Query psy547
Match_columns 282
No_of_seqs 266 out of 2302
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 18:22:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/547hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1278 CspC Cold shock protei 99.9 4.6E-24 9.9E-29 154.9 7.9 66 33-102 1-66 (67)
2 COG1278 CspC Cold shock protei 99.9 2.9E-23 6.2E-28 150.7 7.6 65 201-269 2-66 (67)
3 PRK10943 cold shock-like prote 99.9 8.5E-23 1.8E-27 150.6 8.6 68 32-103 2-69 (69)
4 PRK15464 cold shock-like prote 99.9 1.2E-22 2.6E-27 150.0 9.0 66 33-102 4-69 (70)
5 PRK09507 cspE cold shock prote 99.9 2.8E-22 6.1E-27 147.8 8.8 68 32-103 2-69 (69)
6 PRK15463 cold shock-like prote 99.9 3.4E-22 7.3E-27 147.7 8.8 66 33-102 4-69 (70)
7 PRK10354 RNA chaperone/anti-te 99.9 4.5E-22 9.7E-27 147.2 9.3 66 33-102 4-69 (70)
8 PRK09890 cold shock protein Cs 99.9 5.2E-22 1.1E-26 146.8 9.3 66 33-102 4-69 (70)
9 PRK09937 stationary phase/star 99.9 5.8E-22 1.3E-26 147.9 9.3 68 34-105 2-69 (74)
10 PRK14998 cold shock-like prote 99.9 8.5E-22 1.8E-26 146.7 9.2 68 34-105 2-69 (73)
11 PRK15464 cold shock-like prote 99.9 7.1E-22 1.5E-26 145.9 8.6 66 200-269 4-69 (70)
12 TIGR02381 cspD cold shock doma 99.9 7.4E-22 1.6E-26 145.2 8.2 66 34-103 2-67 (68)
13 PRK15463 cold shock-like prote 99.9 2E-21 4.4E-26 143.6 8.6 66 200-269 4-69 (70)
14 PRK10943 cold shock-like prote 99.9 2.3E-21 5E-26 142.9 8.4 67 199-269 2-68 (69)
15 PRK09507 cspE cold shock prote 99.8 4.5E-21 9.7E-26 141.4 8.7 67 199-269 2-68 (69)
16 PRK09890 cold shock protein Cs 99.8 5.1E-21 1.1E-25 141.5 8.9 66 200-269 4-69 (70)
17 PRK10354 RNA chaperone/anti-te 99.8 7.2E-21 1.6E-25 140.7 8.9 66 200-269 4-69 (70)
18 PRK09937 stationary phase/star 99.8 9.2E-21 2E-25 141.5 8.9 65 202-270 3-67 (74)
19 TIGR02381 cspD cold shock doma 99.8 1E-20 2.2E-25 139.1 8.5 64 202-269 3-66 (68)
20 PRK14998 cold shock-like prote 99.8 1.6E-20 3.5E-25 139.8 8.8 65 201-269 2-66 (73)
21 PF00313 CSD: 'Cold-shock' DNA 99.8 2.7E-19 5.9E-24 130.3 9.3 66 34-103 1-66 (66)
22 cd04458 CSP_CDS Cold-Shock Pro 99.8 8E-19 1.7E-23 127.4 8.8 64 34-101 1-64 (65)
23 PF00313 CSD: 'Cold-shock' DNA 99.8 2.1E-18 4.7E-23 125.6 9.6 65 201-269 1-65 (66)
24 cd04458 CSP_CDS Cold-Shock Pro 99.8 4.2E-18 9.1E-23 123.7 8.6 63 202-268 2-64 (65)
25 KOG3070|consensus 99.5 1.5E-14 3.2E-19 130.0 8.1 93 26-118 49-141 (235)
26 KOG3070|consensus 99.3 2.1E-12 4.7E-17 116.1 6.6 72 197-268 53-124 (235)
27 smart00357 CSP Cold shock prot 98.9 8E-09 1.7E-13 73.3 8.1 61 35-102 1-63 (64)
28 smart00357 CSP Cold shock prot 98.8 3.9E-08 8.6E-13 69.7 8.2 60 202-268 1-62 (64)
29 PF08206 OB_RNB: Ribonuclease 97.7 0.00014 3.1E-09 51.5 5.9 42 44-94 7-48 (58)
30 PRK11642 exoribonuclease R; Pr 97.6 0.0011 2.5E-08 69.7 14.9 47 33-90 84-130 (813)
31 PF08206 OB_RNB: Ribonuclease 97.5 0.00038 8.3E-09 49.3 6.5 42 211-261 7-48 (58)
32 TIGR00358 3_prime_RNase VacB a 97.2 0.0098 2.1E-07 61.4 15.2 47 33-90 16-63 (654)
33 PRK05054 exoribonuclease II; P 97.2 0.013 2.9E-07 60.3 15.7 47 32-90 20-66 (644)
34 TIGR02063 RNase_R ribonuclease 97.0 0.019 4.2E-07 59.7 15.6 47 33-90 68-115 (709)
35 PF14444 S1-like: S1-like 96.9 0.0033 7.2E-08 44.5 6.1 49 199-261 2-50 (58)
36 TIGR02062 RNase_B exoribonucle 96.7 0.051 1.1E-06 56.0 15.3 49 31-91 16-64 (639)
37 PF14444 S1-like: S1-like 96.2 0.018 4E-07 40.8 6.0 48 33-94 3-50 (58)
38 PF07497 Rho_RNA_bind: Rho ter 94.4 0.081 1.8E-06 39.9 4.7 63 34-105 3-73 (78)
39 PF07497 Rho_RNA_bind: Rho ter 94.4 0.17 3.8E-06 38.1 6.4 51 202-261 4-59 (78)
40 PRK13806 rpsA 30S ribosomal pr 93.9 1.1 2.5E-05 44.7 13.2 58 199-259 381-438 (491)
41 cd04459 Rho_CSD Rho_CSD: Rho p 93.8 0.2 4.4E-06 36.7 5.6 44 211-261 9-57 (68)
42 cd04453 S1_RNase_E S1_RNase_E: 93.7 0.42 9.1E-06 36.5 7.6 73 199-273 9-85 (88)
43 cd04459 Rho_CSD Rho_CSD: Rho p 93.6 0.13 2.8E-06 37.8 4.3 41 44-91 9-54 (68)
44 PRK07899 rpsA 30S ribosomal pr 92.4 2.3 5E-05 42.6 12.5 58 199-259 295-352 (486)
45 PRK13806 rpsA 30S ribosomal pr 92.3 2.2 4.8E-05 42.6 12.4 57 199-258 294-351 (491)
46 PRK11642 exoribonuclease R; Pr 91.2 0.51 1.1E-05 50.1 6.9 47 200-257 84-130 (813)
47 PRK12269 bifunctional cytidyla 90.8 5.4 0.00012 42.8 13.9 58 199-259 667-725 (863)
48 PRK12269 bifunctional cytidyla 90.5 3.6 7.7E-05 44.1 12.3 58 199-259 580-638 (863)
49 TIGR00358 3_prime_RNase VacB a 90.3 0.79 1.7E-05 47.5 7.1 47 200-257 16-63 (654)
50 COG0539 RpsA Ribosomal protein 89.9 2.9 6.3E-05 42.4 10.5 142 31-259 193-336 (541)
51 PF00575 S1: S1 RNA binding do 89.7 1.2 2.6E-05 32.0 5.8 60 199-261 6-65 (74)
52 TIGR02062 RNase_B exoribonucle 89.1 1.1 2.3E-05 46.4 7.0 53 199-263 17-69 (639)
53 PRK05054 exoribonuclease II; P 89.1 1.1 2.3E-05 46.5 7.0 52 200-263 21-72 (644)
54 TIGR00717 rpsA ribosomal prote 89.1 9 0.00019 38.2 13.4 57 199-258 448-504 (516)
55 cd00164 S1_like S1_like: Ribos 88.9 1.5 3.3E-05 29.7 5.7 56 202-260 2-57 (65)
56 PF13509 S1_2: S1 domain; PDB: 88.7 1 2.2E-05 31.9 4.7 49 203-262 7-55 (61)
57 cd05698 S1_Rrp5_repeat_hs6_sc5 88.7 2.5 5.5E-05 30.0 6.9 59 200-261 3-61 (70)
58 cd00164 S1_like S1_like: Ribos 88.6 1.5 3.3E-05 29.6 5.5 56 34-92 1-56 (65)
59 cd04461 S1_Rrp5_repeat_hs8_sc7 88.5 2.3 5.1E-05 31.5 6.8 59 199-260 16-74 (83)
60 cd05696 S1_Rrp5_repeat_hs4 S1_ 87.8 2.1 4.6E-05 31.0 6.0 55 203-259 7-61 (71)
61 PRK06299 rpsA 30S ribosomal pr 87.4 11 0.00024 38.1 13.0 57 199-258 375-432 (565)
62 cd04453 S1_RNase_E S1_RNase_E: 87.2 3 6.4E-05 31.8 6.8 62 31-93 8-72 (88)
63 TIGR00717 rpsA ribosomal prote 86.1 14 0.00031 36.8 12.8 57 199-258 361-418 (516)
64 PF00575 S1: S1 RNA binding do 85.8 2.2 4.9E-05 30.5 5.2 58 32-92 6-63 (74)
65 PRK06676 rpsA 30S ribosomal pr 85.8 24 0.00053 33.8 13.9 58 199-259 279-336 (390)
66 TIGR02063 RNase_R ribonuclease 85.6 2.4 5.2E-05 44.3 7.3 48 200-258 68-116 (709)
67 cd04461 S1_Rrp5_repeat_hs8_sc7 85.6 4.6 0.0001 29.8 7.0 58 32-92 16-73 (83)
68 COG2996 Predicted RNA-bindinin 85.4 20 0.00044 33.3 12.2 49 211-265 85-135 (287)
69 cd05698 S1_Rrp5_repeat_hs6_sc5 85.3 4.3 9.3E-05 28.7 6.5 58 33-93 3-60 (70)
70 cd05706 S1_Rrp5_repeat_sc10 S1 85.2 6.3 0.00014 28.1 7.4 59 199-260 5-63 (73)
71 cd05692 S1_RPS1_repeat_hs4 S1_ 85.1 4 8.6E-05 28.2 6.2 56 201-259 4-59 (69)
72 PRK00087 4-hydroxy-3-methylbut 84.5 18 0.0004 37.4 13.1 58 199-259 564-621 (647)
73 cd05704 S1_Rrp5_repeat_hs13 S1 84.5 5.4 0.00012 28.9 6.8 61 199-261 5-65 (72)
74 cd05697 S1_Rrp5_repeat_hs5 S1_ 84.4 5.6 0.00012 28.2 6.7 57 201-260 4-60 (69)
75 cd04472 S1_PNPase S1_PNPase: P 84.4 6.8 0.00015 27.2 7.1 57 201-260 4-60 (68)
76 smart00316 S1 Ribosomal protei 84.2 5.6 0.00012 27.3 6.6 58 200-260 5-62 (72)
77 cd05691 S1_RPS1_repeat_ec6 S1_ 84.2 5.1 0.00011 28.3 6.5 58 201-261 4-61 (73)
78 cd05696 S1_Rrp5_repeat_hs4 S1_ 84.0 4 8.7E-05 29.5 5.9 53 36-90 7-59 (71)
79 PRK06299 rpsA 30S ribosomal pr 84.0 18 0.0004 36.6 12.6 58 199-259 462-519 (565)
80 COG0557 VacB Exoribonuclease R 83.4 16 0.00035 38.3 12.2 47 33-90 69-117 (706)
81 cd05704 S1_Rrp5_repeat_hs13 S1 82.7 8.5 0.00018 27.8 7.2 61 32-94 5-65 (72)
82 cd05689 S1_RPS1_repeat_ec4 S1_ 82.3 9 0.0002 27.2 7.2 57 200-259 6-63 (72)
83 PRK08582 hypothetical protein; 81.3 5.9 0.00013 32.9 6.6 58 199-259 7-64 (139)
84 cd05686 S1_pNO40 S1_pNO40: pNO 81.2 6.3 0.00014 28.5 6.1 59 199-260 5-64 (73)
85 cd05706 S1_Rrp5_repeat_sc10 S1 81.2 8.1 0.00018 27.5 6.6 58 32-92 5-62 (73)
86 cd05690 S1_RPS1_repeat_ec5 S1_ 81.1 5.6 0.00012 27.9 5.6 56 201-259 4-60 (69)
87 cd05697 S1_Rrp5_repeat_hs5 S1_ 81.0 9.4 0.0002 27.0 6.8 58 33-93 3-60 (69)
88 cd04473 S1_RecJ_like S1_RecJ_l 80.7 7.1 0.00015 28.6 6.3 49 199-258 18-66 (77)
89 cd05692 S1_RPS1_repeat_hs4 S1_ 80.5 7.2 0.00016 26.8 6.0 57 33-92 3-59 (69)
90 PRK07400 30S ribosomal protein 80.5 25 0.00053 33.2 11.3 57 200-260 199-255 (318)
91 smart00316 S1 Ribosomal protei 80.4 5.9 0.00013 27.2 5.5 58 32-92 4-61 (72)
92 TIGR01451 B_ant_repeat conserv 80.3 3.3 7.1E-05 28.5 4.0 40 243-282 6-48 (53)
93 cd05707 S1_Rrp5_repeat_sc11 S1 80.1 6.1 0.00013 27.9 5.6 57 201-260 4-60 (68)
94 PRK08582 hypothetical protein; 79.6 18 0.00038 30.1 8.9 70 32-104 7-77 (139)
95 cd05689 S1_RPS1_repeat_ec4 S1_ 79.6 17 0.00036 25.8 7.8 57 33-92 6-63 (72)
96 cd04472 S1_PNPase S1_PNPase: P 79.1 9.4 0.0002 26.4 6.3 57 33-92 3-59 (68)
97 cd05705 S1_Rrp5_repeat_hs14 S1 78.5 8.8 0.00019 28.1 6.1 59 199-260 5-66 (74)
98 cd05687 S1_RPS1_repeat_ec1_hs1 78.2 9.2 0.0002 27.0 6.0 57 200-259 3-59 (70)
99 cd05691 S1_RPS1_repeat_ec6 S1_ 77.7 12 0.00025 26.4 6.5 58 33-93 3-60 (73)
100 cd05686 S1_pNO40 S1_pNO40: pNO 77.7 8.7 0.00019 27.7 5.8 58 32-92 5-63 (73)
101 cd04452 S1_IF2_alpha S1_IF2_al 76.3 14 0.0003 26.4 6.6 59 199-260 5-65 (76)
102 PRK07252 hypothetical protein; 76.2 10 0.00023 30.6 6.4 58 200-260 6-63 (120)
103 cd05694 S1_Rrp5_repeat_hs2_sc2 76.0 15 0.00033 26.8 6.8 52 200-260 7-59 (74)
104 PRK12608 transcription termina 75.8 8.2 0.00018 37.5 6.6 66 33-107 18-88 (380)
105 COG0539 RpsA Ribosomal protein 75.4 30 0.00065 35.2 10.7 58 199-259 365-422 (541)
106 cd05687 S1_RPS1_repeat_ec1_hs1 75.0 12 0.00027 26.3 5.9 56 33-91 3-58 (70)
107 cd05690 S1_RPS1_repeat_ec5 S1_ 74.9 12 0.00027 26.1 5.9 56 33-91 3-59 (69)
108 PF13509 S1_2: S1 domain; PDB: 74.4 6.5 0.00014 27.8 4.2 49 35-94 6-54 (61)
109 cd05703 S1_Rrp5_repeat_hs12_sc 74.1 11 0.00023 27.5 5.4 57 201-260 4-62 (73)
110 cd05685 S1_Tex S1_Tex: The C-t 74.1 13 0.00027 25.6 5.7 56 201-259 4-59 (68)
111 cd05705 S1_Rrp5_repeat_hs14 S1 73.5 13 0.00027 27.2 5.8 57 32-91 5-64 (74)
112 cd05684 S1_DHX8_helicase S1_DH 73.4 20 0.00043 26.1 6.9 58 201-261 4-65 (79)
113 COG4776 Rnb Exoribonuclease II 73.2 3.6 7.8E-05 40.9 3.4 55 31-97 19-73 (645)
114 PRK09376 rho transcription ter 71.6 11 0.00025 36.9 6.5 64 33-105 50-121 (416)
115 PRK05807 hypothetical protein; 71.3 14 0.0003 30.5 6.1 57 199-259 7-63 (136)
116 cd05707 S1_Rrp5_repeat_sc11 S1 71.2 15 0.00033 25.8 5.6 57 33-92 3-59 (68)
117 cd05684 S1_DHX8_helicase S1_DH 70.7 31 0.00068 25.0 7.4 65 34-101 4-72 (79)
118 TIGR00757 RNaseEG ribonuclease 70.1 24 0.00053 34.6 8.5 82 198-280 26-122 (414)
119 cd05703 S1_Rrp5_repeat_hs12_sc 69.5 14 0.00031 26.8 5.2 56 33-91 3-60 (73)
120 PRK09376 rho transcription ter 69.3 10 0.00022 37.2 5.6 52 201-261 51-107 (416)
121 PRK12608 transcription termina 69.0 5.6 0.00012 38.6 3.7 48 201-257 19-71 (380)
122 cd05702 S1_Rrp5_repeat_hs11_sc 68.4 24 0.00051 25.1 6.2 56 201-259 4-61 (70)
123 cd04473 S1_RecJ_like S1_RecJ_l 67.4 26 0.00056 25.5 6.3 50 31-91 17-66 (77)
124 PRK07252 hypothetical protein; 66.9 20 0.00043 29.0 6.1 68 33-103 6-75 (120)
125 PF11604 CusF_Ec: Copper bindi 66.4 10 0.00022 27.6 3.9 27 75-101 40-67 (70)
126 COG1158 Rho Transcription term 65.6 8.4 0.00018 37.1 4.1 51 202-261 55-110 (422)
127 cd04452 S1_IF2_alpha S1_IF2_al 65.4 33 0.00071 24.4 6.5 58 32-92 5-64 (76)
128 COG1158 Rho Transcription term 64.9 8.1 0.00018 37.2 3.8 64 34-106 54-125 (422)
129 PRK08059 general stress protei 64.4 33 0.00071 27.6 6.9 58 199-259 9-66 (123)
130 cd04455 S1_NusA S1_NusA: N-uti 64.2 31 0.00068 24.4 6.1 52 199-260 5-56 (67)
131 cd05688 S1_RPS1_repeat_ec3 S1_ 64.1 23 0.00051 24.3 5.4 56 200-259 4-59 (68)
132 PRK08059 general stress protei 63.9 52 0.0011 26.4 8.0 68 32-102 9-78 (123)
133 cd04465 S1_RPS1_repeat_ec2_hs2 63.7 19 0.00041 25.3 4.8 54 201-260 4-57 (67)
134 cd04471 S1_RNase_R S1_RNase_R: 63.4 50 0.0011 23.7 7.3 57 33-92 4-72 (83)
135 PF11604 CusF_Ec: Copper bindi 63.3 12 0.00026 27.2 3.8 28 242-269 40-68 (70)
136 cd05702 S1_Rrp5_repeat_hs11_sc 63.3 31 0.00068 24.4 6.0 56 33-91 3-60 (70)
137 cd05685 S1_Tex S1_Tex: The C-t 63.0 27 0.00059 23.8 5.5 57 33-92 3-59 (68)
138 cd05694 S1_Rrp5_repeat_hs2_sc2 62.5 45 0.00097 24.3 6.8 51 32-91 6-57 (74)
139 COG1098 VacB Predicted RNA bin 62.2 12 0.00026 30.7 3.9 57 199-258 7-63 (129)
140 cd04455 S1_NusA S1_NusA: N-uti 61.6 26 0.00057 24.8 5.3 50 33-92 6-55 (67)
141 cd04465 S1_RPS1_repeat_ec2_hs2 61.4 19 0.00042 25.2 4.5 52 33-92 3-56 (67)
142 TIGR00767 rho transcription te 59.7 7.3 0.00016 38.3 2.6 50 33-91 50-104 (415)
143 PRK00087 4-hydroxy-3-methylbut 59.0 2.1E+02 0.0046 29.7 13.3 57 31-90 303-359 (647)
144 TIGR00767 rho transcription te 58.2 18 0.00039 35.6 5.1 48 201-257 51-103 (415)
145 cd05695 S1_Rrp5_repeat_hs3 S1_ 57.8 47 0.001 23.4 6.1 54 201-259 4-57 (66)
146 PTZ00248 eukaryotic translatio 57.5 34 0.00075 32.5 6.7 61 199-262 19-83 (319)
147 PHA02945 interferon resistance 57.4 56 0.0012 25.2 6.6 58 31-94 12-73 (88)
148 PRK12678 transcription termina 56.6 16 0.00034 37.8 4.5 51 201-261 296-349 (672)
149 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 56.4 37 0.0008 25.0 5.6 59 199-260 8-70 (86)
150 cd05708 S1_Rrp5_repeat_sc12 S1 55.8 35 0.00077 24.1 5.2 57 33-92 5-62 (77)
151 cd04471 S1_RNase_R S1_RNase_R: 55.8 51 0.0011 23.7 6.2 58 200-260 4-73 (83)
152 cd05688 S1_RPS1_repeat_ec3 S1_ 55.4 37 0.0008 23.2 5.2 56 33-92 4-59 (68)
153 PRK05807 hypothetical protein; 55.0 81 0.0017 25.9 7.8 69 31-103 6-75 (136)
154 PRK12678 transcription termina 54.3 25 0.00055 36.3 5.5 47 34-90 296-345 (672)
155 cd05708 S1_Rrp5_repeat_sc12 S1 53.6 53 0.0011 23.1 5.9 57 200-259 5-62 (77)
156 PHA02945 interferon resistance 53.3 59 0.0013 25.1 6.1 61 201-267 15-79 (88)
157 cd05695 S1_Rrp5_repeat_hs3 S1_ 53.2 48 0.001 23.4 5.5 53 33-90 3-55 (66)
158 COG4776 Rnb Exoribonuclease II 52.9 17 0.00037 36.3 3.9 53 199-263 20-72 (645)
159 PTZ00248 eukaryotic translatio 52.6 59 0.0013 30.9 7.4 72 31-105 18-93 (319)
160 PLN00207 polyribonucleotide nu 52.1 25 0.00055 37.9 5.3 59 199-260 755-814 (891)
161 cd04454 S1_Rrp4_like S1_Rrp4_l 51.8 57 0.0012 23.8 5.9 59 200-261 9-67 (82)
162 PRK09838 periplasmic copper-bi 51.4 24 0.00051 28.5 3.9 64 200-269 44-113 (115)
163 KOG3209|consensus 50.7 93 0.002 33.0 8.8 53 42-94 352-406 (984)
164 PRK09838 periplasmic copper-bi 49.5 31 0.00068 27.8 4.4 64 32-101 43-112 (115)
165 PRK11712 ribonuclease G; Provi 48.6 1.1E+02 0.0024 30.7 9.0 83 197-280 38-135 (489)
166 TIGR00757 RNaseEG ribonuclease 48.5 74 0.0016 31.3 7.6 65 29-94 24-100 (414)
167 PF05606 DUF777: Borrelia burg 48.3 26 0.00055 30.2 3.8 48 34-87 36-83 (181)
168 PRK10811 rne ribonuclease E; R 48.2 70 0.0015 35.0 7.8 75 198-273 39-122 (1068)
169 TIGR03591 polynuc_phos polyrib 48.2 44 0.00094 35.0 6.3 60 198-260 619-678 (684)
170 TIGR02696 pppGpp_PNP guanosine 47.3 42 0.00091 35.4 5.9 59 198-259 648-710 (719)
171 PRK11824 polynucleotide phosph 45.9 53 0.0011 34.5 6.5 58 199-259 623-680 (693)
172 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 45.8 87 0.0019 22.9 6.1 60 31-93 7-70 (86)
173 cd04454 S1_Rrp4_like S1_Rrp4_l 45.7 1E+02 0.0022 22.3 6.5 61 31-94 7-67 (82)
174 PRK03987 translation initiatio 39.8 98 0.0021 28.5 6.6 58 200-260 11-70 (262)
175 PLN00207 polyribonucleotide nu 39.5 98 0.0021 33.6 7.3 67 32-101 755-823 (891)
176 cd04460 S1_RpoE S1_RpoE: RpoE, 39.2 92 0.002 23.7 5.5 55 201-259 3-68 (99)
177 PF01345 DUF11: Domain of unkn 37.8 68 0.0015 23.0 4.3 37 243-279 35-74 (76)
178 cd05701 S1_Rrp5_repeat_hs10 S1 37.2 76 0.0017 23.1 4.2 49 211-259 12-60 (69)
179 PRK11824 polynucleotide phosph 36.9 1E+02 0.0022 32.4 7.0 58 31-91 622-679 (693)
180 PRK07400 30S ribosomal protein 36.1 1.4E+02 0.0029 28.2 7.1 71 31-105 197-269 (318)
181 TIGR03591 polynuc_phos polyrib 35.3 86 0.0019 32.9 6.1 59 31-92 619-677 (684)
182 PRK07899 rpsA 30S ribosomal pr 33.8 97 0.0021 31.2 6.0 68 31-101 294-363 (486)
183 TIGR02696 pppGpp_PNP guanosine 33.3 1E+02 0.0022 32.6 6.2 58 30-90 647-708 (719)
184 cd05693 S1_Rrp5_repeat_hs1_sc1 32.1 92 0.002 24.1 4.4 58 32-93 5-82 (100)
185 PF01336 tRNA_anti-codon: OB-f 30.6 79 0.0017 21.9 3.6 50 33-87 2-54 (75)
186 PRK09521 exosome complex RNA-b 30.5 2.6E+02 0.0057 24.0 7.5 78 199-280 66-154 (189)
187 COG0557 VacB Exoribonuclease R 30.5 1.2E+02 0.0025 32.0 6.2 48 202-260 71-120 (706)
188 PRK06676 rpsA 30S ribosomal pr 30.2 1.5E+02 0.0032 28.4 6.4 59 199-259 19-77 (390)
189 PRK03987 translation initiatio 29.0 1.5E+02 0.0032 27.3 5.9 70 31-103 9-82 (262)
190 PF05606 DUF777: Borrelia burg 28.8 81 0.0018 27.2 3.8 46 202-253 37-82 (181)
191 PF03100 CcmE: CcmE; InterPro 28.8 3.2E+02 0.0069 22.2 8.1 60 35-102 61-121 (131)
192 PF11948 DUF3465: Protein of u 27.8 3.5E+02 0.0077 22.4 7.3 57 200-261 40-104 (131)
193 PRK09202 nusA transcription el 27.7 1.4E+02 0.0031 29.9 6.0 52 199-260 136-187 (470)
194 COG1093 SUI2 Translation initi 27.6 82 0.0018 29.1 3.9 63 201-264 15-77 (269)
195 PRK11712 ribonuclease G; Provi 27.1 2.2E+02 0.0047 28.7 7.2 66 28-94 36-113 (489)
196 COG2996 Predicted RNA-bindinin 26.2 2.3E+02 0.005 26.5 6.5 57 199-265 7-65 (287)
197 PRK09202 nusA transcription el 26.0 1.5E+02 0.0032 29.7 5.7 50 32-91 136-185 (470)
198 PF01551 Peptidase_M23: Peptid 25.8 1.1E+02 0.0023 22.9 3.8 35 200-234 19-56 (96)
199 COG2190 NagE Phosphotransferas 25.3 1.3E+02 0.0028 25.7 4.5 46 34-85 49-100 (156)
200 cd04486 YhcR_OBF_like YhcR_OBF 24.7 2.9E+02 0.0062 20.3 5.9 50 201-259 2-59 (78)
201 PF03459 TOBE: TOBE domain; I 24.3 1.5E+02 0.0033 20.2 4.1 54 199-257 5-59 (64)
202 PRK10811 rne ribonuclease E; R 22.5 2.7E+02 0.0059 30.7 7.1 65 29-94 37-110 (1068)
203 COG1098 VacB Predicted RNA bin 20.7 97 0.0021 25.5 2.7 56 48-104 21-77 (129)
204 COG1095 RPB7 DNA-directed RNA 20.5 1.6E+02 0.0034 25.8 4.1 59 199-261 83-152 (183)
205 PF03100 CcmE: CcmE; InterPro 20.5 4.7E+02 0.01 21.2 8.2 58 203-268 62-120 (131)
206 PRK11637 AmiB activator; Provi 20.3 1.1E+02 0.0023 29.9 3.5 50 200-253 345-397 (428)
No 1
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.90 E-value=4.6e-24 Score=154.86 Aligned_cols=66 Identities=44% Similarity=0.795 Sum_probs=62.8
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~ 102 (282)
+.+|+|||||..||||||+++++++|||+|+|+|+.. |+++|.+|++|+|+++.+.+|++|.+|+.
T Consensus 1 ~~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~----g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~ 66 (67)
T COG1278 1 MATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA----GFRTLREGQKVEFEVEQGRKGPSAANVRA 66 (67)
T ss_pred CCcceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC----CCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence 3589999999999999999999999999999999987 69999999999999999999999999975
No 2
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.89 E-value=2.9e-23 Score=150.70 Aligned_cols=65 Identities=43% Similarity=0.781 Sum_probs=61.5
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
.+|+|||||..||||||+++++++|||||+|+|+ +.|+++|.+||+|+|++++++||++|++|+.
T Consensus 2 ~~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~----~~g~~~L~eGQ~V~f~~~~g~kgp~A~nv~~ 66 (67)
T COG1278 2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQ----RAGFRTLREGQKVEFEVEQGRKGPSAANVRA 66 (67)
T ss_pred CcceEEEeeCCCcceEcCCCCCCcCEEEEeeeec----cCCCcccCCCCEEEEEEecCCCCCceeEEEe
Confidence 4699999999999999999999999999999999 4579999999999999999999999999974
No 3
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.88 E-value=8.5e-23 Score=150.59 Aligned_cols=68 Identities=50% Similarity=0.838 Sum_probs=63.9
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP 103 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~ 103 (282)
++++|+|||||.+||||||+++++++|||||+|+|... |++.|.+|++|+|++..+++|++|.+|+.+
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~~ 69 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEcC
Confidence 57899999999999999999999999999999999986 589999999999999999999999999853
No 4
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.88 E-value=1.2e-22 Score=150.02 Aligned_cols=66 Identities=36% Similarity=0.437 Sum_probs=62.1
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~ 102 (282)
+++|+|||||.+||||||+++++++|||||+|+|... |++.|.+|++|+|+++.+++|++|.+|..
T Consensus 4 ~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~----g~~~l~~G~~V~f~v~~~~kG~~A~~v~~ 69 (70)
T PRK15464 4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR----DAEVLIPGLRVEFCRVNGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 4689999999999999999999999999999999876 58899999999999999999999999974
No 5
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.87 E-value=2.8e-22 Score=147.83 Aligned_cols=68 Identities=49% Similarity=0.806 Sum_probs=63.5
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP 103 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~ 103 (282)
.+.+|+|||||.+||||||+++++++|||||+|+|... |++.|.+|+.|+|+++.+++|++|.+|+.+
T Consensus 2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 69 (69)
T PRK09507 2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIAL 69 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEeC
Confidence 46899999999999999999999999999999999986 589999999999999999999999999753
No 6
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.87 E-value=3.4e-22 Score=147.75 Aligned_cols=66 Identities=36% Similarity=0.464 Sum_probs=62.1
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~ 102 (282)
+++|+|||||.+||||||+++++++|||||+++|... |++.|.+|++|+|++..+++|++|.+|..
T Consensus 4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~----g~~~l~~G~~V~f~v~~~~~G~~A~~V~~ 69 (70)
T PRK15463 4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR----DAEELTTGLRVEFCRINGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 4689999999999999999999999999999999876 58999999999999999999999999974
No 7
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.87 E-value=4.5e-22 Score=147.16 Aligned_cols=66 Identities=47% Similarity=0.822 Sum_probs=62.3
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~ 102 (282)
+++|+|||||.+||||||+++++++|||||+|+|... |++.|.+|++|+|++..+++|++|.+|+.
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK10354 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS 69 (70)
T ss_pred cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 3589999999999999999999999999999999986 58999999999999999999999999985
No 8
>PRK09890 cold shock protein CspG; Provisional
Probab=99.87 E-value=5.2e-22 Score=146.80 Aligned_cols=66 Identities=45% Similarity=0.821 Sum_probs=62.4
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTG 102 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~ 102 (282)
+++|+|||||.+||||||+++++++|||||+|+|... +++.|.+|++|+|+++.+++|++|.+|..
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK09890 4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT 69 (70)
T ss_pred cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 4689999999999999999999999999999999986 58999999999999999999999999975
No 9
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.87 E-value=5.8e-22 Score=147.94 Aligned_cols=68 Identities=38% Similarity=0.720 Sum_probs=63.8
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG 105 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~ 105 (282)
.+|+|||||.+||||||+++++++|||||+|+|... |++.|.+|+.|+|++..+++|++|.+|..++.
T Consensus 2 ~~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~ 69 (74)
T PRK09937 2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHASVIVPVEV 69 (74)
T ss_pred CCeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeeEEEECCc
Confidence 479999999999999999999999999999999986 58999999999999999999999999997643
No 10
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.86 E-value=8.5e-22 Score=146.70 Aligned_cols=68 Identities=38% Similarity=0.739 Sum_probs=63.6
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG 105 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~ 105 (282)
.+|+|||||.+||||||+++++++|||||+|+|+.. |++.|.+|++|+|++..+++|++|.+|..+..
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~~~ 69 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIEA 69 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEECcc
Confidence 479999999999999999999999999999999986 58999999999999999999999999987654
No 11
>PRK15464 cold shock-like protein CspH; Provisional
Probab=99.86 E-value=7.1e-22 Score=145.87 Aligned_cols=66 Identities=33% Similarity=0.420 Sum_probs=61.2
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
+++|+|||||.+||||||+++++++|||||+++|.. .+++.|.+||+|+|++.+++||++|++|..
T Consensus 4 ~~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~----~g~~~l~~G~~V~f~v~~~~kG~~A~~v~~ 69 (70)
T PRK15464 4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTP----RDAEVLIPGLRVEFCRVNGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEECCCCeEEEccCCCCccEEEEehhehh----cCCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 458999999999999999999999999999999984 357889999999999999999999999974
No 12
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.86 E-value=7.4e-22 Score=145.19 Aligned_cols=66 Identities=36% Similarity=0.765 Sum_probs=62.0
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP 103 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~ 103 (282)
.+|+|||||.+||||||+++++++|||||+|+|... |++.|.+|++|+|+++.+++|++|.+|..+
T Consensus 2 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (68)
T TIGR02381 2 AIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVPI 67 (68)
T ss_pred CCeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEEC
Confidence 479999999999999999999999999999999876 589999999999999999999999999753
No 13
>PRK15463 cold shock-like protein CspF; Provisional
Probab=99.85 E-value=2e-21 Score=143.60 Aligned_cols=66 Identities=33% Similarity=0.447 Sum_probs=61.1
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
+++|+|||||.+||||||+++++++|||||+++|.. .|++.|.+|++|+|+++++++|++|.+|..
T Consensus 4 ~~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~----~g~~~l~~G~~V~f~v~~~~~G~~A~~V~~ 69 (70)
T PRK15463 4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNL----RDAEELTTGLRVEFCRINGLRGPTAANVYL 69 (70)
T ss_pred cceEEEEEEeCCCceEEEecCCCCccEEEEehhhhh----cCCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 458999999999999999999999999999999994 357899999999999999999999999863
No 14
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.85 E-value=2.3e-21 Score=142.94 Aligned_cols=67 Identities=46% Similarity=0.768 Sum_probs=62.0
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
++++|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|+.
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~g~~A~~V~~ 68 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVTA 68 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc----CCCCCCCCCEEEEEEEECCCCceeEEEEc
Confidence 36789999999999999999999999999999999943 57899999999999999999999999974
No 15
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.85 E-value=4.5e-21 Score=141.42 Aligned_cols=67 Identities=46% Similarity=0.791 Sum_probs=61.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
.+.+|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|+.
T Consensus 2 ~~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 68 (69)
T PRK09507 2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVIA 68 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc----CCCCCCCCCEEEEEEEECCCCcccEEEEe
Confidence 35789999999999999999999999999999999943 57899999999999999999999999974
No 16
>PRK09890 cold shock protein CspG; Provisional
Probab=99.85 E-value=5.1e-21 Score=141.49 Aligned_cols=66 Identities=42% Similarity=0.784 Sum_probs=61.3
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
+++|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|..
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~----~~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK09890 4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN----EFRTLNENQKVEFSIEQGQRGPAAANVVT 69 (70)
T ss_pred cceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 4589999999999999999999999999999999954 57899999999999999999999999874
No 17
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=99.84 E-value=7.2e-21 Score=140.72 Aligned_cols=66 Identities=42% Similarity=0.756 Sum_probs=61.1
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
+++|+|||||..||||||+++++++|||||+++|... +++.|.+|++|+|++.++++|++|.+|+.
T Consensus 4 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 69 (70)
T PRK10354 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND----GYKSLDEGQKVSFTIESGAKGPAAGNVTS 69 (70)
T ss_pred cceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc----CCCCCCCCCEEEEEEEECCCCceeEEEEe
Confidence 3579999999999999999999999999999999944 57899999999999999999999999974
No 18
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.84 E-value=9.2e-21 Score=141.45 Aligned_cols=65 Identities=40% Similarity=0.784 Sum_probs=60.9
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEec
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKN 270 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~ 270 (282)
+|+|||||..||||||+++++++|||||+++|.. .|++.|.+|++|+|++.++++|++|.+|..-
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~----~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQM----DGYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccc----cCCCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence 6999999999999999999999999999999994 3588999999999999999999999999854
No 19
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=99.84 E-value=1e-20 Score=139.12 Aligned_cols=64 Identities=36% Similarity=0.793 Sum_probs=60.3
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
+|+|||||.+||||||+++++++|||||+|+|... |++.|.+|++|+|++.++++|++|.+|..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 66 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD----GYRTLKAGQKVQFEVVQGPKGAHATHIVP 66 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence 69999999999999999999999999999999843 57899999999999999999999999975
No 20
>PRK14998 cold shock-like protein CspD; Provisional
Probab=99.83 E-value=1.6e-20 Score=139.84 Aligned_cols=65 Identities=40% Similarity=0.799 Sum_probs=60.7
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
.+|+|||||..||||||+++++++|||||+++|... |++.|.+|++|+|+++++++|++|++|..
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~----g~~~l~~G~~V~f~~~~~~~G~~A~~V~~ 66 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVP 66 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc----CCCCCCCCCEEEEEEEECCCCceeEEEEE
Confidence 369999999999999999999999999999999854 57899999999999999999999999975
No 21
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.80 E-value=2.7e-19 Score=130.31 Aligned_cols=66 Identities=41% Similarity=0.814 Sum_probs=59.5
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGP 103 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~ 103 (282)
++|+|||||..||||||+++++.+|||||+++|... +++.|.+|++|+|++..+++|++|.+|+.+
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~~ 66 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRKI 66 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE-
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEECc
Confidence 589999999999999999999999999999999987 378999999999999999999999999853
No 22
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.78 E-value=8e-19 Score=127.45 Aligned_cols=64 Identities=45% Similarity=0.884 Sum_probs=60.4
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVT 101 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~ 101 (282)
++|+|||||.+||||||+++++++|||||+++|... ++..|.+|+.|+|++..+.+|++|.+|+
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~ 64 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVR 64 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeE
Confidence 379999999999999999999999999999999986 4789999999999999999999999986
No 23
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=99.77 E-value=2.1e-18 Score=125.57 Aligned_cols=65 Identities=42% Similarity=0.783 Sum_probs=58.7
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
++|+|+|||..+|||||+++++.+|||||+++|... +++.|..|++|+|++..+++|++|.+|++
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~----~~~~l~~G~~V~F~~~~~~~g~~A~~V~~ 65 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN----GFRSLKEGDRVEFEVEEGKKGPQAVNVRK 65 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS----SSTS--TTSEEEEEEEECTTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccc----ccccCCCCCEEEEEEEECCCCCEEEEEEC
Confidence 579999999999999999999999999999999965 36899999999999999999999999985
No 24
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.75 E-value=4.2e-18 Score=123.66 Aligned_cols=63 Identities=43% Similarity=0.798 Sum_probs=59.1
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL 268 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~ 268 (282)
+|+|||||..||||||+++++++|||||+++|... ++..|.+|++|+|++..+++|++|.+|+
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~----~~~~~~~G~~V~f~~~~~~~g~~A~~V~ 64 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD----GFRSLEEGDRVEFELEEGDKGPQAVNVR 64 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc----CCCcCCCCCEEEEEEEECCCCCeEEEeE
Confidence 69999999999999999999999999999999954 4688999999999999999999999986
No 25
>KOG3070|consensus
Probab=99.54 E-value=1.5e-14 Score=130.04 Aligned_cols=93 Identities=48% Similarity=0.788 Sum_probs=83.9
Q ss_pred CCceeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCC
Q psy547 26 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDG 105 (282)
Q Consensus 26 ~~~~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~ 105 (282)
..+++....+|+|||||..+|||||+++|+.+|||||+++|..+.++.++++|.+++.|+|+++.+.+|..|++|+.+++
T Consensus 49 ~~~~~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt~p~g 128 (235)
T KOG3070|consen 49 AKKVQGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVTGPDG 128 (235)
T ss_pred ccccccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeecCCCC
Confidence 35677888999999999999999999999999999999999997777789999999999999999999999999999999
Q ss_pred CccccccccCCCC
Q psy547 106 RHVQGSQFAANKP 118 (282)
Q Consensus 106 ~~~~~~~~~~~~~ 118 (282)
.++..+.+.....
T Consensus 129 ~~~~~s~~~~~~~ 141 (235)
T KOG3070|consen 129 VPVRGSKGAVKGN 141 (235)
T ss_pred ccccccccccccc
Confidence 8887777665443
No 26
>KOG3070|consensus
Probab=99.32 E-value=2.1e-12 Score=116.10 Aligned_cols=72 Identities=44% Similarity=0.786 Sum_probs=67.6
Q ss_pred eeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL 268 (282)
Q Consensus 197 ~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~ 268 (282)
+....+|+|||||..+|||||+++|+.+|||||+++|.++.++.+++.|.+++.|+|.++...+|.+|++|+
T Consensus 53 ~~~~~~G~~k~fnv~~G~gFi~~~d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g~~a~~vt 124 (235)
T KOG3070|consen 53 QGARVKGTVKWFNVGKGYGFITRDDGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKGTEAANVT 124 (235)
T ss_pred ccccccCcceeEeccCCcceecccCCCCceeEEeeeecccccccchhhcccCCCccceecccCccceeeeec
Confidence 346678999999999999999999999999999999998878889999999999999999999999999988
No 27
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=98.90 E-value=8e-09 Score=73.28 Aligned_cols=61 Identities=46% Similarity=0.822 Sum_probs=50.5
Q ss_pred eeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe--CCCCceEEEEeC
Q psy547 35 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ--GDKGHEAINVTG 102 (282)
Q Consensus 35 ~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~--~~kG~~A~~V~~ 102 (282)
+|+|+|++ +|||||.+++...|+|||.+.+.. + +..+..||.|.|.+.. ..++++|..|..
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-~----~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-G----LKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-C----CCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 58999997 899999998765799999998865 2 5678999999999987 455678877754
No 28
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=98.78 E-value=3.9e-08 Score=69.66 Aligned_cols=60 Identities=42% Similarity=0.749 Sum_probs=48.5
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE--cCCCceeeeeE
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ--GDKGNQFCFVL 268 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~--~~kG~~A~~V~ 268 (282)
+|+|+|++ +|||||.+++...+||||.+.++. ++..+..||.|.|.+.. ..++++|..+.
T Consensus 1 ~G~i~~~~--~g~gfv~~~~~~~~i~v~~~~~~~-----~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~ 62 (64)
T smart00357 1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-----GLKSLREGDEVEFKVVSPRGGGKPEAENVV 62 (64)
T ss_pred CeEEEEEc--CCeeEEecCCCCccEEEEhHHhhc-----CCCcCCCCCEEEEEEEEccCCCCcEEEEEE
Confidence 48999996 799999998766799999998763 24678999999999987 45567776554
No 29
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=97.65 E-value=0.00014 Score=51.50 Aligned_cols=42 Identities=24% Similarity=0.589 Sum_probs=32.4
Q ss_pred CCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 44 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 44 ~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
.+||||+.+++...|||+...++... ..||+|...+....++
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~~A---------~~gD~V~v~i~~~~~~ 48 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLNGA---------MDGDKVLVRITPPSRG 48 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHTTS----------TT-EEEEEEEESSSE
T ss_pred cCCCEEEEECCCCCCEEECHHHHCCC---------CCCCEEEEEEecCCCC
Confidence 89999999999899999999999776 7999999999884433
No 30
>PRK11642 exoribonuclease R; Provisional
Probab=97.64 E-value=0.0011 Score=69.70 Aligned_cols=47 Identities=23% Similarity=0.460 Sum_probs=38.8
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.|+|+.= .+||||+.++++++||||+-..+... ..||+|...+..
T Consensus 84 ~~~G~v~~~--~~GfgFv~~e~~~~difI~~~~l~~A---------~~GD~V~v~i~~ 130 (813)
T PRK11642 84 LLKGTVIGH--RDGYGFLRVEGRKDDLYLSSEQMKTC---------IHGDQVLAQPLG 130 (813)
T ss_pred eEEEEEEEC--CCccEEEEECCCCCCEEEChHHHccC---------CCCCEEEEEEcc
Confidence 477999954 89999999987678999988887664 689999988654
No 31
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=97.51 E-value=0.00038 Score=49.32 Aligned_cols=42 Identities=24% Similarity=0.604 Sum_probs=32.1
Q ss_pred CCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 211 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 211 ~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.+||||+.+++..+|||+...++. ..-.||+|...+....++
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~---------~A~~gD~V~v~i~~~~~~ 48 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLN---------GAMDGDKVLVRITPPSRG 48 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHT---------TS-TT-EEEEEEEESSSE
T ss_pred cCCCEEEEECCCCCCEEECHHHHC---------CCCCCCEEEEEEecCCCC
Confidence 799999999999999999999988 357999999999984433
No 32
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=97.21 E-value=0.0098 Score=61.38 Aligned_cols=47 Identities=30% Similarity=0.477 Sum_probs=38.4
Q ss_pred eeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 33 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.|+|+.= .|||||+.+++ +++|+|+.-..+... ..||+|...+..
T Consensus 16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~~a---------~~GD~V~v~i~~ 63 (654)
T TIGR00358 16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMKKV---------MHGDLVEACPLS 63 (654)
T ss_pred eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhCcC---------CCCCEEEEEEee
Confidence 467999975 89999999986 368999998877654 689999998754
No 33
>PRK05054 exoribonuclease II; Provisional
Probab=97.17 E-value=0.013 Score=60.30 Aligned_cols=47 Identities=26% Similarity=0.451 Sum_probs=37.9
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
..+.|+|+.= .|||||+.+++ .+|+|++-..+... ..||+|...+..
T Consensus 20 ~~~~G~~~~~--~~gfgFv~~~~-~~difI~~~~l~~a---------~~GD~V~v~i~~ 66 (644)
T PRK05054 20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDRIIAVIHT 66 (644)
T ss_pred CeEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEec
Confidence 3467999964 89999998854 46999999988765 689999998754
No 34
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=97.04 E-value=0.019 Score=59.71 Aligned_cols=47 Identities=23% Similarity=0.475 Sum_probs=37.3
Q ss_pred eeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 33 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.|+++. ..+||||+.+++ ...|+|+.-..+.. +..||.|...+..
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~~---------a~~GD~Vlv~I~~ 115 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMNG---------AMHGDRVLVRITG 115 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhCc---------CCCCCEEEEEEec
Confidence 46798886 489999999986 45799998776654 4789999998754
No 35
>PF14444 S1-like: S1-like
Probab=96.94 E-value=0.0033 Score=44.50 Aligned_cols=49 Identities=31% Similarity=0.453 Sum_probs=40.3
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
+..+|+|..+. ..||||. ++|||+.+.+... .++.||+|..+...++.-
T Consensus 2 r~~~GvVTkl~--~~yG~ID-----e~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~~ 50 (58)
T PF14444_consen 2 RVFTGVVTKLC--DDYGFID-----EDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPNM 50 (58)
T ss_pred ceEEEEEEEEe--CCcceEc-----ccEEEEcccEecC-------CCccCCEEEEEEEeCCCC
Confidence 34689999994 6799996 4899999998832 469999999999988754
No 36
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.71 E-value=0.051 Score=56.02 Aligned_cols=49 Identities=24% Similarity=0.435 Sum_probs=38.8
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
...+.|+|+.= .|||||+..++ .+|||++-..+... ..||+|...+...
T Consensus 16 ~~~~~G~i~~~--~kGfgFv~~~~-~~difI~~~~l~~A---------~~GD~V~v~i~~~ 64 (639)
T TIGR02062 16 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMKKV---------MHGDKIIAVIHSE 64 (639)
T ss_pred CceEEEEEEEC--CCccEEEEECC-CCcEEEChHHHccC---------CCCCEEEEEEecC
Confidence 34567999965 89999997654 56999999988765 6899999987543
No 37
>PF14444 S1-like: S1-like
Probab=96.21 E-value=0.018 Score=40.76 Aligned_cols=48 Identities=31% Similarity=0.444 Sum_probs=39.4
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
..+|.|..+ ...||||. +||||+.+.+.+. .++.||+|..+...+++-
T Consensus 3 ~~~GvVTkl--~~~yG~ID-----e~vFF~~~vv~G~-------~P~vGdrV~v~A~~n~~~ 50 (58)
T PF14444_consen 3 VFTGVVTKL--CDDYGFID-----EDVFFQTDVVKGN-------VPKVGDRVLVEAIYNPNM 50 (58)
T ss_pred eEEEEEEEE--eCCcceEc-----ccEEEEcccEecC-------CCccCCEEEEEEEeCCCC
Confidence 358999999 47899997 4899999998763 448999999998877653
No 38
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=94.45 E-value=0.081 Score=39.89 Aligned_cols=63 Identities=32% Similarity=0.582 Sum_probs=39.6
Q ss_pred eeeEEEEeeCCCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC---ceEEEEeCCCC
Q psy547 34 VCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG---HEAINVTGPDG 105 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG---~~A~~V~~~~~ 105 (282)
..|.+--- .+|||||... .+..||||..+.++.. .|+.||.|+=.+.....+ .....|..+++
T Consensus 3 ~~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf-------~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg 73 (78)
T PF07497_consen 3 VEGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRF-------GLRTGDLVEGQVRPPREGEKYFALLRVESVNG 73 (78)
T ss_dssp EEEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCCT-------T--TTEEEEEEEE--STTSSSEEECEECEETT
T ss_pred EEEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHHc-------CCCCCCEEEEEEeCCCCCCcceeeEEEEeECC
Confidence 34555522 5799999997 2678999999999875 579999999888775444 34455665554
No 39
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=94.41 E-value=0.17 Score=38.10 Aligned_cols=51 Identities=33% Similarity=0.614 Sum_probs=33.4
Q ss_pred eeEEEEEEcCCCeeEEecC-----CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 202 CGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~-----d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.|++--. .+|||||... -+..||||..+.++. -.|..||.|+=.+.....+
T Consensus 4 ~GvLei~--~dGyGFLR~~~~~y~~~~~DvYVs~~qIrr-------f~LR~GD~V~G~vr~p~~~ 59 (78)
T PF07497_consen 4 EGVLEIL--PDGYGFLRSPDNNYLPSPDDVYVSPSQIRR-------FGLRTGDLVEGQVRPPREG 59 (78)
T ss_dssp EEEEEE---TTS-EEEE-GGGTTS-STTSEEE-CCCCCC-------TT--TTEEEEEEEE--STT
T ss_pred EEEEEEC--CCCcEEeECCCcCCCCCCCCEEECHHHHHH-------cCCCCCCEEEEEEeCCCCC
Confidence 3555432 5799999987 257899999999994 3599999999988886665
No 40
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=93.93 E-value=1.1 Score=44.68 Aligned_cols=58 Identities=19% Similarity=0.285 Sum_probs=40.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
...+|+|+.. ..||....-+.+-+-|+|.+.+.......-...++.||.|.+.|..-+
T Consensus 381 ~~v~G~V~~i---~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id 438 (491)
T PRK13806 381 TTVTGTVEKR---AQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEID 438 (491)
T ss_pred CEEEEEEEEE---ecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEe
Confidence 3467999886 457765555558899999999975421122456899999999876643
No 41
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=93.78 E-value=0.2 Score=36.72 Aligned_cols=44 Identities=27% Similarity=0.555 Sum_probs=35.1
Q ss_pred CCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 211 KSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 211 ~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.+|||||...+ +..||||+.+-++. ..|..||.|+=.+..-..+
T Consensus 9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr-------~~LR~GD~V~G~vr~p~~~ 57 (68)
T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRR-------FNLRTGDTVVGQIRPPKEG 57 (68)
T ss_pred CCCceEEecCCcCCCCCCCCEEECHHHHHH-------hCCCCCCEEEEEEeCCCCC
Confidence 34999999762 57899999999994 3589999999888764433
No 42
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=93.70 E-value=0.42 Score=36.52 Aligned_cols=73 Identities=22% Similarity=0.237 Sum_probs=48.5
Q ss_pred eeeeeEEEEEEcCCC-eeEEecCCCCccEEEEeccccc---cCCcccccCCCCCCEEEEEEEEcCCCceeeeeEeccee
Q psy547 199 TKVCGVVKWFSVKSG-YGFIATPSSNEDVFVHSKRIKY---NNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLKNIVL 273 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kG-fGFI~~~d~~~dVF~H~s~l~~---~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~~~~~ 273 (282)
..+.|+|+.. .+. ||.+..-+.+.+-|+|++++.. .....-...++.||.|...+..-+.+-.+..++.++.+
T Consensus 9 ~iy~g~V~~i--~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~~~ 85 (88)
T cd04453 9 NIYLGRVKKI--VPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNISL 85 (88)
T ss_pred CEEEEEEEEe--ccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEEEc
Confidence 5578999887 333 4665555557899999999853 00000123599999999999987666555556655543
No 43
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=93.61 E-value=0.13 Score=37.76 Aligned_cols=41 Identities=27% Similarity=0.530 Sum_probs=34.1
Q ss_pred CCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 44 KSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 44 ~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.+|||||... .+..||||+.+.++.. .|+.||.|+=.+...
T Consensus 9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~-------~LR~GD~V~G~vr~p 54 (68)
T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRF-------NLRTGDTVVGQIRPP 54 (68)
T ss_pred CCCceEEecCCcCCCCCCCCEEECHHHHHHh-------CCCCCCEEEEEEeCC
Confidence 3499999986 2678999999999875 579999999887753
No 44
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=92.36 E-value=2.3 Score=42.59 Aligned_cols=58 Identities=16% Similarity=0.168 Sum_probs=41.7
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..++|+|+.. ..||+....+.+-+-|+|++++.......--..++.||.|...|..-+
T Consensus 295 ~vv~G~V~~I---~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID 352 (486)
T PRK07899 295 QIVPGKVTKL---VPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDID 352 (486)
T ss_pred CEEEEEEEEE---eccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEE
Confidence 3467899877 449988877667899999999975321111234799999999987643
No 45
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=92.30 E-value=2.2 Score=42.64 Aligned_cols=57 Identities=21% Similarity=0.288 Sum_probs=40.0
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~ 258 (282)
..+.|+|+.. ..||.+...+.+-+.|+|++++..... ..-...++.||.|.+.+..-
T Consensus 294 ~~v~G~V~~v---~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~i 351 (491)
T PRK13806 294 DKVTGKVVRL---APFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDI 351 (491)
T ss_pred CEEEEEEEEE---eCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEE
Confidence 4467899887 348988776667899999999874210 00013489999999988753
No 46
>PRK11642 exoribonuclease R; Provisional
Probab=91.24 E-value=0.51 Score=50.06 Aligned_cols=47 Identities=26% Similarity=0.480 Sum_probs=38.1
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~ 257 (282)
.+.|+|+. ..+||||+.++++++|||++-..+. ..-.||+|...+..
T Consensus 84 ~~~G~v~~--~~~GfgFv~~e~~~~difI~~~~l~---------~A~~GD~V~v~i~~ 130 (813)
T PRK11642 84 LLKGTVIG--HRDGYGFLRVEGRKDDLYLSSEQMK---------TCIHGDQVLAQPLG 130 (813)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCEEEChHHHc---------cCCCCCEEEEEEcc
Confidence 35688874 3799999999876789999988777 35679999998765
No 47
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=90.75 E-value=5.4 Score=42.79 Aligned_cols=58 Identities=16% Similarity=0.238 Sum_probs=40.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
...+|+|+.. ..||.+..-..+-+-|+|.+++..... ...-..+++||.|.+.|..-+
T Consensus 667 ~~v~G~V~~i---~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID 725 (863)
T PRK12269 667 ARFTRRIVKV---TNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECD 725 (863)
T ss_pred CEEEEEEEEE---ecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEe
Confidence 4467999876 458887766668899999999863210 001125899999999887754
No 48
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=90.52 E-value=3.6 Score=44.13 Aligned_cols=58 Identities=19% Similarity=0.222 Sum_probs=41.0
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
...+|+|+... .||.+..-..+-+-|+|++++... ....-...++.||.|.+.|..-+
T Consensus 580 ~iV~G~V~~I~---~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD 638 (863)
T PRK12269 580 DVVKGRVTKIA---DFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYD 638 (863)
T ss_pred CEEEEEEEEEe---CCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEe
Confidence 44679998873 588777666678889999999741 10111234899999999887744
No 49
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=90.25 E-value=0.79 Score=47.47 Aligned_cols=47 Identities=30% Similarity=0.521 Sum_probs=37.7
Q ss_pred eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547 200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~ 257 (282)
...|+|+.= .+||||+.+++ +++|||+.-..+. ..-.||+|.+.+..
T Consensus 16 ~~~G~i~~~--~~gfgFv~~~~~~~~difI~~~~~~---------~a~~GD~V~v~i~~ 63 (654)
T TIGR00358 16 LVKGVVKAH--NKGFGFLRPDDDDKKDYFIPPPQMK---------KVMHGDLVEACPLS 63 (654)
T ss_pred eEEEEEEEC--CCccEEEEeCCCCCCcEEEchHHhC---------cCCCCCEEEEEEee
Confidence 356999863 79999999886 3689999988776 35689999999865
No 50
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=89.90 E-value=2.9 Score=42.37 Aligned_cols=142 Identities=19% Similarity=0.304 Sum_probs=88.0
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCCCCCcc
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGPDGRHV 108 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~~~~~~ 108 (282)
..-+.|+|+...+ ||-...-. +-|=++|+|.+..........-+++||.|...+-.-+ ++.....+..+...|
T Consensus 193 G~vV~G~V~~It~---~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dP- 267 (541)
T COG0539 193 GEVVEGVVKNITD---YGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDP- 267 (541)
T ss_pred CceEEEEEEEeec---CcEEEEec-CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCc-
Confidence 3447899999865 66444443 4899999999977532222356899999999876543 344444443222100
Q ss_pred ccccccCCCCccccccccccccccCCCcCCccccccccccccccccCCCCcceeeeeeeeccCCCCCccccCCCCCCCCC
Q psy547 109 QGSQFAANKPKYNRRKAKANKRKRKSRRNNRLFGVKYQLEIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASE 188 (282)
Q Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~ 188 (282)
| ....
T Consensus 268 ------------------------------------w-----~~i~---------------------------------- 272 (541)
T COG0539 268 ------------------------------------W-----EGIE---------------------------------- 272 (541)
T ss_pred ------------------------------------H-----HHHh----------------------------------
Confidence 0 0000
Q ss_pred CCCCCceeeeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 189 SPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 189 ~~~~~~~~~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
+......+..|+|..+ .-||.+..-..|-+=|+|+|++.-.....=-.-|+.||.|+..+..-+
T Consensus 273 ----~~~~~g~~v~G~Vt~i---~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id 336 (541)
T COG0539 273 ----KKYPVGDKVEGKVTNL---TDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDID 336 (541)
T ss_pred ----hhcCCCCEEEEEEEEe---ecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeC
Confidence 0000124567999887 458877777778899999998864321111133899999999877644
No 51
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=89.70 E-value=1.2 Score=32.01 Aligned_cols=60 Identities=17% Similarity=0.211 Sum_probs=44.0
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
..+.|+|...+. +|++..-+.+-+.|+|.+++...........+..||.|.+.+..-+..
T Consensus 6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~ 65 (74)
T PF00575_consen 6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKE 65 (74)
T ss_dssp SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETT
T ss_pred CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECC
Confidence 446799998865 776666567899999999998531111246799999999998875543
No 52
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=89.11 E-value=1.1 Score=46.40 Aligned_cols=53 Identities=23% Similarity=0.449 Sum_probs=39.2
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCce
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQ 263 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~ 263 (282)
....|+|+. ..+||||+..++ .+|||++-..+.. .-.||+|.+.+....+..+
T Consensus 17 ~~~~G~i~~--~~kGfgFv~~~~-~~difI~~~~l~~---------A~~GD~V~v~i~~~~~r~~ 69 (639)
T TIGR02062 17 PRVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---------VMHGDKIIAVIHSEKERES 69 (639)
T ss_pred ceEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---------CCCCCEEEEEEecCCCCcE
Confidence 445699975 379999997654 5699999988873 4579999998865433333
No 53
>PRK05054 exoribonuclease II; Provisional
Probab=89.11 E-value=1.1 Score=46.49 Aligned_cols=52 Identities=23% Similarity=0.436 Sum_probs=38.7
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCce
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQ 263 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~ 263 (282)
...|+|+. ..+||||+.+++ .+|||++-..+.. .-.||+|.+.+....++.+
T Consensus 21 ~~~G~~~~--~~~gfgFv~~~~-~~difI~~~~l~~---------a~~GD~V~v~i~~~~~r~~ 72 (644)
T PRK05054 21 RVEGVVKA--TEKGFGFLEVDA-QKSYFIPPPQMKK---------VMHGDRIIAVIHTEKDREI 72 (644)
T ss_pred eEEEEEEE--CCCccEEEEECC-CCcEEEChHHHcc---------CCCCCEEEEEEecCCCCcE
Confidence 45699975 379999998754 5699999888873 4579999999865433333
No 54
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=89.06 E-value=9 Score=38.20 Aligned_cols=57 Identities=14% Similarity=0.215 Sum_probs=40.3
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~ 258 (282)
...+|+|+.. ..||+...-+.+-+-|+|.+++..+....-...++.||.|.+.+..-
T Consensus 448 ~~v~g~V~~v---~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~i 504 (516)
T TIGR00717 448 SVVKGKVTEI---KDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDI 504 (516)
T ss_pred eEEEEEEEEE---ecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEE
Confidence 4467888875 34886655555789999999986542112245689999999988664
No 55
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=88.88 E-value=1.5 Score=29.65 Aligned_cols=56 Identities=16% Similarity=0.267 Sum_probs=38.3
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.|+|+..+ .+|+....+.+.+.|+|.+++...........++.||.|.+.+..-+.
T Consensus 2 ~g~V~~v~---~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 2 TGKVVSIT---KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred EEEEEEEE---eeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence 47888875 355555445578999999999743111112458999999999887543
No 56
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=88.72 E-value=1 Score=31.93 Aligned_cols=49 Identities=16% Similarity=0.287 Sum_probs=31.3
Q ss_pred eEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCc
Q psy547 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262 (282)
Q Consensus 203 G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~ 262 (282)
-+|+..+ .+|+.-..+.+.+||+|.+++. ..+++||.|+.=+-.+.++.
T Consensus 7 L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~D~~~r 55 (61)
T PF13509_consen 7 LKVVDKN---EFGYFLDDGEGKEVLLPKSEVP--------EPLKVGDEVEVFVYLDKEGR 55 (61)
T ss_dssp --EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS-
T ss_pred eEEEEEe---CCEEEEECCCCCEEEechHHcC--------CCCCCCCEEEEEEEECCCCC
Confidence 4565554 4777776776799999999997 35999999999999998883
No 57
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.70 E-value=2.5 Score=29.95 Aligned_cols=59 Identities=15% Similarity=0.179 Sum_probs=41.3
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.+.|+|+... .||.+..-.++-+-|+|.+++..+....-...++.||.|++.+..-++.
T Consensus 3 ~~~g~V~~v~---~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 3 KTHGTIVKVK---PNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred EEEEEEEEEe---cCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCC
Confidence 3568888874 3777666655789999999997432111123489999999999886543
No 58
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=88.57 E-value=1.5 Score=29.63 Aligned_cols=56 Identities=18% Similarity=0.209 Sum_probs=37.3
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
+.|+|+..+ +..-|+..+ .+.+.|+|.+.+...........++.||.|.+.+..-+
T Consensus 1 v~g~V~~v~--~~g~~v~l~-~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d 56 (65)
T cd00164 1 VTGKVVSIT--KFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVD 56 (65)
T ss_pred CEEEEEEEE--eeeEEEEec-CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEc
Confidence 368888886 222345544 46899999999875310001246899999999987643
No 59
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.52 E-value=2.3 Score=31.47 Aligned_cols=59 Identities=15% Similarity=0.120 Sum_probs=42.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
..+.|+|+... .||++..-..+-+.|+|.+++....-..-...++.||.|++.+..-+.
T Consensus 16 ~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 16 MVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 44678998874 488888776678999999999754211112448899999999887553
No 60
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=87.82 E-value=2.1 Score=30.99 Aligned_cols=55 Identities=15% Similarity=0.048 Sum_probs=37.9
Q ss_pred eEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 203 G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
|+|+... ..||.+..-..+-+-|+|++.+..+....-...++.||.|++.+..-+
T Consensus 7 g~V~~v~--~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id 61 (71)
T cd05696 7 VKVTKVE--PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYS 61 (71)
T ss_pred eEEEEEc--cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEe
Confidence 7787763 447776655447899999999964321112345999999999987544
No 61
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=87.42 E-value=11 Score=38.13 Aligned_cols=57 Identities=21% Similarity=0.299 Sum_probs=39.8
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~ 258 (282)
..+.|+|+... .||....-+.+-+.|+|++++..... ..-...++.||.|.+.+..-
T Consensus 375 ~~v~g~V~~v~---~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~v 432 (565)
T PRK06299 375 DVVEGKVKNIT---DFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV 432 (565)
T ss_pred CEEEEEEEEEe---cceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEE
Confidence 34678998863 57877766657899999999974310 11124578999999976554
No 62
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=87.22 E-value=3 Score=31.79 Aligned_cols=62 Identities=19% Similarity=0.221 Sum_probs=40.6
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccC---CCcccccCCCCCCEEEEEEEeCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN---NPRKLYKTLAEGETVEFDIMQGDK 93 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~---~~~~g~~~l~~Gd~V~f~v~~~~k 93 (282)
...+.|+|+-...--.=-||+-.+ +.+-|+|++++... ....--..+++||.|...+..-+.
T Consensus 8 G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~ 72 (88)
T cd04453 8 GNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPI 72 (88)
T ss_pred CCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecC
Confidence 456789999985432225666554 68999999998431 000002458999999999877443
No 63
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=86.13 E-value=14 Score=36.77 Aligned_cols=57 Identities=16% Similarity=0.317 Sum_probs=39.3
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcc-cccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRK-LYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~-g~~~l~~Gd~V~F~i~~~ 258 (282)
....|+|+.. ..||+...-+.+-+.|+|.+++....... -...++.||.|...+..-
T Consensus 361 ~~v~g~V~~v---~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~v 418 (516)
T TIGR00717 361 DRVTGKIKKI---TDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV 418 (516)
T ss_pred CEEEEEEEEE---ecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEE
Confidence 3456899875 45777776666899999999987431100 124588999999976554
No 64
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=85.85 E-value=2.2 Score=30.53 Aligned_cols=58 Identities=16% Similarity=0.205 Sum_probs=41.7
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|...+. +|++..-..+-+.|+|.+++...........+..|++|.+.+..-+
T Consensus 6 ~iv~g~V~~v~~---~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd 63 (74)
T PF00575_consen 6 DIVEGKVTSVED---FGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVD 63 (74)
T ss_dssp SEEEEEEEEEET---TEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEE
T ss_pred CEEEEEEEEEEC---CEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEE
Confidence 457899998876 5555554468899999999985300012468999999999986543
No 65
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.80 E-value=24 Score=33.82 Aligned_cols=58 Identities=19% Similarity=0.317 Sum_probs=39.6
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..++|+|+... .||+...-+.+-+-++|++++.......-...++.||.|...+..-+
T Consensus 279 ~~v~g~V~~i~---~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id 336 (390)
T PRK06676 279 DVIEGTVKRLT---DFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVN 336 (390)
T ss_pred cEEEEEEEEEe---CceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEE
Confidence 44678998864 48887765556788999999864311001134799999999877654
No 66
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=85.61 E-value=2.4 Score=44.31 Aligned_cols=48 Identities=23% Similarity=0.477 Sum_probs=37.9
Q ss_pred eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547 200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~ 258 (282)
.+.|+++. ..+||||+.+++ ...|||+....+. ....||+|.+.+...
T Consensus 68 ~~~G~i~~--~~~g~gFv~~~~~~~~di~I~~~~~~---------~a~~GD~Vlv~I~~~ 116 (709)
T TIGR02063 68 LVKGTVIA--HRDGFGFLRPEDDDEDDIFIPPRQMN---------GAMHGDRVLVRITGK 116 (709)
T ss_pred eEEEEEEE--CCCccEEEEECCCCCCcEEEChHHhC---------cCCCCCEEEEEEecc
Confidence 35688875 478999999876 4679999877665 367899999998764
No 67
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=85.59 E-value=4.6 Score=29.85 Aligned_cols=58 Identities=16% Similarity=0.115 Sum_probs=41.2
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|+-.. -||++..-.++-+.|+|.+.+....-..-...++.||.|++.+..-+
T Consensus 16 ~i~~g~V~~v~---~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 16 MVVHGYVRNIT---PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CEEEEEEEEEe---eceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEc
Confidence 45788988775 37777665557899999999965421111245889999999987654
No 68
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=85.45 E-value=20 Score=33.31 Aligned_cols=49 Identities=14% Similarity=0.201 Sum_probs=35.9
Q ss_pred CCCeeEEecCCCCccEEEEeccccccCCcccccC--CCCCCEEEEEEEEcCCCceee
Q psy547 211 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT--LAEGETVEFDIMQGDKGNQFC 265 (282)
Q Consensus 211 ~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~--l~~Gd~V~F~i~~~~kG~~A~ 265 (282)
.+.-|--...+-.+|++|..+++.. +.+ ++.||++.+.+..+.+|.-..
T Consensus 85 ~~~lGaFlD~Gl~KDl~vp~~elp~------~~~~wpq~Gd~l~v~l~~Dkk~Ri~g 135 (287)
T COG2996 85 NKDLGAFLDWGLPKDLLVPLDELPT------LKSLWPQKGDKLLVYLYVDKKGRIWG 135 (287)
T ss_pred cCCcceEEecCCCcceeeehhhccc------ccccCCCCCCEEEEEEEEccCCcEEE
Confidence 3444443434446899999999984 234 899999999999999994443
No 69
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=85.27 E-value=4.3 Score=28.73 Aligned_cols=58 Identities=16% Similarity=0.185 Sum_probs=38.8
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 93 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k 93 (282)
.+.|+|+-... ||.+..-.++-+-|+|.+.|..+.-..-...++.||.|++.+..-+.
T Consensus 3 ~~~g~V~~v~~---~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 3 KTHGTIVKVKP---NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred EEEEEEEEEec---CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcC
Confidence 46788888843 45554444468999999999643100012348999999999877544
No 70
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=85.24 E-value=6.3 Score=28.14 Aligned_cols=59 Identities=8% Similarity=-0.048 Sum_probs=40.7
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
....|+|+... .+|.+..-+.+-+-|+|.+++..+....-...+..||.|.+.+..-+.
T Consensus 5 ~iv~g~V~~v~---~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 5 DILPGRVTKVN---DRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CEEEEEEEEEe---CCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeC
Confidence 34568888863 366666555578999999999754211112347999999999877553
No 71
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=85.12 E-value=4 Score=28.22 Aligned_cols=56 Identities=21% Similarity=0.338 Sum_probs=39.2
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
+.|+|.... .||+...-+.+.+.|+|.+++.......-...++.||.|...+..-+
T Consensus 4 ~~g~V~~i~---~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 4 VEGTVTRLK---PFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred EEEEEEEEE---eeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 568887764 37877776667899999999974321000134799999999886644
No 72
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=84.54 E-value=18 Score=37.42 Aligned_cols=58 Identities=28% Similarity=0.365 Sum_probs=40.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..++|+|+... .||+...-+.+-+-|+|.+++.......--..++.||.|...+..-+
T Consensus 564 ~~v~g~V~~i~---~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id 621 (647)
T PRK00087 564 SIVLGKVVRIA---PFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD 621 (647)
T ss_pred eEEEEEEEEEE---CCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEe
Confidence 34678998874 37877765667899999999975321111235799999999887654
No 73
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=84.50 E-value=5.4 Score=28.87 Aligned_cols=61 Identities=13% Similarity=0.132 Sum_probs=42.5
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
..+.|+|+... .-||.+..-..+.+-++|++++.+.....-...++.||.|...+..-.+|
T Consensus 5 ~iv~G~V~~i~--~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~ 65 (72)
T cd05704 5 AVTLGMVTKVI--PHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG 65 (72)
T ss_pred CEEEEEEEEee--CCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence 34578888863 23676666666899999999997542111123478899999998887654
No 74
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=84.37 E-value=5.6 Score=28.18 Aligned_cols=57 Identities=14% Similarity=0.160 Sum_probs=41.1
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
+.|+|+..+ .||.+..-+.+-+-|+|++++.......-...++.||.|.+.+..-+.
T Consensus 4 v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 4 VKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred EEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 568888874 478777666678999999999754211112358999999999887654
No 75
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=84.36 E-value=6.8 Score=27.16 Aligned_cols=57 Identities=19% Similarity=0.261 Sum_probs=40.5
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
+.|+|..... ||+...-..+.+-|+|.+++.......-...++.||.|...+..-+.
T Consensus 4 ~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 4 YEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred EEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC
Confidence 5688877753 89888766678999999999743211011347999999999877553
No 76
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=84.25 E-value=5.6 Score=27.27 Aligned_cols=58 Identities=14% Similarity=0.225 Sum_probs=40.7
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+.|+|...+. +|++...+.+-..|+|.+++...........++.||.|.+.+..-+.
T Consensus 5 ~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 5 VVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred EEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 45689988864 56666555578899999999853111112348999999999887654
No 77
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=84.19 E-value=5.1 Score=28.34 Aligned_cols=58 Identities=17% Similarity=0.224 Sum_probs=40.8
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
+.|+|+... .+|.+..-..+-+-|+|.+++..+....-...++.||.|++.+..-+..
T Consensus 4 v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~ 61 (73)
T cd05691 4 VTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRK 61 (73)
T ss_pred EEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCC
Confidence 468888873 4777776655789999999997542111123479999999998886543
No 78
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=83.99 E-value=4 Score=29.50 Aligned_cols=53 Identities=15% Similarity=0.069 Sum_probs=34.8
Q ss_pred eEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 36 G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
|+|+.-...+| -|++..+ +-+-|+|+|.|....-..-...++.|+.|++.+..
T Consensus 7 g~V~~v~~~~G-~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~ 59 (71)
T cd05696 7 VKVTKVEPDLG-AVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIG 59 (71)
T ss_pred eEEEEEccCce-EEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEE
Confidence 78888643333 3455545 58999999999643100113459999999999754
No 79
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.98 E-value=18 Score=36.55 Aligned_cols=58 Identities=16% Similarity=0.207 Sum_probs=39.1
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
....|+|+.... ||.....+.+-.-|+|.+++.......-...+..||.|...+..-+
T Consensus 462 ~vV~G~V~~v~~---~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd 519 (565)
T PRK06299 462 SIVTGTVTEVKD---KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519 (565)
T ss_pred CEEEEEEEEEec---CceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEc
Confidence 345689988753 4644433447789999999964422223456899999999877643
No 80
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=83.38 E-value=16 Score=38.26 Aligned_cols=47 Identities=23% Similarity=0.521 Sum_probs=37.4
Q ss_pred eeeeEEEEeeCCCceEEEeCCC--CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 33 KVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d--~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.|++.+= .+||||+.+++ ...|+|+-...+... ..||.|..++..
T Consensus 69 ~~~~~~~~~--~~gf~f~~~~~~~~~~d~~v~~~~~~~a---------~~gD~V~v~~~~ 117 (706)
T COG0557 69 LVEGIVEAS--AKGFGFLSPDDSKDADDIFVPKDPLNRA---------LHGDRVLVELLP 117 (706)
T ss_pred cccceEEec--cCCceeeccCccCCCCcEEecccccccc---------ccCCEEEEEECc
Confidence 356777665 89999999998 678999998886554 689999998633
No 81
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=82.73 E-value=8.5 Score=27.81 Aligned_cols=61 Identities=13% Similarity=0.131 Sum_probs=40.8
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
+.+.|+|+--... ||.+..-..+.+-|+|+|.+...--..-...+++||.|...+..-+++
T Consensus 5 ~iv~G~V~~i~~~--~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~~ 65 (72)
T cd05704 5 AVTLGMVTKVIPH--SGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDG 65 (72)
T ss_pred CEEEEEEEEeeCC--cEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecCC
Confidence 4468899886433 455555555789999999996641100013468899999998776654
No 82
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=82.35 E-value=9 Score=27.21 Aligned_cols=57 Identities=19% Similarity=0.345 Sum_probs=40.6
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+.|+|+.. +.||+...-+.+.+-|+|++++... ........++.||.|...+..-+
T Consensus 6 ~~~g~V~~i---~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 6 RLFGKVTNL---TDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred EEEEEEEEE---EeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence 467888886 4489888766678999999999632 10111244789999999887754
No 83
>PRK08582 hypothetical protein; Provisional
Probab=81.33 E-value=5.9 Score=32.89 Aligned_cols=58 Identities=19% Similarity=0.337 Sum_probs=42.0
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..+.|+|+.. ..||+....+.+.+-++|++++....-..-...+..||.|...|..-.
T Consensus 7 ~iv~G~V~~I---~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id 64 (139)
T PRK08582 7 SKLQGKVTGI---TNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE 64 (139)
T ss_pred CEEEEEEEEE---ECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC
Confidence 3467888875 448888777768899999999975421111245899999999887754
No 84
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=81.24 E-value=6.3 Score=28.46 Aligned_cols=59 Identities=15% Similarity=0.184 Sum_probs=39.8
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCC-CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~-~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
..+.|+|+... .||....-++ ..+-|+|++++.......-...++.||+|...+..-+.
T Consensus 5 ~~~~g~V~~i~---~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 5 QIFKGEVASVT---EYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM 64 (73)
T ss_pred CEEEEEEEEEE---eeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECC
Confidence 34678888874 4887776543 36899999999754211111226889999998877543
No 85
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=81.19 E-value=8.1 Score=27.55 Aligned_cols=58 Identities=9% Similarity=-0.056 Sum_probs=38.3
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|+-... ||.+..-+.+-+.|+|.++|..+....-...++.||.|++.+..-+
T Consensus 5 ~iv~g~V~~v~~---~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d 62 (73)
T cd05706 5 DILPGRVTKVND---RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVD 62 (73)
T ss_pred CEEEEEEEEEeC---CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEe
Confidence 346888888633 4444444446899999999975421101244799999999987644
No 86
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=81.12 E-value=5.6 Score=27.92 Aligned_cols=56 Identities=23% Similarity=0.360 Sum_probs=39.5
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc-CCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN-NPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~-~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
+.|+|+.. +.||+...-+.+.+-++|++++... ..+.-...++.||.|...+..-+
T Consensus 4 ~~g~V~~i---~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id 60 (69)
T cd05690 4 VSGKIKSI---TDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60 (69)
T ss_pred EEEEEEEE---EeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEE
Confidence 56888876 3588887766678999999999731 10111234799999999887644
No 87
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=80.98 E-value=9.4 Score=26.97 Aligned_cols=58 Identities=14% Similarity=0.147 Sum_probs=39.8
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 93 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k 93 (282)
.+.|+|+-.+ .||.+..-+.+-+-|+|.+.+.......-...++.||.|.+.+..-+.
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 3 VVKGTIRKLR---PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred EEEEEEEEEe---ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEEC
Confidence 3678888874 356665555568999999999654111012458999999999876543
No 88
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=80.74 E-value=7.1 Score=28.58 Aligned_cols=49 Identities=14% Similarity=0.222 Sum_probs=39.4
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~ 258 (282)
..+.|+|... ..||+...-+.+.+-|+|.+++. ..++.||.|...+..-
T Consensus 18 ~~~~g~V~~i---~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 18 KLYKGKVNGV---AKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CEEEEEEEeE---ecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence 4567888876 45888887776789999999986 3589999999887664
No 89
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=80.52 E-value=7.2 Score=26.84 Aligned_cols=57 Identities=21% Similarity=0.321 Sum_probs=38.1
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+-... ||+...-+.+.+.|+|.+.+.......-...++.||.|...+..-+
T Consensus 3 ~~~g~V~~i~~---~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~ 59 (69)
T cd05692 3 VVEGTVTRLKP---FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59 (69)
T ss_pred EEEEEEEEEEe---eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEEC
Confidence 35788887653 6666655556899999999965310000145799999999875543
No 90
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=80.48 E-value=25 Score=33.24 Aligned_cols=57 Identities=16% Similarity=0.187 Sum_probs=41.1
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+.|+|+.. +.||...... +-+-|+|++++.......-...++.||.|.+.+..-+.
T Consensus 199 vv~G~V~~I---~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~ 255 (318)
T PRK07400 199 VVVGTVRGI---KPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDA 255 (318)
T ss_pred EEEEEEEEE---ECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeC
Confidence 456899887 4588877654 67899999999854322223458999999999877553
No 91
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=80.45 E-value=5.9 Score=27.17 Aligned_cols=58 Identities=14% Similarity=0.219 Sum_probs=39.3
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|+-.+. +|++..-+.+-..|+|.+.+...........++.||.|.+.+..-.
T Consensus 4 ~~v~g~V~~v~~---~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 4 DVVEGTVTEITP---FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61 (72)
T ss_pred CEEEEEEEEEEc---cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEe
Confidence 346889998865 4444444446789999999976411111245899999999987644
No 92
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=80.33 E-value=3.3 Score=28.53 Aligned_cols=40 Identities=25% Similarity=0.331 Sum_probs=30.6
Q ss_pred cCCCCCCEEEEEEEEcCCCc-ee--eeeEecceeeeeeeecCC
Q psy547 243 KTLAEGETVEFDIMQGDKGN-QF--CFVLKNIVLYFSFVPQSV 282 (282)
Q Consensus 243 ~~l~~Gd~V~F~i~~~~kG~-~A--~~V~~~~~~~~~~~~~~~ 282 (282)
..+.+||.|+|.|.-...|. .| +.|.-.+.--+.|+|.|+
T Consensus 6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~~v~~S~ 48 (53)
T TIGR01451 6 TVATIGDTITYTITVTNNGNVPATNVVVTDILPSGTTFVSNSV 48 (53)
T ss_pred cccCCCCEEEEEEEEEECCCCceEeEEEEEcCCCCCEEEeCcE
Confidence 46899999999999988883 33 345567777888888763
No 93
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=80.08 E-value=6.1 Score=27.87 Aligned_cols=57 Identities=23% Similarity=0.215 Sum_probs=39.6
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
+.|+|+... .||.+..-..+-+-|+|++++....-..-...+..||.|++.+..-+.
T Consensus 4 v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 4 VRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred EEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeC
Confidence 568888863 477666555578999999999643211112348999999999876553
No 94
>PRK08582 hypothetical protein; Provisional
Probab=79.62 E-value=18 Score=30.05 Aligned_cols=70 Identities=17% Similarity=0.337 Sum_probs=46.4
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC-CCceEEEEeCCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD-KGHEAINVTGPD 104 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~-kG~~A~~V~~~~ 104 (282)
..+.|+|+-. ..||+...-+.+.+-++|++.|....-..-...+..||.|.+.|..-+ .|.....+..+.
T Consensus 7 ~iv~G~V~~I---~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~ 77 (139)
T PRK08582 7 SKLQGKVTGI---TNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAK 77 (139)
T ss_pred CEEEEEEEEE---ECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 3478888875 346766665557899999999975310000145899999999987643 465555555443
No 95
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=79.59 E-value=17 Score=25.81 Aligned_cols=57 Identities=21% Similarity=0.364 Sum_probs=38.9
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCC-cccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~-~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+... -||+...-+.+.+-|+|++.|..... ......++.||.|+..+..-+
T Consensus 6 ~~~g~V~~i~---~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id 63 (72)
T cd05689 6 RLFGKVTNLT---DYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID 63 (72)
T ss_pred EEEEEEEEEE---eeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEee
Confidence 4788888864 47877665556899999999963210 011245789999999876543
No 96
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=79.14 E-value=9.4 Score=26.40 Aligned_cols=57 Identities=19% Similarity=0.246 Sum_probs=39.2
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|.-... ||+...-....+-|+|.+.+....-..-...++.||.|...+..-+
T Consensus 3 ~~~g~V~~v~~---~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 3 IYEGKVVKIKD---FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD 59 (68)
T ss_pred EEEEEEEEEEE---eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEEC
Confidence 35777877754 7877765556899999999975410000135799999999876644
No 97
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=78.47 E-value=8.8 Score=28.05 Aligned_cols=59 Identities=17% Similarity=0.076 Sum_probs=40.4
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcc---cccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRK---LYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~---g~~~l~~Gd~V~F~i~~~~k 260 (282)
....|+|+... .||....-+.+-+-|+|++++....... -...++.||.|.+.+..-++
T Consensus 5 ~~V~g~V~~i~---~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 5 QLLRGYVSSVT---KQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CEEEEEEEEEe---CCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEEC
Confidence 34679998874 4555444445889999999998642111 12457999999999887653
No 98
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=78.17 E-value=9.2 Score=27.01 Aligned_cols=57 Identities=11% Similarity=0.069 Sum_probs=38.2
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.++|+|...+. ..=||.- ..+.+-|+|.+++...........+++||.|++.+..-+
T Consensus 3 iv~g~V~~i~~--~~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 3 IVKGTVVSVDD--DEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59 (70)
T ss_pred EEEEEEEEEeC--CEEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEE
Confidence 35689988743 2344444 446789999999975421111235899999999988744
No 99
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=77.68 E-value=12 Score=26.45 Aligned_cols=58 Identities=17% Similarity=0.219 Sum_probs=39.0
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 93 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~k 93 (282)
.+.|+|+-.. .+|.+..-..+-+-|+|.+.+.....+.-...++.||.|++.+..-+.
T Consensus 3 ~v~g~V~~v~---~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 3 IVTGKVTEVD---AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60 (73)
T ss_pred EEEEEEEEEE---CCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeC
Confidence 3678888874 355555544467999999998764211112347999999999877544
No 100
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=77.68 E-value=8.7 Score=27.73 Aligned_cols=58 Identities=16% Similarity=0.189 Sum_probs=38.0
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCC-CCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~-~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|+.... ||....-++ ..+-|+|++.+.......-...++.||+|...+..-+
T Consensus 5 ~~~~g~V~~i~~---fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd 63 (73)
T cd05686 5 QIFKGEVASVTE---YGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE 63 (73)
T ss_pred CEEEEEEEEEEe---eeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEEC
Confidence 346888888853 776655543 3689999999966421000123688999999876543
No 101
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=76.26 E-value=14 Score=26.38 Aligned_cols=59 Identities=17% Similarity=0.160 Sum_probs=39.8
Q ss_pred eeeeeEEEEEEcCCCeeEEecCC--CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d--~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
..+.|+|... +.||.+..-. .+.+-|+|.+++.......-...+..||.|...+..-+.
T Consensus 5 ~~~~g~V~~v---~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 5 ELVVVTVKSI---ADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred CEEEEEEEEE---EccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence 3457888876 3588776543 257899999999754211112337999999998876543
No 102
>PRK07252 hypothetical protein; Provisional
Probab=76.19 E-value=10 Score=30.62 Aligned_cols=58 Identities=21% Similarity=0.277 Sum_probs=42.2
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+.|+|.... .||++..-+.+.+-|+|++++....-..-...+..||.|...+..-+.
T Consensus 6 iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 6 KLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred EEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeC
Confidence 4678888874 488888777678999999999743211112347999999999888653
No 103
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=76.03 E-value=15 Score=26.84 Aligned_cols=52 Identities=15% Similarity=0.154 Sum_probs=39.8
Q ss_pred eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.++|+|+... .||++..-+ .+-+-|+|.+++... ..+.+||.|...+..-++
T Consensus 7 ~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 7 VLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred EEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEEC
Confidence 4679999873 588876654 466899999999842 569999999999875443
No 104
>PRK12608 transcription termination factor Rho; Provisional
Probab=75.78 E-value=8.2 Score=37.50 Aligned_cols=66 Identities=27% Similarity=0.453 Sum_probs=47.3
Q ss_pred eeeeEEEEeeCCCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEeCCCCCc
Q psy547 33 KVCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRH 107 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~~~~~~~ 107 (282)
...|.+.-.+ +||||+... .+..||||..+.++.. .|+.|+.|.-......+-..--.|..+.+.|
T Consensus 18 ~~~g~l~~~~--~g~gflr~~~~~~~~~~~d~yv~~~~i~~~-------~l~~Gd~V~~~~r~~~~~~~LgrV~~~~G~p 88 (380)
T PRK12608 18 EVLGVLEILG--DGFGFLRSARRNYLPSPDDVFVPPALIRRF-------NLRTGDVVEGVARPRERYRVLVRVDSVNGTD 88 (380)
T ss_pred cceEEEEEcC--CCceEeecCccCCCCCCCCeeeCHHHHHHh-------CCCCCCEEEeccCCCCChhheEEEeccCCcC
Confidence 3578887664 599999985 3678999999999874 6799999999876633223334555555544
No 105
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=75.44 E-value=30 Score=35.21 Aligned_cols=58 Identities=22% Similarity=0.359 Sum_probs=39.8
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
...+|.|+.. ..||-+.-.+++-|=|+|.+++....+..-...++.|+.|+..+..-+
T Consensus 365 ~~v~g~v~~~---t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd 422 (541)
T COG0539 365 DVVEGKVKSI---TDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVD 422 (541)
T ss_pred CeEEEEEeee---cccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEe
Confidence 4567899876 457766655667999999999975421111125699999999776644
No 106
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=74.98 E-value=12 Score=26.33 Aligned_cols=56 Identities=11% Similarity=0.054 Sum_probs=38.3
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.+.|+|+..+. ..-||.- ....+-|+|.+.+...........+++||.|++.+..-
T Consensus 3 iv~g~V~~i~~--~~~~v~l-~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~ 58 (70)
T cd05687 3 IVKGTVVSVDD--DEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV 58 (70)
T ss_pred EEEEEEEEEeC--CEEEEEe-CCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE
Confidence 46899999854 2456665 34678999999996531111124589999999998763
No 107
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=74.86 E-value=12 Score=26.08 Aligned_cols=56 Identities=21% Similarity=0.323 Sum_probs=37.6
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeecccc-CCCcccccCCCCCCEEEEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKY-NNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~-~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.+.|+|+... -||+...-+.+.+-++|+++|.. ...+.-...++.||.|...+..-
T Consensus 3 ~~~g~V~~i~---~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i 59 (69)
T cd05690 3 VVSGKIKSIT---DFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI 59 (69)
T ss_pred EEEEEEEEEE---eeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE
Confidence 3678888764 47777665557899999999963 11000023579999999987553
No 108
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=74.42 E-value=6.5 Score=27.78 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=29.6
Q ss_pred eeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 35 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 35 ~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
+-+|+..+ .+|+.-..+...+||+|.+.+.. .+.+||.|+.=+-.+.++
T Consensus 6 ~L~V~~~~---~~g~fL~~~~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~D~~~ 54 (61)
T PF13509_consen 6 TLKVVDKN---EFGYFLDDGEGKEVLLPKSEVPE--------PLKVGDEVEVFVYLDKEG 54 (61)
T ss_dssp ---EEEE----SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE-TTS
T ss_pred ceEEEEEe---CCEEEEECCCCCEEEechHHcCC--------CCCCCCEEEEEEEECCCC
Confidence 45666665 35666656666899999998853 479999999888888777
No 109
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=74.05 E-value=11 Score=27.49 Aligned_cols=57 Identities=18% Similarity=0.061 Sum_probs=38.7
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccC--CcccccCCCCCCEEEEEEEEcCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN--PRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~--~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+|+|+... .+|.......+-+-|+|++++.... ...-...++.||.|++.+..-++
T Consensus 4 V~g~V~~i~---~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 4 VTGFVNNVS---KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDK 62 (73)
T ss_pred EEEEEEEEe---CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeC
Confidence 568998873 3555444444689999999996431 11123458999999999877543
No 110
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=74.05 E-value=13 Score=25.56 Aligned_cols=56 Identities=18% Similarity=0.290 Sum_probs=38.6
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
+.|+|.... .||....-..+.+-|+|.+++.......-...++.||.|...+..-+
T Consensus 4 ~~g~V~~i~---~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 4 LEGVVTNVT---DFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred EEEEEEEEe---cccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEE
Confidence 568887764 47766665667899999999974321100123799999999887754
No 111
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=73.49 E-value=13 Score=27.21 Aligned_cols=57 Identities=21% Similarity=0.168 Sum_probs=38.2
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC---CcccccCCCCCCEEEEEEEeC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN---PRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~---~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
..+.|+|+... ..| =|+... .+-+-|+|++++.... +..-...+++|+.|++.+..-
T Consensus 5 ~~V~g~V~~i~-~~G-~fV~l~-~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~i 64 (74)
T cd05705 5 QLLRGYVSSVT-KQG-VFFRLS-SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSV 64 (74)
T ss_pred CEEEEEEEEEe-CCc-EEEEeC-CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEE
Confidence 45789999974 222 455554 4789999999987642 100014579999999997654
No 112
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=73.38 E-value=20 Score=26.06 Aligned_cols=58 Identities=14% Similarity=0.307 Sum_probs=39.1
Q ss_pred eeeEEEEEEcCCCeeEEecCC---CCccEEEEeccccccCC-cccccCCCCCCEEEEEEEEcCCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPS---SNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d---~~~dVF~H~s~l~~~~~-r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
+.|+|.... .||+...-+ .+.+-|+|++++..... ..-...++.||+|...+..-+++
T Consensus 4 ~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~ 65 (79)
T cd05684 4 YKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG 65 (79)
T ss_pred EEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCC
Confidence 457887763 478777554 36789999999974321 01113469999999998876633
No 113
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=73.20 E-value=3.6 Score=40.91 Aligned_cols=55 Identities=24% Similarity=0.446 Sum_probs=40.6
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceE
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEA 97 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A 97 (282)
..++.|+||.= +|||||+++|. .+..|+.--.. ..+..||+|.-.+......-+|
T Consensus 19 ~prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~M---------KkvMHGDkIiA~i~te~erE~a 73 (645)
T COG4776 19 TPRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQM---------KKVMHGDKIIAVIHTEKERESA 73 (645)
T ss_pred Ccccceeeeec--cccceeEEEcC-ccccccCCHHH---------hhhcccCeEEEEEEecCccccc
Confidence 45689999975 99999999975 56777654444 4568999999888766544333
No 114
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=71.60 E-value=11 Score=36.90 Aligned_cols=64 Identities=27% Similarity=0.496 Sum_probs=48.1
Q ss_pred eeeeEEEEeeCCCceEEEeCCC-----CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC---CCCceEEEEeCCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG---DKGHEAINVTGPD 104 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d-----~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~---~kG~~A~~V~~~~ 104 (282)
...|.+.-.. .||||+...+ +..||||..+.++.. .|+.||.|+=.+..- ++...-..|..++
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~y~~~~~d~yvs~~~ir~~-------~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vn 120 (416)
T PRK09376 50 FGEGVLEILP--DGFGFLRSPDANYLPGPDDIYVSPSQIRRF-------NLRTGDTVEGKIRPPKEGERYFALLKVETVN 120 (416)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-------CCCCCCEEEEEeeCCCCCCCccceEEEeeeC
Confidence 4577776553 4999999853 568999999999874 579999999988764 3335556777766
Q ss_pred C
Q psy547 105 G 105 (282)
Q Consensus 105 ~ 105 (282)
+
T Consensus 121 g 121 (416)
T PRK09376 121 G 121 (416)
T ss_pred C
Confidence 5
No 115
>PRK05807 hypothetical protein; Provisional
Probab=71.34 E-value=14 Score=30.53 Aligned_cols=57 Identities=16% Similarity=0.268 Sum_probs=40.1
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..+.|+|.... .||+....+ +..-++|++++.......-...+..||.|...|..-.
T Consensus 7 ~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id 63 (136)
T PRK05807 7 SILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID 63 (136)
T ss_pred CEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEEC
Confidence 45678888763 478777664 5789999999974322111245799999999977644
No 116
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=71.22 E-value=15 Score=25.80 Aligned_cols=57 Identities=23% Similarity=0.209 Sum_probs=37.3
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+-.. .||.+..-..+-+-|+|.+.+....-..-...++.||.|++.+..-+
T Consensus 3 ~v~g~V~~v~---~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d 59 (68)
T cd05707 3 VVRGFVKNIA---NNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSID 59 (68)
T ss_pred EEEEEEEEEE---CccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEe
Confidence 3678888874 34554444446899999999965310001234899999999876543
No 117
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=70.69 E-value=31 Score=24.96 Aligned_cols=65 Identities=12% Similarity=0.297 Sum_probs=41.0
Q ss_pred eeeEEEEeeCCCceEEEeCCC---CCCcEEEEeeccccCCC-cccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547 34 VCGVVKWFSVKSGYGFIATPS---SNEDVFVHSKRIKYNNP-RKLYKTLAEGETVEFDIMQGDKGHEAINVT 101 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d---~~~dvF~H~s~l~~~~~-~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~ 101 (282)
+.|+|+-.. -||+...-+ .+.+-|+|++.+..... ..-...++.||+|...+..-+++.....+.
T Consensus 4 ~~g~V~~v~---~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd~~~i~~s~k 72 (79)
T cd05684 4 YKGKVTSIM---DFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMK 72 (79)
T ss_pred EEEEEEEEE---eeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEeCCEEEEEEE
Confidence 567777664 356555544 25789999999965410 000134699999999987755554444444
No 118
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=70.05 E-value=24 Score=34.64 Aligned_cols=82 Identities=18% Similarity=0.277 Sum_probs=53.2
Q ss_pred eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccC---C--------cc-cccCCCCCCEEEEEEEEcCCCceee
Q psy547 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN---P--------RK-LYKTLAEGETVEFDIMQGDKGNQFC 265 (282)
Q Consensus 198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~---~--------r~-g~~~l~~Gd~V~F~i~~~~kG~~A~ 265 (282)
..-+.|+|+...+.-.--||.-.. ++.-|+|++++.... + .. -...|++||.|..+|...+.|....
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp 104 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGA 104 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCC
Confidence 466889999886544478888755 789999999985210 0 00 0013899999999999977554444
Q ss_pred eeEecce---eeeeeeec
Q psy547 266 FVLKNIV---LYFSFVPQ 280 (282)
Q Consensus 266 ~V~~~~~---~~~~~~~~ 280 (282)
.++.+|- =|..|+|.
T Consensus 105 ~lT~~Isl~GrylVl~P~ 122 (414)
T TIGR00757 105 RLTTDISLPGRYLVLMPN 122 (414)
T ss_pred eEEEEEEeccceEEEecC
Confidence 4444433 34445553
No 119
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=69.47 E-value=14 Score=26.79 Aligned_cols=56 Identities=11% Similarity=0.127 Sum_probs=37.7
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC--CcccccCCCCCCEEEEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN--PRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~--~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.+.|+|+... ...=||+..+ +-+-|+|+++|.... ...-...+++||.|++.+..-
T Consensus 3 ~V~g~V~~i~--~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~i 60 (73)
T cd05703 3 EVTGFVNNVS--KEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGV 60 (73)
T ss_pred EEEEEEEEEe--CCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEE
Confidence 4689999884 2224566544 589999999996420 011135689999999997653
No 120
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=69.31 E-value=10 Score=37.23 Aligned_cols=52 Identities=31% Similarity=0.593 Sum_probs=40.0
Q ss_pred eeeEEEEEEcCCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
..|++--. ..||||+...+ +..||||..+.++. ..|..||.|+=.+..-..+
T Consensus 51 ~~g~le~~--~~g~gflr~~~~~y~~~~~d~yvs~~~ir~-------~~lr~gd~v~g~~r~~~~~ 107 (416)
T PRK09376 51 GEGVLEIL--PDGFGFLRSPDANYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKIRPPKEG 107 (416)
T ss_pred EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEeeCCCCC
Confidence 45777655 35999999853 35899999999994 3589999999888775444
No 121
>PRK12608 transcription termination factor Rho; Provisional
Probab=68.99 E-value=5.6 Score=38.64 Aligned_cols=48 Identities=33% Similarity=0.517 Sum_probs=37.8
Q ss_pred eeeEEEEEEcCCCeeEEecC-----CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547 201 VCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~-----d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~ 257 (282)
..|++--. .+||||+... .+..||||..+.++. ..|..|+.|.-....
T Consensus 19 ~~g~l~~~--~~g~gflr~~~~~~~~~~~d~yv~~~~i~~-------~~l~~Gd~V~~~~r~ 71 (380)
T PRK12608 19 VLGVLEIL--GDGFGFLRSARRNYLPSPDDVFVPPALIRR-------FNLRTGDVVEGVARP 71 (380)
T ss_pred ceEEEEEc--CCCceEeecCccCCCCCCCCeeeCHHHHHH-------hCCCCCCEEEeccCC
Confidence 45777765 3599999985 357899999999994 458999999887654
No 122
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=68.43 E-value=24 Score=25.05 Aligned_cols=56 Identities=13% Similarity=0.131 Sum_probs=38.0
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc--CCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN--NPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~--~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
+.|+|+.... +|.+...+.+-+-++|++++... ....-...+++||.|...+..-+
T Consensus 4 V~g~V~~i~~---~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 4 VKAKVKSVKP---TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGH 61 (70)
T ss_pred EEEEEEEEEC---CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEe
Confidence 5688888743 45555445578999999999743 11111244899999999887654
No 123
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=67.38 E-value=26 Score=25.54 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=37.7
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.....|+|.-.. -||+...-+.+.+-|+|.+.+. ..++.||+|...+..-
T Consensus 17 G~~~~g~V~~i~---~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 17 GKLYKGKVNGVA---KYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CCEEEEEEEeEe---cceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE
Confidence 345788888753 4777777666689999999974 4589999999887553
No 124
>PRK07252 hypothetical protein; Provisional
Probab=66.93 E-value=20 Score=28.97 Aligned_cols=68 Identities=19% Similarity=0.281 Sum_probs=44.6
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGP 103 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~ 103 (282)
.+.|+|.-.. -||++..-+.+.+-|+|++.|....-..-...+..||.|...+..-+ ++........+
T Consensus 6 iv~G~V~~V~---~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~ 75 (120)
T PRK07252 6 KLKGTITGIK---PYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL 75 (120)
T ss_pred EEEEEEEEEe---CcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 4678888875 37777766656899999999965310000245799999999987754 34333444433
No 125
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=66.40 E-value=10 Score=27.64 Aligned_cols=27 Identities=22% Similarity=0.374 Sum_probs=21.5
Q ss_pred ccCCCCCCEEEEEEEeCCCC-ceEEEEe
Q psy547 75 YKTLAEGETVEFDIMQGDKG-HEAINVT 101 (282)
Q Consensus 75 ~~~l~~Gd~V~f~v~~~~kG-~~A~~V~ 101 (282)
+..|++||.|.|.+...+.+ +....+.
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 67899999999999999998 7776665
No 126
>COG1158 Rho Transcription termination factor [Transcription]
Probab=65.56 E-value=8.4 Score=37.09 Aligned_cols=51 Identities=27% Similarity=0.572 Sum_probs=40.7
Q ss_pred eeEEEEEEcCCCeeEEecCC-----CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 202 CGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d-----~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.|+.--. ..||||+...+ +..||||.-|.++. -.|..||.|+=.+..-..|
T Consensus 55 ~GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRr-------f~LrtGD~v~G~vR~Pke~ 110 (422)
T COG1158 55 DGVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRR-------FNLRTGDTVEGKVRPPKEG 110 (422)
T ss_pred eeEEEec--cCCcceeecCccccCCCCCceEECHHHHhh-------ccCccCCEEeeeecCCCcc
Confidence 3666555 48999999765 46899999999994 3589999999888777666
No 127
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=65.44 E-value=33 Score=24.36 Aligned_cols=58 Identities=16% Similarity=0.145 Sum_probs=38.2
Q ss_pred eeeeeEEEEeeCCCceEEEeCCC--CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d--~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
..+.|+|+-.. .||.+..-. .+-+.|+|.+.+....-..-...++.||.|+..+..-+
T Consensus 5 ~~~~g~V~~v~---~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d 64 (76)
T cd04452 5 ELVVVTVKSIA---DMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVD 64 (76)
T ss_pred CEEEEEEEEEE---ccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEE
Confidence 34678888774 467655543 24789999999975411000134799999999877644
No 128
>COG1158 Rho Transcription termination factor [Transcription]
Probab=64.86 E-value=8.1 Score=37.21 Aligned_cols=64 Identities=25% Similarity=0.507 Sum_probs=47.4
Q ss_pred eeeEEEEeeCCCceEEEeCCC-----CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC---ceEEEEeCCCC
Q psy547 34 VCGVVKWFSVKSGYGFIATPS-----SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG---HEAINVTGPDG 105 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d-----~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG---~~A~~V~~~~~ 105 (282)
..|++.-. ..||||+...+ +..|||+.-|.++.. .|+.||.|+=.+..-..| .--..|..++.
T Consensus 54 ~~GvLeil--~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf-------~LrtGD~v~G~vR~Pke~Ery~aLl~ve~vN~ 124 (422)
T COG1158 54 GDGVLEIL--PDGFGFLRSADSSYLPGPDDIYVSPSQIRRF-------NLRTGDTVEGKVRPPKEGERYFALLKVEAVNG 124 (422)
T ss_pred eeeEEEec--cCCcceeecCccccCCCCCceEECHHHHhhc-------cCccCCEEeeeecCCCcccceeeeEEEeecCC
Confidence 34666655 48999999865 568999999999874 579999999988766555 22355666655
Q ss_pred C
Q psy547 106 R 106 (282)
Q Consensus 106 ~ 106 (282)
.
T Consensus 125 ~ 125 (422)
T COG1158 125 D 125 (422)
T ss_pred C
Confidence 3
No 129
>PRK08059 general stress protein 13; Validated
Probab=64.37 E-value=33 Score=27.59 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=40.9
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..+.|+|.... .||+...-+.+.+-|+|.+++.......-...+..||.|...+..-+
T Consensus 9 ~iv~G~V~~i~---~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 9 SVVTGKVTGIQ---PYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CEEEEEEEEEe---cceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEE
Confidence 44678887764 38888877767899999999964321111134799999999988754
No 130
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=64.17 E-value=31 Score=24.37 Aligned_cols=52 Identities=15% Similarity=0.235 Sum_probs=36.6
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
...+|+|...+. .+=|+.. + +-+-|++.+++... ..++.||.|.+.+..-++
T Consensus 5 ~iV~G~V~~~~~--~~~~vdi-g-~~eg~lp~~e~~~~------~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 5 EIVTGIVKRVDR--GNVIVDL-G-KVEAILPKKEQIPG------ESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CEEEEEEEEEcC--CCEEEEc-C-CeEEEeeHHHCCCC------CcCCCCCEEEEEEEEEec
Confidence 345799988854 2333443 3 37889999999732 357999999999887543
No 131
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=64.13 E-value=23 Score=24.26 Aligned_cols=56 Identities=20% Similarity=0.325 Sum_probs=37.3
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+.|+|...+. +|++..-+ +.+-|+|.+++.....+.-...++.||.|.+.+..-+
T Consensus 4 ~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 4 VVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred EEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEE
Confidence 35688887753 66666554 5789999999863221111134799999999887754
No 132
>PRK08059 general stress protein 13; Validated
Probab=63.90 E-value=52 Score=26.41 Aligned_cols=68 Identities=21% Similarity=0.333 Sum_probs=44.2
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTG 102 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~ 102 (282)
..+.|+|.-... ||+...-+.+.+-|+|++++.......-...+..||.|...+..-+ ++.....+..
T Consensus 9 ~iv~G~V~~i~~---~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~ 78 (123)
T PRK08059 9 SVVTGKVTGIQP---YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78 (123)
T ss_pred CEEEEEEEEEec---ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEE
Confidence 457888887653 6766666656899999999965310000134699999999987743 4544444443
No 133
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=63.71 E-value=19 Score=25.25 Aligned_cols=54 Identities=19% Similarity=0.212 Sum_probs=37.2
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
++|+|+..+. +|++... .+-+.|+|.+.+...... ... -..|+.+.+.+..-++
T Consensus 4 v~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~~~-~~~-~~vG~~i~~~i~~vd~ 57 (67)
T cd04465 4 VEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRPVE-DLD-EYVGKELKFKIIEIDR 57 (67)
T ss_pred EEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcccC-ChH-HhCCCEEEEEEEEEeC
Confidence 4688888853 6777666 478999999999743210 111 1379999999877654
No 134
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=63.35 E-value=50 Score=23.69 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=37.1
Q ss_pred eeeeEEEEeeCCCceEEEeCCCC-CCcEEEEeeccccCC-----------CcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNN-----------PRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~-~~dvF~H~s~l~~~~-----------~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|.... -||+...-.. +-+-|+|++++..+. .+.....++.||.|...+..-+
T Consensus 4 ~~~g~V~~v~---~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd 72 (83)
T cd04471 4 EFDGVISGVT---SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEEEEEEeEE---eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEec
Confidence 3567777664 3677766554 567899999986420 0001256788999998877654
No 135
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=63.33 E-value=12 Score=27.24 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=21.2
Q ss_pred ccCCCCCCEEEEEEEEcCCC-ceeeeeEe
Q psy547 242 YKTLAEGETVEFDIMQGDKG-NQFCFVLK 269 (282)
Q Consensus 242 ~~~l~~Gd~V~F~i~~~~kG-~~A~~V~~ 269 (282)
+..|++||+|.|.+...+.| +.-..+.+
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~~ 68 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIEP 68 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence 56799999999999999988 76666553
No 136
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=63.26 E-value=31 Score=24.41 Aligned_cols=56 Identities=13% Similarity=0.102 Sum_probs=36.9
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccC--CCcccccCCCCCCEEEEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN--NPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~--~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
.+.|+|+..+.. .=|+... .+-+-++|++++... ....-...+++||.|.+.+..-
T Consensus 3 iV~g~V~~i~~~--gi~v~l~-~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~ 60 (70)
T cd05702 3 LVKAKVKSVKPT--QLNVQLA-DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGG 60 (70)
T ss_pred EEEEEEEEEECC--cEEEEeC-CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEE
Confidence 468899987542 2444544 468999999998643 0001134589999999987653
No 137
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=63.03 E-value=27 Score=23.79 Aligned_cols=57 Identities=18% Similarity=0.257 Sum_probs=36.6
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+-... ||....-....+-|+|.+.+.......-...++.||.|.+.+..-+
T Consensus 3 ~~~g~V~~i~~---~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05685 3 VLEGVVTNVTD---FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59 (68)
T ss_pred EEEEEEEEEec---ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEE
Confidence 36788887643 5544444445889999999965310000124799999999876643
No 138
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=62.53 E-value=45 Score=24.31 Aligned_cols=51 Identities=16% Similarity=0.147 Sum_probs=37.7
Q ss_pred eeeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
+.++|+|+..- -||++..-. ++-+-|+|.+++... ..+++|+.|.+.+..-
T Consensus 6 ~~v~g~V~si~---d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~v 57 (74)
T cd05694 6 MVLSGCVSSVE---DHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKV 57 (74)
T ss_pred CEEEEEEEEEe---CCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEE
Confidence 34789999874 456644433 356899999999752 5789999999997643
No 139
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=62.20 E-value=12 Score=30.73 Aligned_cols=57 Identities=18% Similarity=0.272 Sum_probs=38.2
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~ 258 (282)
..++|+|.-. ..||--..-+++..=+||+|++.++-...--.-|.+||.|...|..-
T Consensus 7 ~~l~GkItgI---~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~i 63 (129)
T COG1098 7 SKLKGKITGI---TPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDI 63 (129)
T ss_pred ceEEEEEEee---EecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEee
Confidence 3456777654 45775555555788999999998542111123499999999987653
No 140
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=61.63 E-value=26 Score=24.77 Aligned_cols=50 Identities=14% Similarity=0.223 Sum_probs=36.6
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|...+. .+=||.. + +-+.|++.+.+... ..++.||+|++.+..-+
T Consensus 6 iV~G~V~~~~~--~~~~vdi-g-~~eg~lp~~e~~~~------~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 6 IVTGIVKRVDR--GNVIVDL-G-KVEAILPKKEQIPG------ESYRPGDRIKAYVLEVR 55 (67)
T ss_pred EEEEEEEEEcC--CCEEEEc-C-CeEEEeeHHHCCCC------CcCCCCCEEEEEEEEEe
Confidence 46899999865 3344544 3 37889999999642 46799999999987643
No 141
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=61.36 E-value=19 Score=25.19 Aligned_cols=52 Identities=19% Similarity=0.221 Sum_probs=35.6
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCccccc--CCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYK--TLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~--~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+..+. +|++... .+-+.|+|.+.+.... .. .-..|+.+++.+..-+
T Consensus 3 iv~g~V~~v~~---~G~~v~l-~g~~gfip~s~~~~~~----~~~~~~~vG~~i~~~i~~vd 56 (67)
T cd04465 3 IVEGKVTEKVK---GGLIVDI-EGVRAFLPASQVDLRP----VEDLDEYVGKELKFKIIEID 56 (67)
T ss_pred EEEEEEEEEEC---CeEEEEE-CCEEEEEEHHHCCCcc----cCChHHhCCCEEEEEEEEEe
Confidence 36889999853 4555555 4689999999996531 11 1147999999976544
No 142
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=59.72 E-value=7.3 Score=38.27 Aligned_cols=50 Identities=28% Similarity=0.551 Sum_probs=39.5
Q ss_pred eeeeEEEEeeCCCceEEEeCC-----CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 33 KVCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~-----d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
...|.+.-.. .||||+... .+..||||..+.++.. .|+.||.|+=.+..-
T Consensus 50 ~~~g~le~~~--~g~gflr~~~~~~~~~~~d~yvs~~~i~~~-------~lr~gd~v~g~~R~~ 104 (415)
T TIGR00767 50 FGEGVLEILP--DGFGFLRSPDSSYLPGPDDIYVSPSQIRRF-------NLRTGDTIEGQIRSP 104 (415)
T ss_pred EEEEEEEEcC--CCCeEEeCCCcCCCCCCCCeeeCHHHHHhc-------CCCCCCEEEEEEecc
Confidence 4678777553 599999985 3678999999999874 579999999877554
No 143
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=58.99 E-value=2.1e+02 Score=29.70 Aligned_cols=57 Identities=12% Similarity=0.253 Sum_probs=37.5
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.+.|+|+..+. .| =||.- ...-+-|++.+.+...........+++|+.|++.+..
T Consensus 303 G~iV~G~V~~v~~-~g-v~Vdi-g~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~ 359 (647)
T PRK00087 303 GDIVKGTVVSVNE-NE-VFVDV-GYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLK 359 (647)
T ss_pred CCEEEEEEEEEEC-CE-EEEEE-CCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEE
Confidence 4557899999964 22 34443 3345789999988643111113458999999999866
No 144
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=58.22 E-value=18 Score=35.55 Aligned_cols=48 Identities=29% Similarity=0.599 Sum_probs=37.3
Q ss_pred eeeEEEEEEcCCCeeEEecC-----CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547 201 VCGVVKWFSVKSGYGFIATP-----SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~-----d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~ 257 (282)
..|++--. ..||||+... .+..||||..+.++. ..|..||.|+=.+..
T Consensus 51 ~~g~le~~--~~g~gflr~~~~~~~~~~~d~yvs~~~i~~-------~~lr~gd~v~g~~R~ 103 (415)
T TIGR00767 51 GEGVLEIL--PDGFGFLRSPDSSYLPGPDDIYVSPSQIRR-------FNLRTGDTIEGQIRS 103 (415)
T ss_pred EEEEEEEc--CCCCeEEeCCCcCCCCCCCCeeeCHHHHHh-------cCCCCCCEEEEEEec
Confidence 35777655 3599999985 357899999999994 358999999877654
No 145
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=57.75 E-value=47 Score=23.41 Aligned_cols=54 Identities=24% Similarity=0.117 Sum_probs=36.8
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+|+|+... .+|-+..-.++-+-|+|++.+.... .....++.|+.|.+.+..-+
T Consensus 4 V~g~V~~i~---~~G~~v~l~~~v~g~v~~~~l~~~~--~~~~~~~~G~~i~~kVi~id 57 (66)
T cd05695 4 VNARVKKVL---SNGLILDFLSSFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILYVD 57 (66)
T ss_pred EEEEEEEEe---CCcEEEEEcCCceEEEEHHHcCCcc--CcccCcCCCCEEEEEEEEEe
Confidence 458888874 3555444333679999999986431 11456999999999876644
No 146
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=57.48 E-value=34 Score=32.48 Aligned_cols=61 Identities=13% Similarity=0.120 Sum_probs=42.4
Q ss_pred eeeeeEEEEEEcCCCeeEEecCC--CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEc--CCCc
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DKGN 262 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d--~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~--~kG~ 262 (282)
..+.|+|+... .||.+..-+ ++-+-|+|+|+|.....+.--.-+++||.|.+.|..- .+|.
T Consensus 19 dvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~ 83 (319)
T PTZ00248 19 DLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGY 83 (319)
T ss_pred CEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence 34569998874 488776553 4789999999997543222223489999999998863 4553
No 147
>PHA02945 interferon resistance protein; Provisional
Probab=57.39 E-value=56 Score=25.20 Aligned_cols=58 Identities=17% Similarity=0.199 Sum_probs=37.7
Q ss_pred eeeeeeEEEEeeCCCceEE-EeCCC-CCCcEEEEeecc--ccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGF-IATPS-SNEDVFVHSKRI--KYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGF-I~~~d-~~~dvF~H~s~l--~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
..-+.|+|+- +.||+ +..++ ++.+-|+|+|.+ ...--+. ...| +|++|.+.+-.-++.
T Consensus 12 GelvigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~ 73 (88)
T PHA02945 12 GDVLKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYT 73 (88)
T ss_pred CcEEEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCC
Confidence 3446899987 55665 44444 578999999966 3320000 2457 999999998765544
No 148
>PRK12678 transcription termination factor Rho; Provisional
Probab=56.59 E-value=16 Score=37.82 Aligned_cols=51 Identities=25% Similarity=0.529 Sum_probs=38.9
Q ss_pred eeeEEEEEEcCCCeeEEecC---CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 201 VCGVVKWFSVKSGYGFIATP---SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~---d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
..|++--. .|||||... -+..||||..+.|+.. .|..||.|.=.+..-..|
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~-------~Lr~Gd~v~G~vr~p~~~ 349 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKN-------GLRKGDAVTGAVRAPREG 349 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHc-------CCCCCCEEEEeecCCCCC
Confidence 45776554 499999976 3578999999999953 589999998777654433
No 149
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=56.39 E-value=37 Score=24.95 Aligned_cols=59 Identities=15% Similarity=0.128 Sum_probs=39.2
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc----CCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN----NPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~----~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
....|+|... ..+|....-+.+-+-|+|++++... ....-...++.||.|.+.+..-.+
T Consensus 8 diV~g~V~~i---~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 8 DVVIGRVTEV---GFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CEEEEEEEEE---CCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 3456888875 3455555555578999999999631 000011248999999999988643
No 150
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=55.80 E-value=35 Score=24.07 Aligned_cols=57 Identities=23% Similarity=0.336 Sum_probs=37.7
Q ss_pred eeeeEEEEeeCCCceEEEeCCC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|+-.. .||++..-. ...+-|+|.+.+.......-...++.||.|+..+..-+
T Consensus 5 ~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 5 KIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred EEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 3678888774 356555443 36789999999976421101234799999999876643
No 151
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=55.77 E-value=51 Score=23.67 Aligned_cols=58 Identities=16% Similarity=0.271 Sum_probs=39.3
Q ss_pred eeeeEEEEEEcCCCeeEEecCCC-CccEEEEeccccccCC-----------cccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSS-NEDVFVHSKRIKYNNP-----------RKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~-~~dVF~H~s~l~~~~~-----------r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+.|+|.... .||+...-.. +.+-|+|++++..+.. +.....++.||.|...+..-+.
T Consensus 4 ~~~g~V~~v~---~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 4 EFDGVISGVT---SFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred EEEEEEEeEE---eeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEecc
Confidence 3567787763 4888887665 6778999999863210 0112457899999998877653
No 152
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=55.41 E-value=37 Score=23.20 Aligned_cols=56 Identities=20% Similarity=0.325 Sum_probs=36.0
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
.+.|+|.-.+. +|++..-+ ..+.|+|.+.+.....+.-...++.||.|.+.+..-+
T Consensus 4 ~~~g~V~~v~~---~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd 59 (68)
T cd05688 4 VVEGTVKSITD---FGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59 (68)
T ss_pred EEEEEEEEEEe---eeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEE
Confidence 46788888753 45554444 5789999998863211101234799999999876543
No 153
>PRK05807 hypothetical protein; Provisional
Probab=54.99 E-value=81 Score=25.95 Aligned_cols=69 Identities=14% Similarity=0.307 Sum_probs=44.5
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe-CCCCceEEEEeCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ-GDKGHEAINVTGP 103 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~-~~kG~~A~~V~~~ 103 (282)
...+.|+|.-.. .||+....+ +.+-|+|++.+...-...-...++.||.|+..+.. +..|.....+..+
T Consensus 6 G~vv~G~Vt~i~---~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~ 75 (136)
T PRK05807 6 GSILEGTVVNIT---NFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQA 75 (136)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 345788888864 356655554 56899999999653111112457999999999765 3456555555543
No 154
>PRK12678 transcription termination factor Rho; Provisional
Probab=54.30 E-value=25 Score=36.35 Aligned_cols=47 Identities=26% Similarity=0.532 Sum_probs=38.2
Q ss_pred eeeEEEEeeCCCceEEEeCC---CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 34 VCGVVKWFSVKSGYGFIATP---SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~---d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
+.|++--. .|||||... .+..||||..+.++.. .|+.||.|.=.+..
T Consensus 296 ~~GiLdi~---dg~gFlR~~~y~~~~~Dvyvs~~qirr~-------~Lr~Gd~v~G~vr~ 345 (672)
T PRK12678 296 VAGILDVL---DNYAFVRTSGYLPGPNDVYVSMNQVRKN-------GLRKGDAVTGAVRA 345 (672)
T ss_pred eeEEEEec---CCeeEeeCCCCCCCCCCeeeCHHHHHHc-------CCCCCCEEEEeecC
Confidence 57777655 499999986 3678999999999875 57899999977665
No 155
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=53.55 E-value=53 Score=23.13 Aligned_cols=57 Identities=23% Similarity=0.336 Sum_probs=39.2
Q ss_pred eeeeEEEEEEcCCCeeEEecCC-CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d-~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+.|+|.... .||++..-. .+.+-|+|++++.......-...+..||.|...+..-+
T Consensus 5 ~v~g~V~~i~---~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 5 KIDGTVRRVE---DYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62 (77)
T ss_pred EEEEEEEEEE---cceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEe
Confidence 3568888774 477666554 36789999999975421111234699999999887755
No 156
>PHA02945 interferon resistance protein; Provisional
Probab=53.27 E-value=59 Score=25.08 Aligned_cols=61 Identities=16% Similarity=0.189 Sum_probs=39.3
Q ss_pred eeeEEEEEEcCCCeeEEec-CC-CCccEEEEeccc--cccCCcccccCCCCCCEEEEEEEEcCCCceeeee
Q psy547 201 VCGVVKWFSVKSGYGFIAT-PS-SNEDVFVHSKRI--KYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFV 267 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~-~d-~~~dVF~H~s~l--~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V 267 (282)
..|+|+. +.||+-.. ++ ++.+-|+|.|.+ ...--+. ...| +|++|...+..-++...-+.+
T Consensus 15 vigtV~~----~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDl 79 (88)
T PHA02945 15 LKGKVYE----NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred EEEEEEe----cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 4588876 56776554 33 488999999966 3221111 3457 999999998887655443333
No 157
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=53.16 E-value=48 Score=23.36 Aligned_cols=53 Identities=21% Similarity=0.083 Sum_probs=36.5
Q ss_pred eeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe
Q psy547 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 33 ~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
.+.|+|+.-. .+| -|+...+ +-+-|+|++.+.... .....+++|+.|.+.+..
T Consensus 3 ~V~g~V~~i~-~~G-~~v~l~~-~v~g~v~~~~l~~~~--~~~~~~~~G~~i~~kVi~ 55 (66)
T cd05695 3 LVNARVKKVL-SNG-LILDFLS-SFTGTVDFLHLDPEK--SSKSTYKEGQKVRARILY 55 (66)
T ss_pred EEEEEEEEEe-CCc-EEEEEcC-CceEEEEHHHcCCcc--CcccCcCCCCEEEEEEEE
Confidence 4678898885 444 4455444 578999999985431 013568999999998654
No 158
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=52.86 E-value=17 Score=36.31 Aligned_cols=53 Identities=23% Similarity=0.448 Sum_probs=39.7
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCce
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQ 263 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~ 263 (282)
.+..|+||.- +|||||+..|. .+..|+.=-.++ .+--||+|.-.+.......+
T Consensus 20 prvEGvVK~t--ekgfGFLEvD~-qkSYFIpPp~MK---------kvMHGDkIiA~i~te~erE~ 72 (645)
T COG4776 20 PRVEGVVKAT--EKGFGFLEVDA-QKSYFIPPPQMK---------KVMHGDKIIAVIHTEKERES 72 (645)
T ss_pred cccceeeeec--cccceeEEEcC-ccccccCCHHHh---------hhcccCeEEEEEEecCcccc
Confidence 4466999975 89999999876 677888766666 35679999887776654433
No 159
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=52.59 E-value=59 Score=30.92 Aligned_cols=72 Identities=11% Similarity=0.085 Sum_probs=49.5
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCC--CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEe--CCCCceEEEEeCCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ--GDKGHEAINVTGPDG 105 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d--~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~--~~kG~~A~~V~~~~~ 105 (282)
...+.|+|+... -||.+..-+ ++-+-|+|+|.|....-+.--..+++|+.|.+.|-. ..+|.....+..+..
T Consensus 18 GdvV~g~V~~I~---d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~ 93 (319)
T PTZ00248 18 DDLVMVKVVRIT---EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP 93 (319)
T ss_pred CCEEEEEEEEEe---CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc
Confidence 456789999875 466554443 468999999999764211112348999999999875 466777777776554
No 160
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=52.12 E-value=25 Score=37.86 Aligned_cols=59 Identities=12% Similarity=0.187 Sum_probs=42.2
Q ss_pred eee-eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKV-CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~-~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
..+ .|+|+.. ..||....-..+.+-|+|+|+|..+....-...++.||.|...+..-+.
T Consensus 755 ~iy~~g~V~~I---~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~ 814 (891)
T PLN00207 755 DIYRNCEIKSI---APYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND 814 (891)
T ss_pred cEEECcEEEEE---eccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC
Confidence 345 3688886 4599887666679999999999754211112458899999999887653
No 161
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=51.81 E-value=57 Score=23.77 Aligned_cols=59 Identities=12% Similarity=0.127 Sum_probs=39.0
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
...|+|.... ..+++..-...-+-|+|.+++.......-...++.||.|.+.+..-.++
T Consensus 9 iV~G~V~~v~---~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 9 IVIGIVTEVN---SRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred EEEEEEEEEc---CCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 3568887763 2333443345789999999997432111234589999999999876654
No 162
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=51.44 E-value=24 Score=28.50 Aligned_cols=64 Identities=16% Similarity=0.092 Sum_probs=39.0
Q ss_pred eeeeEEEEEEcCCCeeEEecCCCCc------cEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeEe
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSSNE------DVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVLK 269 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~~~------dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~~ 269 (282)
..+|+|+..|...+-=-|....-.. -.-|-. .. ..-+..|++||+|.|.++....+.....|++
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v---~~---~~~l~~lk~G~~V~F~~~~~~~~~~i~~i~~ 113 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTI---TP---QTKMSEIKTGDKVAFNFVQQGNLSLLQDIKV 113 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeecccccCCCCCccccccC---CC---hhhhccCCCCCEEEEEEEEcCCcEEEEEEee
Confidence 3469999998766554455432110 001111 10 0124679999999999999998887666654
No 163
>KOG3209|consensus
Probab=50.70 E-value=93 Score=32.95 Aligned_cols=53 Identities=19% Similarity=0.232 Sum_probs=36.4
Q ss_pred eCCCceEEEeCC--CCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 42 SVKSGYGFIATP--SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 42 n~~kGfGFI~~~--d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
...+||||-.-- +...|=|+.+..|..++|-+---.|..||.|...=...--|
T Consensus 352 Kg~~GFGfTliGGdd~~gDefLqVKsvl~DGPAa~dGkle~GDviV~INg~cvlG 406 (984)
T KOG3209|consen 352 KGYMGFGFTLIGGDDVRGDEFLQVKSVLKDGPAAQDGKLETGDVIVHINGECVLG 406 (984)
T ss_pred ecccccceEEecCCcCCCCceeeeeecccCCchhhcCccccCcEEEEECCceecc
Confidence 346899996653 34789999999998876533234689999887654433334
No 164
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=49.52 E-value=31 Score=27.81 Aligned_cols=64 Identities=16% Similarity=0.104 Sum_probs=40.1
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCC------CcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCCceEEEEe
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSN------EDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVT 101 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~------~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG~~A~~V~ 101 (282)
-..+|+|+..|...+-=-|.-..-. --.-|-.. .. .-+..|++|+.|.|++.....+.....|+
T Consensus 43 ~~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~---~~---~~l~~lk~G~~V~F~~~~~~~~~~i~~i~ 112 (115)
T PRK09838 43 ISGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTIT---PQ---TKMSEIKTGDKVAFNFVQQGNLSLLQDIK 112 (115)
T ss_pred EEEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCC---Ch---hhhccCCCCCEEEEEEEEcCCcEEEEEEe
Confidence 4468999999988765444432210 00011111 10 01567899999999999999988776665
No 165
>PRK11712 ribonuclease G; Provisional
Probab=48.57 E-value=1.1e+02 Score=30.75 Aligned_cols=83 Identities=16% Similarity=0.266 Sum_probs=52.8
Q ss_pred eeeeeeeEEEEEEcCCCeeEEecCCCCccEEEEecccccc------CCccc------ccCCCCCCEEEEEEEEcCCCcee
Q psy547 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN------NPRKL------YKTLAEGETVEFDIMQGDKGNQF 264 (282)
Q Consensus 197 ~~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~------~~r~g------~~~l~~Gd~V~F~i~~~~kG~~A 264 (282)
..+-+.|+|+..-+.-.=-||.-.. ++.-|.|++++... ..... -..|++||.|..+|+..+.|...
T Consensus 38 vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG 116 (489)
T PRK11712 38 VGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKG 116 (489)
T ss_pred cccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCC
Confidence 3567889998886665677888765 78999999987310 00000 01289999999999998755434
Q ss_pred eeeEecc---eeeeeeeec
Q psy547 265 CFVLKNI---VLYFSFVPQ 280 (282)
Q Consensus 265 ~~V~~~~---~~~~~~~~~ 280 (282)
..++.+| .=|+-|.|.
T Consensus 117 ~~lT~~Isl~GrylVl~P~ 135 (489)
T PRK11712 117 ARLTTDITLPSRYLVFMPG 135 (489)
T ss_pred CeEEEEEEeccceEEEECC
Confidence 4444333 234444453
No 166
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=48.49 E-value=74 Score=31.31 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=47.1
Q ss_pred eeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC-----------Ccc-cccCCCCCCEEEEEEEeCCCC
Q psy547 29 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN-----------PRK-LYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 29 ~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~-----------~~~-g~~~l~~Gd~V~f~v~~~~kG 94 (282)
....-+.|+|+-..+.-.--||.-.. +..-|+|++++.... ..+ -...|++||.|...+...+.|
T Consensus 24 ~vGnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~ 100 (414)
T TIGR00757 24 LKGNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRG 100 (414)
T ss_pred CCCCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcC
Confidence 34566899999998777789999865 678999999985310 000 012489999999999987543
No 167
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=48.30 E-value=26 Score=30.23 Aligned_cols=48 Identities=27% Similarity=0.423 Sum_probs=40.5
Q ss_pred eeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEE
Q psy547 34 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFD 87 (282)
Q Consensus 34 ~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~ 87 (282)
..|+||.|+.+..=|.++-.+ -+|+=+|-.++..- --.|.+||+|..-
T Consensus 36 rIG~iK~F~~~tQe~iVti~e-~e~LeI~T~nISN~-----~leLs~~D~VlLL 83 (181)
T PF05606_consen 36 RIGTIKSFKFQTQEGIVTIPE-YEDLEIHTKNISNI-----NLELSKGDEVLLL 83 (181)
T ss_pred EEeeeeecccccceEEEEeec-ccCceEEeeecccc-----eeEecCCCEEEEE
Confidence 469999999999999998876 68999999999875 3578999998753
No 168
>PRK10811 rne ribonuclease E; Reviewed
Probab=48.20 E-value=70 Score=34.96 Aligned_cols=75 Identities=20% Similarity=0.178 Sum_probs=52.2
Q ss_pred eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcc--------cc-cCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRK--------LY-KTLAEGETVEFDIMQGDKGNQFCFVL 268 (282)
Q Consensus 198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~--------g~-~~l~~Gd~V~F~i~~~~kG~~A~~V~ 268 (282)
..-+.|+|+.--..-+=-||.-.+ ++.-|+|++++....... .+ ..|.+||.|...|.....|-.+..|+
T Consensus 39 GnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LT 117 (1068)
T PRK10811 39 ANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT 117 (1068)
T ss_pred cceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCcee
Confidence 466889998875555566888776 789999998885210000 01 23889999999999987776666666
Q ss_pred eccee
Q psy547 269 KNIVL 273 (282)
Q Consensus 269 ~~~~~ 273 (282)
.+|-+
T Consensus 118 t~ISL 122 (1068)
T PRK10811 118 TFISL 122 (1068)
T ss_pred eeEEe
Confidence 66544
No 169
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=48.19 E-value=44 Score=35.04 Aligned_cols=60 Identities=23% Similarity=0.311 Sum_probs=43.4
Q ss_pred eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
...+.|+|+... .||....-..+.+-|+|+|.+.......-...++.||.|...+..-++
T Consensus 619 G~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 619 GKIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred CcEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC
Confidence 355789998873 488887766678999999999654211112347899999999877653
No 170
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=47.28 E-value=42 Score=35.39 Aligned_cols=59 Identities=17% Similarity=0.311 Sum_probs=42.0
Q ss_pred eeeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccc---c-CCcccccCCCCCCEEEEEEEEcC
Q psy547 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKY---N-NPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 198 ~~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~---~-~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
...++|+|+.. ..||....-..+.+-|+|+|++.+ . ....-..-++.||.|.+.+..-+
T Consensus 648 G~i~~GkV~~I---~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 648 GERFLGTVVKT---TAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred CCEEEEEEEEE---ECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 35578999887 459988776668999999998841 1 10111234899999999887754
No 171
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=45.90 E-value=53 Score=34.47 Aligned_cols=58 Identities=22% Similarity=0.294 Sum_probs=43.3
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..+.|+|+... .||+...-..+.+-++|++.+.......-...++.||.|...+..-+
T Consensus 623 ~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD 680 (693)
T PRK11824 623 EIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680 (693)
T ss_pred eEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEEC
Confidence 56789998874 58988876668999999999975421111234799999999888754
No 172
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=45.85 E-value=87 Score=22.90 Aligned_cols=60 Identities=15% Similarity=0.137 Sum_probs=37.8
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccC----CCcccccCCCCCCEEEEEEEeCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN----NPRKLYKTLAEGETVEFDIMQGDK 93 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~----~~~~g~~~l~~Gd~V~f~v~~~~k 93 (282)
...+.|+|..-.. ..-|+.- +.+-+-|+|.+++... .-..-...++.||.|.+.+..-..
T Consensus 7 GdiV~g~V~~i~~--~g~~v~i-~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~ 70 (86)
T cd05789 7 GDVVIGRVTEVGF--KRWKVDI-NSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS 70 (86)
T ss_pred CCEEEEEEEEECC--CEEEEEC-CCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC
Confidence 3456888888532 2244444 4467999999999631 000001248999999999877543
No 173
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=45.74 E-value=1e+02 Score=22.34 Aligned_cols=61 Identities=13% Similarity=0.172 Sum_probs=40.1
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG 94 (282)
...+.|+|.-.. ...-++... ...+.|+|.+++....-..-...+++||.|.+.+..-+++
T Consensus 7 GdiV~G~V~~v~--~~~~~V~i~-~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~ 67 (82)
T cd04454 7 GDIVIGIVTEVN--SRFWKVDIL-SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD 67 (82)
T ss_pred CCEEEEEEEEEc--CCEEEEEeC-CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence 345688888873 223445543 4679999999996531111124589999999999876553
No 174
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=39.77 E-value=98 Score=28.46 Aligned_cols=58 Identities=21% Similarity=0.350 Sum_probs=40.1
Q ss_pred eeeeEEEEEEcCCCeeEEecCCC--CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 200 KVCGVVKWFSVKSGYGFIATPSS--NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~d~--~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.+.|+|+.. +.||+...-+. +-+-|+|.+++..+..+.-...++.||.|.+.+..-++
T Consensus 11 iV~G~V~~I---~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~ 70 (262)
T PRK03987 11 LVVGTVKEV---KDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDP 70 (262)
T ss_pred EEEEEEEEE---ECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEec
Confidence 356888876 45777665432 67999999999744211112347999999999887553
No 175
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=39.49 E-value=98 Score=33.56 Aligned_cols=67 Identities=13% Similarity=0.207 Sum_probs=43.1
Q ss_pred eee-eeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC-CCceEEEEe
Q psy547 32 TKV-CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD-KGHEAINVT 101 (282)
Q Consensus 32 ~~~-~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~-kG~~A~~V~ 101 (282)
..+ .|+|+..- -||....-..+.+-|+|+|.|....-..-...++.||.|...+..-+ +|.......
T Consensus 755 ~iy~~g~V~~I~---~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK 823 (891)
T PLN00207 755 DIYRNCEIKSIA---PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRR 823 (891)
T ss_pred cEEECcEEEEEe---ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEe
Confidence 344 36888873 47866555556899999999965410001235889999999976544 454444444
No 176
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=39.20 E-value=92 Score=23.66 Aligned_cols=55 Identities=20% Similarity=0.136 Sum_probs=35.6
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCccc-----------ccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKL-----------YKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g-----------~~~l~~Gd~V~F~i~~~~ 259 (282)
+.|+|...+. +|+...-+ ..+.|+|++++........ -..++.||.|.+.+..-+
T Consensus 3 v~g~V~~i~~---~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd 68 (99)
T cd04460 3 VEGEVVEVVD---FGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVS 68 (99)
T ss_pred EEEEEEEEEe---ccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEe
Confidence 4577777643 56666555 3789999999864321000 134699999999987654
No 177
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=37.83 E-value=68 Score=23.01 Aligned_cols=37 Identities=24% Similarity=0.360 Sum_probs=24.7
Q ss_pred cCCCCCCEEEEEEEEcCCCce-eeeeE--ecceeeeeeee
Q psy547 243 KTLAEGETVEFDIMQGDKGNQ-FCFVL--KNIVLYFSFVP 279 (282)
Q Consensus 243 ~~l~~Gd~V~F~i~~~~kG~~-A~~V~--~~~~~~~~~~~ 279 (282)
..+.+||.|+|.|.-...|.. |.+|. -.+...+.|++
T Consensus 35 ~~~~~Gd~v~ytitvtN~G~~~a~nv~v~D~lp~g~~~v~ 74 (76)
T PF01345_consen 35 STANPGDTVTYTITVTNTGPAPATNVVVTDTLPAGLTFVS 74 (76)
T ss_pred CcccCCCEEEEEEEEEECCCCeeEeEEEEEcCCCCCEEeC
Confidence 468999999999999988833 33343 33344444544
No 178
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.19 E-value=76 Score=23.13 Aligned_cols=49 Identities=6% Similarity=0.151 Sum_probs=39.1
Q ss_pred CCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 211 KSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 211 ~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+.|-.|...+++.-.+|..+.=..+-+|.+...|+.|+.+...+..-.
T Consensus 12 ~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~ 60 (69)
T cd05701 12 DKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPN 60 (69)
T ss_pred hhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCc
Confidence 5678888888888888887766555556777899999999998887654
No 179
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=36.86 E-value=1e+02 Score=32.38 Aligned_cols=58 Identities=21% Similarity=0.270 Sum_probs=41.3
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
...+.|+|+... -||+...-..+.+-++|+|.+....-+.-...++.||.|...+..-
T Consensus 622 G~v~~G~V~~I~---~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~i 679 (693)
T PRK11824 622 GEIYEGKVVRIV---DFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEI 679 (693)
T ss_pred CeEEEEEEEEEE---CCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEE
Confidence 456889999885 3777766555789999999997541100123479999999987654
No 180
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=36.12 E-value=1.4e+02 Score=28.25 Aligned_cols=71 Identities=14% Similarity=0.201 Sum_probs=48.3
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCCCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGPDG 105 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~~~ 105 (282)
...+.|+|+... .||...... +-+-|+|++.+.......-...++.||.|.+.+..-+ ++.....+..+..
T Consensus 197 G~vv~G~V~~I~---~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~ 269 (318)
T PRK07400 197 GEVVVGTVRGIK---PYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEP 269 (318)
T ss_pred CCEEEEEEEEEE---CCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEecccc
Confidence 345789999774 477766553 5689999999976421111345899999999987654 4666666665544
No 181
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=35.34 E-value=86 Score=32.89 Aligned_cols=59 Identities=22% Similarity=0.298 Sum_probs=40.8
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~ 92 (282)
...+.|+|+... .||....-..+.+-|+|+|.+....-..-...++.||.|...+..-+
T Consensus 619 G~i~~G~V~~I~---~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id 677 (684)
T TIGR03591 619 GKIYEGKVVRIM---DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677 (684)
T ss_pred CcEEEEEEEEEe---CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEEC
Confidence 455789999985 37766665556899999999965411111234788999999876544
No 182
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=33.78 E-value=97 Score=31.16 Aligned_cols=68 Identities=12% Similarity=0.167 Sum_probs=45.2
Q ss_pred eeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC--CCCceEEEEe
Q psy547 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DKGHEAINVT 101 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~--~kG~~A~~V~ 101 (282)
...+.|+|+-.. -||+...-+.+-+-|+|++.|........-..++.||+|.+.+..- .++.....+.
T Consensus 294 G~vv~G~V~~I~---~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK 363 (486)
T PRK07899 294 GQIVPGKVTKLV---PFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363 (486)
T ss_pred CCEEEEEEEEEe---ccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 446889999774 4787766655689999999997532100113479999999998653 3444444444
No 183
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=33.35 E-value=1e+02 Score=32.61 Aligned_cols=58 Identities=16% Similarity=0.328 Sum_probs=39.6
Q ss_pred eeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeecccc----CCCcccccCCCCCCEEEEEEEe
Q psy547 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKY----NNPRKLYKTLAEGETVEFDIMQ 90 (282)
Q Consensus 30 ~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~----~~~~~g~~~l~~Gd~V~f~v~~ 90 (282)
....+.|+|+..- -||....-..+.+-|+|+|.|.. ..-..-...+++||.|...+..
T Consensus 647 vG~i~~GkV~~I~---dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ 708 (719)
T TIGR02696 647 VGERFLGTVVKTT---AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIAD 708 (719)
T ss_pred CCCEEEEEEEEEE---CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEE
Confidence 3556899999874 47866655557899999998831 1000012358999999998755
No 184
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.06 E-value=92 Score=24.12 Aligned_cols=58 Identities=26% Similarity=0.267 Sum_probs=38.0
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC--------------------CcccccCCCCCCEEEEEEEeC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN--------------------PRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~--------------------~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
+.+.|+|+--. .+| =||... .+-+-|+|++++.... .+ -...++.||.|.+.+..-
T Consensus 5 ~vV~G~V~~v~-~~g-l~v~L~-~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 5 MLVLGQVKEIT-KLD-LVISLP-NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPD-LEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CEEEEEEEEEc-CCC-EEEECC-CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCC-HHHhccCCCEEEEEEEEc
Confidence 45789999863 333 444444 4679999999996420 00 024579999999998765
Q ss_pred CC
Q psy547 92 DK 93 (282)
Q Consensus 92 ~k 93 (282)
.+
T Consensus 81 d~ 82 (100)
T cd05693 81 DK 82 (100)
T ss_pred cC
Confidence 44
No 185
>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=30.56 E-value=79 Score=21.88 Aligned_cols=50 Identities=18% Similarity=0.121 Sum_probs=37.5
Q ss_pred eeeeEEEEe-eCCCceEEEeCCCCCCcEEEEeec--cccCCCcccccCCCCCCEEEEE
Q psy547 33 KVCGVVKWF-SVKSGYGFIATPSSNEDVFVHSKR--IKYNNPRKLYKTLAEGETVEFD 87 (282)
Q Consensus 33 ~~~G~Vkwf-n~~kGfGFI~~~d~~~dvF~H~s~--l~~~~~~~g~~~l~~Gd~V~f~ 87 (282)
.+.|+|..- ...+.+-|++-+|+...+-+.+.. .... ...|.+|+.|...
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~-----~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERF-----REKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHH-----HHTS-TTSEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHH-----hhcCCCCeEEEEE
Confidence 357888877 888999999998877777666666 2222 5789999999887
No 186
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=30.50 E-value=2.6e+02 Score=23.99 Aligned_cols=78 Identities=10% Similarity=0.123 Sum_probs=48.4
Q ss_pred eeeeeEEEEEEcCCCeeEEecC----------CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCceeeeeE
Q psy547 199 TKVCGVVKWFSVKSGYGFIATP----------SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFCFVL 268 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~----------d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A~~V~ 268 (282)
....|+|+... .+|+...- ..+-+-|+|.+++.......-...+++||.|...+..-. +.-...++
T Consensus 66 diV~GkV~~i~---~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~-~~i~LS~k 141 (189)
T PRK09521 66 DIVYGRVVDVK---EQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT-DPLQLSTK 141 (189)
T ss_pred CEEEEEEEEEc---CCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC-CcEEEEEe
Confidence 34568887763 34443321 235689999999874321112345899999999988877 43323333
Q ss_pred -ecceeeeeeeec
Q psy547 269 -KNIVLYFSFVPQ 280 (282)
Q Consensus 269 -~~~~~~~~~~~~ 280 (282)
..+..=+++|+.
T Consensus 142 ~~~lGvv~a~~~~ 154 (189)
T PRK09521 142 GKDLGVIYAMCSR 154 (189)
T ss_pred cCCceEEEEEccc
Confidence 557777777764
No 187
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=30.49 E-value=1.2e+02 Score=31.97 Aligned_cols=48 Identities=25% Similarity=0.563 Sum_probs=37.2
Q ss_pred eeEEEEEEcCCCeeEEecCC--CCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 202 CGVVKWFSVKSGYGFIATPS--SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d--~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
.|++.+- .+||||+.+++ ...|+|+-...+. ....||.|..++....+
T Consensus 71 ~~~~~~~--~~gf~f~~~~~~~~~~d~~v~~~~~~---------~a~~gD~V~v~~~~~~~ 120 (706)
T COG0557 71 EGIVEAS--AKGFGFLSPDDSKDADDIFVPKDPLN---------RALHGDRVLVELLPSDK 120 (706)
T ss_pred cceEEec--cCCceeeccCccCCCCcEEecccccc---------ccccCCEEEEEECcccc
Confidence 4566554 78999999998 6789999988865 35789999999755443
No 188
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=30.16 E-value=1.5e+02 Score=28.45 Aligned_cols=59 Identities=10% Similarity=0.141 Sum_probs=39.3
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
..++|+|+..+. .+=|+.-+..+-+.|+|.+++...........+.+|+.|++.|..-.
T Consensus 19 ~iv~G~V~~i~~--~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~ 77 (390)
T PRK06676 19 DVVTGEVLKVED--KQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77 (390)
T ss_pred CEEEEEEEEEEC--CeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEE
Confidence 446799999863 33444442446789999999974211112235789999999887754
No 189
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=29.05 E-value=1.5e+02 Score=27.31 Aligned_cols=70 Identities=21% Similarity=0.377 Sum_probs=44.1
Q ss_pred eeeeeeEEEEeeCCCceEEEeC-CC-CCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCC--CCceEEEEeCC
Q psy547 31 ATKVCGVVKWFSVKSGYGFIAT-PS-SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD--KGHEAINVTGP 103 (282)
Q Consensus 31 ~~~~~G~Vkwfn~~kGfGFI~~-~d-~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~--kG~~A~~V~~~ 103 (282)
...+.|+|+-.. .||+... ++ ++-+-|+|+|.+....-+.-...++.||.|.+.+..-+ ++.....+..+
T Consensus 9 GdiV~G~V~~I~---~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v 82 (262)
T PRK03987 9 GELVVGTVKEVK---DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82 (262)
T ss_pred CCEEEEEEEEEE---CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence 445788888773 4565544 33 26799999999965411000134799999999987654 35444444433
No 190
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=28.83 E-value=81 Score=27.25 Aligned_cols=46 Identities=30% Similarity=0.522 Sum_probs=37.2
Q ss_pred eeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEE
Q psy547 202 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEF 253 (282)
Q Consensus 202 ~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F 253 (282)
-|+||.|+.+..-|.++-.+ -+|+=+|-..+..-+ -.|.+||.|..
T Consensus 37 IG~iK~F~~~tQe~iVti~e-~e~LeI~T~nISN~~-----leLs~~D~VlL 82 (181)
T PF05606_consen 37 IGTIKSFKFQTQEGIVTIPE-YEDLEIHTKNISNIN-----LELSKGDEVLL 82 (181)
T ss_pred EeeeeecccccceEEEEeec-ccCceEEeeecccce-----eEecCCCEEEE
Confidence 59999999999999988766 678888987776432 46999999964
No 191
>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=28.78 E-value=3.2e+02 Score=22.16 Aligned_cols=60 Identities=20% Similarity=0.209 Sum_probs=41.6
Q ss_pred eeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeCCCC-ceEEEEeC
Q psy547 35 CGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG-HEAINVTG 102 (282)
Q Consensus 35 ~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~~kG-~~A~~V~~ 102 (282)
.|.|+|=.....+=|+..|. +.++-|+++....+ ..++|+.|..+=.-.++| .+|.+|..
T Consensus 61 ~gSv~~~~~~~~~~F~i~D~-~~~i~V~Y~G~~Pd-------~F~eg~~VVv~G~~~~~g~F~A~~lL~ 121 (131)
T PF03100_consen 61 EGSVEYDPDGNTLTFTITDG-GKEIPVVYTGPLPD-------LFREGQGVVVEGRLGEDGVFEATELLA 121 (131)
T ss_dssp CTTEEE-TTSSEEEEEEE-S-S-EEEEEEES--CT-------T--TTSEEEEEEEECCTSEEEEEEEEE
T ss_pred cCCEEEcCCCCEEEEEEEEC-CcEEEEEECCCCCc-------cccCCCeEEEEEEECCCCEEEEEEEEe
Confidence 34555665788999999887 67899999987654 568999999988876666 88888873
No 192
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=27.78 E-value=3.5e+02 Score=22.39 Aligned_cols=57 Identities=32% Similarity=0.468 Sum_probs=36.7
Q ss_pred eeeeEEEEEEcC--CC---eeEEecCCCCccEEE-EeccccccCCcccccCCCCCCEEEEE--EEEcCCC
Q psy547 200 KVCGVVKWFSVK--SG---YGFIATPSSNEDVFV-HSKRIKYNNPRKLYKTLAEGETVEFD--IMQGDKG 261 (282)
Q Consensus 200 ~~~G~Vk~fn~~--kG---fGFI~~~d~~~dVF~-H~s~l~~~~~r~g~~~l~~Gd~V~F~--i~~~~kG 261 (282)
.-.|+|+..-++ +| -=||.....+..|+| |=-++. || +..|++||.|+|. ...++||
T Consensus 40 ~g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDla---pr--ip~l~~GD~V~f~GeYe~n~kg 104 (131)
T PF11948_consen 40 SGCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLA---PR--IPWLQKGDQVEFYGEYEWNPKG 104 (131)
T ss_pred eccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCcc---cc--CcCcCCCCEEEEEEEEEECCCC
Confidence 346888877443 22 458887766666554 544554 22 6779999999994 5555555
No 193
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=27.74 E-value=1.4e+02 Score=29.85 Aligned_cols=52 Identities=17% Similarity=0.201 Sum_probs=38.6
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 260 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~k 260 (282)
..++|+|+... + +|++... ++-+.|+|.+.+... ..+..||+|.+.+..=.+
T Consensus 136 eIV~G~V~ri~--~-~giiVDL-ggvea~LP~sE~ip~------E~~~~GdrIka~I~~Vd~ 187 (470)
T PRK09202 136 EIITGVVKRVE--R-GNIIVDL-GRAEAILPRKEQIPR------ENFRPGDRVRAYVYEVRK 187 (470)
T ss_pred CEEEEEEEEEe--c-CCEEEEE-CCeEEEecHHHcCCC------ccCCCCCEEEEEEEEEec
Confidence 44679999985 3 4666644 467999999998733 468999999998776543
No 194
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=27.60 E-value=82 Score=29.14 Aligned_cols=63 Identities=17% Similarity=0.242 Sum_probs=40.1
Q ss_pred eeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCCcee
Q psy547 201 VCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQF 264 (282)
Q Consensus 201 ~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG~~A 264 (282)
.-|+|+.-....-|.-+..= ++.+-|+|+|++...--++=..-+.+|++|.+.+..-++...-
T Consensus 15 Vv~tV~~V~~~GAyv~L~EY-~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~ 77 (269)
T COG1093 15 VVGTVKQVADYGAYVELDEY-PGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGH 77 (269)
T ss_pred EEEEEEEeeccccEEEeecc-CCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCe
Confidence 34888887544444444432 3789999999997432111123489999999988776554433
No 195
>PRK11712 ribonuclease G; Provisional
Probab=27.10 E-value=2.2e+02 Score=28.75 Aligned_cols=66 Identities=14% Similarity=0.223 Sum_probs=48.2
Q ss_pred ceeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccC------CCccc------ccCCCCCCEEEEEEEeCCCC
Q psy547 28 VVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYN------NPRKL------YKTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 28 ~~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~------~~~~g------~~~l~~Gd~V~f~v~~~~kG 94 (282)
.....-+.|+|+---+.-.=-||.-.. +..-|+|++++... ..... -..|++||.|..+|...+.|
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~ 113 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLG 113 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcC
Confidence 345666899999998888889998875 68999999988321 00000 01289999999999987644
No 196
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=26.15 E-value=2.3e+02 Score=26.48 Aligned_cols=57 Identities=14% Similarity=0.140 Sum_probs=40.1
Q ss_pred eeeeeEEEEEEcCCCeeEEecC-CCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC-ceee
Q psy547 199 TKVCGVVKWFSVKSGYGFIATP-SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG-NQFC 265 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~-d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG-~~A~ 265 (282)
..++..|+.+ ..||+.-.. ..+..|+.|.++... ..+++||.|++=+-.+.++ +.|+
T Consensus 7 ~~~~l~V~~~---~~~g~fL~~~~~~~~ilL~k~~~~~-------~e~evGdev~vFiY~D~~~rl~aT 65 (287)
T COG2996 7 QINSLEVVEF---SDFGYFLDAGEDGTTILLPKSEPEE-------DELEVGDEVTVFIYVDSEDRLIAT 65 (287)
T ss_pred ceEEEEEEEe---eceeEEEecCCCceEEeccccCCcC-------CccccCcEEEEEEEECCCCceehe
Confidence 3455677666 456655544 445599999998863 4699999999988888777 4444
No 197
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=25.95 E-value=1.5e+02 Score=29.74 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=38.0
Q ss_pred eeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEEeC
Q psy547 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91 (282)
Q Consensus 32 ~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~~~ 91 (282)
..++|+|+... ++ |+|... ++-+.|+|.+.+.. -..++.|++|.+.+..=
T Consensus 136 eIV~G~V~ri~--~~-giiVDL-ggvea~LP~sE~ip------~E~~~~GdrIka~I~~V 185 (470)
T PRK09202 136 EIITGVVKRVE--RG-NIIVDL-GRAEAILPRKEQIP------RENFRPGDRVRAYVYEV 185 (470)
T ss_pred CEEEEEEEEEe--cC-CEEEEE-CCeEEEecHHHcCC------CccCCCCCEEEEEEEEE
Confidence 45799999986 54 555544 46799999999854 36789999999887653
No 198
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=25.83 E-value=1.1e+02 Score=22.89 Aligned_cols=35 Identities=20% Similarity=0.296 Sum_probs=23.0
Q ss_pred eeeeEEEEEEcCCCeeEEec---CCCCccEEEEecccc
Q psy547 200 KVCGVVKWFSVKSGYGFIAT---PSSNEDVFVHSKRIK 234 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~---~d~~~dVF~H~s~l~ 234 (282)
...|+|......+++|-... .++-.-+|.|+..+.
T Consensus 19 ~~~G~V~~~~~~~~~g~~V~i~~~~g~~~~y~~l~~~~ 56 (96)
T PF01551_consen 19 PADGKVVFVGEDPGYGNYVIIQHGNGYITVYGHLDSVS 56 (96)
T ss_dssp SSSEEEEEEEEETTTEEEEEEEETTSEEEEEEEESEES
T ss_pred CccEEEEEEEeccCCccEEEEEeCCcCCEEEecccccc
Confidence 34689988877767666553 333456788877754
No 199
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=25.33 E-value=1.3e+02 Score=25.65 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=30.1
Q ss_pred eeeEEEEeeCCC-ceEEEeCCCCCCcEEEEee----ccccCCCccccc-CCCCCCEEE
Q psy547 34 VCGVVKWFSVKS-GYGFIATPSSNEDVFVHSK----RIKYNNPRKLYK-TLAEGETVE 85 (282)
Q Consensus 34 ~~G~Vkwfn~~k-GfGFI~~~d~~~dvF~H~s----~l~~~~~~~g~~-~l~~Gd~V~ 85 (282)
..|+|....+.| -||+.+ +.+-+|++|+- .|.+. |+. .+++||.|.
T Consensus 49 vdG~v~~iFpTkHAigi~t--~~GvEiLiHiGiDTV~L~Ge----gF~~~v~~Gd~Vk 100 (156)
T COG2190 49 VDGTVVLIFPTKHAIGIET--DEGVEILIHIGIDTVKLNGE----GFESLVKEGDKVK 100 (156)
T ss_pred cCcEEEEEeeCCcEEEEEc--CCCcEEEEEeceeeEEECCc----ceEEEeeCCCEEc
Confidence 578877766665 566544 44789999986 55554 453 467777764
No 200
>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=24.74 E-value=2.9e+02 Score=20.33 Aligned_cols=50 Identities=24% Similarity=0.224 Sum_probs=31.1
Q ss_pred eeeEEEEEEcCC-CeeEEecCCC-------CccEEEEeccccccCCcccccCCCCCCEEEEEEEEcC
Q psy547 201 VCGVVKWFSVKS-GYGFIATPSS-------NEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259 (282)
Q Consensus 201 ~~G~Vk~fn~~k-GfGFI~~~d~-------~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~ 259 (282)
.+|+|....... ..||-..+.. .+-|||.... . ..+++||.|+..=...+
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~-~--------~~~~~Gd~V~vtG~v~e 59 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGS-G--------ADVAVGDLVRVTGTVTE 59 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCC-C--------CCCCCCCEEEEEEEEEe
Confidence 357776664433 2566554431 3569998776 2 35899999998644443
No 201
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=24.33 E-value=1.5e+02 Score=20.20 Aligned_cols=54 Identities=11% Similarity=-0.013 Sum_probs=33.8
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCc-cEEEEeccccccCCcccccCCCCCCEEEEEEEE
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNE-DVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~-dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~ 257 (282)
+.+.|+|.........=+|...-++. .+...++.-... --.|++|++|.+.+..
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~-----~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAE-----ELGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHH-----HCT-STT-EEEEEE-G
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHH-----HcCCCCCCEEEEEEeh
Confidence 56779999998777777777543333 377776443311 1248999999998764
No 202
>PRK10811 rne ribonuclease E; Reviewed
Probab=22.53 E-value=2.7e+02 Score=30.69 Aligned_cols=65 Identities=20% Similarity=0.211 Sum_probs=47.5
Q ss_pred eeeeeeeeEEEEeeCCCceEEEeCCCCCCcEEEEeeccccCC--------Ccccc-cCCCCCCEEEEEEEeCCCC
Q psy547 29 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNN--------PRKLY-KTLAEGETVEFDIMQGDKG 94 (282)
Q Consensus 29 ~~~~~~~G~Vkwfn~~kGfGFI~~~d~~~dvF~H~s~l~~~~--------~~~g~-~~l~~Gd~V~f~v~~~~kG 94 (282)
....-+.|+|+---+.-+=-||.-.+ +...|+|++++.... ..+.. ..|++||.|...|...+.+
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence 34666899999988877778999876 678999999885320 00001 2489999999999987555
No 203
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=20.72 E-value=97 Score=25.54 Aligned_cols=56 Identities=14% Similarity=0.312 Sum_probs=36.7
Q ss_pred EEEeCCCCCCcEEEEeeccccCCCcccccCCCCCCEEEEEEE-eCCCCceEEEEeCCC
Q psy547 48 GFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM-QGDKGHEAINVTGPD 104 (282)
Q Consensus 48 GFI~~~d~~~dvF~H~s~l~~~~~~~g~~~l~~Gd~V~f~v~-~~~kG~~A~~V~~~~ 104 (282)
.|++-++ +..=+||+|.+...-=..=-..|.+||.|...|- .+++|..-..|+...
T Consensus 21 AFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~ 77 (129)
T COG1098 21 AFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLE 77 (129)
T ss_pred eEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhh
Confidence 4777655 6678999999977410000145999999999864 456776666666433
No 204
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=20.52 E-value=1.6e+02 Score=25.82 Aligned_cols=59 Identities=20% Similarity=0.152 Sum_probs=40.2
Q ss_pred eeeeeEEEEEEcCCCeeEEecCCCCccEEEEeccccccCC-----------cccccCCCCCCEEEEEEEEcCCC
Q psy547 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNP-----------RKLYKTLAEGETVEFDIMQGDKG 261 (282)
Q Consensus 199 ~~~~G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~-----------r~g~~~l~~Gd~V~F~i~~~~kG 261 (282)
.-+.|.|...+ .||+-..-. .-|+|+|.+.+-+..- +..-+.|+.||.|.+.|+.....
T Consensus 83 EVV~GeVv~~~---~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~ 152 (183)
T COG1095 83 EVVEGEVVEVV---EFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLK 152 (183)
T ss_pred cEEEEEEEEEe---ecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecc
Confidence 34568888874 477766555 6789999998865410 00112589999999999876543
No 205
>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=20.46 E-value=4.7e+02 Score=21.16 Aligned_cols=58 Identities=19% Similarity=0.169 Sum_probs=38.8
Q ss_pred eEEEEEEcCCCeeEEecCCCCccEEEEeccccccCCcccccCCCCCCEEEEEEEEcCCC-ceeeeeE
Q psy547 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG-NQFCFVL 268 (282)
Q Consensus 203 G~Vk~fn~~kGfGFI~~~d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F~i~~~~kG-~~A~~V~ 268 (282)
|.|+|-.....+=|+..|. +.+|-|+++...- ...++|+.|..+=.-++.| .+|.++.
T Consensus 62 gSv~~~~~~~~~~F~i~D~-~~~i~V~Y~G~~P-------d~F~eg~~VVv~G~~~~~g~F~A~~lL 120 (131)
T PF03100_consen 62 GSVEYDPDGNTLTFTITDG-GKEIPVVYTGPLP-------DLFREGQGVVVEGRLGEDGVFEATELL 120 (131)
T ss_dssp TTEEE-TTSSEEEEEEE-S-S-EEEEEEES--C-------TT--TTSEEEEEEEECCTSEEEEEEEE
T ss_pred CCEEEcCCCCEEEEEEEEC-CcEEEEEECCCCC-------ccccCCCeEEEEEEECCCCEEEEEEEE
Confidence 4444433566799999877 6789999998874 3578999998888776666 8888876
No 206
>PRK11637 AmiB activator; Provisional
Probab=20.32 E-value=1.1e+02 Score=29.93 Aligned_cols=50 Identities=12% Similarity=0.189 Sum_probs=28.6
Q ss_pred eeeeEEEEEEcCCCeeEEecC---CCCccEEEEeccccccCCcccccCCCCCCEEEE
Q psy547 200 KVCGVVKWFSVKSGYGFIATP---SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEF 253 (282)
Q Consensus 200 ~~~G~Vk~fn~~kGfGFI~~~---d~~~dVF~H~s~l~~~~~r~g~~~l~~Gd~V~F 253 (282)
-..|+|.+.....|||-+..- ++---+|-|.+.+.-. .| ..+..|+.+-+
T Consensus 345 ~~~G~V~~~~~~~~~G~~vii~hg~g~~t~Y~~~~~~~v~---~G-~~V~~G~~ig~ 397 (428)
T PRK11637 345 IADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSALVS---VG-AQVRAGQPIAL 397 (428)
T ss_pred cCCeEEEEeeccCCcccEEEEEeCCCcEEEccCCCcCCCC---Cc-CEECCCCeEEe
Confidence 356999888778899954432 2233456676655421 12 34556665543
Done!