 34-70 (79)
126 KOG0556 Aspartyl-tRNA syntheta 34.5 2.5E+02 0.0055 23.8 7.4 54 16-69 78-148 (533)
127 PF07013 DUF1314: Protein of u 34.5 66 0.0014 23.6 3.6 57 25-81 8-65 (177)
128 COG5496 Predicted thioesterase 34.4 93 0.002 21.8 4.2 37 10-46 63-102 (130)
129 PF10670 DUF4198: Domain of un 33.7 1.3E+02 0.0028 21.1 5.1 19 36-54 184-202 (215)
130 PRK14285 chaperone protein Dna 33.6 2.5E+02 0.0054 22.4 9.1 72 31-104 279-356 (365)
131 PLN00208 translation initiatio 33.0 1.3E+02 0.0027 21.5 4.8 29 25-53 34-63 (145)
132 COG2088 SpoVG Uncharacterized 32.8 66 0.0014 21.2 3.1 22 65-86 8-29 (95)
133 PRK12442 translation initiatio 32.5 1.4E+02 0.0031 19.4 5.4 31 22-52 6-37 (87)
134 PF03061 4HBT: Thioesterase su 32.3 1E+02 0.0022 17.6 3.9 30 11-40 37-67 (79)
135 PRK07211 replication factor A; 31.7 2.1E+02 0.0046 24.2 6.6 55 18-77 427-482 (485)
136 cd04486 YhcR_OBF_like YhcR_OBF 31.6 62 0.0013 20.1 2.8 19 18-36 46-64 (78)
137 cd01716 Hfq Hfq, an abundant, 31.0 1E+02 0.0022 18.7 3.5 28 21-49 20-47 (61)
138 PF12272 DUF3610: Protein of u 30.5 79 0.0017 22.8 3.4 29 39-69 24-52 (157)
139 PF00868 Transglut_N: Transglu 30.3 37 0.00081 22.8 1.7 26 36-61 84-110 (118)
140 PRK10409 hydrogenase assembly 29.9 1.6E+02 0.0035 19.1 5.3 43 23-66 3-52 (90)
141 PRK09618 flgD flagellar basal 29.8 61 0.0013 22.9 2.8 11 15-25 87-97 (142)
142 PF10054 DUF2291: Predicted pe 29.7 74 0.0016 23.6 3.3 30 22-51 90-125 (205)
143 PHA02581 9 baseplate wedge tai 29.5 1.2E+02 0.0025 24.0 4.4 36 34-75 80-115 (284)
144 PRK14337 (dimethylallyl)adenos 29.4 2.3E+02 0.005 23.1 6.4 55 10-64 372-430 (446)
145 PF03931 Skp1_POZ: Skp1 family 29.0 69 0.0015 18.7 2.6 55 36-99 2-58 (62)
146 PF01203 T2SN: Type II secreti 28.9 2.3E+02 0.005 20.6 8.6 83 9-94 106-201 (221)
147 COG0621 MiaB 2-methylthioadeni 28.8 3.4E+02 0.0075 22.6 7.5 66 9-76 367-433 (437)
148 PRK13450 atpC F0F1 ATP synthas 28.8 1.9E+02 0.0042 19.6 7.0 53 43-99 46-102 (132)
149 PF11148 DUF2922: Protein of u 28.6 1.2E+02 0.0027 18.1 3.7 19 37-55 5-23 (69)
150 PF09853 DUF2080: Putative tra 28.5 42 0.00092 19.9 1.5 20 7-26 28-47 (53)
151 cd03524 RPA2_OBF_family RPA2_O 28.0 1.1E+02 0.0024 16.7 7.1 47 24-70 1-61 (75)
152 COG3798 Uncharacterized protei 27.8 61 0.0013 20.5 2.2 26 20-45 15-40 (75)
153 CHL00010 infA translation init 27.7 1.6E+02 0.0034 18.3 5.4 44 22-65 6-56 (78)
154 PTZ00329 eukaryotic translatio 27.6 1.7E+02 0.0038 21.0 4.8 29 25-53 34-63 (155)
155 KOG0054 Multidrug resistance-a 27.2 15 0.00032 34.7 -1.0 41 57-99 573-621 (1381)
156 PF01556 CTDII: DnaJ C termina 26.7 1.6E+02 0.0034 18.0 4.3 58 31-89 13-77 (81)
157 PF09776 Mitoc_L55: Mitochondr 26.1 48 0.001 22.7 1.6 58 37-96 47-115 (116)
158 TIGR02383 Hfq RNA chaperone Hf 26.0 1.4E+02 0.003 18.1 3.5 24 22-46 25-48 (61)
159 PF04351 PilP: Pilus assembly 26.0 1.8E+02 0.004 20.1 4.7 39 13-51 69-107 (149)
160 PF15232 DUF4585: Domain of un 25.9 1.3E+02 0.0029 19.0 3.5 36 27-65 8-45 (75)
161 cd04488 RecG_wedge_OBF RecG_we 24.8 1.4E+02 0.0031 16.8 3.9 23 19-42 48-70 (75)
162 PF07443 HARP: HepA-related pr 24.4 71 0.0015 19.0 2.0 19 85-104 31-49 (55)
163 cd01736 LSm14_N LSm14 (also kn 24.3 94 0.002 19.6 2.6 15 16-30 2-16 (74)
164 cd01721 Sm_D3 The eukaryotic S 24.2 1.2E+02 0.0026 18.3 3.1 22 13-34 3-32 (70)
165 PF12971 NAGLU_N: Alpha-N-acet 23.8 95 0.002 19.6 2.6 22 33-54 30-51 (86)
166 cd01723 LSm4 The eukaryotic Sm 23.5 1.9E+02 0.004 17.7 5.0 22 13-34 4-33 (76)
167 COG3277 GAR1 RNA-binding prote 23.5 1.4E+02 0.0031 19.8 3.5 44 25-70 3-51 (98)
168 PRK14327 (dimethylallyl)adenos 23.2 2.8E+02 0.0062 23.3 6.0 53 10-64 435-488 (509)
169 PRK06792 flgD flagellar basal 22.8 1E+02 0.0022 22.9 2.9 49 16-68 114-167 (190)
170 PF00924 MS_channel: Mechanose 22.6 1.6E+02 0.0034 20.7 3.9 25 25-49 72-96 (206)
171 PRK13149 H/ACA RNA-protein com 22.5 87 0.0019 19.3 2.2 42 25-70 3-50 (73)
172 cd00210 PTS_IIA_glc PTS_IIA, P 22.1 2.1E+02 0.0045 19.5 4.2 39 27-65 44-85 (124)
173 COG2139 RPL21A Ribosomal prote 21.8 1.8E+02 0.0039 19.4 3.7 34 17-54 55-88 (98)
174 PF13861 FLgD_tudor: FlgD Tudo 21.8 1.8E+02 0.0039 16.9 3.7 15 16-30 8-22 (61)
175 PF03947 Ribosomal_L2_C: Ribos 21.7 54 0.0012 22.6 1.2 44 27-70 29-74 (130)
176 PF00337 Gal-bind_lectin: Gala 21.6 1.7E+02 0.0037 19.2 3.7 37 18-54 11-51 (133)
177 COG3168 PilP Tfp pilus assembl 21.5 1.7E+02 0.0037 21.3 3.8 46 5-51 80-125 (170)
178 PF01868 UPF0086: Domain of un 21.4 2.3E+02 0.005 18.0 4.4 34 16-49 10-54 (89)
179 PF11720 Inhibitor_I78: Peptid 21.3 1.3E+02 0.0027 17.7 2.7 16 11-26 2-17 (60)
180 PRK00539 atpC F0F1 ATP synthas 21.2 2.8E+02 0.0061 18.9 7.2 56 40-99 43-102 (133)
181 PRK14736 atpC F0F1 ATP synthas 21.2 2.8E+02 0.0061 19.0 7.6 56 40-99 43-102 (133)
182 cd01732 LSm5 The eukaryotic Sm 21.0 1.4E+02 0.0031 18.5 3.0 13 13-25 6-18 (76)
183 cd04490 PolII_SU_OBF PolII_SU_ 21.0 2.2E+02 0.0047 17.5 4.9 55 23-78 2-71 (79)
184 PF14299 PP2: Phloem protein 2 20.8 3E+02 0.0065 19.1 5.4 55 9-65 50-114 (154)
185 PHA01634 hypothetical protein 20.7 82 0.0018 22.5 2.0 41 9-49 106-153 (156)
186 PF01247 Ribosomal_L35Ae: Ribo 20.6 2.6E+02 0.0057 18.4 4.8 32 25-64 61-94 (95)
187 TIGR02603 CxxCH_TIGR02603 puta 20.4 2.8E+02 0.0061 18.6 4.7 27 25-51 70-96 (133)
188 PHA02099 hypothetical protein 20.3 2.2E+02 0.0049 18.0 3.7 35 64-99 24-66 (84)
189 PF09642 YonK: YonK protein; 20.2 1.3E+02 0.0028 18.3 2.5 19 12-30 35-53 (62)
190 PRK03879 ribonuclease P protei 20.2 2.6E+02 0.0057 18.2 5.2 58 10-68 3-79 (96)
191 PF11525 CopK: Copper resistan 20.1 1.3E+02 0.0029 18.9 2.6 16 38-53 43-58 (73)
192 cd00070 GLECT Galectin/galacto 20.1 2.6E+02 0.0057 18.3 4.4 34 18-53 11-46 (127)
193 PRK10917 ATP-dependent DNA hel 20.0 4.2E+02 0.0092 22.9 6.6 52 19-70 58-122 (681)
No 1
>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=100.00 E-value=5.2e-41 Score=226.37 Aligned_cols=103 Identities=41% Similarity=0.669 Sum_probs=82.6
Q ss_pred CCCCCCceeeehhhhhccCCCeEEEEEEEeecc--CCeEEEEeCCCCEEEEEccCCC-CCCCCEEEEEEEECCCC---CE
Q 033976 1 MDTSNPAVFVNGGLMRMYVGRRIRTVIQVIQSD--GGGVTGKSTDGHQLVVKGPQPG-FPLTTFVEVIGIADTDR---SI 74 (107)
Q Consensus 1 Md~~~~~pRVn~~~L~~~~Gk~VrlvGkV~~~~--g~~~~~~s~D~g~V~v~l~~~~-~~~~~~vEViG~V~~~~---si 74 (107)
|| .|+||||+++|++|+||+|||+|||.+++ |++++++|+||++|+|.+++|. ...++||||||+|++++ +|
T Consensus 1 M~--~~~pRVn~~~L~~~~gk~VrivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~~~~~~~~vEviG~V~~~~~~~~i 78 (109)
T PF08661_consen 1 MD--APTPRVNGSMLSQFVGKTVRIVGKVESVDPDGGSATLSTSDGGQVTVSLNPPSDEELSKYVEVIGKVNDDGTVLSI 78 (109)
T ss_dssp GG--S--EEE-GGGGGGGTTSEEEEEEEEEEE-TTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-TTS-EEEE
T ss_pred CC--CCcceECHHHHHhhCCCeEEEEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCCCCCCCCEEEEEEEEcCCCCceEE
Confidence 78 67999999999999999999999999998 9999999999999999999883 45799999999999999 99
Q ss_pred EEEEEEeCCCCCCHHHHHHHHHHHhccccCCC
Q 033976 75 RAEIWNNFGNTFDTQSYNQLCQLANGEFKHLF 106 (107)
Q Consensus 75 ~~~~~~~~g~~fD~~~yn~lv~l~~~~~~~lF 106 (107)
++..+++||++||+++||++|+++| +||+||
T Consensus 79 ~~~~~~~~g~~~D~~~y~~lv~l~~-~~p~lf 109 (109)
T PF08661_consen 79 RYFSFTDFGDDFDMDLYNELVQLTH-KFPELF 109 (109)
T ss_dssp EEEE---SSS---HHHHHHHHHHHH-HSGGGS
T ss_pred EEEEeccCCCCcCHHHHHHHHHHHh-hCCccC
Confidence 9999999999999999999999999 999998
No 2
>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=100.00 E-value=1.6e-40 Score=221.98 Aligned_cols=100 Identities=37% Similarity=0.684 Sum_probs=97.4
Q ss_pred CceeeehhhhhccCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEccCC-CCCCCCEEEEEEEECCCCCEEEEEEEeCCC
Q 033976 6 PAVFVNGGLMRMYVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKGPQP-GFPLTTFVEVIGIADTDRSIRAEIWNNFGN 84 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l~~~-~~~~~~~vEViG~V~~~~si~~~~~~~~g~ 84 (107)
|+||||++||++|+||+|||+|||.+++|++++++|+||++|+|.|++| +.+.++||||+|+|+++++|++.++++||+
T Consensus 1 p~prVn~~~L~~f~gk~V~ivGkV~~~~~~~~~~~~~Dg~~v~v~l~~~~~~~~~~~vEViG~V~~~~~I~~~~~~~~g~ 80 (101)
T cd04479 1 PTPRINGAMLSQFVGKTVRIVGKVEKVDGDSLTLISSDGVNVTVELNRPLDLPISGYVEVIGKVSPDLTIRVLSYIDFGD 80 (101)
T ss_pred CCceeCHHHHHhhCCCEEEEEEEEEEecCCeEEEEcCCCCEEEEEeCCCCCcccCCEEEEEEEECCCCeEEEEEEEECCC
Confidence 6899999999999999999999999999999999999999999999988 578899999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHhccccCCC
Q 033976 85 TFDTQSYNQLCQLANGEFKHLF 106 (107)
Q Consensus 85 ~fD~~~yn~lv~l~~~~~~~lF 106 (107)
+||+++||++|+++| +||++|
T Consensus 81 ~~D~~~yn~lv~l~~-~~~~~f 101 (101)
T cd04479 81 DFDMDLYNELVKLSH-KFKNLF 101 (101)
T ss_pred ccCHHHHHHHHHHHh-hCcccC
Confidence 999999999999999 899998
No 3
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=98.02 E-value=0.00014 Score=49.92 Aligned_cols=85 Identities=21% Similarity=0.203 Sum_probs=58.9
Q ss_pred ccCCCeEEEEEEEeeccC--CeEEEE---eCCCCEEEE--EccCC-CCCCCCEEEEEEEECCC----CCEEEEEEEeCCC
Q 033976 17 MYVGRRIRTVIQVIQSDG--GGVTGK---STDGHQLVV--KGPQP-GFPLTTFVEVIGIADTD----RSIRAEIWNNFGN 84 (107)
Q Consensus 17 ~~~Gk~VrlvGkV~~~~g--~~~~~~---s~D~g~V~v--~l~~~-~~~~~~~vEViG~V~~~----~si~~~~~~~~g~ 84 (107)
...|+.||+.|++.+.|- ..+++. ..++..+.| ++-+| ....+..|.|+|-.... ..+-..-..-+=|
T Consensus 18 ~~~g~svR~~GrL~~yD~~~~~a~l~~~~~~~~~~l~V~t~~l~~~~~~~gslyq~iGEl~~~~~~~~~~L~ARV~r~Vd 97 (118)
T PF15490_consen 18 VPEGKSVRTFGRLQSYDVATSRATLTAQHESDQHSLKVDTKLLEPFQARVGSLYQFIGELEHQPQDGGIVLKARVLRCVD 97 (118)
T ss_pred ccCCCeEEEEEEEEEEeccCCEEEEEeeccCCCcEEEEEeeEccccccCCCCEEEEEEEEEEEcCCCcEEEEEEEEEecC
Confidence 457999999999998765 456561 234555555 45455 35579999999998632 2222223334448
Q ss_pred CCCHHHHHHHHHHHhccc
Q 033976 85 TFDTQSYNQLCQLANGEF 102 (107)
Q Consensus 85 ~fD~~~yn~lv~l~~~~~ 102 (107)
.+|+++|++++++-. +|
T Consensus 98 G~Dl~Ly~~al~~rR-kf 114 (118)
T PF15490_consen 98 GMDLNLYEQALQERR-KF 114 (118)
T ss_pred CcCHHHHHHHHHHHH-HH
Confidence 899999999999987 66
No 4
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=96.84 E-value=0.014 Score=40.31 Aligned_cols=90 Identities=17% Similarity=0.196 Sum_probs=54.5
Q ss_pred Cceeeehhhhhc-cCCCeEEEEEEEeeccCCe--EEEEeC-------CCCEEEEEccCC--C-----CCCCCEEEEEEEE
Q 033976 6 PAVFVNGGLMRM-YVGRRIRTVIQVIQSDGGG--VTGKST-------DGHQLVVKGPQP--G-----FPLTTFVEVIGIA 68 (107)
Q Consensus 6 ~~pRVn~~~L~~-~~Gk~VrlvGkV~~~~g~~--~~~~s~-------D~g~V~v~l~~~--~-----~~~~~~vEViG~V 68 (107)
|+..+..+.|+. -.|++||++|-|.+.+..+ ++++-. +...+.|..+.- + ...+.||.|+|-+
T Consensus 10 ~~~l~fl~~l~s~~~g~KVRfLgcV~~Y~~~~~~L~l~h~~p~~~~~~~~~v~VdI~~vL~tv~~~~~rvG~WvNV~Gy~ 89 (124)
T PF12658_consen 10 PSQLLFLSQLPSCSPGDKVRFLGCVSSYDTSTGTLTLEHNYPRENDSQPSSVSVDINLVLETVSSEELRVGEWVNVVGYI 89 (124)
T ss_dssp GHCCH-CCGGGCTTCTEEEEEEEEEEEEECCCTEEEEEETCCC---S----EEEE-TTTTTTS-GGGGSTT-EEEEEEEE
T ss_pred chhHhCccccccCCCCCEEEEEEEEeEEecCccEEEEeecCCCCcCCCCceEEEEHHHHhhhcCccceecceEEEEEEEe
Confidence 345555566655 4799999999999887654 444431 222455554332 1 1238999999999
Q ss_pred CCCCC--------EEEEEEEeCCCCCCHHHHHHHHH
Q 033976 69 DTDRS--------IRAEIWNNFGNTFDTQSYNQLCQ 96 (107)
Q Consensus 69 ~~~~s--------i~~~~~~~~g~~fD~~~yn~lv~ 96 (107)
++... +++..+...| .+|+..|.+.++
T Consensus 90 ~~~~~~~~~~~v~Vqai~i~~ag-~~dl~~ye~~l~ 124 (124)
T PF12658_consen 90 RGEKPSQTQSPVYVQAIMIWSAG-PIDLGEYEESLQ 124 (124)
T ss_dssp ECTT--------EEEEEEEEE-T-CGGHHHHHHHHH
T ss_pred cccccccccccceEEEEEEEecC-chhhhhhhcccC
Confidence 86553 5555555544 588999988765
No 5
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.29 E-value=0.027 Score=48.11 Aligned_cols=73 Identities=19% Similarity=0.160 Sum_probs=49.8
Q ss_pred CCceeeehhhhhccCCCeEEEEEEEeec---cCCe-EEEEeCCCCEEEE-EccCC------CCCCCCEEEEEEEEC-CCC
Q 033976 5 NPAVFVNGGLMRMYVGRRIRTVIQVIQS---DGGG-VTGKSTDGHQLVV-KGPQP------GFPLTTFVEVIGIAD-TDR 72 (107)
Q Consensus 5 ~~~pRVn~~~L~~~~Gk~VrlvGkV~~~---~g~~-~~~~s~D~g~V~v-~l~~~------~~~~~~~vEViG~V~-~~~ 72 (107)
.-.||....-|.+++|++|+|-|+|.++ .|-+ |+++ ...|.+.+ -+-.+ .-..+.+|+|||.|+ -++
T Consensus 198 ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GPTVFtlt-Detg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V~~r~g 276 (715)
T COG1107 198 KELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLT-DETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEVTRRDG 276 (715)
T ss_pred hhcccccHHHHHhhcCceEEEEEEEEEEEEcCCCEEEEEe-cCCCceehhhhccCCcccCCCCCCCceEEEEEEEeecCC
Confidence 3469999999999999999999999954 4544 4443 22344444 22222 123599999999998 366
Q ss_pred CEEEEE
Q 033976 73 SIRAEI 78 (107)
Q Consensus 73 si~~~~ 78 (107)
.++.+.
T Consensus 277 ~lQiE~ 282 (715)
T COG1107 277 RLQIEI 282 (715)
T ss_pred cEEEee
Confidence 666543
No 6
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=94.74 E-value=0.26 Score=33.64 Aligned_cols=55 Identities=16% Similarity=0.098 Sum_probs=38.3
Q ss_pred hccCCCeEEEEEEEeecc--CCeEEEEeCCC-CEEEEEccCC---------CCCCCCEEEEEEEECC
Q 033976 16 RMYVGRRIRTVIQVIQSD--GGGVTGKSTDG-HQLVVKGPQP---------GFPLTTFVEVIGIADT 70 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~--g~~~~~~s~D~-g~V~v~l~~~---------~~~~~~~vEViG~V~~ 70 (107)
..+.|++|++.|.|.+.. |+..-+.-.|+ +.+++.++.. ....+.+|+|.|++..
T Consensus 10 ~~~~g~~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~ 76 (135)
T cd04317 10 ESHVGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRA 76 (135)
T ss_pred hhHCCCEEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEEC
Confidence 477899999999999653 44444444444 6777776542 1245899999998863
No 7
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=94.69 E-value=0.37 Score=31.71 Aligned_cols=68 Identities=16% Similarity=0.127 Sum_probs=44.1
Q ss_pred hccCCCeEEEEEEEeecc--CCeEEEEeCCC-CEEEEEccCCC-----------CCCCCEEEEEEEECCC------CCEE
Q 033976 16 RMYVGRRIRTVIQVIQSD--GGGVTGKSTDG-HQLVVKGPQPG-----------FPLTTFVEVIGIADTD------RSIR 75 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~--g~~~~~~s~D~-g~V~v~l~~~~-----------~~~~~~vEViG~V~~~------~si~ 75 (107)
.++.|+.|++-|.|.+.. |+..-+...|+ +.+++.+.... ...+..|+|.|++... ..|.
T Consensus 8 ~~~~g~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~ 87 (108)
T cd04316 8 PELDGEEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEII 87 (108)
T ss_pred hhhCCCEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEE
Confidence 377899999999999653 45444444444 56777664321 2458999999998632 2355
Q ss_pred EEEEEeCC
Q 033976 76 AEIWNNFG 83 (107)
Q Consensus 76 ~~~~~~~g 83 (107)
+..+.-++
T Consensus 88 ~~~i~il~ 95 (108)
T cd04316 88 PEEIEVLS 95 (108)
T ss_pred EeEEEEEe
Confidence 55555554
No 8
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding 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 dependent manner in response to DNA dam
Probab=94.37 E-value=0.78 Score=29.07 Aligned_cols=69 Identities=22% Similarity=0.203 Sum_probs=44.0
Q ss_pred eEEEEEEEeecc--CCeEEEEeCCC-CEEEEEccCCCC----------CCCCEEEEEEEECC---CCCEEEEEEEeCCCC
Q 033976 22 RIRTVIQVIQSD--GGGVTGKSTDG-HQLVVKGPQPGF----------PLTTFVEVIGIADT---DRSIRAEIWNNFGNT 85 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~~~~~~s~D~-g~V~v~l~~~~~----------~~~~~vEViG~V~~---~~si~~~~~~~~g~~ 85 (107)
.|++||.|.+++ +..++++-.|+ |.+.++.-.+++ ..+.+|.|.|++.. ...|+........ +
T Consensus 1 ~v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~~v~-d 79 (95)
T cd04478 1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVT-D 79 (95)
T ss_pred CEEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEEEeC-C
Confidence 389999999775 45566655553 578876654421 23789999999974 4456655555443 3
Q ss_pred CCHHHH
Q 033976 86 FDTQSY 91 (107)
Q Consensus 86 fD~~~y 91 (107)
++--.|
T Consensus 80 ~ne~~~ 85 (95)
T cd04478 80 FNEVTY 85 (95)
T ss_pred ccHHHH
Confidence 444443
No 9
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=93.91 E-value=0.78 Score=37.46 Aligned_cols=77 Identities=12% Similarity=-0.036 Sum_probs=51.9
Q ss_pred eeeehhhhhc-cCCCeEEEEEEEeec--cCCeEEEEeC-CCCEEEEEccCC----------CCCCCCEEEEEEEECC---
Q 033976 8 VFVNGGLMRM-YVGRRIRTVIQVIQS--DGGGVTGKST-DGHQLVVKGPQP----------GFPLTTFVEVIGIADT--- 70 (107)
Q Consensus 8 pRVn~~~L~~-~~Gk~VrlvGkV~~~--~g~~~~~~s~-D~g~V~v~l~~~----------~~~~~~~vEViG~V~~--- 70 (107)
.|+..+-|.. +.|++|+|-|+|.+. .|+..-+.-. ..+.+++.++.. ....+.+|.|.|+|..
T Consensus 3 ~~~~~~~l~~~~~g~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~~~ 82 (437)
T PRK05159 3 KRHLTSELTPELDGEEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPK 82 (437)
T ss_pred ceeEhhhCChhhCCCEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcCCC
Confidence 3666777765 459999999999966 4554323333 336788887542 1346999999999963
Q ss_pred ---CCCEEEEEEEeCCC
Q 033976 71 ---DRSIRAEIWNNFGN 84 (107)
Q Consensus 71 ---~~si~~~~~~~~g~ 84 (107)
+..|.+..+.-++.
T Consensus 83 ~~~~~el~~~~i~vls~ 99 (437)
T PRK05159 83 APGGVEVIPEEIEVLNK 99 (437)
T ss_pred CCCCEEEEEeEEEEEeC
Confidence 23477777766653
No 10
>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=93.83 E-value=0.33 Score=32.48 Aligned_cols=57 Identities=11% Similarity=-0.024 Sum_probs=41.9
Q ss_pred hhccCCCeEEEEEEEe-eccCCeEEEEeCCCCEEEEEccCC-CC----CCCCEEEEEEEECCCC
Q 033976 15 MRMYVGRRIRTVIQVI-QSDGGGVTGKSTDGHQLVVKGPQP-GF----PLTTFVEVIGIADTDR 72 (107)
Q Consensus 15 L~~~~Gk~VrlvGkV~-~~~g~~~~~~s~D~g~V~v~l~~~-~~----~~~~~vEViG~V~~~~ 72 (107)
+...-+..|.|-|++. +++++....+-.- |+|.|.+... .. ..+.-|+|.|+|+.+.
T Consensus 29 ~~~~Dd~~V~L~G~Iv~~l~~d~Y~F~D~T-G~I~VeId~~~w~g~~vt~~~~Vri~GeVDk~~ 91 (103)
T PF04076_consen 29 KNAKDDTPVTLEGNIVKQLGDDKYLFRDAT-GEIEVEIDDDVWRGQTVTPDDKVRISGEVDKDW 91 (103)
T ss_dssp TTS-SSEEEEEEEEEEEEEETTEEEEEETT-EEEEEE--GGGSTT----TTSEEEEEEEEEEET
T ss_pred hhCcCCCeEEEEEEEEEEecCCEEEEECCC-CcEEEEEChhhcCCcccCCCCEEEEEEEEeCCC
Confidence 4557799999999988 7788888787665 5999999665 21 2378999999998444
No 11
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=93.17 E-value=1.8 Score=35.53 Aligned_cols=69 Identities=17% Similarity=0.107 Sum_probs=46.7
Q ss_pred hccCCCeEEEEEEEeec--cCCeEEEEeCCC-CEEEEEccCC---C-------CCCCCEEEEEEEECC------CCCEEE
Q 033976 16 RMYVGRRIRTVIQVIQS--DGGGVTGKSTDG-HQLVVKGPQP---G-------FPLTTFVEVIGIADT------DRSIRA 76 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~--~g~~~~~~s~D~-g~V~v~l~~~---~-------~~~~~~vEViG~V~~------~~si~~ 76 (107)
..+.|++|++.|+|.++ .|+.+-+.-.|+ |.+++.+... . ...+.+|+|.|+|.. +..|.+
T Consensus 12 ~~~~~~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~ 91 (450)
T PRK03932 12 GKYVGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVESPRAGQGYELQA 91 (450)
T ss_pred cccCCCEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEcCCCCCCCEEEEE
Confidence 57889999999999955 355444444444 4444444221 1 246999999999974 345888
Q ss_pred EEEEeCCC
Q 033976 77 EIWNNFGN 84 (107)
Q Consensus 77 ~~~~~~g~ 84 (107)
..+.-++.
T Consensus 92 ~~i~vl~~ 99 (450)
T PRK03932 92 TKIEVIGE 99 (450)
T ss_pred EEEEEccC
Confidence 88877774
No 12
>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=93.09 E-value=0.28 Score=27.45 Aligned_cols=27 Identities=33% Similarity=0.506 Sum_probs=24.3
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
+.|+|.+.+|+.+++++.||.+++|.-
T Consensus 14 v~g~I~~~~g~~vtV~~~~G~~~tv~~ 40 (42)
T PF02736_consen 14 VKGEIIEEEGDKVTVKTEDGKEVTVKK 40 (42)
T ss_dssp EEEEEEEEESSEEEEEETTTEEEEEEG
T ss_pred EEEEEEEEcCCEEEEEECCCCEEEeCC
Confidence 679999999999999999999998864
No 13
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=92.79 E-value=1.1 Score=36.83 Aligned_cols=68 Identities=13% Similarity=0.059 Sum_probs=46.7
Q ss_pred hccCCCeEEEEEEEeec--cCCeEEEEeCCC---CEEEEEccCC-C---------CCCCCEEEEEEEECC------CCCE
Q 033976 16 RMYVGRRIRTVIQVIQS--DGGGVTGKSTDG---HQLVVKGPQP-G---------FPLTTFVEVIGIADT------DRSI 74 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~--~g~~~~~~s~D~---g~V~v~l~~~-~---------~~~~~~vEViG~V~~------~~si 74 (107)
..+.|++|++.|+|.++ .|+.+-+...|+ |.+++.++.. . ...+.+|+|.|+|.. +..|
T Consensus 12 ~~~~g~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El 91 (453)
T TIGR00457 12 YKFVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESPGKGQPVEL 91 (453)
T ss_pred hhcCCCEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCCCCCCCEEE
Confidence 47889999999999965 345555666666 4788876543 1 245999999999863 2345
Q ss_pred EEEEEEeCC
Q 033976 75 RAEIWNNFG 83 (107)
Q Consensus 75 ~~~~~~~~g 83 (107)
.+....-++
T Consensus 92 ~~~~i~vl~ 100 (453)
T TIGR00457 92 QVKKIEVVG 100 (453)
T ss_pred EEeEEEEEe
Confidence 555555554
No 14
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=92.60 E-value=2.7 Score=29.83 Aligned_cols=93 Identities=18% Similarity=0.050 Sum_probs=63.8
Q ss_pred ceeeehhhhhc---cCCCeEEEEEEEe--ec---cCCeEEEEeCC-CCEEEEEccCC--C-CCCCCEEEEEEEECCCCCE
Q 033976 7 AVFVNGGLMRM---YVGRRIRTVIQVI--QS---DGGGVTGKSTD-GHQLVVKGPQP--G-FPLTTFVEVIGIADTDRSI 74 (107)
Q Consensus 7 ~pRVn~~~L~~---~~Gk~VrlvGkV~--~~---~g~~~~~~s~D-~g~V~v~l~~~--~-~~~~~~vEViG~V~~~~si 74 (107)
.+.++.+.+.+ +.||.||+-|.|. ++ ++..++..-+| +..+.|..... + ...+.-|=++|+.++++..
T Consensus 35 ~yf~tpse~~~~~~~~g~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~lPd~F~eg~~VVv~G~~~~~g~F 114 (148)
T PRK13254 35 VFFYTPSEVAEGEAPAGRRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGILPDLFREGQGVVAEGRLQDGGVF 114 (148)
T ss_pred ceeeCHHHHhcCCccCCCeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCCCCccccCCCEEEEEEEECCCCeE
Confidence 45666776644 7899999999998 33 44444443333 56778877543 2 2238888899999988888
Q ss_pred EEEEE-EeCCCCCCHHHHHHHHHHHh
Q 033976 75 RAEIW-NNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 75 ~~~~~-~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+... ..+.+++-.....+..+-.+
T Consensus 115 ~A~~vLaKc~skY~p~ev~~~~~~~~ 140 (148)
T PRK13254 115 VADEVLAKHDENYMPKEVADALKKAG 140 (148)
T ss_pred EEEEEEecCCCCCCCHHHHHHHHHhc
Confidence 88776 67777877666666666555
No 15
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=91.24 E-value=1.9 Score=35.25 Aligned_cols=67 Identities=16% Similarity=0.117 Sum_probs=44.9
Q ss_pred ccCCCeEEEEEEEeec--cCCeEEEE-eCCCCEEEEEccCCC-----------CCCCCEEEEEEEECC------CCCEEE
Q 033976 17 MYVGRRIRTVIQVIQS--DGGGVTGK-STDGHQLVVKGPQPG-----------FPLTTFVEVIGIADT------DRSIRA 76 (107)
Q Consensus 17 ~~~Gk~VrlvGkV~~~--~g~~~~~~-s~D~g~V~v~l~~~~-----------~~~~~~vEViG~V~~------~~si~~ 76 (107)
.+.||.|++-|+|.+. .|+..-+. ....+.|++.++... ...+..|+|.|+|.. +..|.+
T Consensus 9 ~~~g~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~ 88 (428)
T TIGR00458 9 EMDGQEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEKAPGGFEIIP 88 (428)
T ss_pred hhCCCEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCCCCCcEEEEE
Confidence 6789999999999965 34432233 333467888775421 235999999999862 345666
Q ss_pred EEEEeCC
Q 033976 77 EIWNNFG 83 (107)
Q Consensus 77 ~~~~~~g 83 (107)
..+.-++
T Consensus 89 ~~i~vl~ 95 (428)
T TIGR00458 89 TKIEVIN 95 (428)
T ss_pred eEEEEEe
Confidence 6665555
No 16
>PRK10053 hypothetical protein; Provisional
Probab=90.98 E-value=2.8 Score=29.26 Aligned_cols=58 Identities=12% Similarity=0.084 Sum_probs=44.6
Q ss_pred hhhccCCCeEEEEEEEe-eccCCeEEEEeCCCCEEEEEccCC-C----CCCCCEEEEEEEECCCC
Q 033976 14 LMRMYVGRRIRTVIQVI-QSDGGGVTGKSTDGHQLVVKGPQP-G----FPLTTFVEVIGIADTDR 72 (107)
Q Consensus 14 ~L~~~~Gk~VrlvGkV~-~~~g~~~~~~s~D~g~V~v~l~~~-~----~~~~~~vEViG~V~~~~ 72 (107)
.+..+-+..|.|-|++. ++.++....+-.- |+|+|.+... . .....-|++.|.|+.+.
T Consensus 55 a~~~~Dd~~V~L~G~Iv~~lg~d~Y~F~D~t-G~I~VeID~~~w~G~~v~p~~kV~I~GevDk~~ 118 (130)
T PRK10053 55 AKTMHDGATVSLRGNLIDHKGDDRYVFRDKS-GEINVIIPAAVFDGREVQPDQMININGSLDKKS 118 (130)
T ss_pred hhcCcCCCeEEEEEEEEEEeCCceEEEECCC-CcEEEEeCHHHcCCCcCCCCCEEEEEEEECCCC
Confidence 45567899999999999 6777877666554 6899998654 2 22488999999998653
No 17
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=90.45 E-value=2.5 Score=35.20 Aligned_cols=63 Identities=13% Similarity=0.112 Sum_probs=43.4
Q ss_pred CeEEEEEEEeecc--CCeEEEEeCC-CCEEEEEccCCC-----------CCCCCEEEEEEEEC----CCCCEEEEEEEeC
Q 033976 21 RRIRTVIQVIQSD--GGGVTGKSTD-GHQLVVKGPQPG-----------FPLTTFVEVIGIAD----TDRSIRAEIWNNF 82 (107)
Q Consensus 21 k~VrlvGkV~~~~--g~~~~~~s~D-~g~V~v~l~~~~-----------~~~~~~vEViG~V~----~~~si~~~~~~~~ 82 (107)
++|++-|+|.++. |+..-+...| .|.|+|.++... ...+.+|+|.|+|. ++.+|.+..+.-+
T Consensus 55 ~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~ge~el~~~~~~vl 134 (491)
T PRK00484 55 IEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTGELSVKATELTLL 134 (491)
T ss_pred cEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCCcEEEEEeEEEEE
Confidence 8899999999663 5543344433 367888775431 23589999999996 4566777777666
Q ss_pred C
Q 033976 83 G 83 (107)
Q Consensus 83 g 83 (107)
+
T Consensus 135 s 135 (491)
T PRK00484 135 T 135 (491)
T ss_pred e
Confidence 5
No 18
>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=90.43 E-value=3.3 Score=28.74 Aligned_cols=57 Identities=14% Similarity=0.107 Sum_probs=42.8
Q ss_pred hhccCCCeEEEEEEEe-eccCCeEEEEeCCCCEEEEEccCC-C----CCCCCEEEEEEEECCCC
Q 033976 15 MRMYVGRRIRTVIQVI-QSDGGGVTGKSTDGHQLVVKGPQP-G----FPLTTFVEVIGIADTDR 72 (107)
Q Consensus 15 L~~~~Gk~VrlvGkV~-~~~g~~~~~~s~D~g~V~v~l~~~-~----~~~~~~vEViG~V~~~~ 72 (107)
+...-+..|.|-|++. +++++....+-.- |+|+|..... . ...+.-|+|.|+|+.+.
T Consensus 52 ~~~~Ddt~V~L~G~Iv~~l~~d~Y~F~D~T-G~I~VeId~~~w~G~~v~p~d~V~I~GeVDk~~ 114 (126)
T TIGR00156 52 KSMHDGASVTLRGNIISHIGDDRYVFRDKS-GEINVVIPAAVWNGREVQPKDMVNISGSLDKKS 114 (126)
T ss_pred hhCCCCCEEEEEEEEEEEeCCceEEEECCC-CCEEEEECHHHcCCCcCCCCCEEEEEEEECCCC
Confidence 3345689999999999 6777877676554 6899998653 2 22488999999998653
No 19
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=90.38 E-value=0.77 Score=31.20 Aligned_cols=55 Identities=16% Similarity=0.035 Sum_probs=33.2
Q ss_pred hccCCCeEEEEEEEeec----cCCeEEEEeC--CCCEEEEEccCCC--------CCCCCEEEEEEEECC
Q 033976 16 RMYVGRRIRTVIQVIQS----DGGGVTGKST--DGHQLVVKGPQPG--------FPLTTFVEVIGIADT 70 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~----~g~~~~~~s~--D~g~V~v~l~~~~--------~~~~~~vEViG~V~~ 70 (107)
.+|.||.+.+-|+|.++ .+.++++... +...|.+.+..++ ...+.-|-|.|++.+
T Consensus 63 ~kY~gK~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g 131 (144)
T PF12869_consen 63 KKYKGKIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKGICTG 131 (144)
T ss_dssp HHHTT-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEEEE---
T ss_pred hhcCCCEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEEEEEEe
Confidence 45799999999999977 3455555544 4455778886654 235999999999975
No 20
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=90.11 E-value=3.1 Score=35.56 Aligned_cols=71 Identities=20% Similarity=0.132 Sum_probs=46.2
Q ss_pred hhhhccCCCeEEEEEEEeecc--CCeEEEEeCC-CCEEEEEccCC--------CCCCCCEEEEEEEECC-----------
Q 033976 13 GLMRMYVGRRIRTVIQVIQSD--GGGVTGKSTD-GHQLVVKGPQP--------GFPLTTFVEVIGIADT----------- 70 (107)
Q Consensus 13 ~~L~~~~Gk~VrlvGkV~~~~--g~~~~~~s~D-~g~V~v~l~~~--------~~~~~~~vEViG~V~~----------- 70 (107)
+.-..++|++|++.|+|.+.. |+..-+..-| .|.++|.++.. ....+.+|+|.|+|..
T Consensus 8 ~l~~~~~g~~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~ 87 (583)
T TIGR00459 8 QLRTEHLGQTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLD 87 (583)
T ss_pred hcchhhCCCEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCC
Confidence 333478999999999999653 4443333333 35788877543 1245899999999952
Q ss_pred --CCCEEEEEEEeCC
Q 033976 71 --DRSIRAEIWNNFG 83 (107)
Q Consensus 71 --~~si~~~~~~~~g 83 (107)
+..|.+..+.-++
T Consensus 88 tg~iEl~~~~i~iL~ 102 (583)
T TIGR00459 88 TGEIEILAESITLLN 102 (583)
T ss_pred CCcEEEEEeEEEEee
Confidence 2346666665555
No 21
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=89.76 E-value=3.9 Score=28.52 Aligned_cols=56 Identities=13% Similarity=0.070 Sum_probs=45.1
Q ss_pred hhccCCCeEEEEEEEe-eccCCeEEEEeCCCCEEEEEccCC-C----CCCCCEEEEEEEECCC
Q 033976 15 MRMYVGRRIRTVIQVI-QSDGGGVTGKSTDGHQLVVKGPQP-G----FPLTTFVEVIGIADTD 71 (107)
Q Consensus 15 L~~~~Gk~VrlvGkV~-~~~g~~~~~~s~D~g~V~v~l~~~-~----~~~~~~vEViG~V~~~ 71 (107)
+.-+-+..|.|-|.+. +++++.+..+...| +|+|.+... . .....-|++-|+|+.+
T Consensus 52 k~~~Dda~V~l~GnIv~qi~~D~y~FrD~sG-eI~VeIdd~~w~g~tv~P~dkV~I~GevDk~ 113 (128)
T COG3111 52 KTLHDDAWVSLEGNIVRQIGDDRYVFRDASG-EINVDIDDKVWNGQTVTPKDKVRIQGEVDKD 113 (128)
T ss_pred hccccCCeEEEEeeEEEeeCCceEEEEcCCc-cEEEEecccccCCcccCcccEEEEEeEEcCC
Confidence 4456799999999999 78999998887765 999999665 2 2248899999999876
No 22
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=89.12 E-value=3.4 Score=34.52 Aligned_cols=64 Identities=9% Similarity=0.079 Sum_probs=43.6
Q ss_pred CCeEEEEEEEeecc--CCeEEEEeC-CCCEEEEEccCCC------------CCCCCEEEEEEEEC----CCCCEEEEEEE
Q 033976 20 GRRIRTVIQVIQSD--GGGVTGKST-DGHQLVVKGPQPG------------FPLTTFVEVIGIAD----TDRSIRAEIWN 80 (107)
Q Consensus 20 Gk~VrlvGkV~~~~--g~~~~~~s~-D~g~V~v~l~~~~------------~~~~~~vEViG~V~----~~~si~~~~~~ 80 (107)
|++|++-|+|.+.. |+..-+.-. +.|.|++.++... ..++.+|.|.|++. ++.+|.+..+.
T Consensus 53 ~~~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~i~ 132 (496)
T TIGR00499 53 NIEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTELQ 132 (496)
T ss_pred CCEEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeEEE
Confidence 88999999999664 444333333 3467888765421 24589999999995 45667777766
Q ss_pred eCC
Q 033976 81 NFG 83 (107)
Q Consensus 81 ~~g 83 (107)
-++
T Consensus 133 ils 135 (496)
T TIGR00499 133 ILT 135 (496)
T ss_pred EEe
Confidence 655
No 23
>PLN02221 asparaginyl-tRNA synthetase
Probab=88.89 E-value=2 Score=36.61 Aligned_cols=54 Identities=22% Similarity=0.119 Sum_probs=41.0
Q ss_pred hccCCCeEEEEEEEeecc--CC--eEEEEeCCC---CEEEEEccCCC------CCCCCEEEEEEEEC
Q 033976 16 RMYVGRRIRTVIQVIQSD--GG--GVTGKSTDG---HQLVVKGPQPG------FPLTTFVEVIGIAD 69 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~--g~--~~~~~s~D~---g~V~v~l~~~~------~~~~~~vEViG~V~ 69 (107)
..++|+.|+|-|.|.++. |+ .+-+.-.|| |.++|.+.... ...+..|+|.|+|.
T Consensus 46 ~~~~g~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~ES~V~V~G~V~ 112 (572)
T PLN02221 46 AGLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLYDLSTLVATGTCVTVDGVLK 112 (572)
T ss_pred hhcCCCEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchhhHHhcCCCceEEEEEEEEE
Confidence 578999999999999764 43 355778888 57888775431 13589999999996
No 24
>PLN02903 aminoacyl-tRNA ligase
Probab=88.54 E-value=4.4 Score=35.20 Aligned_cols=58 Identities=21% Similarity=0.048 Sum_probs=39.0
Q ss_pred hhhhhccCCCeEEEEEEEeec--cCCeEEEE-eCCCCEEEEEccCCC----------CCCCCEEEEEEEEC
Q 033976 12 GGLMRMYVGRRIRTVIQVIQS--DGGGVTGK-STDGHQLVVKGPQPG----------FPLTTFVEVIGIAD 69 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGkV~~~--~g~~~~~~-s~D~g~V~v~l~~~~----------~~~~~~vEViG~V~ 69 (107)
++.-..++|++|+|.|.|.+. .|+..-+. -...|.++|.++... ...+.+|+|.|+|.
T Consensus 64 g~l~~~~~gk~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~ 134 (652)
T PLN02903 64 GALSVNDVGSRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVR 134 (652)
T ss_pred hhcchhhCCCEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEE
Confidence 444467899999999999965 34433333 333466787765321 23489999999996
No 25
>PRK14639 hypothetical protein; Provisional
Probab=88.24 E-value=2.1 Score=29.94 Aligned_cols=46 Identities=7% Similarity=0.096 Sum_probs=35.4
Q ss_pred CceeeehhhhhccCCCeEEEE--------EEEeeccCCeEEEEe-CCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV--------IQVIQSDGGGVTGKS-TDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv--------GkV~~~~g~~~~~~s-~D~g~V~v~l 51 (107)
-+|--+.....+|+|+.|++- |++...+++.++++. .+++++++.+
T Consensus 74 ~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~ 128 (140)
T PRK14639 74 ERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINF 128 (140)
T ss_pred CCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEh
Confidence 368888999999999999985 777788888877754 3455666655
No 26
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=88.18 E-value=4.4 Score=37.09 Aligned_cols=69 Identities=20% Similarity=0.209 Sum_probs=46.6
Q ss_pred hhccCCCeEEEEEEEeec--cCCeEEEEe-CCCCEEEEEccCCC------------CCCCCEEEEEEEEC----CCCCEE
Q 033976 15 MRMYVGRRIRTVIQVIQS--DGGGVTGKS-TDGHQLVVKGPQPG------------FPLTTFVEVIGIAD----TDRSIR 75 (107)
Q Consensus 15 L~~~~Gk~VrlvGkV~~~--~g~~~~~~s-~D~g~V~v~l~~~~------------~~~~~~vEViG~V~----~~~si~ 75 (107)
..++.|++|++-|+|.++ .|+..-+.- ...|.++|.++... ..++..|+|.|+|. +..+|.
T Consensus 646 ~~~~~~~~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~ 725 (1094)
T PRK02983 646 LDAPTGEEVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLL 725 (1094)
T ss_pred HHhcCCCEEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEE
Confidence 346789999999999965 344433332 33478888775541 24689999999995 455666
Q ss_pred EEEEEeCC
Q 033976 76 AEIWNNFG 83 (107)
Q Consensus 76 ~~~~~~~g 83 (107)
+..+.-++
T Consensus 726 ~~~i~ll~ 733 (1094)
T PRK02983 726 VTSWRLAG 733 (1094)
T ss_pred EeEEEEEe
Confidence 66665444
No 27
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=88.16 E-value=4.3 Score=31.20 Aligned_cols=78 Identities=18% Similarity=0.213 Sum_probs=45.8
Q ss_pred CCeEEEEEEEeecc------CCe--EEEEeCCCC-EEEEEccCC---------CCCCCCEEEEEEEEC-CCCCEEEEEEE
Q 033976 20 GRRIRTVIQVIQSD------GGG--VTGKSTDGH-QLVVKGPQP---------GFPLTTFVEVIGIAD-TDRSIRAEIWN 80 (107)
Q Consensus 20 Gk~VrlvGkV~~~~------g~~--~~~~s~D~g-~V~v~l~~~---------~~~~~~~vEViG~V~-~~~si~~~~~~ 80 (107)
=+.|||+|+|.+.+ .+. +++..+.|. .+.+..... ....+..|+|.|.++ +...+.+....
T Consensus 66 I~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~~G~~V~VkG~vsr~~~ql~ve~i~ 145 (256)
T PF10451_consen 66 IRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDLIGKVVEVKGTVSRNERQLDVERIE 145 (256)
T ss_dssp E-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT-TT-EEEEEEEEESSSEEEEEEEEE
T ss_pred cEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcccccccCCCccCCCCcEEEEEEEEccCcEEEEEEEEE
Confidence 36899999999764 333 555555554 566655432 123699999999998 33445555555
Q ss_pred eCCCCCC--HHHHHHHHHHH
Q 033976 81 NFGNTFD--TQSYNQLCQLA 98 (107)
Q Consensus 81 ~~g~~fD--~~~yn~lv~l~ 98 (107)
-+. +++ ++-+++.+++-
T Consensus 146 ~~~-~l~~Ei~fW~~~~~~R 164 (256)
T PF10451_consen 146 LVR-DLNAEIEFWKERMRFR 164 (256)
T ss_dssp EET-SCCHHHHHHHHHHHHH
T ss_pred ccC-ChHHHHHHHHHHHHHH
Confidence 443 444 44466666663
No 28
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=88.11 E-value=6.6 Score=26.93 Aligned_cols=71 Identities=24% Similarity=0.243 Sum_probs=44.6
Q ss_pred eeeehhhhh---ccCCCeEEEEEEEe--ec----cCCe--EEEEeCCCCEEEEEccCC--C-CCCCCEEEEEEEECCCCC
Q 033976 8 VFVNGGLMR---MYVGRRIRTVIQVI--QS----DGGG--VTGKSTDGHQLVVKGPQP--G-FPLTTFVEVIGIADTDRS 73 (107)
Q Consensus 8 pRVn~~~L~---~~~Gk~VrlvGkV~--~~----~g~~--~~~~s~D~g~V~v~l~~~--~-~~~~~~vEViG~V~~~~s 73 (107)
.....+.+. +..||.||+-|.|. ++ ++.. |.++ ..+.++.|....+ + ...+.=|=|+|+..+++.
T Consensus 35 yy~t~se~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~-D~~~~i~V~Y~G~~Pd~F~eg~~VVv~G~~~~~g~ 113 (131)
T PF03100_consen 35 YYLTPSELAAEPQKVGRKVRVGGLVVEGSVEYDPDGNTLTFTIT-DGGKEIPVVYTGPLPDLFREGQGVVVEGRLGEDGV 113 (131)
T ss_dssp -EE-TTTTTTTST-TTSEEEEEEEEECTTEEE-TTSSEEEEEEE--SS-EEEEEEES--CTT--TTSEEEEEEEECCTSE
T ss_pred EEcCHHHHhhccccCCceEEEeeEEccCCEEEcCCCCEEEEEEE-ECCcEEEEEECCCCCccccCCCeEEEEEEECCCCE
Confidence 344444442 24799999999998 32 3444 4443 3367788877654 2 224788899999988888
Q ss_pred EEEEEE
Q 033976 74 IRAEIW 79 (107)
Q Consensus 74 i~~~~~ 79 (107)
..+...
T Consensus 114 F~A~~l 119 (131)
T PF03100_consen 114 FEATEL 119 (131)
T ss_dssp EEEEEE
T ss_pred EEEEEE
Confidence 888765
No 29
>PRK14630 hypothetical protein; Provisional
Probab=87.79 E-value=1.4 Score=31.02 Aligned_cols=45 Identities=11% Similarity=0.214 Sum_probs=35.6
Q ss_pred CceeeehhhhhccCCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--+.....+|+|+.|++- |++...+++.+++.+ +++++.+.+
T Consensus 83 dRpL~~~~df~r~~G~~v~V~l~~~~~~G~L~~~~d~~i~l~~-~~~~~~i~~ 134 (143)
T PRK14630 83 NRKIKSDREFKIFEGKKIKLMLDNDFEEGFILEAKADSFIFKT-DSKEVNVLY 134 (143)
T ss_pred CCcCCCHHHHHHhCCCEEEEEEcCcceEEEEEEEeCCEEEEEE-CCEEEEEEh
Confidence 368888999999999999984 888888888877774 566666655
No 30
>PLN02502 lysyl-tRNA synthetase
Probab=87.63 E-value=5.4 Score=33.89 Aligned_cols=67 Identities=12% Similarity=0.092 Sum_probs=45.9
Q ss_pred cCCCeEEEEEEEeec--cCCeEEEE-eCCCCEEEEEccCCC--------------CCCCCEEEEEEEEC----CCCCEEE
Q 033976 18 YVGRRIRTVIQVIQS--DGGGVTGK-STDGHQLVVKGPQPG--------------FPLTTFVEVIGIAD----TDRSIRA 76 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~--~g~~~~~~-s~D~g~V~v~l~~~~--------------~~~~~~vEViG~V~----~~~si~~ 76 (107)
..|++|++-|+|.+. .|+..-+. -.+++.|+|..+... ...+..|+|.|.+. ++.+|.+
T Consensus 106 ~~~~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~ 185 (553)
T PLN02502 106 LEDVSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFP 185 (553)
T ss_pred cCCCEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEE
Confidence 368999999999965 45543333 334467887664320 23599999999995 4677888
Q ss_pred EEEEeCCC
Q 033976 77 EIWNNFGN 84 (107)
Q Consensus 77 ~~~~~~g~ 84 (107)
..+.-++.
T Consensus 186 ~~i~vLs~ 193 (553)
T PLN02502 186 TSFEVLTK 193 (553)
T ss_pred eEEEEEec
Confidence 77766663
No 31
>PRK14633 hypothetical protein; Provisional
Probab=87.50 E-value=1.9 Score=30.52 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=33.2
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|-.+.....+|+|+.|++. |++...+++.+++...+|+++.+.+
T Consensus 80 dRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~~~~~~i~~ 137 (150)
T PRK14633 80 NRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLEDGKEISFDF 137 (150)
T ss_pred CCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcCCcEEEEEh
Confidence 478889999999999998873 6666666666666654555655544
No 32
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=87.43 E-value=3.9 Score=34.94 Aligned_cols=58 Identities=17% Similarity=0.121 Sum_probs=39.2
Q ss_pred hhhhhccCCCeEEEEEEEeec--cCCeEEEE-eCCCCEEEEEccCC--------CCCCCCEEEEEEEEC
Q 033976 12 GGLMRMYVGRRIRTVIQVIQS--DGGGVTGK-STDGHQLVVKGPQP--------GFPLTTFVEVIGIAD 69 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGkV~~~--~g~~~~~~-s~D~g~V~v~l~~~--------~~~~~~~vEViG~V~ 69 (107)
++....++|++|++.|.|.+. -|+..-+. -...|.+++.++.. ....+.+|+|.|+|.
T Consensus 9 ~~l~~~~~g~~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~ 77 (588)
T PRK00476 9 GELRESHVGQTVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSEYVIQVTGTVR 77 (588)
T ss_pred HHhhHHhCCCEEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEE
Confidence 344468899999999999965 34433333 33346677766531 134589999999996
No 33
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=87.41 E-value=4.3 Score=34.04 Aligned_cols=65 Identities=11% Similarity=0.088 Sum_probs=44.2
Q ss_pred CCeEEEEEEEeec--cCCeEEEEeCC-CCEEEEEccCCC------------CCCCCEEEEEEEEC----CCCCEEEEEEE
Q 033976 20 GRRIRTVIQVIQS--DGGGVTGKSTD-GHQLVVKGPQPG------------FPLTTFVEVIGIAD----TDRSIRAEIWN 80 (107)
Q Consensus 20 Gk~VrlvGkV~~~--~g~~~~~~s~D-~g~V~v~l~~~~------------~~~~~~vEViG~V~----~~~si~~~~~~ 80 (107)
|++|++-|+|.++ .|+..-+..-| .|.++|.++... ..++.+|.|.|+|. +..+|.+..+.
T Consensus 65 ~~~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~~~ 144 (505)
T PRK12445 65 NIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELR 144 (505)
T ss_pred CCEEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeEEE
Confidence 7889999999965 35443333333 367887665321 22488999999995 56778887776
Q ss_pred eCCC
Q 033976 81 NFGN 84 (107)
Q Consensus 81 ~~g~ 84 (107)
-++.
T Consensus 145 llsk 148 (505)
T PRK12445 145 LLTK 148 (505)
T ss_pred EEec
Confidence 6663
No 34
>PRK14638 hypothetical protein; Provisional
Probab=87.22 E-value=1.7 Score=30.77 Aligned_cols=45 Identities=9% Similarity=0.027 Sum_probs=35.1
Q ss_pred ceeeehhhhhccCCCeEEEE--------EEEeeccCCeEEEEeCCCCEEEEEcc
Q 033976 7 AVFVNGGLMRMYVGRRIRTV--------IQVIQSDGGGVTGKSTDGHQLVVKGP 52 (107)
Q Consensus 7 ~pRVn~~~L~~~~Gk~Vrlv--------GkV~~~~g~~~~~~s~D~g~V~v~l~ 52 (107)
+|--......+|+|+.|++- |++...+++.+++. .+++++.+.++
T Consensus 87 RpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~-~~~~~~~i~~~ 139 (150)
T PRK14638 87 RPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDGTITIS-DEKEKYEINID 139 (150)
T ss_pred CCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEE-ECCcEEEEEhH
Confidence 67778889999999999985 88888888887776 35677776553
No 35
>PRK14631 hypothetical protein; Provisional
Probab=86.85 E-value=2 Score=31.27 Aligned_cols=46 Identities=13% Similarity=0.252 Sum_probs=35.6
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeecc--CCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSD--GGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~--g~~~~~~s~D~g~V~v~l 51 (107)
-+|.-......+|+|+.|++- |++..++ ++.+++...++.++.+.+
T Consensus 103 dRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~~~~~i~~ 162 (174)
T PRK14631 103 DRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGKHVLDIDS 162 (174)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCCcEEEEEh
Confidence 367888899999999999875 7777777 777777766566666655
No 36
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=86.64 E-value=0.69 Score=26.86 Aligned_cols=21 Identities=10% Similarity=0.339 Sum_probs=17.7
Q ss_pred hhhhhccCCCeEEEEEEEeec
Q 033976 12 GGLMRMYVGRRIRTVIQVIQS 32 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGkV~~~ 32 (107)
.+.++++.||.|++-|++-..
T Consensus 11 ~~~~~~~~Gk~V~V~G~l~~a 31 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVTGKLFHA 31 (48)
T ss_pred hHHHHHhcCCeEEEEEEEeec
Confidence 467788999999999999843
No 37
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=86.36 E-value=3.5 Score=25.98 Aligned_cols=46 Identities=13% Similarity=0.074 Sum_probs=30.6
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCC---CCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTD---GHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D---~g~V~v~l 51 (107)
-+|-.......+|+|+.|.+. |++..++++.+++.... ++++++.+
T Consensus 11 ~RpL~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~ 71 (83)
T cd01734 11 ERPLKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPL 71 (83)
T ss_pred CCcCCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEh
Confidence 467888899999999988763 55556666666555432 44555544
No 38
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.36 E-value=2.5 Score=30.27 Aligned_cols=48 Identities=15% Similarity=0.282 Sum_probs=38.2
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCCEEEEEccCC
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGHQLVVKGPQP 54 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g~V~v~l~~~ 54 (107)
-+|-...+....|.|+.|.+. |++..++++++++. .|+++|.|-++..
T Consensus 85 dRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~-~~~k~v~Ip~~~i 144 (153)
T COG0779 85 DRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLE-VDGKEVEIPFSDI 144 (153)
T ss_pred CCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEE-ECCEEEEEEcccc
Confidence 368899999999999999764 67777888887777 6778888877554
No 39
>PRK14636 hypothetical protein; Provisional
Probab=86.23 E-value=2.3 Score=30.92 Aligned_cols=46 Identities=13% Similarity=0.106 Sum_probs=30.0
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|-.......+|+|+.|++- |++...+++.+++...++++++|.+
T Consensus 84 dRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~~~~~~i~~ 141 (176)
T PRK14636 84 DRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNKAGEVILPF 141 (176)
T ss_pred CCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcCCcEEEEEh
Confidence 367888899999999988863 4455555555555544445554443
No 40
>PRK14647 hypothetical protein; Provisional
Probab=86.20 E-value=2.3 Score=30.27 Aligned_cols=46 Identities=17% Similarity=0.121 Sum_probs=33.1
Q ss_pred CceeeehhhhhccCCCeEEEE-----------------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV-----------------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv-----------------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--...+..+|+|+.|.+- |++...+++.+++...+++.+++.+
T Consensus 85 ~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~i~~ 147 (159)
T PRK14647 85 DRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKEGQQARIPL 147 (159)
T ss_pred CCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcCCcEEEEEH
Confidence 367888899999999998874 6666667777666655556666554
No 41
>PLN02603 asparaginyl-tRNA synthetase
Probab=85.85 E-value=5.3 Score=34.08 Aligned_cols=67 Identities=13% Similarity=0.059 Sum_probs=47.3
Q ss_pred ccCCCeEEEEEEEeec--cCCeEEEEeCCCC---EEEEEccCC-C---------CCCCCEEEEEEEECC------CCCEE
Q 033976 17 MYVGRRIRTVIQVIQS--DGGGVTGKSTDGH---QLVVKGPQP-G---------FPLTTFVEVIGIADT------DRSIR 75 (107)
Q Consensus 17 ~~~Gk~VrlvGkV~~~--~g~~~~~~s~D~g---~V~v~l~~~-~---------~~~~~~vEViG~V~~------~~si~ 75 (107)
.+.|++|++-|.|.++ .|+..-+.-.||. +++|.+... . ...+..|+|.|+|.. +..|.
T Consensus 104 ~~~g~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~gs~V~V~G~v~~~~~~~~~~EL~ 183 (565)
T PLN02603 104 ARVGKTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTGASVLVQGTVVSSQGGKQKVELK 183 (565)
T ss_pred ccCCCEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCCCEEEEEEEEEecCCCCccEEEE
Confidence 7889999999999965 3455556777765 588877543 1 235899999999952 13566
Q ss_pred EEEEEeCC
Q 033976 76 AEIWNNFG 83 (107)
Q Consensus 76 ~~~~~~~g 83 (107)
+..+.-+|
T Consensus 184 v~~i~vlg 191 (565)
T PLN02603 184 VSKIVVVG 191 (565)
T ss_pred EeEEEEEE
Confidence 66665565
No 42
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=85.46 E-value=5.9 Score=26.30 Aligned_cols=75 Identities=17% Similarity=0.177 Sum_probs=46.5
Q ss_pred hhhhccC--CCeEEEEEEEeec---cCCe--EEEEe----------CCCCEEEEEccCCCC---CCCCEEEEEEEECCCC
Q 033976 13 GLMRMYV--GRRIRTVIQVIQS---DGGG--VTGKS----------TDGHQLVVKGPQPGF---PLTTFVEVIGIADTDR 72 (107)
Q Consensus 13 ~~L~~~~--Gk~VrlvGkV~~~---~g~~--~~~~s----------~D~g~V~v~l~~~~~---~~~~~vEViG~V~~~~ 72 (107)
..++++. |+.|.+.|+|.+. ++.. ++++. ...+.|.+.+..++. ..+..+++.|+..+..
T Consensus 66 ~~~~~~~~~~~~~~v~g~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l~~~~ 145 (176)
T PF13567_consen 66 QDLSQLLPSGKEVTVQGTVESVPQIDGRGQRFTLRVERVLAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVRGKLKPPS 145 (176)
T ss_pred cccchhhccCceEEEEEEEcccccccCceEEEEEEEEEeeccccccccceeeEEEeccccccccCCCCEEEEEEEEecCC
Confidence 3444544 9999999999844 3332 44431 134667777766643 3599999999987422
Q ss_pred CEEEEEEEeCCCCCCHHHHHH
Q 033976 73 SIRAEIWNNFGNTFDTQSYNQ 93 (107)
Q Consensus 73 si~~~~~~~~g~~fD~~~yn~ 93 (107)
. -.....||...|-.
T Consensus 146 ~------~~Npg~FD~~~yl~ 160 (176)
T PF13567_consen 146 G------PTNPGGFDYQRYLR 160 (176)
T ss_pred C------CCCCCCcCHHHHHH
Confidence 1 11124688888754
No 43
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=85.22 E-value=2.3 Score=27.29 Aligned_cols=33 Identities=9% Similarity=0.138 Sum_probs=27.6
Q ss_pred CCCeEE----EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIR----TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
.|..|. +.|+|.+++++++.++.++|..+++.-
T Consensus 40 ~Gd~VvT~gGi~G~V~~i~d~~v~vei~~g~~i~~~r 76 (84)
T TIGR00739 40 KGDKVLTIGGIIGTVTKIAENTIVIELNDNTEITFSK 76 (84)
T ss_pred CCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 577776 689999999999999999887777754
No 44
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=85.13 E-value=8.2 Score=25.11 Aligned_cols=62 Identities=13% Similarity=0.124 Sum_probs=38.3
Q ss_pred eEEEEEEEeecc--CCeEEEEeCCC-CEEEEEccCCC------------CCCCCEEEEEEEEC----CCCCEEEEEEEeC
Q 033976 22 RIRTVIQVIQSD--GGGVTGKSTDG-HQLVVKGPQPG------------FPLTTFVEVIGIAD----TDRSIRAEIWNNF 82 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~~~~~~s~D~-g~V~v~l~~~~------------~~~~~~vEViG~V~----~~~si~~~~~~~~ 82 (107)
.|++.|+|.++. |+.+-+.--|| +.+++..+... ...+.+|+|.|++. ++..|.+..+.-+
T Consensus 1 ~v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~il 80 (108)
T cd04322 1 EVSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLL 80 (108)
T ss_pred CEEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEe
Confidence 488999999664 44443443333 66777664321 34599999999985 3344555555444
Q ss_pred C
Q 033976 83 G 83 (107)
Q Consensus 83 g 83 (107)
+
T Consensus 81 s 81 (108)
T cd04322 81 S 81 (108)
T ss_pred e
Confidence 4
No 45
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=84.73 E-value=2.3 Score=28.55 Aligned_cols=33 Identities=12% Similarity=0.125 Sum_probs=27.1
Q ss_pred CCCeEE----EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIR----TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
.|..|. |.|+|.+++++++.+++++|..+++.-
T Consensus 55 ~Gd~VvT~gGi~G~Vv~i~~~~v~lei~~g~~i~~~r 91 (106)
T PRK05585 55 KGDEVVTNGGIIGKVTKVSEDFVIIELNDDTEIKIQK 91 (106)
T ss_pred CCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 577775 689999999999999999986666654
No 46
>PRK14634 hypothetical protein; Provisional
Probab=84.61 E-value=2.6 Score=29.97 Aligned_cols=45 Identities=4% Similarity=0.018 Sum_probs=32.3
Q ss_pred CceeeehhhhhccCCCeEEE------------EEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRT------------VIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrl------------vGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|-.......+|+|+.|++ .|++...+++.+++.. +++.+++.+
T Consensus 86 dRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~-~~~~~~i~~ 142 (155)
T PRK14634 86 GDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI-RGRIKRIPR 142 (155)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE-CCEEEEEEH
Confidence 36888889999999998876 5666666777766654 456666544
No 47
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=84.07 E-value=6.3 Score=34.57 Aligned_cols=60 Identities=13% Similarity=-0.042 Sum_probs=40.8
Q ss_pred ehhhhhccCCCeEEEEEEEeec--cCCeEEEE-eCCCCEEEEEccCCC-----------CCCCCEEEEEEEECC
Q 033976 11 NGGLMRMYVGRRIRTVIQVIQS--DGGGVTGK-STDGHQLVVKGPQPG-----------FPLTTFVEVIGIADT 70 (107)
Q Consensus 11 n~~~L~~~~Gk~VrlvGkV~~~--~g~~~~~~-s~D~g~V~v~l~~~~-----------~~~~~~vEViG~V~~ 70 (107)
.+++-..++|++|++.|.|.+. -|+..-+. -...|.++|.++... ...+.+|.|.|+|..
T Consensus 9 cg~l~~~~~g~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~ 82 (706)
T PRK12820 9 CGHLSLDDTGREVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQK 82 (706)
T ss_pred cccCChhhCCCEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEec
Confidence 3455577899999999999965 34433333 333467888775321 234899999999864
No 48
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=83.96 E-value=2.3 Score=29.33 Aligned_cols=47 Identities=9% Similarity=0.157 Sum_probs=32.4
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCC---EEEEEcc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGH---QLVVKGP 52 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g---~V~v~l~ 52 (107)
-+|-.+...+..|+|+.|++. |++..+++++++++..+++ +++|.+.
T Consensus 73 ~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~ 134 (141)
T PF02576_consen 73 DRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFS 134 (141)
T ss_dssp SS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS
T ss_pred CCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHH
Confidence 367778889999999988765 6777888888888777664 6666663
No 49
>PRK14646 hypothetical protein; Provisional
Probab=83.82 E-value=3.3 Score=29.45 Aligned_cols=44 Identities=5% Similarity=-0.039 Sum_probs=34.2
Q ss_pred ceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 7 AVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 7 ~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
+|--+.....+|.|+.|++- |++...+++.+++.. +|+++.+.+
T Consensus 87 RpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~-~g~~~~i~~ 142 (155)
T PRK14646 87 DELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINI-KGKIKKIPF 142 (155)
T ss_pred CcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEE-CCEEEEEEH
Confidence 67778899999999999874 777777888887764 566666655
No 50
>PRK14637 hypothetical protein; Provisional
Probab=83.45 E-value=2.8 Score=29.76 Aligned_cols=45 Identities=20% Similarity=0.316 Sum_probs=31.7
Q ss_pred CceeeehhhhhccCCCeEEE---------EEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRT---------VIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrl---------vGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--...+..+|+|+.|++ .|++...+++.+++.. +++++.|.+
T Consensus 84 dRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~-~~~~~~i~~ 137 (151)
T PRK14637 84 ERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADETCLVLTS-DGVPVTIPY 137 (151)
T ss_pred CCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE-CCEEEEEEH
Confidence 36788889999999999988 3555566666666653 455555544
No 51
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=83.20 E-value=9.8 Score=24.44 Aligned_cols=49 Identities=14% Similarity=0.055 Sum_probs=32.1
Q ss_pred eEEEEEEEeecc--C-CeEEEEe-CCCCEEEEEccCCC-------------CCCCCEEEEEEEECC
Q 033976 22 RIRTVIQVIQSD--G-GGVTGKS-TDGHQLVVKGPQPG-------------FPLTTFVEVIGIADT 70 (107)
Q Consensus 22 ~VrlvGkV~~~~--g-~~~~~~s-~D~g~V~v~l~~~~-------------~~~~~~vEViG~V~~ 70 (107)
.|++-|+|.+.. | +.+-+.- ...+.+++.++... ...+..|+|.|++..
T Consensus 1 ~V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 66 (102)
T cd04320 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKK 66 (102)
T ss_pred CEEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEEC
Confidence 489999999664 3 3332332 23478888775431 234899999999864
No 52
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=82.35 E-value=11 Score=24.36 Aligned_cols=63 Identities=14% Similarity=0.055 Sum_probs=38.2
Q ss_pred eEEEEEEEeecc--CCeEEEEeCCC-CEEEEEccCC----------CCCCCCEEEEEEEECCC------CCEEEEEEEeC
Q 033976 22 RIRTVIQVIQSD--GGGVTGKSTDG-HQLVVKGPQP----------GFPLTTFVEVIGIADTD------RSIRAEIWNNF 82 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~~~~~~s~D~-g~V~v~l~~~----------~~~~~~~vEViG~V~~~------~si~~~~~~~~ 82 (107)
+|++-|.|.+.. |+..-+.-.|+ |.+++.+... ....+..|+|.|+|... --|.+..+.-+
T Consensus 1 ~V~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl 80 (103)
T cd04319 1 KVTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEII 80 (103)
T ss_pred CEEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEE
Confidence 489999999553 44333444443 5677766532 12458999999998632 22555555555
Q ss_pred CC
Q 033976 83 GN 84 (107)
Q Consensus 83 g~ 84 (107)
|+
T Consensus 81 ~~ 82 (103)
T cd04319 81 QN 82 (103)
T ss_pred ec
Confidence 53
No 53
>PLN02850 aspartate-tRNA ligase
Probab=82.24 E-value=8 Score=32.64 Aligned_cols=61 Identities=11% Similarity=0.089 Sum_probs=42.3
Q ss_pred eeehhhh-hccCCCeEEEEEEEeecc--CCe-EEEEeCCCCEEEEEccCCC-------------CCCCCEEEEEEEEC
Q 033976 9 FVNGGLM-RMYVGRRIRTVIQVIQSD--GGG-VTGKSTDGHQLVVKGPQPG-------------FPLTTFVEVIGIAD 69 (107)
Q Consensus 9 RVn~~~L-~~~~Gk~VrlvGkV~~~~--g~~-~~~~s~D~g~V~v~l~~~~-------------~~~~~~vEViG~V~ 69 (107)
+++-+.| ..+.|++|++-|+|.++. |+. |..--..++.|++.+.... ...+.+|.|.|+|.
T Consensus 69 ~~~i~~l~~~~~g~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~ 146 (530)
T PLN02850 69 WTDVSDLGEELAGSEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVS 146 (530)
T ss_pred EeEhhhcchhhCCCEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEEEEEEEEE
Confidence 5666666 468899999999999653 443 3333334578888764321 23489999999997
No 54
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=81.59 E-value=4.1 Score=28.65 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=31.4
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCC--EEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGH--QLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g--~V~v~l 51 (107)
-+|--+..+..+|+|+.|++- |++...+++.+++... ++ ++++.+
T Consensus 84 ~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~-~~~~~~~i~~ 142 (154)
T PRK00092 84 DRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVE-GKEKEVEIPL 142 (154)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEEC-CCeEEEEEEH
Confidence 367888899999999999986 5566666666666543 34 455544
No 55
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=80.20 E-value=11 Score=23.11 Aligned_cols=48 Identities=15% Similarity=-0.046 Sum_probs=32.9
Q ss_pred eEEEEEEEeecc--CCeEEEEeCCCCE---EEEEccCCC--------CCCCCEEEEEEEEC
Q 033976 22 RIRTVIQVIQSD--GGGVTGKSTDGHQ---LVVKGPQPG--------FPLTTFVEVIGIAD 69 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~~~~~~s~D~g~---V~v~l~~~~--------~~~~~~vEViG~V~ 69 (107)
.|++-|.|.+.. |..+-+.-.||.. +++.++... ...+..|+|.|++.
T Consensus 1 ~v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~ 61 (82)
T cd04318 1 EVTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLV 61 (82)
T ss_pred CEEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEE
Confidence 488999999653 4555566656543 777665431 24589999999985
No 56
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=80.14 E-value=13 Score=31.62 Aligned_cols=61 Identities=11% Similarity=0.104 Sum_probs=40.5
Q ss_pred eeehhhhh-cc-CCCeEEEEEEEeecc--CCeEEEE-eCCCCEEEEEccCC---C---------CCCCCEEEEEEEEC
Q 033976 9 FVNGGLMR-MY-VGRRIRTVIQVIQSD--GGGVTGK-STDGHQLVVKGPQP---G---------FPLTTFVEVIGIAD 69 (107)
Q Consensus 9 RVn~~~L~-~~-~Gk~VrlvGkV~~~~--g~~~~~~-s~D~g~V~v~l~~~---~---------~~~~~~vEViG~V~ 69 (107)
+++=+.|. +. .|++|++-|+|.++. |+.+-+. -...+.|++.++.. + ...+.+|+|.|+|.
T Consensus 65 ~~~i~~l~~~~~~g~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~V~G~v~ 142 (550)
T PTZ00401 65 FIPVAVLSKPELVDKTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVDVEATVC 142 (550)
T ss_pred eEEHHHCCccccCCCEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEEEEEEEE
Confidence 56666664 33 799999999999653 4433333 33346788766321 1 24589999999886
No 57
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=79.91 E-value=12 Score=23.38 Aligned_cols=49 Identities=8% Similarity=0.022 Sum_probs=32.6
Q ss_pred eEEEEEEEeeccC---Ce--EEEEeCCCCEEEEEccCC--------CCCCCCEEEEEEEECC
Q 033976 22 RIRTVIQVIQSDG---GG--VTGKSTDGHQLVVKGPQP--------GFPLTTFVEVIGIADT 70 (107)
Q Consensus 22 ~VrlvGkV~~~~g---~~--~~~~s~D~g~V~v~l~~~--------~~~~~~~vEViG~V~~ 70 (107)
+|++.|.|.+... +. +.++...|..++|.++.. ..+.+..|.|.|++..
T Consensus 1 ~V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~ 62 (86)
T cd04321 1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQL 62 (86)
T ss_pred CEEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEe
Confidence 4899999997653 33 334444443578876543 1345899999999963
No 58
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=79.84 E-value=4.5 Score=27.40 Aligned_cols=33 Identities=12% Similarity=0.071 Sum_probs=26.7
Q ss_pred CCCeEE----EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIR----TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
.|..|. |+|+|.+++.+++.++.++|..+++.-
T Consensus 41 ~GD~VvT~gGi~G~V~~I~d~~v~leia~gv~i~~~r 77 (109)
T PRK05886 41 PGDRVHTTSGLQATIVGITDDTVDLEIAPGVVTTWMK 77 (109)
T ss_pred CCCEEEECCCeEEEEEEEeCCEEEEEECCCeEEEEEh
Confidence 577776 689999999999999999887777644
No 59
>PRK14640 hypothetical protein; Provisional
Probab=79.12 E-value=6.1 Score=27.92 Aligned_cols=45 Identities=18% Similarity=0.166 Sum_probs=31.6
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--...+..+|+|+.|++- |++...+++.+++.. +|+++.+.+
T Consensus 83 ~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~-~~~~~~i~~ 139 (152)
T PRK14640 83 DRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTV-DGKDEVLAF 139 (152)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEE-CCeEEEEEh
Confidence 468888999999999998764 566666666666653 455555544
No 60
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=79.06 E-value=9.2 Score=32.84 Aligned_cols=57 Identities=16% Similarity=0.039 Sum_probs=39.9
Q ss_pred hhhhccCCCeEEEEEEEeecc--CC--eEEEEeCCCCE---EEEEccCC--------CCCCCCEEEEEEEEC
Q 033976 13 GLMRMYVGRRIRTVIQVIQSD--GG--GVTGKSTDGHQ---LVVKGPQP--------GFPLTTFVEVIGIAD 69 (107)
Q Consensus 13 ~~L~~~~Gk~VrlvGkV~~~~--g~--~~~~~s~D~g~---V~v~l~~~--------~~~~~~~vEViG~V~ 69 (107)
+-+..++|+.|+|.|-|.++. |+ ..-+...||-- ++|.+... ....+..|+|.|+|.
T Consensus 74 ~~~~~~~g~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~~~~~~~~~l~~l~~gs~v~v~G~v~ 145 (586)
T PTZ00425 74 SRKNKYIDQIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVDQSIENYEKLLKCGVGCCFRFTGKLI 145 (586)
T ss_pred ccccccCCCEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEECCchHHHHHHhcCCCccEEEEEEEEE
Confidence 445688999999999999664 32 34466666653 67765432 123589999999996
No 61
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=79.05 E-value=16 Score=31.29 Aligned_cols=64 Identities=13% Similarity=0.071 Sum_probs=43.2
Q ss_pred CCeEEEEEEEeec--cC-CeEEEEe-CCCCEEEEEccCC--------------CCCCCCEEEEEEEEC----CCCCEEEE
Q 033976 20 GRRIRTVIQVIQS--DG-GGVTGKS-TDGHQLVVKGPQP--------------GFPLTTFVEVIGIAD----TDRSIRAE 77 (107)
Q Consensus 20 Gk~VrlvGkV~~~--~g-~~~~~~s-~D~g~V~v~l~~~--------------~~~~~~~vEViG~V~----~~~si~~~ 77 (107)
++.|++-|+|.++ .| +..-+.- .|++.++|.++.. ...++.+|+|.|.+. +..+|.+.
T Consensus 132 ~~~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~~gel~i~~~ 211 (585)
T PTZ00417 132 DTILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPK 211 (585)
T ss_pred CCeEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCCCceEEEEEE
Confidence 3569999999965 35 3333433 6788899877532 124599999999986 34456776
Q ss_pred EEEeCC
Q 033976 78 IWNNFG 83 (107)
Q Consensus 78 ~~~~~g 83 (107)
.+.-++
T Consensus 212 ~i~lls 217 (585)
T PTZ00417 212 ETIILS 217 (585)
T ss_pred EEEEEe
Confidence 665555
No 62
>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=77.24 E-value=12 Score=21.81 Aligned_cols=56 Identities=13% Similarity=-0.054 Sum_probs=35.5
Q ss_pred EEEEEEEeec---cCCe--EEEEeCCCCEEEEEccCC-C------CCCCCEEEEEEEECC---C-CCEEEEEE
Q 033976 23 IRTVIQVIQS---DGGG--VTGKSTDGHQLVVKGPQP-G------FPLTTFVEVIGIADT---D-RSIRAEIW 79 (107)
Q Consensus 23 VrlvGkV~~~---~g~~--~~~~s~D~g~V~v~l~~~-~------~~~~~~vEViG~V~~---~-~si~~~~~ 79 (107)
|++.|+|.+. .+.. ++++..- |.+++.+-.+ . ...+..|.|.|++.. . ..|.+..+
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~~~i 72 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYNGGELELIVPKI 72 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEETTSSEEEEEEEE
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEECCccEEEEECEE
Confidence 7899999966 2333 3444333 7888877661 1 245999999999972 2 34555444
No 63
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=76.65 E-value=14 Score=25.21 Aligned_cols=50 Identities=16% Similarity=0.126 Sum_probs=35.3
Q ss_pred cCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEccCC-CCCCCCEEEEEEEECC
Q 033976 18 YVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKGPQP-GFPLTTFVEVIGIADT 70 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l~~~-~~~~~~~vEViG~V~~ 70 (107)
|+||.=||.|||.+++---+.++=.... -.-+.+ .......+||+|+|.-
T Consensus 61 ~IG~~q~L~Gkv~kL~kPLaVLrk~~~~---~~~~~~~~~~~~~e~evv~II~~ 111 (122)
T PF09696_consen 61 YIGKHQRLEGKVVKLKKPLAVLRKRKSN---DDSSDDSEEESSTEYEVVDIIRY 111 (122)
T ss_pred EECCCEEEEEEEeccCCCEEEEEEcccC---cccccccCCCCCeEEEEEEeeee
Confidence 6899999999999998887777644332 011111 2456889999999864
No 64
>PRK14645 hypothetical protein; Provisional
Probab=73.64 E-value=12 Score=26.62 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=29.3
Q ss_pred CceeeehhhhhccCCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--......+|+|+.|.+- |++...+++.+++.. +|+++.+.+
T Consensus 88 dRpL~~~~df~r~~G~~v~v~~~~k~~~G~L~~~~d~~i~l~~-~~~~~~i~~ 139 (154)
T PRK14645 88 KRPLFTARHFERFAGLKAKVRGPGENFTGRIKAVSGDQVTFDV-GGEDRTLRI 139 (154)
T ss_pred CCCCCCHHHHHHhCCCEEEEEcCCeEEEEEEEEEeCCEEEEEE-CCeEEEEEH
Confidence 367788889999999998873 455555555555542 445555443
No 65
>PRK14643 hypothetical protein; Provisional
Probab=72.27 E-value=13 Score=26.62 Aligned_cols=46 Identities=11% Similarity=-0.099 Sum_probs=32.0
Q ss_pred CceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEe-----CCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKS-----TDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s-----~D~g~V~v~l 51 (107)
-+|--+......|+|+.|.+- |++...+++..++.. .+++.+++.+
T Consensus 90 eRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~ 152 (164)
T PRK14643 90 EKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKY 152 (164)
T ss_pred CCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeH
Confidence 367888899999999999874 666666666555541 2356666654
No 66
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=71.98 E-value=6.8 Score=23.96 Aligned_cols=25 Identities=16% Similarity=0.056 Sum_probs=21.8
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEE
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVV 49 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v 49 (107)
.=|+|.++|..++++...||+.-++
T Consensus 5 veG~I~~id~~~~titLdDGksy~l 29 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYKL 29 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEEC
Confidence 3489999999999999999997764
No 67
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=71.95 E-value=16 Score=24.42 Aligned_cols=42 Identities=26% Similarity=0.393 Sum_probs=27.9
Q ss_pred hccCCCeEEE---------EEEEeeccCCeEEEEeCCCCEEEEEccCC--CCCCCCEEEEE
Q 033976 16 RMYVGRRIRT---------VIQVIQSDGGGVTGKSTDGHQLVVKGPQP--GFPLTTFVEVI 65 (107)
Q Consensus 16 ~~~~Gk~Vrl---------vGkV~~~~g~~~~~~s~D~g~V~v~l~~~--~~~~~~~vEVi 65 (107)
+.|+||.||- .|||....|++ |-|.+.+..+ ...++..|||.
T Consensus 42 ~~y~gk~v~yk~~~~G~Vi~G~V~R~HGns--------GaVrarF~~~LP~qa~G~~v~v~ 94 (100)
T COG2451 42 QFYLGKRVCYKYRSSGRVIKGKVVRTHGNS--------GAVRARFERNLPGQALGTSVEVK 94 (100)
T ss_pred HhhhccEEEEEeCCCCcEEEEEEEEecCCc--------ceEEEEecCCCCchhcCcEEEEE
Confidence 5578887764 46666666653 5677777665 34568888885
No 68
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=71.51 E-value=9.6 Score=25.27 Aligned_cols=34 Identities=18% Similarity=0.169 Sum_probs=26.9
Q ss_pred CCCeEE----EEEEEeeccCCeEEEEeCCCCEEEEEcc
Q 033976 19 VGRRIR----TVIQVIQSDGGGVTGKSTDGHQLVVKGP 52 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g~~~~~~s~D~g~V~v~l~ 52 (107)
.|-.|- |+|+|.+++.+.++++..||..+++.-+
T Consensus 46 kGD~VvT~gGi~G~V~~v~d~~v~I~l~~~~~i~~~k~ 83 (97)
T COG1862 46 KGDEVVTIGGIVGTVTKVGDDTVEIELGDGTKIKFEKE 83 (97)
T ss_pred CCCEEEEcCCeEEEEEEEecCcEEEEECCCeEEEEEHH
Confidence 355555 6789999998889999998888887653
No 69
>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=70.83 E-value=13 Score=22.33 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=23.9
Q ss_pred EEEEEEeecc-CCeEEEEeCCCCEEEEEccC
Q 033976 24 RTVIQVIQSD-GGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 24 rlvGkV~~~~-g~~~~~~s~D~g~V~v~l~~ 53 (107)
-+.|+|.+.- +..+.+++.||.++.+.++.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~g 34 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPG 34 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-H
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc
Confidence 3679999664 46799999999999999853
No 70
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=68.44 E-value=42 Score=24.20 Aligned_cols=82 Identities=20% Similarity=0.147 Sum_probs=53.9
Q ss_pred cCCCeEEEEEEEe--ec--c--CCeEEEEeCC-CCEEEEEccC--CC-CCCCCEEEEEEEECCCCCEEEEEE-EeCCCCC
Q 033976 18 YVGRRIRTVIQVI--QS--D--GGGVTGKSTD-GHQLVVKGPQ--PG-FPLTTFVEVIGIADTDRSIRAEIW-NNFGNTF 86 (107)
Q Consensus 18 ~~Gk~VrlvGkV~--~~--~--g~~~~~~s~D-~g~V~v~l~~--~~-~~~~~~vEViG~V~~~~si~~~~~-~~~g~~f 86 (107)
..||++|+-|.|. |+ + +..+...-+| ..+|.|.... |+ .-.+.-|=+.|+..+++...+... ....+++
T Consensus 55 ~~g~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~~~~g~F~A~evLAKhdekY 134 (159)
T PRK13150 55 AVGQRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGILPDLFREGQGVVVQGTLEKGNHVLAHEVLAKHDENY 134 (159)
T ss_pred CCCCEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEeccCCccccCCCeEEEEEEECCCCEEEEeEEEeCCCCCC
Confidence 4699999999999 43 2 3344444444 4567776533 22 223778889999998888887776 5666777
Q ss_pred CHHHHHHHHHHHh
Q 033976 87 DTQSYNQLCQLAN 99 (107)
Q Consensus 87 D~~~yn~lv~l~~ 99 (107)
-..-..++++-.+
T Consensus 135 mPpEv~~al~~~~ 147 (159)
T PRK13150 135 TPPEVEKAMQENH 147 (159)
T ss_pred CCHHHHHHHHHhC
Confidence 6555555555444
No 71
>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=68.26 E-value=18 Score=22.82 Aligned_cols=40 Identities=20% Similarity=0.279 Sum_probs=29.3
Q ss_pred EEEEEeeccC-CeEEEEeCCCCEEEEEccCCC-----CCCCCEEEE
Q 033976 25 TVIQVIQSDG-GGVTGKSTDGHQLVVKGPQPG-----FPLTTFVEV 64 (107)
Q Consensus 25 lvGkV~~~~g-~~~~~~s~D~g~V~v~l~~~~-----~~~~~~vEV 64 (107)
.+|+|...-| +.+.+++.||.++.++++.-- -..+.+|-|
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV 47 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIV 47 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEE
Confidence 5799997655 578899999999999995431 123666666
No 72
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=68.10 E-value=45 Score=28.31 Aligned_cols=62 Identities=10% Similarity=0.096 Sum_probs=46.3
Q ss_pred EEEEEEEeecc--CC-eEEEEeCCCCEEEEEccCCC------------CCCCCEEEEEEEEC----CCCCEEEEEEEeCC
Q 033976 23 IRTVIQVIQSD--GG-GVTGKSTDGHQLVVKGPQPG------------FPLTTFVEVIGIAD----TDRSIRAEIWNNFG 83 (107)
Q Consensus 23 VrlvGkV~~~~--g~-~~~~~s~D~g~V~v~l~~~~------------~~~~~~vEViG~V~----~~~si~~~~~~~~g 83 (107)
|.+.||+.... |+ .+.-.-.++|++++.++... ..++.+|+|.|.+- +..||.+..+..+.
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLs 143 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLS 143 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeec
Confidence 99999999665 43 34334455679999877441 13599999999994 68899999998877
Q ss_pred C
Q 033976 84 N 84 (107)
Q Consensus 84 ~ 84 (107)
.
T Consensus 144 K 144 (502)
T COG1190 144 K 144 (502)
T ss_pred c
Confidence 4
No 73
>PRK02001 hypothetical protein; Validated
Probab=67.68 E-value=24 Score=25.06 Aligned_cols=35 Identities=11% Similarity=0.171 Sum_probs=24.5
Q ss_pred CceeeehhhhhccCCCeEEEE--------EEEeeccCCeEEEE
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV--------IQVIQSDGGGVTGK 40 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv--------GkV~~~~g~~~~~~ 40 (107)
-+|--...+..+|+|+.|++. |++..++++.+++.
T Consensus 76 dRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~ 118 (152)
T PRK02001 76 TSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADENDITLE 118 (152)
T ss_pred CCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCCEEEEE
Confidence 367788889999999999875 44445544444443
No 74
>PRK14644 hypothetical protein; Provisional
Probab=66.03 E-value=32 Score=23.91 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=30.5
Q ss_pred ceeeehhhhhccCCCeEEEE------------EEEeeccCCeEEEEe-CCCCEEEEEc
Q 033976 7 AVFVNGGLMRMYVGRRIRTV------------IQVIQSDGGGVTGKS-TDGHQLVVKG 51 (107)
Q Consensus 7 ~pRVn~~~L~~~~Gk~Vrlv------------GkV~~~~g~~~~~~s-~D~g~V~v~l 51 (107)
+|.-. ....+|+|+.|++- |++..++++.+++.. ..|...++.+
T Consensus 73 RpL~~-~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~ 129 (136)
T PRK14644 73 MDYET-DELENHIGEIIDVSLNKEVNKTDFITGELLENNPETITLKWNCKGQFRKVEI 129 (136)
T ss_pred CCCCH-HHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCCEEEEEEecCCcEEEEEE
Confidence 55555 47899999998873 777788888777753 3344555555
No 75
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=65.91 E-value=47 Score=29.04 Aligned_cols=64 Identities=19% Similarity=0.176 Sum_probs=42.6
Q ss_pred CCeEEEEEEEeec--cCCe--EEEEeCCCCEEEEEccCCC-------------CCCCCEEEEEEEEC----CCCCEEEEE
Q 033976 20 GRRIRTVIQVIQS--DGGG--VTGKSTDGHQLVVKGPQPG-------------FPLTTFVEVIGIAD----TDRSIRAEI 78 (107)
Q Consensus 20 Gk~VrlvGkV~~~--~g~~--~~~~s~D~g~V~v~l~~~~-------------~~~~~~vEViG~V~----~~~si~~~~ 78 (107)
.+.|+|-|+|.+. -|+. +.++ ..+|.|+|...... ..++.+|.|.|+|. +..+|.+..
T Consensus 107 ~~~V~vaGrV~~~R~~Gk~~F~~Lr-D~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~~GeleI~~~~ 185 (659)
T PTZ00385 107 QATVRVAGRVTSVRDIGKIIFVTIR-SNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASR 185 (659)
T ss_pred CCEEEEEEEEEeeeccCCeEEEEEE-ECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecCCceEEEEeeE
Confidence 3469999999965 3544 3333 34578888775421 23589999999885 345676676
Q ss_pred EEeCCC
Q 033976 79 WNNFGN 84 (107)
Q Consensus 79 ~~~~g~ 84 (107)
+.-++.
T Consensus 186 i~lLsk 191 (659)
T PTZ00385 186 MLILSP 191 (659)
T ss_pred EEEech
Confidence 666553
No 76
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=65.62 E-value=62 Score=26.96 Aligned_cols=62 Identities=19% Similarity=0.072 Sum_probs=41.7
Q ss_pred eeehhhhhccCC-CeEEEEEEEeec--cCCeEEEEeCCC-CEEEEEccCC-C---------CCCCCEEEEEEEECC
Q 033976 9 FVNGGLMRMYVG-RRIRTVIQVIQS--DGGGVTGKSTDG-HQLVVKGPQP-G---------FPLTTFVEVIGIADT 70 (107)
Q Consensus 9 RVn~~~L~~~~G-k~VrlvGkV~~~--~g~~~~~~s~D~-g~V~v~l~~~-~---------~~~~~~vEViG~V~~ 70 (107)
|+.-+-+.++.+ +.|++-|-|-.. .|+..-+..-|| +.|++.+..+ . ..+...|+|.|+|..
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~G~v~~ 79 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVTGIVKA 79 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccEEEEEEEEEc
Confidence 455566677776 999999999954 455544544444 4566666532 1 235889999999973
No 77
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=64.68 E-value=2.2 Score=27.18 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=0.0
Q ss_pred CCCeEE----EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIR----TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
.|..|. +.|+|.+++++++.+++++|-.+++.-
T Consensus 39 ~Gd~VvT~gGi~G~V~~i~~~~v~lei~~g~~i~v~k 75 (82)
T PF02699_consen 39 PGDEVVTIGGIYGTVVEIDDDTVVLEIAPGVEITVEK 75 (82)
T ss_dssp -------------------------------------
T ss_pred CCCEEEECCcEEEEEEEEeCCEEEEEECCCeEEEEEH
Confidence 466665 468888999999999999876665543
No 78
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=64.49 E-value=16 Score=23.86 Aligned_cols=42 Identities=21% Similarity=0.391 Sum_probs=28.0
Q ss_pred hccCCCeEE--------EEEEEeeccCCeEEEEeCCCCEEEEEccCC--CCCCCCEEEEE
Q 033976 16 RMYVGRRIR--------TVIQVIQSDGGGVTGKSTDGHQLVVKGPQP--GFPLTTFVEVI 65 (107)
Q Consensus 16 ~~~~Gk~Vr--------lvGkV~~~~g~~~~~~s~D~g~V~v~l~~~--~~~~~~~vEVi 65 (107)
..|+||.|. ++|||....|++ |.|..++... ...++..|+|+
T Consensus 36 ~fylGKrv~yvyk~grviwGKItR~HGns--------GvVrAkF~~nLP~~a~G~~vrv~ 87 (87)
T PRK04337 36 AKLIGRKVIWKDPTGNKYVGKIVRVHGNR--------GEVRARFKPGLPGQALGDYVEII 87 (87)
T ss_pred HhhcCceEEEEeCCCCEEEEEEEeeeCCC--------ceEEEEECCCCChHHcCCEEEeC
Confidence 457788774 678888888854 6677777544 23357777763
No 79
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=63.92 E-value=32 Score=21.17 Aligned_cols=49 Identities=14% Similarity=0.048 Sum_probs=31.0
Q ss_pred eEEEEEEEeecc--CC-eEEEEeCCCCEEEEEccCC----------CCCCCCEEEEEEEECC
Q 033976 22 RIRTVIQVIQSD--GG-GVTGKSTDGHQLVVKGPQP----------GFPLTTFVEVIGIADT 70 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~-~~~~~s~D~g~V~v~l~~~----------~~~~~~~vEViG~V~~ 70 (107)
+|++-|.|.+.. |+ .|..--...+.+++.++.. ..+.+.+|+|.|++..
T Consensus 1 ~V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~ 62 (85)
T cd04100 1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVK 62 (85)
T ss_pred CEEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEE
Confidence 488999999553 33 3322233346777766442 1245899999999863
No 80
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=62.58 E-value=27 Score=22.25 Aligned_cols=40 Identities=23% Similarity=0.278 Sum_probs=29.5
Q ss_pred EEEEEeeccC-CeEEEEeCCCCEEEEEccCCC-----CCCCCEEEE
Q 033976 25 TVIQVIQSDG-GGVTGKSTDGHQLVVKGPQPG-----FPLTTFVEV 64 (107)
Q Consensus 25 lvGkV~~~~g-~~~~~~s~D~g~V~v~l~~~~-----~~~~~~vEV 64 (107)
+.|+|...-| +.+.++|.||.++.++++.-- -..+.+|-|
T Consensus 7 ~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlV 52 (83)
T smart00652 7 EIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLV 52 (83)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEE
Confidence 6799997655 568899999999999985431 123777766
No 81
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=62.50 E-value=30 Score=27.11 Aligned_cols=46 Identities=20% Similarity=0.227 Sum_probs=37.7
Q ss_pred EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECCCC
Q 033976 27 IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADTDR 72 (107)
Q Consensus 27 GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~~ 72 (107)
|++..+.|.++++-.-|++-++|+|++.. .....+.-.||.|...+
T Consensus 152 Gq~aRSaGtyA~vv~~~~~y~~vrLpSGe~r~v~~~CrATIGvV~n~~ 199 (275)
T COG0090 152 GQLARSAGTYAQVVGKEGNYVIVRLPSGEMRKVLSECRATIGVVANGG 199 (275)
T ss_pred ceEEEeCCceEEEEEccCCEEEEECCCCCeEeecccccEEEEEecCCc
Confidence 66778889999999999999999998773 23488889999997544
No 82
>TIGR00752 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.
Probab=62.32 E-value=54 Score=24.03 Aligned_cols=55 Identities=15% Similarity=0.049 Sum_probs=34.1
Q ss_pred hccCCCeEEEEEEEeecc----CCeEEEE-------------eCCCCEEEEEccCC-C--CCCCCEEEEEEEECC
Q 033976 16 RMYVGRRIRTVIQVIQSD----GGGVTGK-------------STDGHQLVVKGPQP-G--FPLTTFVEVIGIADT 70 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~----g~~~~~~-------------s~D~g~V~v~l~~~-~--~~~~~~vEViG~V~~ 70 (107)
..|+||.||+=|+|.++. ...+.+- ....|..-+..+.- + ...+..|.|+|++.+
T Consensus 44 ~~y~G~~Vr~GG~I~~v~N~~~~T~lEVv~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y~Gr~VTVvG~i~G 118 (182)
T TIGR00752 44 LLYVGQTARFGGKVVNVTNLANQTKLEIASLPLDSIAKPFVELQSDGRFIAYFNGFLDPVNLRERYVTVGGQIAG 118 (182)
T ss_pred hhcCCCEEEECCEEEEEEECCCceEEEEEEcccCCCCCcCCCCCCCCEEEEEeCCCcChhhcCCCEEEEEEEecc
Confidence 458999999999999652 2222221 22334454544332 1 124899999999974
No 83
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. This entry represents Gar1 and Naf1. Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex being replaced by GAR1 to yield mature H/ACA snoRNPs complex. Naf1 reveals a striking structural homology with the core domain of archaeal Gar1 [].; GO: 0030515 snoRNA binding, 0031120 snRNA pseudouridine synthesis, 0042254 ribosome biogenesis; PDB: 2EY4_C 3MQK_C 2RFK_C 2HVY_B 3HAY_B 3U28_C 3UAI_C 2EQN_A 2V3M_F.
Probab=62.27 E-value=13 Score=26.12 Aligned_cols=53 Identities=19% Similarity=0.108 Sum_probs=35.7
Q ss_pred CCCeEEEEEEEeeccCCeEEEEeCCCCEEE----EEccCCCCCCCCEEEEEEEECCC
Q 033976 19 VGRRIRTVIQVIQSDGGGVTGKSTDGHQLV----VKGPQPGFPLTTFVEVIGIADTD 71 (107)
Q Consensus 19 ~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~----v~l~~~~~~~~~~vEViG~V~~~ 71 (107)
-.-.+.-+|+|.++-++.+.++++....+- +...+.-..++...||.|-|+..
T Consensus 19 ~~~~i~~lG~v~~i~~~~vVvk~~~~~~vl~~~s~v~~edr~~iG~V~eiFGpV~~P 75 (154)
T PF04410_consen 19 PPEEIKPLGTVSHIVENLVVVKSTPSKQVLDFGSVVCLEDRTKIGKVDEIFGPVNNP 75 (154)
T ss_dssp TTSSEEEEEEEEEEETTEEEEEE-SS-CEEBTT-EEEETTSBEEEEEEEEESESSS-
T ss_pred CCceEEEeeeEEEEeCCcEEEEeCCCCcCCCCCCEEECCCCCEeEEEeeEeCCCCce
Confidence 456789999999998888989988762221 11112224568999999999753
No 84
>PRK14632 hypothetical protein; Provisional
Probab=62.14 E-value=25 Score=25.34 Aligned_cols=21 Identities=33% Similarity=0.499 Sum_probs=17.7
Q ss_pred CceeeehhhhhccCCCeEEEE
Q 033976 6 PAVFVNGGLMRMYVGRRIRTV 26 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~Vrlv 26 (107)
-+|-....+..+|+|+.|++-
T Consensus 84 dRpL~~~~~f~r~iG~~V~V~ 104 (172)
T PRK14632 84 ERPFFRAEQMSPYVGRQIELT 104 (172)
T ss_pred CCcCCCHHHHHHhCCCEEEEE
Confidence 367888889999999999874
No 85
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=60.04 E-value=48 Score=21.97 Aligned_cols=29 Identities=10% Similarity=0.079 Sum_probs=23.1
Q ss_pred EEEEEeec-cCCeEEEEeCCCCEEEEEccC
Q 033976 25 TVIQVIQS-DGGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 25 lvGkV~~~-~g~~~~~~s~D~g~V~v~l~~ 53 (107)
+-|+|.++ ||+++.+...++..++|.|..
T Consensus 3 ~~~~V~~V~DGDT~~v~~~~~~~~~vrL~g 32 (138)
T smart00318 3 IRGVVERVLDGDTIRVRLPKNKLITIRLSG 32 (138)
T ss_pred eeEEEEEEecCCEEEEEeCCCCEEEEEEEe
Confidence 45778865 999999998887788887754
No 86
>PRK14635 hypothetical protein; Provisional
Probab=58.75 E-value=32 Score=24.49 Aligned_cols=46 Identities=15% Similarity=0.109 Sum_probs=27.5
Q ss_pred CceeeehhhhhccCCCeEEEEEEEe---eccCCeEEEEeCCCCEEEEEc
Q 033976 6 PAVFVNGGLMRMYVGRRIRTVIQVI---QSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 6 ~~pRVn~~~L~~~~Gk~VrlvGkV~---~~~g~~~~~~s~D~g~V~v~l 51 (107)
-+|--...+..+|+|+.|++--+.. ...|....|..-|+..|++..
T Consensus 85 dRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~ 133 (162)
T PRK14635 85 ERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEK 133 (162)
T ss_pred CCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEE
Confidence 3677788899999999988643222 112222245555555666544
No 87
>CHL00052 rpl2 ribosomal protein L2
Probab=57.88 E-value=34 Score=26.68 Aligned_cols=53 Identities=17% Similarity=0.213 Sum_probs=41.6
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECCC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADTD 71 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~ 71 (107)
.|-.|+=+ |++....|..+++..-+++-+.|+|++.. .......=.||+|...
T Consensus 135 ~Gt~I~NIE~~pg~Ggk~~RsAGt~A~ii~k~~~~~~vkLPSGe~r~v~~~c~AtIG~Vsn~ 196 (273)
T CHL00052 135 LGTAIHNIEITPGKGGQLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATIGQVGNV 196 (273)
T ss_pred CCCEEEEEEecCCCCceEEEecCCeEEEEEecCCEEEEECCCCCeEEECCcCeEEEEEccCC
Confidence 46666655 88889999999999889999999997763 2247778899999653
No 88
>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane
Probab=57.65 E-value=66 Score=22.83 Aligned_cols=55 Identities=13% Similarity=0.210 Sum_probs=35.4
Q ss_pred hccCCCeEEEEEEEeecc----CCeEEEE-------------eCCCCEEEEEccCC-C---CCCCCEEEEEEEECC
Q 033976 16 RMYVGRRIRTVIQVIQSD----GGGVTGK-------------STDGHQLVVKGPQP-G---FPLTTFVEVIGIADT 70 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~----g~~~~~~-------------s~D~g~V~v~l~~~-~---~~~~~~vEViG~V~~ 70 (107)
..|.||.||+=|+|.+++ +..+.+. ....|...+..+.- + ...+..|.|+|+|.+
T Consensus 30 ~~~~G~~VrwGG~I~~v~n~~~~T~leV~~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y~~Gr~vTV~G~v~g 105 (160)
T PF03843_consen 30 DAYQGQQVRWGGVIVNVRNLPDQTELEVVQYPLDSSGRPQTDDPSQGRFLARVPGFLDPAIYAPGRLVTVVGTVTG 105 (160)
T ss_pred hhcCCCEEEECCEEEEEEECCCceEEEEEEccCCCCCCcCCCCCCCCEEEEEeCCCcCHHHcCCCCEEEEEEEecc
Confidence 568999999999999552 2223221 22345555655433 2 235899999999974
No 89
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=57.09 E-value=26 Score=23.22 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=28.5
Q ss_pred eeeehhhh--hccCCCeEEEE-----------EEEeeccCCeEEEEeCCCCEEEEE
Q 033976 8 VFVNGGLM--RMYVGRRIRTV-----------IQVIQSDGGGVTGKSTDGHQLVVK 50 (107)
Q Consensus 8 pRVn~~~L--~~~~Gk~Vrlv-----------GkV~~~~g~~~~~~s~D~g~V~v~ 50 (107)
+++...+| ..++|..|+++ |+|..-.-+++.+.+.+ ++.+|-
T Consensus 3 ~~i~p~~i~~hEliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t~~-~~~~Vp 57 (95)
T COG1588 3 GRITPRNIIRHELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDTGS-REKVVP 57 (95)
T ss_pred CCccCCCcChHHhcCcEEEEEecCCCCccceeEEEEeeeccEEEEECCC-ceEEEe
Confidence 34444444 55788888876 66776677788888876 666653
No 90
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=56.46 E-value=37 Score=26.03 Aligned_cols=53 Identities=15% Similarity=0.166 Sum_probs=41.8
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECCC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADTD 71 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~ 71 (107)
.|-.|+=+ |++....|..+++..-|++.++|+|++.. .......=.||+|...
T Consensus 102 ~Gt~I~NIE~~pG~Ggkl~RSAGt~A~Ii~k~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~ 163 (238)
T PRK09612 102 EGTPVCNIESRPGDGGKFARSSGTYALVVGHEGDKVIVQLPSGKIKELNPRCRATIGVVAGG 163 (238)
T ss_pred CCCEEEEEEecCCCCcceEEcCCCeEEEEEecCCEEEEECCCCCeEEECCcCeEEEEEccCC
Confidence 56666666 78888899999999889999999997763 2247778899999653
No 91
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=56.15 E-value=32 Score=26.90 Aligned_cols=52 Identities=19% Similarity=0.247 Sum_probs=41.3
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADT 70 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~ 70 (107)
.|-.|.=+ |++....|..+++..-++..++|+|++.. .......=.||+|..
T Consensus 137 ~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k~~~~~~vkLPSGe~r~i~~~c~AtIG~Vsn 197 (276)
T PRK09374 137 VGTTVHNIELKPGKGGQLARSAGTSAQLVAKEGKYATLRLPSGEVRKVLAECRATIGEVGN 197 (276)
T ss_pred CCCEEEEEEecCCCCceeEeecCCeEEEEEecCCEEEEECCCCCeEEEcccccEEEEeecC
Confidence 46666655 88889999999999989999999997763 224777889999975
No 92
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=56.08 E-value=38 Score=26.40 Aligned_cols=54 Identities=19% Similarity=0.283 Sum_probs=42.6
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECCCC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADTDR 72 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~~ 72 (107)
.|-.|.=+ |+.....|..+++..-++..++|+|++.. .......=.||+|...+
T Consensus 135 ~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~~ 197 (273)
T TIGR01171 135 VGTTVHNIELKPGKGGQLARSAGTSAQILAKEGGYVTLRLPSGEMRMVLKECRATIGEVGNED 197 (273)
T ss_pred CCCEEEEEEecCCCCceEEEecCCeEEEEEecCCEEEEECCCCCeEEECCcCeEEEEEccCCc
Confidence 56666666 88889999999999999999999997763 22477788999997533
No 93
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=55.13 E-value=40 Score=22.33 Aligned_cols=29 Identities=24% Similarity=0.141 Sum_probs=24.0
Q ss_pred EEEEEeeccC-CeEEEEeCCCCEEEEEccC
Q 033976 25 TVIQVIQSDG-GGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 25 lvGkV~~~~g-~~~~~~s~D~g~V~v~l~~ 53 (107)
+.|+|...-| +.+.+.+.||.++.++++.
T Consensus 23 ~~g~V~~~lG~~~~~V~~~dG~~~la~i~G 52 (100)
T PRK04012 23 VFGVVEQMLGANRVRVRCMDGVERMGRIPG 52 (100)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEEch
Confidence 7899996654 5788999999999999854
No 94
>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=54.63 E-value=45 Score=20.88 Aligned_cols=41 Identities=20% Similarity=0.054 Sum_probs=29.1
Q ss_pred EEEEEeeccC-CeEEEEeCCCCEEEEEccCCC-C----CCCCEEEEE
Q 033976 25 TVIQVIQSDG-GGVTGKSTDGHQLVVKGPQPG-F----PLTTFVEVI 65 (107)
Q Consensus 25 lvGkV~~~~g-~~~~~~s~D~g~V~v~l~~~~-~----~~~~~vEVi 65 (107)
+.|+|...-| +.+.+++.||.++.+.++.-- . ..+.+|-|-
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve 48 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVA 48 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEE
Confidence 5789997655 578899999999999985441 1 126666554
No 95
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=53.63 E-value=51 Score=28.46 Aligned_cols=58 Identities=19% Similarity=0.093 Sum_probs=38.9
Q ss_pred hhhhhccCCCeEEEEEEEeec--cCCeEEEEeCC-CCEEEEEccCC-CC---------CCCCEEEEEEEEC
Q 033976 12 GGLMRMYVGRRIRTVIQVIQS--DGGGVTGKSTD-GHQLVVKGPQP-GF---------PLTTFVEVIGIAD 69 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGkV~~~--~g~~~~~~s~D-~g~V~v~l~~~-~~---------~~~~~vEViG~V~ 69 (107)
+..-..++|++|+|-|-|.+. -|+..-+..-| .|.|+|..+.+ +. -..-+++|.|+|.
T Consensus 7 g~l~~~~vG~~V~L~GWV~r~Rd~GgliFiDLRDr~GivQvv~~~~~~~~~~~~a~~lr~E~vi~V~G~V~ 77 (585)
T COG0173 7 GELRESHVGQTVTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEFVIQVTGTVR 77 (585)
T ss_pred cccCHHHCCCEEEEEeeeeeccccCCeEEEEcccCCCeEEEEECCccCHHHHHHHHhcCceEEEEEEEEEE
Confidence 344456999999999999954 34443344333 36888888663 11 1277899999995
No 96
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=52.19 E-value=45 Score=19.25 Aligned_cols=46 Identities=28% Similarity=0.584 Sum_probs=27.4
Q ss_pred ccCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEE
Q 033976 17 MYVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVI 65 (107)
Q Consensus 17 ~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEVi 65 (107)
+++|+++.+.-.=.+ ++......+.++..|-|.-..| .++.+++|.
T Consensus 2 ~~~G~~~~VlVe~~~-~~g~~~gr~~~~~~V~v~~~~~--~iG~~v~v~ 47 (61)
T PF01938_consen 2 SYVGKTLEVLVEELG-DEGQGIGRTDNGKVVFVPGGLP--LIGEFVKVR 47 (61)
T ss_dssp --TTEEEEEEEEEE--TTSEEEEEET-TEEEEETT--T----TEEEEEE
T ss_pred ccCCcEEEEEEEEec-CCCEEEEEeCCCeEEEECCCCC--CCCCEEEEE
Confidence 578888887633334 6677888998877777766544 278888774
No 97
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=50.59 E-value=12 Score=24.71 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=11.3
Q ss_pred hhhhccCCCeEEEEEEE
Q 033976 13 GLMRMYVGRRIRTVIQV 29 (107)
Q Consensus 13 ~~L~~~~Gk~VrlvGkV 29 (107)
+|..+|+|++|.|+-|-
T Consensus 1 ~m~~~~IGs~ISlisk~ 17 (96)
T PF12701_consen 1 SMADPYIGSKISLISKS 17 (96)
T ss_dssp --CCCCTTCEEEEEETT
T ss_pred CccccccCCEEEEEECC
Confidence 36678999998876443
No 98
>PTZ00031 ribosomal protein L2; Provisional
Probab=50.35 E-value=53 Score=26.27 Aligned_cols=53 Identities=23% Similarity=0.108 Sum_probs=42.4
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECCC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADTD 71 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~ 71 (107)
.|-.|+=+ |+.....|..+++..-+++.++|+|++.. .......=.||+|...
T Consensus 168 ~GT~IhNIE~~pG~Ggkl~RSAGt~A~Ii~k~~~~~~VkLPSGe~r~i~~~C~ATIG~Vsn~ 229 (317)
T PTZ00031 168 VGSIVHNVEMRPGAGGQIIRAGGTYATVVSKDEQFATLKLKSTEIRKFPLDCWATIGQVSNL 229 (317)
T ss_pred CCCEEEEEEecCCCCceEEEecCCeEEEEEccCCEEEEECCCCCEEEECccCeEEEEEccCC
Confidence 56666666 88889999999999999999999997763 2247778899999753
No 99
>PF09939 DUF2171: Uncharacterized protein conserved in bacteria (DUF2171); InterPro: IPR018684 This family of various hypothetical prokaryotic proteins has no known function.
Probab=50.22 E-value=23 Score=22.02 Aligned_cols=19 Identities=21% Similarity=0.186 Sum_probs=15.9
Q ss_pred EEEEEeeccCCeEEEEeCC
Q 033976 25 TVIQVIQSDGGGVTGKSTD 43 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D 43 (107)
-+|+|.+++|+...|+-.|
T Consensus 15 ~vGtVDhveGd~IKLtk~d 33 (67)
T PF09939_consen 15 HVGTVDHVEGDRIKLTKDD 33 (67)
T ss_pred EEEEEeeEeCCEEEEeccC
Confidence 4799999999888887776
No 100
>PRK12366 replication factor A; Reviewed
Probab=50.04 E-value=67 Score=27.72 Aligned_cols=59 Identities=10% Similarity=-0.075 Sum_probs=38.7
Q ss_pred eeeehhhhhcc-CCCeEEEEEEEeecc-----------CCeEEEEeC-CCCEEEEEccCCC----CC--CCCEEEEEE
Q 033976 8 VFVNGGLMRMY-VGRRIRTVIQVIQSD-----------GGGVTGKST-DGHQLVVKGPQPG----FP--LTTFVEVIG 66 (107)
Q Consensus 8 pRVn~~~L~~~-~Gk~VrlvGkV~~~~-----------g~~~~~~s~-D~g~V~v~l~~~~----~~--~~~~vEViG 66 (107)
+.+.=+-|..| .|+++.|-|||.+.+ |..+.+.-. +.|+|.+.+=.+. .. .+++|+|.+
T Consensus 278 ~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l~~G~vy~is~ 355 (637)
T PRK12366 278 EIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILENLKEGDAVKIEN 355 (637)
T ss_pred CceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCCeEEEEEeCchhhhhcccCCCCEEEEec
Confidence 34555778888 899999999999653 333334333 3378888775541 12 477888765
No 101
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=48.46 E-value=60 Score=21.44 Aligned_cols=40 Identities=23% Similarity=0.129 Sum_probs=28.9
Q ss_pred EEEEEeeccC-CeEEEEeCCCCEEEEEccCCC-----CCCCCEEEE
Q 033976 25 TVIQVIQSDG-GGVTGKSTDGHQLVVKGPQPG-----FPLTTFVEV 64 (107)
Q Consensus 25 lvGkV~~~~g-~~~~~~s~D~g~V~v~l~~~~-----~~~~~~vEV 64 (107)
+.|+|...-| ..+.+.|.||.++.++++.-- -..+.+|-|
T Consensus 21 ~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlV 66 (99)
T TIGR00523 21 ILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIV 66 (99)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEE
Confidence 7889997655 578889999999999985431 112666665
No 102
>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=47.78 E-value=66 Score=19.91 Aligned_cols=32 Identities=16% Similarity=0.172 Sum_probs=26.2
Q ss_pred eEEEEEEEeec-cCCeEEEEeCCCCEEEEEccC
Q 033976 22 RIRTVIQVIQS-DGGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 22 ~VrlvGkV~~~-~g~~~~~~s~D~g~V~v~l~~ 53 (107)
.+.+-|+|... .+..+.+++.||.++..+++-
T Consensus 4 ~ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~G 36 (68)
T TIGR00008 4 KIEMEGKVTESLPNAMFRVELENGHEVLAHISG 36 (68)
T ss_pred EEEEEEEEEEECCCCEEEEEECCCCEEEEEecC
Confidence 57788999954 667799999999999998843
No 103
>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=47.62 E-value=57 Score=20.69 Aligned_cols=55 Identities=22% Similarity=0.265 Sum_probs=34.7
Q ss_pred EEEEEeeccCC-eEEEEeCCCCEEEEEccCCC---CC--CCCEEEEEEEECCCCCEEEEEEE
Q 033976 25 TVIQVIQSDGG-GVTGKSTDGHQLVVKGPQPG---FP--LTTFVEVIGIADTDRSIRAEIWN 80 (107)
Q Consensus 25 lvGkV~~~~g~-~~~~~s~D~g~V~v~l~~~~---~~--~~~~vEViG~V~~~~si~~~~~~ 80 (107)
.+.+|.+..|+ .+.++|.||.+.-+.++.-- .. -+.||=|- .-+.+..++++-..
T Consensus 2 ~i~rV~~~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~-p~~~~~kvkgeIv~ 62 (78)
T cd05792 2 QIVRVLGSKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVE-PIEEGDKVKAEIVK 62 (78)
T ss_pred eEEEEEEcCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEE-ecccCCceEEEEEE
Confidence 35688877664 68899999999999995431 11 27777652 22223345555443
No 104
>KOG2411 consensus Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]
Probab=47.54 E-value=71 Score=27.55 Aligned_cols=57 Identities=14% Similarity=-0.043 Sum_probs=40.5
Q ss_pred hhhhccCCCeEEEEEEEeecc---CCeEEEEeCCCCEEEEEccCCC----------CCCCCEEEEEEEEC
Q 033976 13 GLMRMYVGRRIRTVIQVIQSD---GGGVTGKSTDGHQLVVKGPQPG----------FPLTTFVEVIGIAD 69 (107)
Q Consensus 13 ~~L~~~~Gk~VrlvGkV~~~~---g~~~~~~s~D~g~V~v~l~~~~----------~~~~~~vEViG~V~ 69 (107)
+....-+|++|.|.|-++... +.++..--...|+|++.++..+ .++..+|.|.|+|.
T Consensus 40 el~~~~vg~kv~l~GWl~~~~~~k~~~F~~LRD~~G~vq~lls~~s~~l~~~~~~~v~~e~vv~v~gtvv 109 (628)
T KOG2411|consen 40 ELSVNDVGKKVVLCGWLELHRVHKMLTFFNLRDAYGIVQQLLSPDSFPLAQKLENDVPLEDVVQVEGTVV 109 (628)
T ss_pred hhccCccCCEEEEeeeeeeeeccccceEEEeeccCcceEEEecchhhhHHhcccCCCChhheEeeeeeEe
Confidence 344556999999999999443 5555444444688888886543 23478999999995
No 105
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=46.98 E-value=80 Score=24.55 Aligned_cols=53 Identities=19% Similarity=0.144 Sum_probs=41.2
Q ss_pred CCCeEEEE-------EEEeeccCCeEEEEe--CCCCEEEEEccCCC--CCCCCEEEEEEEECCC
Q 033976 19 VGRRIRTV-------IQVIQSDGGGVTGKS--TDGHQLVVKGPQPG--FPLTTFVEVIGIADTD 71 (107)
Q Consensus 19 ~Gk~Vrlv-------GkV~~~~g~~~~~~s--~D~g~V~v~l~~~~--~~~~~~vEViG~V~~~ 71 (107)
.|-.|.=| |++....|..+++.. -|++.++|+|++.. .......=.||+|...
T Consensus 109 ~GT~IhNIE~~pG~GgklaRSAGt~A~ii~k~k~~~~~~vkLPSGe~r~v~~~c~ATIG~Vsn~ 172 (260)
T PTZ00180 109 EGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGG 172 (260)
T ss_pred CCCeEEEEeccCCCCceEEEecCCeEEEEEEcccCCEEEEECCCCCeEeECCCCeEEEEEccCC
Confidence 56666666 788889999999987 56899999997763 2247778899999643
No 106
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=46.43 E-value=52 Score=18.36 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=16.6
Q ss_pred CCCeEEE-------EEEEeeccC-CeEEEEeCCC
Q 033976 19 VGRRIRT-------VIQVIQSDG-GGVTGKSTDG 44 (107)
Q Consensus 19 ~Gk~Vrl-------vGkV~~~~g-~~~~~~s~D~ 44 (107)
.||.|++ .|++..+|. ..+.+++.||
T Consensus 2 lG~~V~v~~~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 2 LGQEVRVETGDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp TTSEEEEEETSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCEEEEEECCeEEEEEEEEECCCCEEEEEECCC
Confidence 4666665 577777755 3566777765
No 107
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=43.63 E-value=58 Score=22.50 Aligned_cols=32 Identities=9% Similarity=0.032 Sum_probs=19.1
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEEEccCC--CCCCCCEEEE
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVVKGPQP--GFPLTTFVEV 64 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v~l~~~--~~~~~~~vEV 64 (107)
++|||....|++ |.|..++... ...++..|+|
T Consensus 80 iwGKVtR~HGns--------GvVrAkF~~nLPp~A~G~~VrV 113 (120)
T PTZ00041 80 IWGKITRPHGNS--------GVVRARFNKNLPPKAIGSRVRV 113 (120)
T ss_pred EEEEEEcccCCC--------cEEEEEeCCCCChHHcCCeEEE
Confidence 447777777753 6677766543 2235666665
No 108
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=42.74 E-value=46 Score=23.49 Aligned_cols=11 Identities=18% Similarity=0.474 Sum_probs=8.2
Q ss_pred hccCCCeEEEE
Q 033976 16 RMYVGRRIRTV 26 (107)
Q Consensus 16 ~~~~Gk~Vrlv 26 (107)
..++||.|...
T Consensus 93 ~slIGk~V~~~ 103 (140)
T PRK06009 93 EGLIGRTVTSA 103 (140)
T ss_pred HHhcCCEEEec
Confidence 45789999854
No 109
>PF11495 Regulator_TrmB: Archaeal transcriptional regulator TrmB; InterPro: IPR021586 TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus []. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif []. ; PDB: 3QPH_A 2F5T_X.
Probab=41.74 E-value=44 Score=24.65 Aligned_cols=32 Identities=22% Similarity=0.389 Sum_probs=22.3
Q ss_pred CCCeEEEEEEEee--cc--C--CeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIRTVIQVIQ--SD--G--GGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~VrlvGkV~~--~~--g--~~~~~~s~D~g~V~v~l 51 (107)
.|.++.+-|+|.. .+ + .+++++|.|| +++|-.
T Consensus 179 t~~~~~i~G~v~~~~~~~~~~~~~~~vet~~g-~~~VGG 216 (233)
T PF11495_consen 179 TGEPVTITGRVVDVRFNSFPGVASFTVETDDG-EVTVGG 216 (233)
T ss_dssp T--EEEEEEEEEEEEEETTTTEEEEEEEETTE-EEEEE-
T ss_pred CCCceEEEEEEEEEEeccCCceeEEEEEeCCc-eEEecC
Confidence 7889999999996 32 2 3678888776 888865
No 110
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=41.60 E-value=84 Score=19.34 Aligned_cols=38 Identities=8% Similarity=0.192 Sum_probs=27.2
Q ss_pred hhhhccCCCeEEE-------EEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 13 GLMRMYVGRRIRT-------VIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 13 ~~L~~~~Gk~Vrl-------vGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
..|++.+||+|.+ -|++..+..+...++.. +...=|.+
T Consensus 14 q~lq~liG~~vvV~T~~g~v~G~L~~V~pDhIvl~~~-~~~~~IR~ 58 (66)
T PF10842_consen 14 QTLQSLIGQRVVVQTTRGSVRGILVDVKPDHIVLEEN-GTPFFIRI 58 (66)
T ss_pred HHHHHhcCCEEEEEEcCCcEEEEEEeecCCEEEEEeC-CcEEEEEe
Confidence 5688899999865 57777777777777766 55555554
No 111
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=41.15 E-value=20 Score=22.73 Aligned_cols=17 Identities=18% Similarity=0.493 Sum_probs=13.9
Q ss_pred eeehhhhhccCCCeEEE
Q 033976 9 FVNGGLMRMYVGRRIRT 25 (107)
Q Consensus 9 RVn~~~L~~~~Gk~Vrl 25 (107)
-..++.|++++||+|.+
T Consensus 5 ~~~~~fl~~iiGr~V~V 21 (77)
T KOG1783|consen 5 SMPGEFLKAIIGRTVVV 21 (77)
T ss_pred cCcHHHHHHHhCCeEEE
Confidence 45689999999999854
No 112
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=41.09 E-value=33 Score=21.28 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=13.9
Q ss_pred hhhhhccCCCeEEEEEE
Q 033976 12 GGLMRMYVGRRIRTVIQ 28 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGk 28 (107)
+|.|.+|+||+|++.-+
T Consensus 2 ~~~l~~~l~~~V~V~l~ 18 (79)
T cd01717 2 SSKMLQLINYRLRVTLQ 18 (79)
T ss_pred cchhHHHcCCEEEEEEC
Confidence 57899999999988544
No 113
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=41.03 E-value=93 Score=19.68 Aligned_cols=32 Identities=19% Similarity=0.198 Sum_probs=26.2
Q ss_pred CeEEEEEEEeec-cCCeEEEEeCCCCEEEEEcc
Q 033976 21 RRIRTVIQVIQS-DGGGVTGKSTDGHQLVVKGP 52 (107)
Q Consensus 21 k~VrlvGkV~~~-~g~~~~~~s~D~g~V~v~l~ 52 (107)
....+-|+|... -+..+.++|.||..+.-+++
T Consensus 5 d~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~ 37 (75)
T COG0361 5 DEIEMEGTVIEMLPNGRFRVELENGHERLAHIS 37 (75)
T ss_pred cccEEEEEEEEecCCCEEEEEecCCcEEEEEcc
Confidence 346788999954 66789999999999998884
No 114
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=40.83 E-value=58 Score=22.09 Aligned_cols=32 Identities=19% Similarity=0.081 Sum_probs=22.9
Q ss_pred CCCeEE----EEEEEeeccC--CeEEEEeCCCCEEEEEc
Q 033976 19 VGRRIR----TVIQVIQSDG--GGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~Vr----lvGkV~~~~g--~~~~~~s~D~g~V~v~l 51 (107)
.|-.|. |+|+|.+++. .++.+++ +|..+++.-
T Consensus 39 ~GD~VvT~GGi~G~V~~I~~~~~~v~le~-~gv~i~v~r 76 (113)
T PRK06531 39 KGDEVVTIGGLYGTVDEVDTEAKTIVLDV-DGVYLTFEL 76 (113)
T ss_pred CCCEEEECCCcEEEEEEEecCCCEEEEEE-CCEEEEEEh
Confidence 466666 6899988875 5788887 776666644
No 115
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=40.04 E-value=87 Score=19.06 Aligned_cols=44 Identities=14% Similarity=0.031 Sum_probs=31.6
Q ss_pred eEEEEEEEeecc-CCeEEEEeCCCCEEEEEccCC------CCCCCCEEEEE
Q 033976 22 RIRTVIQVIQSD-GGGVTGKSTDGHQLVVKGPQP------GFPLTTFVEVI 65 (107)
Q Consensus 22 ~VrlvGkV~~~~-g~~~~~~s~D~g~V~v~l~~~------~~~~~~~vEVi 65 (107)
.+.+-|+|.+.- |..+.+++.||..+.+.+..- ....+.+|||.
T Consensus 6 ~~~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve 56 (72)
T PRK00276 6 VIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVE 56 (72)
T ss_pred eEEEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEE
Confidence 567789999765 547888888888888877431 12348888876
No 116
>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=39.67 E-value=76 Score=18.30 Aligned_cols=40 Identities=18% Similarity=0.043 Sum_probs=27.9
Q ss_pred EEEEeeccCCeEEEEeCCCCEEEEEccCC-----C-CCCCCEEEEE
Q 033976 26 VIQVIQSDGGGVTGKSTDGHQLVVKGPQP-----G-FPLTTFVEVI 65 (107)
Q Consensus 26 vGkV~~~~g~~~~~~s~D~g~V~v~l~~~-----~-~~~~~~vEVi 65 (107)
.|+|.+..++...+.+.+++.+.+.+... . ...+.||++-
T Consensus 2 ~grVv~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~ 47 (68)
T cd04466 2 EGLIIKAIGGFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFE 47 (68)
T ss_pred CEEEEEEECCEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEE
Confidence 37788777777778877677888776542 1 2349999875
No 117
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=39.29 E-value=91 Score=19.07 Aligned_cols=48 Identities=17% Similarity=-0.036 Sum_probs=30.1
Q ss_pred eEEEEEEEeecc--CCeEEEEeCC-CCEEEEEccCCC---------CCCCCEEEEEEEEC
Q 033976 22 RIRTVIQVIQSD--GGGVTGKSTD-GHQLVVKGPQPG---------FPLTTFVEVIGIAD 69 (107)
Q Consensus 22 ~VrlvGkV~~~~--g~~~~~~s~D-~g~V~v~l~~~~---------~~~~~~vEViG~V~ 69 (107)
.|++-|.|.+.. |+..-+.-.| .+.+++.+.... .+.+..|+|.|++.
T Consensus 1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~ 60 (84)
T cd04323 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVK 60 (84)
T ss_pred CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEE
Confidence 478999999553 3333333333 355777664321 23589999999986
No 118
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=38.94 E-value=1.8 Score=28.15 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=36.4
Q ss_pred EEEeCCCCEEEEEccCCC-CCCCCEEEEEEEECCCCCEEEEEEEeC-CC
Q 033976 38 TGKSTDGHQLVVKGPQPG-FPLTTFVEVIGIADTDRSIRAEIWNNF-GN 84 (107)
Q Consensus 38 ~~~s~D~g~V~v~l~~~~-~~~~~~vEViG~V~~~~si~~~~~~~~-g~ 84 (107)
.+++.+||.|.=..+.|. .......|+||.|-++.+..++.|-+= ||
T Consensus 4 RIk~p~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~aT~tAFeYEDE~gD 52 (91)
T cd06395 4 RIKIPNGGAVDWTVQSGPQLLFRDVLDVIGQVLPEATTTAFEYEDEDGD 52 (91)
T ss_pred EEeCCCCCcccccccCcccccHHHHHHHHHHhcccccccceeeccccCC
Confidence 467888888877776653 334788999999999999999988554 45
No 119
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=38.80 E-value=1.5e+02 Score=21.38 Aligned_cols=92 Identities=17% Similarity=0.200 Sum_probs=58.8
Q ss_pred eeeehhhhhc---------cCCCeEEEEEEEe--ec--cCC--eEEEEeCCC-CEEEEEccC--CC-CCCCCEEEEEEEE
Q 033976 8 VFVNGGLMRM---------YVGRRIRTVIQVI--QS--DGG--GVTGKSTDG-HQLVVKGPQ--PG-FPLTTFVEVIGIA 68 (107)
Q Consensus 8 pRVn~~~L~~---------~~Gk~VrlvGkV~--~~--~g~--~~~~~s~D~-g~V~v~l~~--~~-~~~~~~vEViG~V 68 (107)
...+.+.+.+ ..||.+|+-|.|. |+ +++ .+..+-+|+ .+|.|.... |+ .-.+.-|=+.|+.
T Consensus 36 yF~tPsev~~~~~~~~~~~~~g~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~~ 115 (160)
T PRK13165 36 LFYTPGEILYGKRETQQKPEVGQRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGILPDLFREGQGIVAQGVL 115 (160)
T ss_pred EEeCHHHHhccccccccccCCCCEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEcccCCccccCCCeEEEEEEE
Confidence 4455555543 4699999999999 43 334 334444444 566776533 22 2237788899999
Q ss_pred CCCCCEEEEEE-EeCCCCCCHHHHHHHHHHHh
Q 033976 69 DTDRSIRAEIW-NNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 69 ~~~~si~~~~~-~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+++...+... ....+++-..-..++++-.+
T Consensus 116 ~~~g~F~A~~vLAKhdekYmPpEv~~al~~~~ 147 (160)
T PRK13165 116 EEGNHIEAKEVLAKHDENYTPPEVEEAMKKNH 147 (160)
T ss_pred CCCCeEEEEEEEecCCCCCCCHHHHHHHHhcc
Confidence 98888877776 56667776555555555443
No 120
>PRK14699 replication factor A; Provisional
Probab=38.74 E-value=2.1e+02 Score=24.05 Aligned_cols=50 Identities=10% Similarity=-0.025 Sum_probs=34.9
Q ss_pred CCeEEEEEEEeecc---------C---CeEEEEeCCC-CEEEEEccCCCC--------CCCCEEEEEEEEC
Q 033976 20 GRRIRTVIQVIQSD---------G---GGVTGKSTDG-HQLVVKGPQPGF--------PLTTFVEVIGIAD 69 (107)
Q Consensus 20 Gk~VrlvGkV~~~~---------g---~~~~~~s~D~-g~V~v~l~~~~~--------~~~~~vEViG~V~ 69 (107)
++.|+|.|||.++. | ....+.-.|. |+|.+.|=.... ..+.+|+|.|.|.
T Consensus 67 ~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv~I~~~~r 137 (484)
T PRK14699 67 SGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQISGYAK 137 (484)
T ss_pred CceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEEEEcceec
Confidence 38899999999763 3 2344455666 789988755421 2367999999884
No 121
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=38.72 E-value=70 Score=19.70 Aligned_cols=33 Identities=15% Similarity=-0.002 Sum_probs=23.6
Q ss_pred CCCeEEEEEEEeeccCCe--EEEEeCCCCEEEEEc
Q 033976 19 VGRRIRTVIQVIQSDGGG--VTGKSTDGHQLVVKG 51 (107)
Q Consensus 19 ~Gk~VrlvGkV~~~~g~~--~~~~s~D~g~V~v~l 51 (107)
-|...++.|+|.++|... +.+...++....|.+
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~ 86 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPF 86 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEh
Confidence 488889999999887754 555554566666665
No 122
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=37.01 E-value=1.1e+02 Score=19.48 Aligned_cols=13 Identities=23% Similarity=0.337 Sum_probs=11.0
Q ss_pred CCCEEEEEEEECC
Q 033976 58 LTTFVEVIGIADT 70 (107)
Q Consensus 58 ~~~~vEViG~V~~ 70 (107)
.+.++.|.|++..
T Consensus 65 ~G~vvrV~G~i~~ 77 (92)
T cd04483 65 IGDLLRVRGSIRT 77 (92)
T ss_pred CCCEEEEEEEEec
Confidence 4889999999973
No 123
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=36.86 E-value=49 Score=21.59 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=17.6
Q ss_pred ccCCeEEEEeCCCCEEEEEccC
Q 033976 32 SDGGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 32 ~~g~~~~~~s~D~g~V~v~l~~ 53 (107)
+||+++.+...++..++|.|..
T Consensus 3 ~dGDt~~v~~~~~~~~~vrL~g 24 (129)
T cd00175 3 IDGDTIRVRLPPGPLITVRLSG 24 (129)
T ss_pred ecCcEEEEEeCCCCEEEEEEEe
Confidence 4899999998888788887743
No 124
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=36.65 E-value=1e+02 Score=18.77 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=27.7
Q ss_pred EEeeccCCeEEEEeCCCC-EEEEEccC-C-CCCCCCEEEE
Q 033976 28 QVIQSDGGGVTGKSTDGH-QLVVKGPQ-P-GFPLTTFVEV 64 (107)
Q Consensus 28 kV~~~~g~~~~~~s~D~g-~V~v~l~~-~-~~~~~~~vEV 64 (107)
-|.+++|+.|.+...+++ .+.|-.+. | ..-.+.++++
T Consensus 3 ivDRiE~~~AVl~~~~~~~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 3 IVDRIEGDYAVLELEDGEKEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred EEEEEeCCEEEEEECCCeEEEEEEHHHCCCCCCcccEEEE
Confidence 466889999999999998 77775542 3 3445888888
No 125
>PF13457 SH3_8: SH3-like domain; PDB: 1M9S_A.
Probab=36.45 E-value=96 Score=18.53 Aligned_cols=37 Identities=19% Similarity=0.362 Sum_probs=24.0
Q ss_pred eehhhhhccCCCeEEEEEEEeeccCCeEEEEeCCCCEE
Q 033976 10 VNGGLMRMYVGRRIRTVIQVIQSDGGGVTGKSTDGHQL 47 (107)
Q Consensus 10 Vn~~~L~~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V 47 (107)
-+-+.+.+|.|+.|.+.....-.+|.-..+.. +|+++
T Consensus 34 ~~~~~~~~y~~~~v~v~k~~~t~~~tw~~i~~-~~~~i 70 (79)
T PF13457_consen 34 GNNGSAKQYNGKKVKVTKEATTKNGTWYQISL-NGKQI 70 (79)
T ss_dssp EE--EGGGCTTS-EEEEEEEEETTEEEEEEEE-TTCEE
T ss_pred cccchhHhhCCcEEEEEEEEEeCccEEEEEEE-CCeEE
Confidence 34456889999999999777766665566655 55543
No 126
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.50 E-value=2.5e+02 Score=23.75 Aligned_cols=54 Identities=13% Similarity=0.041 Sum_probs=35.8
Q ss_pred hccCCCeEEEEEEEee--ccCCe-EEEEeCCCCEEEEEccCCC--------------CCCCCEEEEEEEEC
Q 033976 16 RMYVGRRIRTVIQVIQ--SDGGG-VTGKSTDGHQLVVKGPQPG--------------FPLTTFVEVIGIAD 69 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~--~~g~~-~~~~s~D~g~V~v~l~~~~--------------~~~~~~vEViG~V~ 69 (107)
.+..|+.|.+-|+|-. ..|.. +.+--.-+-+|++....+. .....+|+|+|+|.
T Consensus 78 ~~~~~~~V~vRgrVhtsr~~GK~~FlvLRq~~~tVQ~~~~~~~~~~isk~Mvkf~~~is~ESiV~v~g~v~ 148 (533)
T KOG0556|consen 78 ESNDGSEVLVRGRVHTSRLKGKLCFLVLRQQGSTVQCLVAVNEDGTISKQMVKFAGSISKESIVDVRGVVV 148 (533)
T ss_pred hhcCCceEEEEEEEeeccccceEEEEEEeccCceEEEEEEcCCCchHHHHHHHHHhhcCcceEEEEEEEEe
Confidence 4567999999999984 45655 3332233456666554331 13488999999996
No 127
>PF07013 DUF1314: Protein of unknown function (DUF1314); InterPro: IPR010741 This family consists of several alphaherpesvirus proteins of around 200 residues in length. They belong to the varicellovirus ORF2 family and their function is unknown.
Probab=34.45 E-value=66 Score=23.59 Aligned_cols=57 Identities=19% Similarity=0.028 Sum_probs=43.3
Q ss_pred EEEEEeec-cCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEECCCCCEEEEEEEe
Q 033976 25 TVIQVIQS-DGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIADTDRSIRAEIWNN 81 (107)
Q Consensus 25 lvGkV~~~-~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~~~~si~~~~~~~ 81 (107)
|-|++..+ .|+.+.+.+.-|..++.++..+...-..++-.||+.-.++.-|.+-...
T Consensus 8 LaGR~iDLPgG~el~I~~~~g~~~~~~f~~~g~~~~~~~~~IGRA~a~g~~RkF~iy~ 65 (177)
T PF07013_consen 8 LAGRTIDLPGGDELRISANTGRPNTGKFVRSGSSRLMPVHFIGRAYAIGSCRKFVIYL 65 (177)
T ss_pred hcCcceecCCCCeEEEecCCCCceEEEEecCCCCceehhheehhhhccCCCceEEEEE
Confidence 44555544 5778889988888889999877555677899999999888888765543
No 128
>COG5496 Predicted thioesterase [General function prediction only]
Probab=34.37 E-value=93 Score=21.77 Aligned_cols=37 Identities=11% Similarity=0.039 Sum_probs=25.4
Q ss_pred eehhhhhc-cCCCeEEEEEEEeeccCCe--EEEEeCCCCE
Q 033976 10 VNGGLMRM-YVGRRIRTVIQVIQSDGGG--VTGKSTDGHQ 46 (107)
Q Consensus 10 Vn~~~L~~-~~Gk~VrlvGkV~~~~g~~--~~~~s~D~g~ 46 (107)
|+.++|+. -.|.+|++.-++..++|+. +.++.-+|++
T Consensus 63 v~vrHla~~~~G~~V~i~~~l~~v~Gr~v~f~i~a~~~~~ 102 (130)
T COG5496 63 VLVRHLAATPPGLTVTIGARLEKVEGRKVKFRIIAMEGGD 102 (130)
T ss_pred EEeeeccCCCCCCeEEEEEEEEEEeccEEEEEEEEeeCCc
Confidence 44445533 4799999999999999985 4445555443
No 129
>PF10670 DUF4198: Domain of unknown function (DUF4198)
Probab=33.73 E-value=1.3e+02 Score=21.10 Aligned_cols=19 Identities=21% Similarity=0.232 Sum_probs=16.5
Q ss_pred eEEEEeCCCCEEEEEccCC
Q 033976 36 GVTGKSTDGHQLVVKGPQP 54 (107)
Q Consensus 36 ~~~~~s~D~g~V~v~l~~~ 54 (107)
...++|.++|.+++.+..+
T Consensus 184 ~~~~~TD~~G~~~~~~~~~ 202 (215)
T PF10670_consen 184 AKTLKTDANGRATFTLPRP 202 (215)
T ss_pred eEEEEECCCCEEEEecCCC
Confidence 7788999999999999666
No 130
>PRK14285 chaperone protein DnaJ; Provisional
Probab=33.57 E-value=2.5e+02 Score=22.41 Aligned_cols=72 Identities=11% Similarity=0.069 Sum_probs=50.5
Q ss_pred eccCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEECC------CCCEEEEEEEeCCCCCCHHHHHHHHHHHhccccC
Q 033976 31 QSDGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIADT------DRSIRAEIWNNFGNTFDTQSYNQLCQLANGEFKH 104 (107)
Q Consensus 31 ~~~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~~------~~si~~~~~~~~g~~fD~~~yn~lv~l~~~~~~~ 104 (107)
.+-|.++.+.+-||..|+|.++.. ...+..+-+-|+-.+ .+.+-..--+.+...|.-+.-..+-+++. .+++
T Consensus 279 Al~G~~~~i~tldG~~v~V~Ip~g-~~~g~~irl~GkG~p~~~~~~~GDL~V~~~v~~P~~l~~~q~~~l~~l~~-~~~~ 356 (365)
T PRK14285 279 AALGKEIKIQTIASKKIKIKIPKG-TENDEQIIIKNEGMPILHTEKFGNLILIIKIKTPKNLNSNAIKLLENLSK-ELKD 356 (365)
T ss_pred HhCCCEEEEECCCCCEEEEEeCCC-cCCCcEEEECCCCccCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHH-Hhcc
Confidence 346888999999998899988543 344566666665532 26677777888888888877666666655 4554
No 131
>PLN00208 translation initiation factor (eIF); Provisional
Probab=33.04 E-value=1.3e+02 Score=21.46 Aligned_cols=29 Identities=17% Similarity=0.153 Sum_probs=23.7
Q ss_pred EEEEEeecc-CCeEEEEeCCCCEEEEEccC
Q 033976 25 TVIQVIQSD-GGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 25 lvGkV~~~~-g~~~~~~s~D~g~V~v~l~~ 53 (107)
.+|+|...- +..+.+.|.||.++.++++.
T Consensus 34 ~~g~V~~~lGn~~~~V~c~dG~~rLa~IpG 63 (145)
T PLN00208 34 EYAQVLRMLGNGRCEALCIDGTKRLCHIRG 63 (145)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEec
Confidence 678999664 46788999999999998854
No 132
>COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane]
Probab=32.84 E-value=66 Score=21.23 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=18.3
Q ss_pred EEEECCCCCEEEEEEEeCCCCC
Q 033976 65 IGIADTDRSIRAEIWNNFGNTF 86 (107)
Q Consensus 65 iG~V~~~~si~~~~~~~~g~~f 86 (107)
+=||++++.+++...+.|.+.|
T Consensus 8 irkv~~dgrmkA~vsvT~D~ef 29 (95)
T COG2088 8 IRKVDTDGRMKAYVSVTLDNEF 29 (95)
T ss_pred EEEecCCCcEEEEEEEEecceE
Confidence 4578899999999999998754
No 133
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=32.50 E-value=1.4e+02 Score=19.39 Aligned_cols=31 Identities=10% Similarity=-0.105 Sum_probs=25.2
Q ss_pred eEEEEEEEee-ccCCeEEEEeCCCCEEEEEcc
Q 033976 22 RIRTVIQVIQ-SDGGGVTGKSTDGHQLVVKGP 52 (107)
Q Consensus 22 ~VrlvGkV~~-~~g~~~~~~s~D~g~V~v~l~ 52 (107)
.+.+-|+|.. +.+..+.+++.||.+|..+++
T Consensus 6 ~ie~~G~V~e~Lp~~~frV~LenG~~vla~is 37 (87)
T PRK12442 6 LIELDGIVDEVLPDSRFRVTLENGVEVGAYAS 37 (87)
T ss_pred eEEEEEEEEEECCCCEEEEEeCCCCEEEEEec
Confidence 5778899994 566788899999998888874
No 134
>PF03061 4HBT: Thioesterase superfamily; InterPro: IPR006683 This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (3.1.2.23 from EC) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. ; PDB: 3F5O_F 2F0X_D 2H4U_C 2PRX_A 2OV9_D 1YLI_B 3BJK_F 1IXL_A 3DKZ_B 2EIS_B ....
Probab=32.31 E-value=1e+02 Score=17.60 Aligned_cols=30 Identities=17% Similarity=0.250 Sum_probs=23.0
Q ss_pred ehhhhh-ccCCCeEEEEEEEeeccCCeEEEE
Q 033976 11 NGGLMR-MYVGRRIRTVIQVIQSDGGGVTGK 40 (107)
Q Consensus 11 n~~~L~-~~~Gk~VrlvGkV~~~~g~~~~~~ 40 (107)
+-++++ -..|.++++.+++.+..+++++++
T Consensus 37 ~i~f~~p~~~gd~l~~~~~v~~~g~~~~~~~ 67 (79)
T PF03061_consen 37 SIDFLRPVRPGDTLRVEARVVRVGRKSFTVE 67 (79)
T ss_dssp EEEESS-BBTTSEEEEEEEEEEEESSEEEEE
T ss_pred EEEEccccCCCeEEEEEEEEEEECCEEEEEE
Confidence 334443 357999999999999999987765
No 135
>PRK07211 replication factor A; Reviewed
Probab=31.70 E-value=2.1e+02 Score=24.15 Aligned_cols=55 Identities=24% Similarity=0.126 Sum_probs=39.4
Q ss_pred cCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEccCC-CCCCCCEEEEEEEECCCCCEEEE
Q 033976 18 YVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKGPQP-GFPLTTFVEVIGIADTDRSIRAE 77 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l~~~-~~~~~~~vEViG~V~~~~si~~~ 77 (107)
.-|+.|.+-|.|.+.....+ | |+|+=+..+..+ +.+++.-|+|.|.+. ++.|.+.
T Consensus 427 ~~~~~~~~~g~v~~~~~~~~-l---d~g~~~~~~~~~~~~~~g~~v~~~g~~~-~~~~~~~ 482 (485)
T PRK07211 427 GDGEEVEFTGTVVQAGDPVV-L---DDGEETMSVETDADVRLGEEVTVRGSLR-DGRIDAE 482 (485)
T ss_pred CCCceEEEEEEEEeCCCCeE-E---eCCCeEEEEecCCcCCCCCEEEEEEeec-CCEeehh
Confidence 46899999999998755443 3 445555555555 467899999999985 4666554
No 136
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=31.55 E-value=62 Score=20.10 Aligned_cols=19 Identities=26% Similarity=0.169 Sum_probs=16.0
Q ss_pred cCCCeEEEEEEEeeccCCe
Q 033976 18 YVGRRIRTVIQVIQSDGGG 36 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~~g~~ 36 (107)
-+|..||+-|+|....|.+
T Consensus 46 ~~Gd~V~vtG~v~ey~g~t 64 (78)
T cd04486 46 AVGDLVRVTGTVTEYYGLT 64 (78)
T ss_pred CCCCEEEEEEEEEeeCCeE
Confidence 3699999999999888843
No 137
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=30.98 E-value=1e+02 Score=18.71 Aligned_cols=28 Identities=25% Similarity=0.125 Sum_probs=20.8
Q ss_pred CeEEEEEEEeeccCCeEEEEeCCCCEEEE
Q 033976 21 RRIRTVIQVIQSDGGGVTGKSTDGHQLVV 49 (107)
Q Consensus 21 k~VrlvGkV~~~~g~~~~~~s~D~g~V~v 49 (107)
.-+++-|+|.+.|.=++.+++. |++--|
T Consensus 20 NG~~l~G~I~~fD~ftVll~~~-g~qqLI 47 (61)
T cd01716 20 NGVQLKGQIESFDNFTVLLESD-GKQQLV 47 (61)
T ss_pred CCcEEEEEEEEEcceEEEEEEC-CcEEEE
Confidence 3478899999999999888775 444333
No 138
>PF12272 DUF3610: Protein of unknown function (DUF3610); InterPro: IPR022058 This domain family is found in eukaryotes, and is typically between 146 and 160 amino acids in length. There are two conserved sequence motifs: FNN and IDS.
Probab=30.48 E-value=79 Score=22.81 Aligned_cols=29 Identities=34% Similarity=0.541 Sum_probs=19.8
Q ss_pred EEeCCCCEEEEEccCCCCCCCCEEEEEEEEC
Q 033976 39 GKSTDGHQLVVKGPQPGFPLTTFVEVIGIAD 69 (107)
Q Consensus 39 ~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~ 69 (107)
-..-+++....+-- ...++.|||-.|++.
T Consensus 24 ~~~~~~~PMam~gF--NNsLGTFVE~~Gqas 52 (157)
T PF12272_consen 24 DREEDGNPMAMRGF--NNSLGTFVEYSGQAS 52 (157)
T ss_pred CccccCCceeeeec--cCccceeEeecceEE
Confidence 34455666665432 246899999999995
No 139
>PF00868 Transglut_N: Transglutaminase family; InterPro: IPR001102 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) (TGase) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ]. Transglutaminases are widely distributed in various organs, tissues and body fluids. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. There are commonly three domains: N-terminal, middle (IPR013808 from INTERPRO) and C-terminal (IPR013807 from INTERPRO). This entry represents the N-terminal domain found in transglutaminases.; GO: 0018149 peptide cross-linking; PDB: 1L9N_B 1NUF_A 1NUD_A 1NUG_B 1L9M_A 1KV3_C 3S3S_A 2Q3Z_A 3LY6_A 3S3P_A ....
Probab=30.31 E-value=37 Score=22.76 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=17.3
Q ss_pred eEEEEeCCCCEEEEEccCC-CCCCCCE
Q 033976 36 GVTGKSTDGHQLVVKGPQP-GFPLTTF 61 (107)
Q Consensus 36 ~~~~~s~D~g~V~v~l~~~-~~~~~~~ 61 (107)
.+.+...+|..++|.+..| +.+.+.|
T Consensus 84 ~a~v~~~~~~~~tv~V~spa~A~VG~y 110 (118)
T PF00868_consen 84 SARVESQDGNSVTVSVTSPANAPVGRY 110 (118)
T ss_dssp EEEEEEEETTEEEEEEE--TTS--EEE
T ss_pred EEEEEecCCCEEEEEEECCCCCceEEE
Confidence 6888888888899988888 4555555
No 140
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=29.90 E-value=1.6e+02 Score=19.14 Aligned_cols=43 Identities=16% Similarity=0.013 Sum_probs=28.3
Q ss_pred EEEEEEEeeccCCeEEEEeCCCC--EEEEEccCC-----CCCCCCEEEEEE
Q 033976 23 IRTVIQVIQSDGGGVTGKSTDGH--QLVVKGPQP-----GFPLTTFVEVIG 66 (107)
Q Consensus 23 VrlvGkV~~~~g~~~~~~s~D~g--~V~v~l~~~-----~~~~~~~vEViG 66 (107)
+-+-|||.++++.++++... |. +|.+.|-.. ....+.||=|..
T Consensus 3 LgiP~kVv~i~~~~A~vd~~-Gv~reV~l~Lv~~~~~~~~~~vGDyVLVHa 52 (90)
T PRK10409 3 IGVPGQIRTIDGNQAKVDVC-GIQRDVDLTLVGSCDENGQPRVGQWVLVHV 52 (90)
T ss_pred cccceEEEEEcCCeEEEEcC-CeEEEEEEeeecccCCCCccCCCCEEEEec
Confidence 44679999999988777655 22 566666431 234688887653
No 141
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=29.79 E-value=61 Score=22.90 Aligned_cols=11 Identities=9% Similarity=0.317 Sum_probs=8.7
Q ss_pred hhccCCCeEEE
Q 033976 15 MRMYVGRRIRT 25 (107)
Q Consensus 15 L~~~~Gk~Vrl 25 (107)
...++||.|.+
T Consensus 87 a~slVGk~V~~ 97 (142)
T PRK09618 87 YSELIGKEVEW 97 (142)
T ss_pred HHHHhCCEEEE
Confidence 35689999986
No 142
>PF10054 DUF2291: Predicted periplasmic lipoprotein (DUF2291); InterPro: IPR014582 There is currently no experimental data for members of this group of predicted periplasmic lipoproteins or their homologues, nor do they exhibit features indicative of any function.; PDB: 2F4I_B.
Probab=29.68 E-value=74 Score=23.64 Aligned_cols=30 Identities=20% Similarity=0.167 Sum_probs=20.8
Q ss_pred eEEEEEEEeecc----CCeEEEEeCCCC--EEEEEc
Q 033976 22 RIRTVIQVIQSD----GGGVTGKSTDGH--QLVVKG 51 (107)
Q Consensus 22 ~VrlvGkV~~~~----g~~~~~~s~D~g--~V~v~l 51 (107)
.||+-|+|.+.+ ...++++....+ .|+|.+
T Consensus 90 ~Vk~~G~V~~vdt~sr~g~~~v~~~g~~~~~v~vQ~ 125 (205)
T PF10054_consen 90 FVKGSGTVVAVDTSSRSGKMTVKVDGDGKADVRVQI 125 (205)
T ss_dssp EEEEEEEEEEEE----TTEEEEESSSSSS-SEEEES
T ss_pred EEEEEEEEEEeeeccccceEEEEcCCCCcccEEEEe
Confidence 699999999887 777777755332 444444
No 143
>PHA02581 9 baseplate wedge tail fiber connector; Provisional
Probab=29.53 E-value=1.2e+02 Score=23.97 Aligned_cols=36 Identities=28% Similarity=0.250 Sum_probs=24.1
Q ss_pred CCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEECCCCCEE
Q 033976 34 GGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIADTDRSIR 75 (107)
Q Consensus 34 g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~~~~si~ 75 (107)
|+.-.+.|+- |.|+|.|+.. ..+.++|+| +.++|+.
T Consensus 80 Gs~~didTS~-g~itv~LPkg--~~ge~~~fI---ns~gS~s 115 (284)
T PHA02581 80 GSLHDIDTST-GGLTVTLPKG--KLGEGVEFI---NSNGSIS 115 (284)
T ss_pred cceEEEecCC-CcEEEEecCC--ccccceEEE---eCCceec
Confidence 4555677774 5599999664 577788888 5555544
No 144
>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=29.40 E-value=2.3e+02 Score=23.08 Aligned_cols=55 Identities=18% Similarity=0.259 Sum_probs=34.8
Q ss_pred eehhhhhccCCCeEEEEEEEeecc----CCeEEEEeCCCCEEEEEccCCCCCCCCEEEE
Q 033976 10 VNGGLMRMYVGRRIRTVIQVIQSD----GGGVTGKSTDGHQLVVKGPQPGFPLTTFVEV 64 (107)
Q Consensus 10 Vn~~~L~~~~Gk~VrlvGkV~~~~----g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEV 64 (107)
+..+.+++++|+++.++-.=..-+ +......+.++..|.|.+..+....+.++.|
T Consensus 372 ~~~~~~~~~vG~~~~vlve~~~~~~~~~~~~~~g~~~~~~~v~v~~~~~~~~~g~~~~v 430 (446)
T PRK14337 372 LTERWLQARVGRKTTVLLEGPSRKPGEGGDSWQGRDPGGRVVNVPLPAGADLTGRLVPV 430 (446)
T ss_pred HHHHHHHHhCCCEEEEEEEeccccCCCCCceEEEECCCCeEEEEecCCCcCCCCCEEEE
Confidence 445677889999999886421111 2356678887777667654332236777765
No 145
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=29.05 E-value=69 Score=18.73 Aligned_cols=55 Identities=13% Similarity=0.181 Sum_probs=32.4
Q ss_pred eEEEEeCCCCEEEEEccCC--CCCCCCEEEEEEEECCCCCEEEEEEEeCCCCCCHHHHHHHHHHHh
Q 033976 36 GVTGKSTDGHQLVVKGPQP--GFPLTTFVEVIGIADTDRSIRAEIWNNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 36 ~~~~~s~D~g~V~v~l~~~--~~~~~~~vEViG~V~~~~si~~~~~~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+++.|+||..+.|...-- +..+...+|=.| .+.. .+++. +++-+..++++++..
T Consensus 2 ~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~---~~~~-----~Ipl~-~v~~~~L~kViewc~ 58 (62)
T PF03931_consen 2 YVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLG---DEDE-----PIPLP-NVSSRILKKVIEWCE 58 (62)
T ss_dssp EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTC---CCGT-----EEEET-TS-HHHHHHHHHHHH
T ss_pred EEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhc---cccc-----ccccC-ccCHHHHHHHHHHHH
Confidence 4688999999999875322 111122222111 1111 55555 699999999999986
No 146
>PF01203 T2SN: Type II secretion system (T2SS), protein N; InterPro: IPR022792 The secretion pathway (GSP) for the export of proteins (also called the type II pathway) [] requires a number of protein components. One of them is known as the 'N' protein and has been sequenced in a variety of bacteria such as Aeromonas hydrophila (gene exeN); Erwinia carotovora (gene outN); Klebsiella pneumoniae (gene pulN); or Vibrio cholerae (gene epsN). The size of the 'N' protein is around 250 amino acids. It apparently contains a single transmembrane domain located in the N-terminal section. The short N-terminal domain is predicted to be cytoplasmic and the large C-terminal domain periplasmic.
Probab=28.86 E-value=2.3e+02 Score=20.59 Aligned_cols=83 Identities=16% Similarity=0.022 Sum_probs=57.2
Q ss_pred eeehhhhhccCCCeEEEEEEEe----e---c------cCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEECCCCCEE
Q 033976 9 FVNGGLMRMYVGRRIRTVIQVI----Q---S------DGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIADTDRSIR 75 (107)
Q Consensus 9 RVn~~~L~~~~Gk~VrlvGkV~----~---~------~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~~~~si~ 75 (107)
+++-..+....+.+..+=|++. . . ..=.+.+.|. ++.+.+.+..++.++ -++..+.+++++..+
T Consensus 106 ~l~~~~~~~~~~~c~~a~G~l~w~~a~v~~~~~~~~lg~~~~~l~c~-~g~l~~~l~~~~g~l--~l~g~~~l~~~g~y~ 182 (221)
T PF01203_consen 106 ELDIDELRFGDGRCQQAEGQLVWQNAAVASPLGWLPLGSLSGDLSCQ-DGQLVLTLSDQSGPL--QLDGQASLSPDGRYR 182 (221)
T ss_pred EEEeeeeEecCCCeEeeEEEEEEecccccccCCCCcccCEEEEEEec-CCEEEEEEeCCCCce--EEEEEEEEcCCCeEE
Confidence 4555556655678888888884 1 1 1123566676 689999997764444 367777777999999
Q ss_pred EEEEEeCCCCCCHHHHHHH
Q 033976 76 AEIWNNFGNTFDTQSYNQL 94 (107)
Q Consensus 76 ~~~~~~~g~~fD~~~yn~l 94 (107)
......=++.+|.++...+
T Consensus 183 ~~~~~~p~~~~~~~l~~~L 201 (221)
T PF01203_consen 183 LDGTVKPGASAPPALRQAL 201 (221)
T ss_pred EEEEEecCcCCCHHHHHHH
Confidence 8888887778887764444
No 147
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.76 E-value=3.4e+02 Score=22.57 Aligned_cols=66 Identities=17% Similarity=0.266 Sum_probs=44.1
Q ss_pred eeehhhhhccCCCeEEEEEEEe-eccCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEECCCCCEEE
Q 033976 9 FVNGGLMRMYVGRRIRTVIQVI-QSDGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIADTDRSIRA 76 (107)
Q Consensus 9 RVn~~~L~~~~Gk~VrlvGkV~-~~~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~~~~si~~ 76 (107)
++....+++++||+++++-.=. +-.| .+...|.....|.+....+ ...++|++|.=+=....++.+
T Consensus 367 ~~~~~~~~~~vG~~~~VLVe~~~~~~~-~~~Grt~~~~~v~~~~~~~-~~~G~~v~VkIt~~~~~~L~g 433 (437)
T COG0621 367 QISAEFNQKLVGKTLEVLVEEGGSKKG-ELIGRTENYRPVVFGGVYT-EDIGEFVEVKITEADEYSLIG 433 (437)
T ss_pred HHHHHHHHHhcCCEEEEEEEeccCcCC-ceEEEcCCCCEEEecCccc-CCCCCEEEEEEEecCCCceEE
Confidence 3456778889999999987632 3344 7888988888777766322 227899988654444444443
No 148
>PRK13450 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=28.76 E-value=1.9e+02 Score=19.64 Aligned_cols=53 Identities=8% Similarity=-0.009 Sum_probs=32.1
Q ss_pred CCCEEEEEccCCC----CCCCCEEEEEEEECCCCCEEEEEEEeCCCCCCHHHHHHHHHHHh
Q 033976 43 DGHQLVVKGPQPG----FPLTTFVEVIGIADTDRSIRAEIWNNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 43 D~g~V~v~l~~~~----~~~~~~vEViG~V~~~~si~~~~~~~~g~~fD~~~yn~lv~l~~ 99 (107)
+-|.++++..... .-.++|+||. ++...-......+++++|.+.+.+..+-+.
T Consensus 46 ~~G~l~i~~~~~~~~~~~v~gGf~~v~----~~~v~Il~~~a~~~~~ID~~~a~~~~~~A~ 102 (132)
T PRK13450 46 KPTITKIIDENGEKKKIFTSSGVLKVE----NNEVYILCDASEWPEEIDIKRAENAKKRAE 102 (132)
T ss_pred ccEEEEEEECCCcEEEEEEcCeEEEEE----CCEEEEEehhhcccccCCHHHHHHHHHHHH
Confidence 4466666653221 1248888873 333233333457789999999988877664
No 149
>PF11148 DUF2922: Protein of unknown function (DUF2922); InterPro: IPR021321 This bacterial family of proteins has no known function.
Probab=28.62 E-value=1.2e+02 Score=18.14 Aligned_cols=19 Identities=26% Similarity=0.503 Sum_probs=15.7
Q ss_pred EEEEeCCCCEEEEEccCCC
Q 033976 37 VTGKSTDGHQLVVKGPQPG 55 (107)
Q Consensus 37 ~~~~s~D~g~V~v~l~~~~ 55 (107)
+...+++|+..++.++.|-
T Consensus 5 l~F~~~~gk~~ti~i~~pk 23 (69)
T PF11148_consen 5 LVFKTEDGKTFTISIPNPK 23 (69)
T ss_pred EEEEcCCCCEEEEEcCCCC
Confidence 4567899999999998883
No 150
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=28.48 E-value=42 Score=19.90 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=16.1
Q ss_pred ceeeehhhhhccCCCeEEEE
Q 033976 7 AVFVNGGLMRMYVGRRIRTV 26 (107)
Q Consensus 7 ~pRVn~~~L~~~~Gk~Vrlv 26 (107)
+-|+..+.-+.|+||+|.|+
T Consensus 28 sa~v~p~lPkeyiGK~v~ii 47 (53)
T PF09853_consen 28 SARVYPSLPKEYIGKKVIII 47 (53)
T ss_pred ceeEcCCCChHHcCcEEEEE
Confidence 45777778889999999875
No 151
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=28.01 E-value=1.1e+02 Score=16.70 Aligned_cols=47 Identities=17% Similarity=0.003 Sum_probs=31.1
Q ss_pred EEEEEEeeccC-----CeEEEEeCCC--CEEEEEccCCC-------CCCCCEEEEEEEECC
Q 033976 24 RTVIQVIQSDG-----GGVTGKSTDG--HQLVVKGPQPG-------FPLTTFVEVIGIADT 70 (107)
Q Consensus 24 rlvGkV~~~~g-----~~~~~~s~D~--g~V~v~l~~~~-------~~~~~~vEViG~V~~ 70 (107)
++.|+|.++.. ..+.+...|+ +.+.+.+-++. ...+.++.|.|+++.
T Consensus 1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~ 61 (75)
T cd03524 1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKK 61 (75)
T ss_pred CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEe
Confidence 46788886642 3455655554 58888776542 133789999999974
No 152
>COG3798 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.80 E-value=61 Score=20.47 Aligned_cols=26 Identities=23% Similarity=0.129 Sum_probs=18.9
Q ss_pred CCeEEEEEEEeeccCCeEEEEeCCCC
Q 033976 20 GRRIRTVIQVIQSDGGGVTGKSTDGH 45 (107)
Q Consensus 20 Gk~VrlvGkV~~~~g~~~~~~s~D~g 45 (107)
|+-=-=+|+|.+++|+...+.-.|-|
T Consensus 15 ~aDG~hvGtVDh~dG~~iklakddsg 40 (75)
T COG3798 15 GADGKHVGTVDHLDGEYIKLAKDDSG 40 (75)
T ss_pred cCCCcEeccEeeccCcEEEEeeccCC
Confidence 33334579999999999888766655
No 153
>CHL00010 infA translation initiation factor 1
Probab=27.70 E-value=1.6e+02 Score=18.31 Aligned_cols=44 Identities=18% Similarity=0.021 Sum_probs=32.2
Q ss_pred eEEEEEEEeecc-CCeEEEEeCCCCEEEEEccCC----C--CCCCCEEEEE
Q 033976 22 RIRTVIQVIQSD-GGGVTGKSTDGHQLVVKGPQP----G--FPLTTFVEVI 65 (107)
Q Consensus 22 ~VrlvGkV~~~~-g~~~~~~s~D~g~V~v~l~~~----~--~~~~~~vEVi 65 (107)
.+.+-|+|.+.- +..+.+++.||..+.+.+..- . ...+.+|||.
T Consensus 6 ~~~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve 56 (78)
T CHL00010 6 KIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVE 56 (78)
T ss_pred eEEEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEE
Confidence 455789999877 477888888888888877432 1 2348889887
No 154
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=27.61 E-value=1.7e+02 Score=20.98 Aligned_cols=29 Identities=17% Similarity=0.182 Sum_probs=23.5
Q ss_pred EEEEEeec-cCCeEEEEeCCCCEEEEEccC
Q 033976 25 TVIQVIQS-DGGGVTGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 25 lvGkV~~~-~g~~~~~~s~D~g~V~v~l~~ 53 (107)
.+|+|... -+..+.+.|.||.++.++++.
T Consensus 34 ~~g~V~~~LGn~~f~V~c~dG~~rLa~I~G 63 (155)
T PTZ00329 34 EYAQVLRMLGNGRLEAYCFDGVKRLCHIRG 63 (155)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEeec
Confidence 57888866 456789999999999998854
No 155
>KOG0054 consensus Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]
Probab=27.20 E-value=15 Score=34.73 Aligned_cols=41 Identities=22% Similarity=0.401 Sum_probs=30.4
Q ss_pred CCCCEEEEEEEEC--------CCCCEEEEEEEeCCCCCCHHHHHHHHHHHh
Q 033976 57 PLTTFVEVIGIAD--------TDRSIRAEIWNNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 57 ~~~~~vEViG~V~--------~~~si~~~~~~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+++-|+|-|.+. -++|||. -+-||..||-+-|+++++...
T Consensus 573 ~~sG~v~v~gsiaYv~Q~pWI~ngTvre--NILFG~~~d~~rY~~Vi~aC~ 621 (1381)
T KOG0054|consen 573 KLSGSVAVNGSVAYVPQQPWIQNGTVRE--NILFGSPYDEERYDKVIKACA 621 (1381)
T ss_pred cccceEEEcCeEEEeccccHhhCCcHHH--hhhcCccccHHHHHHHHHHcc
Confidence 3466777777764 2555653 477999999999999998754
No 156
>PF01556 CTDII: DnaJ C terminal domain; InterPro: IPR002939 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. This domain consists of the C-terminal region of the DnaJ protein. The function of this domain is unknown. It is found associated with IPR001623 from INTERPRO and IPR001305 from INTERPRO. ; GO: 0051082 unfolded protein binding, 0006457 protein folding; PDB: 2Q2G_A 2QLD_A 3AGX_A 3AGZ_A 3AGY_A 3I38_J 3LZ8_B 2B26_B 1C3G_A 1XAO_B ....
Probab=26.72 E-value=1.6e+02 Score=17.98 Aligned_cols=58 Identities=14% Similarity=0.174 Sum_probs=35.0
Q ss_pred eccCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEEEEEC-------CCCCEEEEEEEeCCCCCCHH
Q 033976 31 QSDGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVIGIAD-------TDRSIRAEIWNNFGNTFDTQ 89 (107)
Q Consensus 31 ~~~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V~-------~~~si~~~~~~~~g~~fD~~ 89 (107)
.+-|....+.+-||++++|..... ...+..+-|-|+-- ..+.+-..--+.|.++++-+
T Consensus 13 al~G~~i~i~~l~g~~~~i~ip~~-~~~g~~~~i~g~G~p~~~~~~~~GdL~v~~~V~~P~~ls~~ 77 (81)
T PF01556_consen 13 ALLGGTISIPTLDGKTIKIKIPPG-TQPGQQLRIKGKGMPKPKGGGKRGDLIVKFEVEFPKKLSPE 77 (81)
T ss_dssp HHH-EEEEEE-TTS-EEEEEETST--STT-EEEETTESEEESSSTTSBEEEEEEEEEE--SSTSHH
T ss_pred HhCCCEEEEECCCCCEEEEeccCc-cCCCcEEeecCCCCCcCCCCCCcCCEEEEEEEECCCCCCHH
Confidence 345778889999999999998544 44466666666632 24467777777788877754
No 157
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=26.12 E-value=48 Score=22.74 Aligned_cols=58 Identities=21% Similarity=0.418 Sum_probs=31.2
Q ss_pred EEEEeCCCCEEEEEccCC-C---CCC--CCEEEE-----EEEECCCCCEEEEEEEeCCCCCCHHHHHHHHH
Q 033976 37 VTGKSTDGHQLVVKGPQP-G---FPL--TTFVEV-----IGIADTDRSIRAEIWNNFGNTFDTQSYNQLCQ 96 (107)
Q Consensus 37 ~~~~s~D~g~V~v~l~~~-~---~~~--~~~vEV-----iG~V~~~~si~~~~~~~~g~~fD~~~yn~lv~ 96 (107)
+.+--+||.+|+|...+| - -|+ +..=|= .-+=.+.. +...--++.|+||.+.|.++.+
T Consensus 47 v~lV~pDGSTI~Iry~EPR~ii~mPlDl~~LSeeERk~rl~kR~pk~--k~~~~~e~eD~Fd~~~Y~~fwk 115 (116)
T PF09776_consen 47 VLLVRPDGSTINIRYHEPRRIIKMPLDLDTLSEEERKARLRKRKPKK--KIKIEEELEDDFDAEKYKKFWK 115 (116)
T ss_pred EEEEecCCCEEEEeccChHHHhccccCcccCCHHHHHHHHHHhCCcc--ccccchhhcccCCHHHHHHHhh
Confidence 455677888888888777 2 111 111100 00001111 2222236789999999988753
No 158
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=26.00 E-value=1.4e+02 Score=18.15 Aligned_cols=24 Identities=21% Similarity=0.033 Sum_probs=18.8
Q ss_pred eEEEEEEEeeccCCeEEEEeCCCCE
Q 033976 22 RIRTVIQVIQSDGGGVTGKSTDGHQ 46 (107)
Q Consensus 22 ~VrlvGkV~~~~g~~~~~~s~D~g~ 46 (107)
=+++-|+|.+.|.=++.+++. |++
T Consensus 25 G~~l~G~I~~fD~ftVll~~~-g~q 48 (61)
T TIGR02383 25 GVQLKGVIESFDNFTVLLESQ-GKQ 48 (61)
T ss_pred CcEEEEEEEEEeeeEEEEEEC-CcE
Confidence 368899999999988877764 444
No 159
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=25.99 E-value=1.8e+02 Score=20.10 Aligned_cols=39 Identities=18% Similarity=0.089 Sum_probs=31.4
Q ss_pred hhhhccCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 13 GLMRMYVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 13 ~~L~~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
.-|.+|-=...+++|-+.+-+...+.+++.||.-..|+.
T Consensus 69 ~~LE~~~Ld~LklvG~l~~~~~~~ALv~~pdg~v~~V~~ 107 (149)
T PF04351_consen 69 EPLERYPLDQLKLVGTLSQGGQPWALVQDPDGKVYRVKV 107 (149)
T ss_dssp SGGGGS-CCCEEEEEEEEETTEEEEEEEE-TTEEEEEET
T ss_pred cccccCchhHeEEEEEEeeCCEEEEEEEeCCCCEEEecC
Confidence 567888888899999998877778999999998888876
No 160
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=25.85 E-value=1.3e+02 Score=19.04 Aligned_cols=36 Identities=19% Similarity=0.098 Sum_probs=23.4
Q ss_pred EEEe--eccCCeEEEEeCCCCEEEEEccCCCCCCCCEEEEE
Q 033976 27 IQVI--QSDGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEVI 65 (107)
Q Consensus 27 GkV~--~~~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEVi 65 (107)
|||. --+|+.+.+++. .++..++-= +.+.++||||-
T Consensus 8 rKvL~DP~SG~Yy~vd~P--~Qp~~k~lf-DPETGqYVeV~ 45 (75)
T PF15232_consen 8 RKVLQDPESGQYYVVDAP--VQPKTKTLF-DPETGQYVEVL 45 (75)
T ss_pred ccEeecCCCCCEEEEecC--CCcceeeee-cCCCCcEEEEe
Confidence 3454 247888889988 455554322 35689999985
No 161
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=24.77 E-value=1.4e+02 Score=16.77 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=16.4
Q ss_pred CCCeEEEEEEEeeccCCeEEEEeC
Q 033976 19 VGRRIRTVIQVIQSDGGGVTGKST 42 (107)
Q Consensus 19 ~Gk~VrlvGkV~~~~g~~~~~~s~ 42 (107)
.|+.+.+.||+....+ ..++.-+
T Consensus 48 ~G~~~~v~Gkv~~~~~-~~qi~~P 70 (75)
T cd04488 48 PGTRVRVSGKVKRFRG-GLQIVHP 70 (75)
T ss_pred CCCEEEEEEEEeecCC-eeEEeCC
Confidence 5999999999987654 3444443
No 162
>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus
Probab=24.37 E-value=71 Score=19.02 Aligned_cols=19 Identities=16% Similarity=0.422 Sum_probs=16.1
Q ss_pred CCCHHHHHHHHHHHhccccC
Q 033976 85 TFDTQSYNQLCQLANGEFKH 104 (107)
Q Consensus 85 ~fD~~~yn~lv~l~~~~~~~ 104 (107)
+|+++-|+++++.+. ..|+
T Consensus 31 ~F~L~Dy~~L~~~~~-~l~~ 49 (55)
T PF07443_consen 31 NFSLEDYSTLMKKVR-NLPQ 49 (55)
T ss_pred eeeHHHHHHHHHHHh-cCCc
Confidence 799999999999988 4554
No 163
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=24.28 E-value=94 Score=19.64 Aligned_cols=15 Identities=20% Similarity=0.399 Sum_probs=9.5
Q ss_pred hccCCCeEEEEEEEe
Q 033976 16 RMYVGRRIRTVIQVI 30 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~ 30 (107)
.+|+|+++.|+-|-.
T Consensus 2 ~~~IG~~isLISk~~ 16 (74)
T cd01736 2 TPYIGSKISLISKSD 16 (74)
T ss_pred ccccCceEEEEecCC
Confidence 468888876654433
No 164
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=24.16 E-value=1.2e+02 Score=18.29 Aligned_cols=22 Identities=14% Similarity=0.219 Sum_probs=15.0
Q ss_pred hhhhccCCCeEEE--------EEEEeeccC
Q 033976 13 GLMRMYVGRRIRT--------VIQVIQSDG 34 (107)
Q Consensus 13 ~~L~~~~Gk~Vrl--------vGkV~~~~g 34 (107)
+.|.+..|+.|.+ .|++.++|+
T Consensus 3 ~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~ 32 (70)
T cd01721 3 KLLHEAEGHIVTVELKTGEVYRGKLIEAED 32 (70)
T ss_pred HHHhhCCCCEEEEEECCCcEEEEEEEEEcC
Confidence 4677888888876 455555555
No 165
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=23.79 E-value=95 Score=19.58 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=16.3
Q ss_pred cCCeEEEEeCCCCEEEEEccCC
Q 033976 33 DGGGVTGKSTDGHQLVVKGPQP 54 (107)
Q Consensus 33 ~g~~~~~~s~D~g~V~v~l~~~ 54 (107)
..+.++++++++|.|.|.-+++
T Consensus 30 ~~d~F~l~~~~~gki~I~G~s~ 51 (86)
T PF12971_consen 30 GKDVFELSSADNGKIVIRGNSG 51 (86)
T ss_dssp TBEEEEEEE-SSS-EEEEESSH
T ss_pred CCCEEEEEeCCCCeEEEEeCCH
Confidence 4568999887889999998765
No 166
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=23.51 E-value=1.9e+02 Score=17.71 Aligned_cols=22 Identities=9% Similarity=0.173 Sum_probs=15.1
Q ss_pred hhhhccCCCeEEE--------EEEEeeccC
Q 033976 13 GLMRMYVGRRIRT--------VIQVIQSDG 34 (107)
Q Consensus 13 ~~L~~~~Gk~Vrl--------vGkV~~~~g 34 (107)
+.|++..|++|.+ .|++.++|+
T Consensus 4 ~~L~~~~g~~V~VeLkng~~~~G~L~~~D~ 33 (76)
T cd01723 4 SLLKTAQNHPMLVELKNGETYNGHLVNCDN 33 (76)
T ss_pred HHHHhcCCCEEEEEECCCCEEEEEEEEEcC
Confidence 4677888888876 466666655
No 167
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=23.46 E-value=1.4e+02 Score=19.75 Aligned_cols=44 Identities=18% Similarity=0.201 Sum_probs=27.7
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEEEccCC--C---CCCCCEEEEEEEECC
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVVKGPQP--G---FPLTTFVEVIGIADT 70 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v~l~~~--~---~~~~~~vEViG~V~~ 70 (107)
-+|+|.+..+..+.+.+++.... .++.| + ...+..+||.|-|+.
T Consensus 3 ~lG~vlh~~~~g~vi~~~~~~iP--~l~~~V~~~~~k~IG~V~dVfGPv~~ 51 (98)
T COG3277 3 RLGKVLHVCGTGMVIVRDNDRIP--PLNAPVYDANLKRIGKVVDVFGPVDE 51 (98)
T ss_pred cceeEEEecCCceEEEeCCCCCC--CCCCeeEecCCCEEEEEEEEEccCCC
Confidence 36899998888777776642211 22222 1 335888899998863
No 168
>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.18 E-value=2.8e+02 Score=23.31 Aligned_cols=53 Identities=15% Similarity=0.255 Sum_probs=34.6
Q ss_pred eehhhhhccCCCeEEEEEEEeec-cCCeEEEEeCCCCEEEEEccCCCCCCCCEEEE
Q 033976 10 VNGGLMRMYVGRRIRTVIQVIQS-DGGGVTGKSTDGHQLVVKGPQPGFPLTTFVEV 64 (107)
Q Consensus 10 Vn~~~L~~~~Gk~VrlvGkV~~~-~g~~~~~~s~D~g~V~v~l~~~~~~~~~~vEV 64 (107)
+..+.+++++|++++++-.=.+. ++..++..|..++.|.+. .+....+.+|.|
T Consensus 435 ~~~~~~~~~~G~~~~VLve~~~~~~~~~~~Grt~~~~~V~~~--~~~~~~G~~v~v 488 (509)
T PRK14327 435 YSAKKMKRYEGQTVEVLVEGESKKNPEVLAGYTRKNKLVNFK--GPKSLIGQLVKV 488 (509)
T ss_pred HHHHHHHHhCCCEEEEEEEecccCCCceEEEECCCCcEEEEC--CCCCCCCCEEEE
Confidence 34556788999999988653222 334677888877766553 332346778776
No 169
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=22.80 E-value=1e+02 Score=22.94 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=25.6
Q ss_pred hccCCCeEEEEEEEeeccCCeE-----EEEeCCCCEEEEEccCCCCCCCCEEEEEEEE
Q 033976 16 RMYVGRRIRTVIQVIQSDGGGV-----TGKSTDGHQLVVKGPQPGFPLTTFVEVIGIA 68 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~~~~g~~~-----~~~s~D~g~V~v~l~~~~~~~~~~vEViG~V 68 (107)
..++||.|...+ .+|... .++..+++.+.+.+.....+++..++|--+-
T Consensus 114 ~slIGK~V~~~~----~dG~~vtG~V~sV~~~~~g~v~l~vdg~~v~l~~V~~Vsd~~ 167 (190)
T PRK06792 114 MKFLGKYVRGVS----NDGKQVTGQVETVRLAENNDVQLIVDNQVVSLRFVERVSDKP 167 (190)
T ss_pred HHhcCcEEEEEc----CCCCEEEEEEEEEEEccCCcEEEEECCEEEeccceeEecCCC
Confidence 357999997432 233211 1223355666655543234566666665553
No 170
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=22.62 E-value=1.6e+02 Score=20.66 Aligned_cols=25 Identities=12% Similarity=0.065 Sum_probs=20.0
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEE
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVV 49 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v 49 (107)
..|+|.++.=.+.++++.||..+.+
T Consensus 72 ~~G~V~~I~l~~t~l~~~~g~~v~I 96 (206)
T PF00924_consen 72 VEGRVEEIGLRSTRLRTWDGEIVII 96 (206)
T ss_dssp -EEEEEEE-SSEEEEEETTS-EEEE
T ss_pred eehHHHhcCcceeeeecCCCCEEEE
Confidence 4799999999999999999888877
No 171
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=22.49 E-value=87 Score=19.30 Aligned_cols=42 Identities=14% Similarity=0.064 Sum_probs=26.0
Q ss_pred EEEEEeecc-CCeEEEEeCCCCEEEEEccCC-----CCCCCCEEEEEEEECC
Q 033976 25 TVIQVIQSD-GGGVTGKSTDGHQLVVKGPQP-----GFPLTTFVEVIGIADT 70 (107)
Q Consensus 25 lvGkV~~~~-g~~~~~~s~D~g~V~v~l~~~-----~~~~~~~vEViG~V~~ 70 (107)
-+|++.|.. .+.+..++ + + .-.++++ -...++.+||.|-|+.
T Consensus 3 ~~G~~~h~~~~g~lI~~~-~-~--~P~~n~~V~~~~~~~IGkV~dIfGPV~~ 50 (73)
T PRK13149 3 RLGKVLHYAPKGKLIIRL-D-K--QPPIGSVVYDKKLKKIGKVVDVFGPVKE 50 (73)
T ss_pred EeEEEEEEcCCCCEEEEc-C-C--CCCCCCEeECCCCCEeEEEEEEECCCCC
Confidence 478899887 45566666 2 1 1122222 1345899999999874
No 172
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=22.06 E-value=2.1e+02 Score=19.54 Aligned_cols=39 Identities=10% Similarity=0.009 Sum_probs=26.4
Q ss_pred EEEeec--cCCeEEEEeCCCCEEEEEccCCCCCC-CCEEEEE
Q 033976 27 IQVIQS--DGGGVTGKSTDGHQLVVKGPQPGFPL-TTFVEVI 65 (107)
Q Consensus 27 GkV~~~--~g~~~~~~s~D~g~V~v~l~~~~~~~-~~~vEVi 65 (107)
|+|..+ .+..+.+++.+|-+|.+++--+...+ +.-.|+.
T Consensus 44 G~v~~i~~T~HA~~i~~~~G~eiLiHiGidTv~l~g~gF~~~ 85 (124)
T cd00210 44 GTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGEGFTSH 85 (124)
T ss_pred eEEEEEccCCCEEEEEeCCCcEEEEEeeeeeeecCCCceEEE
Confidence 777765 55778899999999999886553222 4444443
No 173
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=21.81 E-value=1.8e+02 Score=19.40 Aligned_cols=34 Identities=18% Similarity=0.208 Sum_probs=25.2
Q ss_pred ccCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEccCC
Q 033976 17 MYVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKGPQP 54 (107)
Q Consensus 17 ~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l~~~ 54 (107)
.|.|++ |+|.-..|++..++.-||+........|
T Consensus 55 rf~G~T----G~Vvg~~g~ay~V~v~~G~k~K~liv~p 88 (98)
T COG2139 55 RFQGKT----GTVVGVRGRAYKVEVYDGNKEKTLIVRP 88 (98)
T ss_pred cccCcc----eEEEeccCCEEEEEEecCCceEEEEeCH
Confidence 466765 6666678999888888888776666566
No 174
>PF13861 FLgD_tudor: FlgD Tudor-like domain; PDB: 3OSV_A 3C12_A.
Probab=21.76 E-value=1.8e+02 Score=16.87 Aligned_cols=15 Identities=13% Similarity=0.237 Sum_probs=10.5
Q ss_pred hccCCCeEEEEEEEe
Q 033976 16 RMYVGRRIRTVIQVI 30 (107)
Q Consensus 16 ~~~~Gk~VrlvGkV~ 30 (107)
..++||.|..-..+.
T Consensus 8 ~~lIGk~V~~~~~~~ 22 (61)
T PF13861_consen 8 ASLIGKEVLVPKSVA 22 (61)
T ss_dssp TCTTTSEEEEEEEEE
T ss_pred HHhcCCEEEECCcEe
Confidence 468999998854443
No 175
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=21.72 E-value=54 Score=22.65 Aligned_cols=44 Identities=18% Similarity=0.195 Sum_probs=33.3
Q ss_pred EEEeeccCCeEEEEeCCCCEEEEEccCCC--CCCCCEEEEEEEECC
Q 033976 27 IQVIQSDGGGVTGKSTDGHQLVVKGPQPG--FPLTTFVEVIGIADT 70 (107)
Q Consensus 27 GkV~~~~g~~~~~~s~D~g~V~v~l~~~~--~~~~~~vEViG~V~~ 70 (107)
|+.....|..+++..-++..+.|+|++.. .......=++|+|..
T Consensus 29 ~~~~RaAGt~a~ii~k~~~~~~ikLPSG~~k~v~~~c~AtiG~vsn 74 (130)
T PF03947_consen 29 GKLARAAGTYAQIISKEGNYVVIKLPSGEIKLVSSNCRATIGRVSN 74 (130)
T ss_dssp EEBSSSTTBBEEEEEEESSEEEEEETTSEEEEEETTSEEEESCBSS
T ss_pred ceEEeeCCCEEEEEEeccceeEEEecCCCeEeecccceEEEEEecC
Confidence 45667788889998888899999997662 123667778888864
No 176
>PF00337 Gal-bind_lectin: Galactoside-binding lectin; InterPro: IPR001079 Galectins (also known as galaptins or S-lectin) are a family of proteins defined by having at least one characteristic carbohydrate recognition domain (CRD) with an affinity for beta-galactosides and sharing certain sequence elements. Members of the galectins family are found in mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Galectins are known to carry out intra- and extracellular functions through glycoconjugate-mediated recogntion. From the cytosol they may be secreted by non-classical pathways, but they may also be targeted to the nucleus or specific sub-cytosolic sites. Within the same peptide chain some galectins have a CRD with only a few additional amino acids, whereas others have two CRDs joined by a link peptide, and one (galectin-3) has one CRD joined to a different type of domain [, ]. The galectin carbohydrate recognition domain (CRD) is a beta-sandwich of about 135 amino acid. The two sheets are slightly bent with 6 strands forming the concave side and 5 strands forming the convex side. The concave side forms a groove in which carbohydrate is bound, and which is long enough to hold about a linear tetrasaccharide [, ].; GO: 0005529 sugar binding; PDB: 2WSU_B 2WT0_A 2WT1_A 2WT2_B 2WSV_A 1HLC_A 2ZGQ_A 3M3Q_B 1WW5_C 3M3E_A ....
Probab=21.57 E-value=1.7e+02 Score=19.21 Aligned_cols=37 Identities=8% Similarity=-0.034 Sum_probs=25.2
Q ss_pred cCCCeEEEEEEEeeccCC-eEEEEeC---CCCEEEEEccCC
Q 033976 18 YVGRRIRTVIQVIQSDGG-GVTGKST---DGHQLVVKGPQP 54 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~~g~-~~~~~s~---D~g~V~v~l~~~ 54 (107)
..|+.+.+-|++..-..+ ++.+.+. +...|-++++.-
T Consensus 11 ~~G~~i~i~G~~~~~~~~f~inl~~~~~~~~~~i~lH~~~r 51 (133)
T PF00337_consen 11 SPGDSIIIRGTVPPDAKRFSINLQTGPNDPDDDIALHFNPR 51 (133)
T ss_dssp ETTEEEEEEEEEBTTSSBEEEEEEES-STTTTEEEEEEEEE
T ss_pred CCCcEEEEEEEECCCCCEEEEEecCCCcCCCCCEEEEEEEE
Confidence 579999999999943322 3444554 458888888543
No 177
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=21.50 E-value=1.7e+02 Score=21.32 Aligned_cols=46 Identities=13% Similarity=0.055 Sum_probs=36.5
Q ss_pred CCceeeehhhhhccCCCeEEEEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 5 NPAVFVNGGLMRMYVGRRIRTVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 5 ~~~pRVn~~~L~~~~Gk~VrlvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
+|-|+=-.+-|..|-=.+-|++|...+-.+-++.+++.|+- .+|+.
T Consensus 80 ~Pdp~r~kepLE~fpLe~~rlvGtm~~g~~~~A~i~~~~~v-~~V~v 125 (170)
T COG3168 80 APDPKRRKEPLEKFPLETFRLVGTLKSGQGVSALIEAPGGV-YRVRV 125 (170)
T ss_pred CCCcccccCchhhCChhheeeEEEecCCCceEEEEEcCCce-EEEee
Confidence 35555556778889889999999999888888988888655 77765
No 178
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=21.42 E-value=2.3e+02 Score=18.00 Aligned_cols=34 Identities=15% Similarity=0.161 Sum_probs=24.1
Q ss_pred hccCCCeEE-----------EEEEEeeccCCeEEEEeCCCCEEEE
Q 033976 16 RMYVGRRIR-----------TVIQVIQSDGGGVTGKSTDGHQLVV 49 (107)
Q Consensus 16 ~~~~Gk~Vr-----------lvGkV~~~~g~~~~~~s~D~g~V~v 49 (107)
..|+|-.++ +-|.|..=.-+++.+.+.+|...+|
T Consensus 10 ~dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~t~~~~~~~I 54 (89)
T PF01868_consen 10 ADLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIVTEDGKVKTI 54 (89)
T ss_dssp S--TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEEETTEEEEEE
T ss_pred hhhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEEecCCcEEEE
Confidence 346777777 5688888888999999998866665
No 179
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=21.34 E-value=1.3e+02 Score=17.74 Aligned_cols=16 Identities=13% Similarity=0.208 Sum_probs=10.0
Q ss_pred ehhhhhccCCCeEEEE
Q 033976 11 NGGLMRMYVGRRIRTV 26 (107)
Q Consensus 11 n~~~L~~~~Gk~Vrlv 26 (107)
+++.++.++||++.-.
T Consensus 2 ~A~~~q~lvGq~~~~~ 17 (60)
T PF11720_consen 2 GAAAAQSLVGQPASAA 17 (60)
T ss_pred CHHHHHHhhCCCcccc
Confidence 3566777777776433
No 180
>PRK00539 atpC F0F1 ATP synthase subunit epsilon; Validated
Probab=21.23 E-value=2.8e+02 Score=18.94 Aligned_cols=56 Identities=5% Similarity=-0.091 Sum_probs=34.2
Q ss_pred EeCCCCEEEEEccCCC----CCCCCEEEEEEEECCCCCEEEEEEEeCCCCCCHHHHHHHHHHHh
Q 033976 40 KSTDGHQLVVKGPQPG----FPLTTFVEVIGIADTDRSIRAEIWNNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 40 ~s~D~g~V~v~l~~~~----~~~~~~vEViG~V~~~~si~~~~~~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+-+-|.+.|+..... ...++|+||. ++...-......+.+++|.+.+.+..+-+.
T Consensus 43 t~L~~G~~~i~~~~~~~~~~~v~gGf~ev~----~n~v~Ilad~ae~~eeID~~~a~~a~erAe 102 (133)
T PRK00539 43 AAIQSHVCKITFADKTKRSAIIGAGLLLIK----KTEAKIFTENFVFADELDYDETLKRKKELE 102 (133)
T ss_pred eEecceEEEEEECCCcEEEEEEeeeEEEEE----CCEEEEEECeEEchhhCCHHHHHHHHHHHH
Confidence 3334467777653221 1136777664 334444455677889999999988877654
No 181
>PRK14736 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=21.18 E-value=2.8e+02 Score=18.96 Aligned_cols=56 Identities=5% Similarity=-0.032 Sum_probs=33.9
Q ss_pred EeCCCCEEEEEccCCC----CCCCCEEEEEEEECCCCCEEEEEEEeCCCCCCHHHHHHHHHHHh
Q 033976 40 KSTDGHQLVVKGPQPG----FPLTTFVEVIGIADTDRSIRAEIWNNFGNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 40 ~s~D~g~V~v~l~~~~----~~~~~~vEViG~V~~~~si~~~~~~~~g~~fD~~~yn~lv~l~~ 99 (107)
.+=+-|.++|+..... .-.++|+||. ++.-.-.-....+.+++|.+.+.+..+-+.
T Consensus 43 t~L~~G~l~i~~~~~~~~~~~v~gGf~eV~----~n~v~Ila~~ae~~eeID~~~a~~a~~~Ae 102 (133)
T PRK14736 43 TTLKVGVITVTETTGNGKRIYVRGGFAEIG----PTSVTVLAERAAPVEELTPEMIDREIEAVE 102 (133)
T ss_pred eEecceEEEEEECCCcEEEEEEeceEEEEE----CCEEEEEeeeeEEhhhCCHHHHHHHHHHHH
Confidence 3334577777653321 1237888873 332222334456789999999988877654
No 182
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=21.05 E-value=1.4e+02 Score=18.48 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=10.3
Q ss_pred hhhhccCCCeEEE
Q 033976 13 GLMRMYVGRRIRT 25 (107)
Q Consensus 13 ~~L~~~~Gk~Vrl 25 (107)
+.|.++++|+|.+
T Consensus 6 ~~L~~~~~~~V~V 18 (76)
T cd01732 6 ELIDKCIGSRIWI 18 (76)
T ss_pred HHHHHhCCCEEEE
Confidence 5678888888877
No 183
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=20.96 E-value=2.2e+02 Score=17.53 Aligned_cols=55 Identities=18% Similarity=0.074 Sum_probs=30.5
Q ss_pred EEEEEEEeec----cCC-eEEEEeCCCCEEEEEccCCC-C--------CCCCEEEEEEEECCC-CCEEEEE
Q 033976 23 IRTVIQVIQS----DGG-GVTGKSTDGHQLVVKGPQPG-F--------PLTTFVEVIGIADTD-RSIRAEI 78 (107)
Q Consensus 23 VrlvGkV~~~----~g~-~~~~~s~D~g~V~v~l~~~~-~--------~~~~~vEViG~V~~~-~si~~~~ 78 (107)
|++.|.|.++ .|+ .++++.. .|.+.+.+-+.. + ..+..|-|.|+++.+ ..+.+.+
T Consensus 2 v~i~GiI~~v~~TK~g~~~~~leD~-~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~~~~~l~~~~ 71 (79)
T cd04490 2 VSIIGMVNDVRSTKNGHRIVELEDT-TGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSKDGGLIFADE 71 (79)
T ss_pred EEEEEEEeEEEEcCCCCEEEEEECC-CCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEecCCCEEEEEE
Confidence 5667776643 333 3444433 366777664431 2 237899999999632 2344443
No 184
>PF14299 PP2: Phloem protein 2
Probab=20.81 E-value=3e+02 Score=19.08 Aligned_cols=55 Identities=16% Similarity=0.085 Sum_probs=37.5
Q ss_pred eeehhhhhccCCCeEEEEEEEeec----c--CCeEEEEeCCCCE----EEEEccCCCCCCCCEEEEE
Q 033976 9 FVNGGLMRMYVGRRIRTVIQVIQS----D--GGGVTGKSTDGHQ----LVVKGPQPGFPLTTFVEVI 65 (107)
Q Consensus 9 RVn~~~L~~~~Gk~VrlvGkV~~~----~--g~~~~~~s~D~g~----V~v~l~~~~~~~~~~vEVi 65 (107)
++|..+|+.-.-=.|-++=|+..- + +-.+.+..+|+++ -.+.+ |...-++|+||.
T Consensus 50 ~i~~~~Lsp~t~Y~vy~v~kl~~~~~Gw~~~pv~~~v~~~~~~~~~~~~~~~~--~~~r~dgW~Eie 114 (154)
T PF14299_consen 50 KINTRMLSPGTTYAVYFVFKLKDDAYGWDSPPVEFSVKVPDGEKYEQERKVCL--PKERGDGWMEIE 114 (154)
T ss_pred EEEceEcCCCCEEEEEEEEEecCCCCCCCcCCEEEEEEeCCCccccceeeEEc--CCCCCCCEEEEE
Confidence 678888888777788888888732 2 2357778887766 23333 334568999984
No 185
>PHA01634 hypothetical protein
Probab=20.69 E-value=82 Score=22.48 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=31.0
Q ss_pred eeehhhhhccCCCeEEEEE----EEe---eccCCeEEEEeCCCCEEEE
Q 033976 9 FVNGGLMRMYVGRRIRTVI----QVI---QSDGGGVTGKSTDGHQLVV 49 (107)
Q Consensus 9 RVn~~~L~~~~Gk~VrlvG----kV~---~~~g~~~~~~s~D~g~V~v 49 (107)
++|-++|.+|.-=.|-|.- ||+ +..|.++|--|.||.++++
T Consensus 106 ~l~v~~l~ky~q~ci~ihdwt~nrvel~rk~~g~~ftyvsddgre~~l 153 (156)
T PHA01634 106 KLNVSMLKKYKQWCIGIHDWTKNRVELMRKMEGATFTYVSDDGREITL 153 (156)
T ss_pred hcCHHHHHHHHhheeeeehhhhhHHHHHHHhcCcEEEEEccCCcEEEE
Confidence 6788899888655555543 333 5689999999999999885
No 186
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 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 ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=20.59 E-value=2.6e+02 Score=18.37 Aligned_cols=32 Identities=16% Similarity=0.050 Sum_probs=20.2
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEEEccCC--CCCCCCEEEE
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVVKGPQP--GFPLTTFVEV 64 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v~l~~~--~~~~~~~vEV 64 (107)
++|||.+..|++ |.|..++... ...++.-|.|
T Consensus 61 iwGkV~r~HGns--------GvVrAkF~~nLP~~a~G~~VrV 94 (95)
T PF01247_consen 61 IWGKVTRPHGNS--------GVVRAKFKKNLPPQAIGSRVRV 94 (95)
T ss_dssp EEEEEEEESTTT--------TEEEEEESS--STTGCSSEEEE
T ss_pred EEEEEEeEEcCC--------CEEEEEeCCCCChHHcCCEEEe
Confidence 467777777763 6777777654 2345777665
No 187
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=20.38 E-value=2.8e+02 Score=18.58 Aligned_cols=27 Identities=26% Similarity=0.145 Sum_probs=15.5
Q ss_pred EEEEEeeccCCeEEEEeCCCCEEEEEc
Q 033976 25 TVIQVIQSDGGGVTGKSTDGHQLVVKG 51 (107)
Q Consensus 25 lvGkV~~~~g~~~~~~s~D~g~V~v~l 51 (107)
+.|.+.+-+++..++...+|...+|.-
T Consensus 70 ~~G~~~~e~~~~~~l~~~~g~~~~i~~ 96 (133)
T TIGR02603 70 LSGIVASETADGVTVKMPGGVEQSVPR 96 (133)
T ss_pred EEEEEEecCCCeEEEEcCCCcEEEEEH
Confidence 345555666666666666655555543
No 188
>PHA02099 hypothetical protein
Probab=20.34 E-value=2.2e+02 Score=17.97 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=22.1
Q ss_pred EEEEECCCCCEEEEEEEeC--------CCCCCHHHHHHHHHHHh
Q 033976 64 VIGIADTDRSIRAEIWNNF--------GNTFDTQSYNQLCQLAN 99 (107)
Q Consensus 64 ViG~V~~~~si~~~~~~~~--------g~~fD~~~yn~lv~l~~ 99 (107)
=+|+|.+.++ .+....+| .+.+|.++|+++-..+|
T Consensus 24 n~~rv~pg~~-emhilr~~~g~diifha~gy~p~ly~e~~r~~~ 66 (84)
T PHA02099 24 NAGRVGPGES-EMHILRNFEGVDIVFHAEGYNPDLYAELKRHVC 66 (84)
T ss_pred ccCccCCCCc-EEEEEeecCCccEEEEcCCCCHHHHHHHHHhhe
Confidence 3677766444 22223333 25899999999977665
No 189
>PF09642 YonK: YonK protein; InterPro: IPR018600 YonK protein is expressed by the bacterial prophage SPbetaC []. It is a 63 residue protein that associates into a homo-octamer in the form of a beta-stranded barrel with four outer helical features at points of the compass. Its function is unknown. ; PDB: 2H4O_C.
Probab=20.23 E-value=1.3e+02 Score=18.28 Aligned_cols=19 Identities=11% Similarity=0.329 Sum_probs=14.8
Q ss_pred hhhhhccCCCeEEEEEEEe
Q 033976 12 GGLMRMYVGRRIRTVIQVI 30 (107)
Q Consensus 12 ~~~L~~~~Gk~VrlvGkV~ 30 (107)
.+.|+.|.||.|.|--|=.
T Consensus 35 ~eil~~F~gk~VsitIkEe 53 (62)
T PF09642_consen 35 NEILSEFNGKNVSITIKEE 53 (62)
T ss_dssp HHHHHTTTTSEEEEEEEEE
T ss_pred HHHHHHhCCceEEEEEeec
Confidence 5678999999999865533
No 190
>PRK03879 ribonuclease P protein component 1; Validated
Probab=20.20 E-value=2.6e+02 Score=18.20 Aligned_cols=58 Identities=17% Similarity=0.183 Sum_probs=34.5
Q ss_pred eehhhh--hccCCCeEEEE-----------EEEeeccCCeEEEEeCCCCEEEEEccCC--C----CCCCCEEEEEEEE
Q 033976 10 VNGGLM--RMYVGRRIRTV-----------IQVIQSDGGGVTGKSTDGHQLVVKGPQP--G----FPLTTFVEVIGIA 68 (107)
Q Consensus 10 Vn~~~L--~~~~Gk~Vrlv-----------GkV~~~~g~~~~~~s~D~g~V~v~l~~~--~----~~~~~~vEViG~V 68 (107)
++++.| ..|+|-.|+++ |.|..=.-.++.+. ++++..+|--..- . .+.+..++|.|..
T Consensus 3 it~~nl~~~eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~-~~~~~~~VPK~~~iF~f~~~~~~~~~v~I~G~~ 79 (96)
T PRK03879 3 ITPSNILRHELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE-TDGKEWMVPKDGATFEFELGRDDVVKVKVDGRL 79 (96)
T ss_pred ccHHHHHHHHhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE-cCCcEEEEeCCCeEEEEEEcCCCCeEEEEECce
Confidence 344444 45788888875 77777677788888 6666555422111 0 1235567777754
No 191
>PF11525 CopK: Copper resistance protein K; InterPro: IPR021604 CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation []. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site []. ; PDB: 3N7E_B 3N7D_B 3DSP_A 3DSO_A 2K0Q_A 2KM0_A 2LEL_A.
Probab=20.13 E-value=1.3e+02 Score=18.90 Aligned_cols=16 Identities=19% Similarity=0.540 Sum_probs=12.2
Q ss_pred EEEeCCCCEEEEEccC
Q 033976 38 TGKSTDGHQLVVKGPQ 53 (107)
Q Consensus 38 ~~~s~D~g~V~v~l~~ 53 (107)
+++|.||..|..+-++
T Consensus 43 ~meTkDG~kI~m~gdE 58 (73)
T PF11525_consen 43 VMETKDGQKITMHGDE 58 (73)
T ss_dssp EEEBTTS-EEEEETTE
T ss_pred EEEccCCCEEEecchH
Confidence 4899999999987654
No 192
>cd00070 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
Probab=20.07 E-value=2.6e+02 Score=18.33 Aligned_cols=34 Identities=6% Similarity=0.030 Sum_probs=22.9
Q ss_pred cCCCeEEEEEEEeeccCCeEE--EEeCCCCEEEEEccC
Q 033976 18 YVGRRIRTVIQVIQSDGGGVT--GKSTDGHQLVVKGPQ 53 (107)
Q Consensus 18 ~~Gk~VrlvGkV~~~~g~~~~--~~s~D~g~V~v~l~~ 53 (107)
..|+.+++.|++..- .+.+. +.++++ .|-++++.
T Consensus 11 ~~G~~i~i~G~~~~~-~~~f~Inl~~~~~-~i~lH~n~ 46 (127)
T cd00070 11 KPGSTLTVKGRVLPN-AKRFSINLGTGSS-DIALHFNP 46 (127)
T ss_pred cCCCEEEEEEEECCC-CCEEEEEEecCCC-CEEEEEee
Confidence 479999999999865 34443 444433 67777743
No 193
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=20.03 E-value=4.2e+02 Score=22.90 Aligned_cols=52 Identities=21% Similarity=0.266 Sum_probs=35.9
Q ss_pred CCCeEEEEEEEeecc----C-CeEEEEeCCC-CEEEEEcc---CCC----CCCCCEEEEEEEECC
Q 033976 19 VGRRIRTVIQVIQSD----G-GGVTGKSTDG-HQLVVKGP---QPG----FPLTTFVEVIGIADT 70 (107)
Q Consensus 19 ~Gk~VrlvGkV~~~~----g-~~~~~~s~D~-g~V~v~l~---~~~----~~~~~~vEViG~V~~ 70 (107)
.|..|++.|+|.+.. + ..+.+...|+ |.+.+..- +|. ...+..+=|.|||+.
T Consensus 58 ~g~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G~~~~v~Gkv~~ 122 (681)
T PRK10917 58 PGEKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVYGKVKR 122 (681)
T ss_pred CCCEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCCCEEEEEEEEEe
Confidence 599999999998542 2 3455665555 36766543 442 345999999999974
Done!