Query 008167
Match_columns 575
No_of_seqs 283 out of 1914
Neff 7.6
Searched_HMMs 46136
Date Thu Mar 28 20:20:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 100.0 8E-121 2E-125 1022.9 64.4 548 10-575 93-654 (654)
2 PRK11642 exoribonuclease R; Pr 100.0 9E-120 2E-124 1025.1 64.1 547 11-575 161-725 (813)
3 TIGR02063 RNase_R ribonuclease 100.0 2E-118 4E-123 1016.4 65.4 547 11-575 147-709 (709)
4 COG0557 VacB Exoribonuclease R 100.0 4E-114 9E-119 977.2 59.4 546 12-575 150-704 (706)
5 PRK05054 exoribonuclease II; P 100.0 3E-113 6E-118 957.4 62.1 532 11-575 95-644 (644)
6 TIGR02062 RNase_B exoribonucle 100.0 1E-111 2E-116 942.4 64.1 529 11-573 92-638 (639)
7 KOG2102 Exosomal 3'-5' exoribo 100.0 7E-105 2E-109 908.8 44.0 555 5-574 366-925 (941)
8 PF00773 RNB: RNB domain CAUTI 100.0 3.5E-79 7.5E-84 637.9 30.3 317 111-441 1-324 (325)
9 COG4776 Rnb Exoribonuclease II 100.0 1.1E-75 2.5E-80 592.5 24.9 526 9-571 93-640 (645)
10 cd04471 S1_RNase_R S1_RNase_R: 99.2 1E-10 2.2E-15 96.9 11.1 81 490-575 3-83 (83)
11 cd04460 S1_RpoE S1_RpoE: RpoE, 98.7 5.7E-08 1.2E-12 83.5 9.3 80 490-574 1-83 (99)
12 cd05686 S1_pNO40 S1_pNO40: pNO 98.7 7.8E-08 1.7E-12 77.8 9.2 69 490-575 5-73 (73)
13 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.6 9.4E-08 2E-12 76.3 7.2 68 490-574 2-69 (69)
14 cd05706 S1_Rrp5_repeat_sc10 S1 98.5 5.1E-07 1.1E-11 72.8 9.0 68 490-574 5-72 (73)
15 cd05690 S1_RPS1_repeat_ec5 S1_ 98.5 2.8E-07 6.1E-12 73.3 6.9 68 490-573 2-69 (69)
16 cd05689 S1_RPS1_repeat_ec4 S1_ 98.5 6.1E-07 1.3E-11 72.1 7.9 68 490-573 5-72 (72)
17 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.5 5.8E-07 1.2E-11 72.3 7.5 68 490-574 2-71 (71)
18 cd05703 S1_Rrp5_repeat_hs12_sc 98.5 5.1E-07 1.1E-11 73.0 7.2 70 490-574 2-71 (73)
19 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 4.6E-07 1E-11 72.1 6.5 67 490-573 2-68 (68)
20 cd05708 S1_Rrp5_repeat_sc12 S1 98.4 1.1E-06 2.4E-11 71.4 8.7 69 490-574 4-72 (77)
21 cd05698 S1_Rrp5_repeat_hs6_sc5 98.4 8E-07 1.7E-11 71.0 7.3 68 490-574 2-69 (70)
22 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 7.8E-07 1.7E-11 72.1 7.3 70 490-573 5-74 (74)
23 TIGR00448 rpoE DNA-directed RN 98.4 5.4E-07 1.2E-11 86.0 7.4 88 482-574 74-165 (179)
24 cd04461 S1_Rrp5_repeat_hs8_sc7 98.4 8.2E-07 1.8E-11 73.6 7.0 68 490-574 16-83 (83)
25 COG1098 VacB Predicted RNA bin 98.4 2.8E-07 6E-12 79.9 4.2 67 490-574 7-73 (129)
26 PF00575 S1: S1 RNA binding do 98.4 1.3E-06 2.7E-11 70.6 7.6 68 490-574 6-73 (74)
27 PRK07252 hypothetical protein; 98.4 1.5E-06 3.2E-11 77.2 8.6 68 490-574 5-72 (120)
28 cd05684 S1_DHX8_helicase S1_DH 98.4 2.1E-06 4.5E-11 70.5 8.8 68 490-574 2-71 (79)
29 PRK08582 hypothetical protein; 98.4 1.9E-06 4.2E-11 78.6 9.3 67 490-574 7-73 (139)
30 cd04452 S1_IF2_alpha S1_IF2_al 98.3 2.6E-06 5.7E-11 69.1 8.6 69 490-574 5-74 (76)
31 COG1095 RPB7 DNA-directed RNA 98.3 3.5E-06 7.5E-11 78.8 9.1 80 490-574 83-165 (183)
32 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.3 2.8E-06 6E-11 67.3 7.3 64 491-573 3-66 (66)
33 cd05685 S1_Tex S1_Tex: The C-t 98.3 1.8E-06 3.9E-11 68.1 6.0 67 490-573 2-68 (68)
34 PTZ00248 eukaryotic translatio 98.3 1.7E-06 3.7E-11 88.6 7.0 77 482-574 7-88 (319)
35 cd05704 S1_Rrp5_repeat_hs13 S1 98.2 4.5E-06 9.7E-11 67.3 6.5 66 490-574 5-71 (72)
36 cd05691 S1_RPS1_repeat_ec6 S1_ 98.2 7.9E-06 1.7E-10 65.6 7.8 68 490-574 2-69 (73)
37 PHA02945 interferon resistance 98.2 1.4E-05 3E-10 65.5 8.8 66 490-574 13-81 (88)
38 PRK05807 hypothetical protein; 98.1 1.7E-05 3.8E-10 72.1 9.2 66 490-574 7-72 (136)
39 cd04472 S1_PNPase S1_PNPase: P 98.1 1.4E-05 3.1E-10 63.1 7.6 67 490-574 2-68 (68)
40 cd05692 S1_RPS1_repeat_hs4 S1_ 98.1 1.5E-05 3.4E-10 62.8 7.6 67 490-574 2-68 (69)
41 cd05688 S1_RPS1_repeat_ec3 S1_ 98.1 1.6E-05 3.4E-10 62.8 7.4 66 490-573 3-68 (68)
42 PRK08059 general stress protei 98.0 1.5E-05 3.2E-10 71.3 7.8 68 490-574 9-76 (123)
43 cd04473 S1_RecJ_like S1_RecJ_l 98.0 2.7E-05 5.9E-10 63.6 8.4 60 490-575 18-77 (77)
44 PRK08563 DNA-directed RNA poly 98.0 5.2E-05 1.1E-09 73.0 11.0 80 490-574 83-165 (187)
45 PLN00207 polyribonucleotide nu 98.0 2.8E-05 6.1E-10 89.4 10.0 78 479-574 743-822 (891)
46 smart00316 S1 Ribosomal protei 97.9 4E-05 8.8E-10 60.5 7.8 68 490-574 4-71 (72)
47 cd05694 S1_Rrp5_repeat_hs2_sc2 97.9 5.3E-05 1.1E-09 61.4 8.4 63 490-574 6-68 (74)
48 PRK03987 translation initiatio 97.9 2.6E-05 5.7E-10 78.6 7.8 69 490-574 10-79 (262)
49 COG0539 RpsA Ribosomal protein 97.9 3.7E-05 8.1E-10 83.9 9.5 67 490-574 194-260 (541)
50 COG0539 RpsA Ribosomal protein 97.9 2.9E-05 6.4E-10 84.7 7.6 68 490-574 279-346 (541)
51 cd05687 S1_RPS1_repeat_ec1_hs1 97.9 6E-05 1.3E-09 60.1 7.5 68 490-574 2-69 (70)
52 cd00164 S1_like S1_like: Ribos 97.8 5.3E-05 1.2E-09 58.5 6.7 65 492-573 1-65 (65)
53 PRK07899 rpsA 30S ribosomal pr 97.8 7E-05 1.5E-09 81.9 9.3 68 490-574 295-362 (486)
54 cd04465 S1_RPS1_repeat_ec2_hs2 97.7 0.00018 4E-09 56.9 7.6 65 490-574 2-66 (67)
55 cd05693 S1_Rrp5_repeat_hs1_sc1 97.7 6.7E-05 1.5E-09 64.5 5.0 84 490-574 5-94 (100)
56 cd05702 S1_Rrp5_repeat_hs11_sc 97.6 0.0002 4.4E-09 57.2 6.7 62 490-564 2-63 (70)
57 PRK12269 bifunctional cytidyla 97.6 0.0002 4.3E-09 83.4 9.0 71 490-574 754-824 (863)
58 PRK07400 30S ribosomal protein 97.6 0.00021 4.6E-09 74.3 8.5 67 490-574 198-264 (318)
59 PRK07899 rpsA 30S ribosomal pr 97.5 0.0004 8.7E-09 76.1 10.5 67 490-574 210-276 (486)
60 PRK13806 rpsA 30S ribosomal pr 97.5 0.00019 4.1E-09 79.3 7.6 68 490-574 381-448 (491)
61 PRK11824 polynucleotide phosph 97.5 0.00071 1.5E-08 77.6 11.7 67 490-574 623-689 (693)
62 PRK13806 rpsA 30S ribosomal pr 97.4 0.00037 8E-09 77.0 7.6 69 490-574 294-362 (491)
63 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.4 0.00052 1.1E-08 57.1 6.7 71 490-574 8-78 (86)
64 TIGR02696 pppGpp_PNP guanosine 97.3 0.00047 1E-08 77.9 7.5 69 490-573 649-718 (719)
65 PRK12269 bifunctional cytidyla 97.3 0.00051 1.1E-08 80.0 7.8 69 490-574 667-735 (863)
66 PTZ00162 DNA-directed RNA poly 97.3 0.0016 3.5E-08 61.9 9.9 70 490-565 83-154 (176)
67 TIGR00717 rpsA ribosomal prote 97.3 0.00063 1.4E-08 75.8 8.3 68 490-574 448-515 (516)
68 PRK06299 rpsA 30S ribosomal pr 97.3 0.00053 1.1E-08 77.3 7.4 69 490-574 375-443 (565)
69 COG1093 SUI2 Translation initi 97.3 0.00025 5.4E-09 69.7 4.1 69 490-574 13-82 (269)
70 cd04453 S1_RNase_E S1_RNase_E: 97.2 0.0014 3.1E-08 54.9 7.6 63 490-564 9-73 (88)
71 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.2 0.0029 6.3E-08 53.0 9.4 68 490-564 3-72 (88)
72 PRK06676 rpsA 30S ribosomal pr 97.2 0.00098 2.1E-08 71.6 8.3 68 490-574 279-346 (390)
73 PRK00087 4-hydroxy-3-methylbut 97.2 0.00098 2.1E-08 76.2 8.1 68 490-574 564-631 (647)
74 cd04455 S1_NusA S1_NusA: N-uti 97.1 0.0024 5.2E-08 50.5 7.4 62 490-573 5-66 (67)
75 TIGR03591 polynuc_phos polyrib 97.1 0.0019 4.2E-08 74.0 9.6 65 490-572 620-684 (684)
76 cd04454 S1_Rrp4_like S1_Rrp4_l 97.0 0.0021 4.6E-08 52.9 6.9 67 490-574 8-74 (82)
77 PRK06676 rpsA 30S ribosomal pr 97.0 0.0032 7E-08 67.6 9.6 67 490-574 194-260 (390)
78 TIGR00717 rpsA ribosomal prote 96.9 0.0017 3.7E-08 72.4 7.4 69 490-574 361-429 (516)
79 COG2183 Tex Transcriptional ac 96.8 0.0015 3.3E-08 73.6 5.6 68 490-574 660-727 (780)
80 PRK07400 30S ribosomal protein 96.8 0.0066 1.4E-07 63.3 9.9 64 489-574 119-182 (318)
81 PRK06299 rpsA 30S ribosomal pr 96.8 0.0025 5.3E-08 71.9 7.0 69 490-574 288-356 (565)
82 PRK09202 nusA transcription el 96.3 0.038 8.1E-07 60.5 11.8 63 489-573 135-197 (470)
83 PRK00087 4-hydroxy-3-methylbut 96.1 0.021 4.5E-07 65.5 9.4 68 489-574 478-545 (647)
84 COG1185 Pnp Polyribonucleotide 96.0 0.013 2.9E-07 65.1 6.9 67 490-574 621-687 (692)
85 PRK12327 nusA transcription el 95.7 0.093 2E-06 55.5 11.4 70 482-573 128-197 (362)
86 PRK09521 exosome complex RNA-b 95.5 0.032 6.9E-07 53.8 6.4 66 490-574 66-140 (189)
87 PRK04163 exosome complex RNA-b 95.2 0.058 1.3E-06 53.8 7.5 71 490-574 65-135 (235)
88 TIGR01953 NusA transcription t 95.1 0.2 4.4E-06 52.6 11.5 70 482-573 125-195 (341)
89 PHA02858 EIF2a-like PKR inhibi 94.8 0.042 9E-07 44.9 4.1 64 495-575 22-86 (86)
90 cd05699 S1_Rrp5_repeat_hs7 S1_ 94.5 0.093 2E-06 42.0 5.5 67 491-573 3-70 (72)
91 PF08206 OB_RNB: Ribonuclease 93.2 0.093 2E-06 40.2 3.2 52 8-61 6-58 (58)
92 KOG3298 DNA-directed RNA polym 93.2 0.47 1E-05 43.7 8.1 70 490-564 83-152 (170)
93 KOG1067 Predicted RNA-binding 91.7 0.41 8.9E-06 52.2 6.8 60 490-564 670-729 (760)
94 TIGR00008 infA translation ini 91.5 1.2 2.7E-05 35.2 7.5 62 490-572 5-67 (68)
95 KOG1070 rRNA processing protei 91.3 0.18 4E-06 60.1 3.9 68 490-574 601-668 (1710)
96 COG2996 Predicted RNA-bindinin 91.0 0.58 1.3E-05 46.8 6.6 59 490-574 157-215 (287)
97 PRK12442 translation initiatio 90.2 2 4.4E-05 35.6 7.9 63 490-573 7-70 (87)
98 PRK12328 nusA transcription el 89.8 3.4 7.4E-05 43.8 11.4 70 482-573 132-203 (374)
99 PRK12329 nusA transcription el 89.5 3.7 8E-05 44.3 11.5 71 483-573 147-222 (449)
100 cd05791 S1_CSL4 S1_CSL4: CSL4, 88.2 1.2 2.7E-05 37.5 5.7 69 490-574 8-84 (92)
101 KOG1070 rRNA processing protei 87.2 1.8 3.8E-05 52.3 7.9 68 490-574 1164-1231(1710)
102 PF08292 RNA_pol_Rbc25: RNA po 84.8 9.9 0.00022 33.8 9.8 69 490-563 5-76 (122)
103 TIGR02063 RNase_R ribonuclease 84.4 2 4.4E-05 49.9 6.8 60 9-68 77-137 (709)
104 COG0361 InfA Translation initi 82.3 10 0.00022 30.7 7.9 63 490-573 7-70 (75)
105 COG1107 Archaea-specific RecJ- 82.2 1 2.2E-05 49.6 2.9 62 490-574 124-185 (715)
106 TIGR00757 RNaseEG ribonuclease 80.4 4.4 9.5E-05 43.9 7.0 69 490-561 27-97 (414)
107 smart00357 CSP Cold shock prot 79.2 6.5 0.00014 29.7 5.9 51 10-62 9-64 (64)
108 cd05790 S1_Rrp40 S1_Rrp40: Rrp 74.7 14 0.00031 30.8 6.9 59 490-564 8-66 (86)
109 PF13509 S1_2: S1 domain; PDB: 74.5 20 0.00043 27.6 7.3 48 492-562 5-52 (61)
110 COG1097 RRP4 RNA-binding prote 63.7 21 0.00046 35.4 6.6 64 490-564 66-129 (239)
111 PRK04012 translation initiatio 58.6 51 0.0011 28.3 7.3 62 490-573 21-83 (100)
112 cd05793 S1_IF1A S1_IF1A: Trans 56.7 53 0.0011 26.7 6.8 60 492-573 2-62 (77)
113 PF10447 EXOSC1: Exosome compo 52.4 21 0.00047 29.4 3.9 59 490-560 6-81 (82)
114 PRK10811 rne ribonuclease E; R 51.7 42 0.00092 39.9 7.4 67 490-563 40-109 (1068)
115 KOG1856 Transcription elongati 46.2 24 0.00052 42.3 4.4 59 491-564 988-1049(1299)
116 PRK15464 cold shock-like prote 43.7 64 0.0014 25.7 5.3 53 492-562 5-59 (70)
117 PF02599 CsrA: Global regulato 43.5 66 0.0014 24.3 5.0 23 541-563 5-27 (54)
118 PRK00276 infA translation init 43.1 1.6E+02 0.0034 23.4 7.5 62 490-572 7-69 (72)
119 smart00652 eIF1a eukaryotic tr 39.9 1.6E+02 0.0034 24.3 7.2 61 490-572 5-66 (83)
120 cd04456 S1_IF1A_like S1_IF1A_l 39.7 1.5E+02 0.0033 24.1 7.0 49 493-561 3-52 (78)
121 COG1096 Predicted RNA-binding 38.9 85 0.0018 30.0 6.1 57 490-562 66-133 (188)
122 PRK15463 cold shock-like prote 38.6 84 0.0018 25.0 5.2 52 492-561 5-58 (70)
123 PRK09937 stationary phase/star 37.2 98 0.0021 24.9 5.5 52 493-562 3-56 (74)
124 COG1551 CsrA RNA-binding globa 37.0 51 0.0011 26.3 3.6 23 541-563 5-27 (73)
125 PRK11712 ribonuclease G; Provi 35.8 88 0.0019 34.8 6.6 71 490-563 40-112 (489)
126 PRK01712 carbon storage regula 34.9 88 0.0019 24.5 4.6 22 542-563 6-27 (64)
127 PF03544 TonB_C: Gram-negative 34.9 68 0.0015 25.2 4.3 22 203-224 17-38 (79)
128 PRK09507 cspE cold shock prote 33.0 1.4E+02 0.003 23.5 5.7 54 491-562 3-58 (69)
129 PTZ00329 eukaryotic translatio 32.8 1.3E+02 0.0029 27.9 6.2 62 490-573 32-94 (155)
130 PF13103 TonB_2: TonB C termin 32.4 64 0.0014 26.0 3.8 25 200-224 24-48 (85)
131 cd05701 S1_Rrp5_repeat_hs10 S1 31.4 98 0.0021 24.3 4.2 58 492-563 4-61 (69)
132 PRK00568 carbon storage regula 30.9 79 0.0017 25.7 3.9 22 542-563 6-27 (76)
133 TIGR00358 3_prime_RNase VacB a 30.2 1.2E+02 0.0026 35.1 6.9 58 9-67 25-83 (654)
134 CHL00010 infA translation init 29.5 3.1E+02 0.0066 22.2 7.3 61 491-572 8-69 (78)
135 PRK10354 RNA chaperone/anti-te 28.0 1.8E+02 0.004 22.9 5.6 52 493-562 6-59 (70)
136 cd04508 TUDOR Tudor domains ar 28.0 85 0.0018 22.2 3.4 33 490-522 13-46 (48)
137 KOG2916 Translation initiation 27.9 23 0.00049 35.5 0.4 77 481-573 5-86 (304)
138 PRK10943 cold shock-like prote 27.6 1.7E+02 0.0038 23.0 5.4 54 491-562 3-58 (69)
139 TIGR01352 tonB_Cterm TonB fami 27.5 1E+02 0.0022 23.8 4.2 20 204-223 12-31 (74)
140 PF01176 eIF-1a: Translation i 26.3 1.7E+02 0.0037 22.7 5.1 52 491-562 4-56 (65)
141 COG4871 Uncharacterized protei 26.2 1.3E+02 0.0028 28.0 4.9 50 271-321 64-113 (193)
142 cd04458 CSP_CDS Cold-Shock Pro 26.0 1.8E+02 0.0038 22.2 5.1 51 493-561 2-54 (65)
143 PRK14998 cold shock-like prote 25.8 2E+02 0.0044 23.0 5.5 52 493-562 3-56 (73)
144 TIGR00523 eIF-1A eukaryotic/ar 25.7 4.2E+02 0.0092 22.6 8.0 49 490-558 19-68 (99)
145 TIGR00202 csrA carbon storage 25.5 1.3E+02 0.0028 24.0 4.1 22 542-563 6-27 (69)
146 PLN00208 translation initiatio 24.3 2.3E+02 0.0051 26.0 6.2 61 490-572 32-93 (145)
147 PF10615 DUF2470: Protein of u 23.1 4.1E+02 0.0088 21.5 8.4 61 453-522 8-68 (83)
148 PRK06763 F0F1 ATP synthase sub 22.4 2.3E+02 0.0051 27.4 6.0 34 486-519 36-69 (213)
149 smart00333 TUDOR Tudor domain. 21.9 1.4E+02 0.003 21.9 3.7 33 490-522 17-50 (57)
150 PRK11642 exoribonuclease R; Pr 20.9 2E+02 0.0044 34.1 6.6 58 8-67 92-150 (813)
No 1
>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=100.00 E-value=8.1e-121 Score=1022.93 Aligned_cols=548 Identities=26% Similarity=0.415 Sum_probs=503.0
Q ss_pred ccEEEEEeCCCCCCc-eEecCCcc--CcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCC
Q 008167 10 VAHALFVPKDRRIPK-IRIQTRQL--GNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPF 86 (575)
Q Consensus 10 ~~~~~~~P~d~r~p~-i~i~~~~~--~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f 86 (575)
++..+++|.|+|++. |.|++... ....|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|||+. .|
T Consensus 93 ~~~~~v~p~~~~~~~~i~i~~~~~~~~~~~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~-~f 171 (654)
T TIGR00358 93 NDFGFVVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF-EF 171 (654)
T ss_pred CCeEEEEECCCCCCCcEEEcCCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC-CC
Confidence 346789999999984 88877632 345799999999999999999999999999999999999999999999998 69
Q ss_pred cHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHH
Q 008167 87 STQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDE 166 (575)
Q Consensus 87 ~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~e 166 (575)
|++++++++..++.+++++.. +|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+|
T Consensus 172 ~~~v~~~a~~~~~~~~~~~~~--~R~Dlr~~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~e 249 (654)
T TIGR00358 172 PDGVEQQAAKLQFDVDEQAKK--YREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKE 249 (654)
T ss_pred CHHHHHHHHhccccCChhHhh--CccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHH
Confidence 999999999888888777776 899999999999999999999999999999889999999999999999999999999
Q ss_pred HHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC
Q 008167 167 ASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL 246 (575)
Q Consensus 167 A~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~ 246 (575)
|++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|.+++|++|+|+|+++|||++|+++|+++..
T Consensus 250 A~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~ 329 (654)
T TIGR00358 250 AKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDE 329 (654)
T ss_pred HHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999987532
Q ss_pred ----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHH
Q 008167 247 ----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQI 322 (575)
Q Consensus 247 ----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l 322 (575)
..++.++|..|+++|++|+++|.++|+++|+.||.+|.+|++ |.+..+...+++.||.|||||||+||++||+|+
T Consensus 330 ~~~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~~~d~~-g~~~~i~~~~~~~a~~lIeE~MilAN~~vA~~~ 408 (654)
T TIGR00358 330 LQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEE-GRVIDIVAEVRRIAEKIIEEAMIVANICAARFL 408 (654)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeEEECCC-CCeeEEEeccCcHHHHHHHHHHHHHHHHHHHHH
Confidence 235678999999999999999999999999999999999875 678888888899999999999999999999999
Q ss_pred HHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC-----CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167 323 LRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS-----SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF 397 (575)
Q Consensus 323 ~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~-----~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~ 397 (575)
.++ +.|++||+|++|+++++++|.++++.+|+.++.. ++.+++..|.++.+. + ...+++.+++|+|++|+|
T Consensus 409 ~~~-~~p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~~l~~~llr~m~~A~y- 484 (654)
T TIGR00358 409 HNH-KVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDR-P-EYEILVTRLLRSLSQAEY- 484 (654)
T ss_pred HHc-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHHHHhhCC-C-HHHHHHHHHHHhhccccc-
Confidence 987 8899999999999999999999999999986431 467788888877652 2 344788899999999999
Q ss_pred ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCC-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 008167 398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL-PSVFQDRPQLTSIADNLNYRHRNAQMASRGS 476 (575)
Q Consensus 398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~-~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~ 476 (575)
+.+|.+|||||++.|||||||||||+||+|||||+++|.+++. +....+.++|..+|.+||.+++.|++|||++
T Consensus 485 -----~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~ 559 (654)
T TIGR00358 485 -----SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDV 559 (654)
T ss_pred -----CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999999999999999987642 1112355789999999999999999999999
Q ss_pred HHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEE
Q 008167 477 VELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVN 555 (575)
Q Consensus 477 ~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~ 555 (575)
.++|.|+||+++. ++|+|+|++|+++|++|.|+++|+||+||++++++++ |.||+.++++.|+++++.|++||+|+
T Consensus 560 ~~~~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~---y~~d~~~~~l~g~~~~~~~~lGD~V~ 636 (654)
T TIGR00358 560 ADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDY---YVFDQEKMALIGKGTGKVYRIGDRVT 636 (654)
T ss_pred HHHHHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcc---eEEeccccEEEeccCCcEECCCCEEE
Confidence 9999999999987 7899999999999999999999999999999999886 99999999999998899999999999
Q ss_pred EEEEEecCCCCCCceEEEeC
Q 008167 556 IHMEVVEPQPNRPKLQLTLI 575 (575)
Q Consensus 556 V~V~~vd~~~~~~~i~l~l~ 575 (575)
|+|.++|.+ +++|.|+++
T Consensus 637 Vki~~vd~~--~~~I~f~l~ 654 (654)
T TIGR00358 637 VKLTEVNME--TRSIIFELV 654 (654)
T ss_pred EEEEEEecc--cCeEEEEEC
Confidence 999999976 899999974
No 2
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=8.7e-120 Score=1025.06 Aligned_cols=547 Identities=27% Similarity=0.430 Sum_probs=501.5
Q ss_pred cEEEEEeCCCCCC-ceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcH
Q 008167 11 AHALFVPKDRRIP-KIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFST 88 (575)
Q Consensus 11 ~~~~~~P~d~r~p-~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~ 88 (575)
+..+++|.|.|++ .|.|+..... ...|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|+|+. .||+
T Consensus 161 ~~~~v~P~d~r~~~~i~i~~~~~~~~~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~-~Fp~ 239 (813)
T PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPY-IWPQ 239 (813)
T ss_pred CeEEEEECCCCCCCcEEeccccccCCCCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCC-CCCH
Confidence 4578999999998 5999876543 34689999999999999999999999999999999999999999999998 5999
Q ss_pred HHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHH
Q 008167 89 QVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEAS 168 (575)
Q Consensus 89 ~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~ 168 (575)
+|++++..+++.+++++.+ +|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||+
T Consensus 240 ~v~~ea~~~~~~~~~~~~~--~R~DLr~l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~ 317 (813)
T PRK11642 240 AVEQQVAGLKEEVPEEAKA--GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREAR 317 (813)
T ss_pred HHHHHHHhccccCChhHhc--cccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHH
Confidence 9999999888888777766 89999999999999999999999999999988899999999999999999999999999
Q ss_pred hCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC--
Q 008167 169 KRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL-- 246 (575)
Q Consensus 169 ~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~-- 246 (575)
+||||+|||++++||||+.||+++|||+||++|+||||.|+||.+|+|.+++|++|+|+|+++|||++|+++|+++..
T Consensus 318 ~RgtSvYlpd~viPMLP~~Lsn~lcSL~p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~ 397 (813)
T PRK11642 318 NRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLR 397 (813)
T ss_pred HhCCeEeCCCceeeCCCHHHhcCccccCCCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999987532
Q ss_pred --CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHH
Q 008167 247 --MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILR 324 (575)
Q Consensus 247 --~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~ 324 (575)
..++.++|..|+++|+.|+++|.++|+|+|+.||.+|.+|++ |.+..+...++.+||.|||||||+||++||+|+.+
T Consensus 398 ~~~~~~~~~L~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~ld~~-g~~~~i~~~~~~~a~~lIEE~MllAN~~vA~~l~~ 476 (813)
T PRK11642 398 EQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAE-RRIERIEQTQRNDAHKLIEECMILANISAARFVEK 476 (813)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceEEEECCC-CCEeeEEecccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 235678899999999999999999999999999999999976 67888888899999999999999999999999998
Q ss_pred hCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC---CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCC
Q 008167 325 QFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGD 401 (575)
Q Consensus 325 ~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~ 401 (575)
+ +.|++||+|+.|+++++++|.+++..+|+.++.. +++.+++.++.+.+ .| ...+++.+++|+|++|.|
T Consensus 477 ~-~~p~lyR~H~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~~~~-~~-~~~~l~~~llRsm~~A~Y----- 548 (813)
T PRK11642 477 A-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVAD-RP-DAEMLQTMLLRSMKQAIY----- 548 (813)
T ss_pred C-CCCEEEEeCCCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHHHhC-Cc-HHHHHHHHHHHhcccccc-----
Confidence 6 8999999999999999999999999999988542 46778888887755 33 235788999999999999
Q ss_pred CCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCC-------C-CCCChhHHHHHHHHHHHHHHHHHHHH
Q 008167 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP-------S-VFQDRPQLTSIADNLNYRHRNAQMAS 473 (575)
Q Consensus 402 ~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~-------~-~~~~~~~l~~~~~~~n~~~~~a~~a~ 473 (575)
++++.+|||||++.|||||||||||+||+|||+|+++|.++... . .....+.|..+|++||.++++|.+|+
T Consensus 549 -~~~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~ae 627 (813)
T PRK11642 549 -DPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEAT 627 (813)
T ss_pred -CCCCCCccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCcccccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999999999999764311 0 01123568999999999999999999
Q ss_pred HHHHHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCc
Q 008167 474 RGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQ 552 (575)
Q Consensus 474 r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD 552 (575)
|++.+++.|+||++++ ++|+|+|++|.++|+||.|+++++||+||+++++++| |.|++.+++++|+++++.|++||
T Consensus 628 R~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~---y~~d~~~~~L~g~~~~~~~~lGD 704 (813)
T PRK11642 628 RDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDY---YRFDQVGQRLIGESSGQTYRLGD 704 (813)
T ss_pred HHHHHHHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcc---eEecchheEEecccCCcEECCCC
Confidence 9999999999999877 7899999999999999999998899999999999888 99999999999999999999999
Q ss_pred EEEEEEEEecCCCCCCceEEEeC
Q 008167 553 TVNIHMEVVEPQPNRPKLQLTLI 575 (575)
Q Consensus 553 ~V~V~V~~vd~~~~~~~i~l~l~ 575 (575)
+|+|+|..+|.. +++|.|+++
T Consensus 705 ~V~VkV~~vD~~--~rkI~f~l~ 725 (813)
T PRK11642 705 RVEVRVEAVNMD--ERKIDFSLI 725 (813)
T ss_pred EEEEEEEEeecC--CCeEEEEEe
Confidence 999999999976 899999974
No 3
>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=100.00 E-value=1.7e-118 Score=1016.36 Aligned_cols=547 Identities=31% Similarity=0.480 Sum_probs=503.4
Q ss_pred cEEEEEeCCCCCC-ceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcH
Q 008167 11 AHALFVPKDRRIP-KIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFST 88 (575)
Q Consensus 11 ~~~~~~P~d~r~p-~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~ 88 (575)
+..+++|.|+|++ .|.|++....+ ..|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|||+. .||+
T Consensus 147 ~~~~v~p~d~~~~~~I~i~~~~~~~~~~g~~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~-~f~~ 225 (709)
T TIGR02063 147 GIGFVIPDDKRIYLDIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY-EFPE 225 (709)
T ss_pred cEEEEEECCCCCCCCEEECCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCC-CCCH
Confidence 4688999999998 59998775433 4689999999999999999999999999999999999999999999998 6999
Q ss_pred HHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHH
Q 008167 89 QVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEAS 168 (575)
Q Consensus 89 ~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~ 168 (575)
++++++...++.+++++.+ +|+|||++++|||||++|+|+||||||++.++|+|+|||||||||+||++||+||+||+
T Consensus 226 ~v~~~a~~~~~~~~~~~~~--~R~Dl~~~~~~tID~~~a~D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~ 303 (709)
T TIGR02063 226 EVLDEAAKIPEEVPEEEIK--GRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEAL 303 (709)
T ss_pred HHHHHHHhCCCCCChhHhh--cccccccCcEEEECCCCCcccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHH
Confidence 9999999888888766666 89999999999999999999999999999988899999999999999999999999999
Q ss_pred hCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC--
Q 008167 169 KRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL-- 246 (575)
Q Consensus 169 ~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~-- 246 (575)
+||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++++|++|+|+|+++|||++|+++|+++..
T Consensus 304 ~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~ 383 (709)
T TIGR02063 304 KRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALD 383 (709)
T ss_pred HhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEEEEECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999987542
Q ss_pred --CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHH
Q 008167 247 --MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILR 324 (575)
Q Consensus 247 --~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~ 324 (575)
..++.++|..|+++|+.|+++|.++|+++|+.|+.+|.+|++ |.+..+...+++.||.|||||||+||++||+++.+
T Consensus 384 ~~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~~d~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~ 462 (709)
T TIGR02063 384 KKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDEN-GKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEK 462 (709)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeEECCC-CCeEEEEeccchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 235778999999999999999999999999999999999976 77889988899999999999999999999999987
Q ss_pred hCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCC-----CCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceeccc
Q 008167 325 QFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDV-----SSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCS 399 (575)
Q Consensus 325 ~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~-----~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~ 399 (575)
+ +.|++||+|++|+++++++|.++++.+|++++. .++++++++|+++.+ .+ ...+++.+++|+|++|.|
T Consensus 463 ~-~~p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~~l~~~llr~m~~A~y--- 536 (709)
T TIGR02063 463 A-KLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKG-RP-EEELINTVLLRSMQQAKY--- 536 (709)
T ss_pred C-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHHHHhhC-Cc-HHHHHHHHHHHHhcCccc---
Confidence 5 899999999999999999999999999998753 367888999887765 23 335788999999999999
Q ss_pred CCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCC-C-CC--CCChhHHHHHHHHHHHHHHHHHHHHHH
Q 008167 400 GDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL-P-SV--FQDRPQLTSIADNLNYRHRNAQMASRG 475 (575)
Q Consensus 400 ~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~-~-~~--~~~~~~l~~~~~~~n~~~~~a~~a~r~ 475 (575)
+..|.+|||||++.|||||||||||+||+|||||+++|.+++. + .. ....+.|+.+|.+||.++++|++|||+
T Consensus 537 ---~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~ 613 (709)
T TIGR02063 537 ---SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERD 613 (709)
T ss_pred ---CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6688999999999999999999999999999999999987632 1 11 223567999999999999999999999
Q ss_pred HHHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEE
Q 008167 476 SVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTV 554 (575)
Q Consensus 476 ~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V 554 (575)
+.++|+|+||+.+. ++++|+|++|.++|+||.|+++|++|+||++++++++ |.|++..+.+.|++.++.|++||+|
T Consensus 614 ~~~~~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~---~~~d~~~~~l~g~~~~~~~~lGd~V 690 (709)
T TIGR02063 614 VNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY---YVFDEKGLALVGERTGKVFRLGDRV 690 (709)
T ss_pred HHHHHHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc---EEEcccceEEEeccCCcEECCCCEE
Confidence 99999999999887 7899999999999999999998999999999999887 8999999999999889999999999
Q ss_pred EEEEEEecCCCCCCceEEEeC
Q 008167 555 NIHMEVVEPQPNRPKLQLTLI 575 (575)
Q Consensus 555 ~V~V~~vd~~~~~~~i~l~l~ 575 (575)
+|+|.+||.. +++|.|+|.
T Consensus 691 ~Vkv~~vd~~--~~~I~~~l~ 709 (709)
T TIGR02063 691 KVRVVKADLD--TGKIDFELV 709 (709)
T ss_pred EEEEEEEecc--cCeEEEEEC
Confidence 9999999975 899999974
No 4
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=4e-114 Score=977.25 Aligned_cols=546 Identities=36% Similarity=0.593 Sum_probs=507.1
Q ss_pred EEEEEeCCCCCC-ceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcHH
Q 008167 12 HALFVPKDRRIP-KIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQ 89 (575)
Q Consensus 12 ~~~~~P~d~r~p-~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~~ 89 (575)
+++++|.|+|++ .|.|++++.+ ...|++++|+|+.||.++.+|.|+++++||..+++..++++++++|++++. ||++
T Consensus 150 ~~~~~p~d~r~~~~i~i~~~~~~~~~~~~~v~~~i~~~~~~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i~~~-f~~~ 228 (706)
T COG0557 150 IGRVLPDDKRLPFLIAIPPEQAPGAEEGHLVVVEITRWPDTSRPPFGEVVEVLGDLGDPGADIEAILRDHGIPSE-FPEK 228 (706)
T ss_pred eEEEEecCCCCccceeeccccccccccCCEEEEEecccCCcCCCCceeEEEeecCCCCcchhHHHHHHHcCCCCC-CCHH
Confidence 799999999999 6999987765 567999999999999999999999999999999999999999999999995 9999
Q ss_pred HHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHh
Q 008167 90 VLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169 (575)
Q Consensus 90 v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~ 169 (575)
+++++...+..+.+++.. +|.|||++++|||||++|+|+|||||++++.+|+|+|||||||||+||+|||+||+||++
T Consensus 229 v~~~a~~~~~~~~~~~~~--~R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~ 306 (706)
T COG0557 229 VLDEAAALPDEVPEEDLK--GRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARK 306 (706)
T ss_pred HHHHHHhccCcCChhhhc--CccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHH
Confidence 999999888877677777 999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCC--CCC
Q 008167 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDS--RLM 247 (575)
Q Consensus 170 R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~--~~~ 247 (575)
||||||||++++||||+.||+++|||+|+++|+|+||.|++|++|+|.+++|++|+|+|+++|||++|+++|++. ...
T Consensus 307 RgtSVYlp~~vipMLPe~Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~ 386 (706)
T COG0557 307 RGTSVYLPDRVIPMLPEALSNGLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKY 386 (706)
T ss_pred cCCeEEcCCcccCCCchhhcCCccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcchhc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999986 344
Q ss_pred CchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHHhCC
Q 008167 248 DPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFP 327 (575)
Q Consensus 248 ~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~~~~ 327 (575)
.++.+.|..|.++++.++++|.++|+++|+.+|.++.+|++ |.|..|...++..+|.||||||++||++||+++.++ .
T Consensus 387 ~~l~~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~~-~~~~~i~~~~r~~a~~lIee~Ml~AN~~vA~~l~~~-~ 464 (706)
T COG0557 387 APLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDEE-GRPVEIEIRERLDAEKLIEEFMLLANETVAEHLEKH-K 464 (706)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECCC-CCeeeEEEecccHHHHHHHHHHHHHHHHHHHHHHHc-C
Confidence 56778999999999999999999999999999999999976 678999999999999999999999999999999998 5
Q ss_pred CceeeeeCCCCChhhHHHHHHHHHHcCCccCCCC----HHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCC
Q 008167 328 LCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS----SKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLT 403 (575)
Q Consensus 328 ~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~----~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~ 403 (575)
.|.+||+|+.|+.++++.|.+++..+|+.+.... +..++..+++..+ .| ...+++.+++|+|++|.| +
T Consensus 465 ~~~~~R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~v~~~~~lRsm~~a~Y------s 536 (706)
T COG0557 465 IPLLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKG-RP-LEAVLQTLLLRSMKQAEY------S 536 (706)
T ss_pred CCcceeCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccC-Ch-HHHHHHHHHHHhhhcCee------c
Confidence 6789999999999999999999999999887442 5567777766542 23 456788899999999999 6
Q ss_pred CCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167 404 PPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLI 483 (575)
Q Consensus 404 ~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~ 483 (575)
+.+.+|||||++.|||||||||||+||+|||||+++|.++..+......++|..+|.+||.++|+|..|+|++.++|+|.
T Consensus 537 ~~~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~ 616 (706)
T COG0557 537 PDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAE 616 (706)
T ss_pred CCCCCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Confidence 77999999999999999999999999999999999999876654332347899999999999999999999999999999
Q ss_pred HHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 484 YFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 484 ~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
||++++ ++|+|+|++|.++|++|.|+++|++|+||++.+++++ |.|++..+.+.|++.+..|++||.|+|+|.+++
T Consensus 617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~---y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~ 693 (706)
T COG0557 617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDY---YHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD 693 (706)
T ss_pred HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCce---eeeccccceeeccccccccccCCEEEEEEEEEc
Confidence 999998 5999999999999999999999999999999999987 999999999999999999999999999999999
Q ss_pred CCCCCCceEEEeC
Q 008167 563 PQPNRPKLQLTLI 575 (575)
Q Consensus 563 ~~~~~~~i~l~l~ 575 (575)
.. .++|.|+++
T Consensus 694 ~~--~~~i~~~~v 704 (706)
T COG0557 694 LD--ERKIDFELV 704 (706)
T ss_pred cc--ccceEEEec
Confidence 75 899999875
No 5
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=2.6e-113 Score=957.38 Aligned_cols=532 Identities=21% Similarity=0.287 Sum_probs=466.9
Q ss_pred cEEEEEeCCCCCC-ceEecCC-c-c-CcCCCCEEEEEEeecCCC-CCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCC
Q 008167 11 AHALFVPKDRRIP-KIRIQTR-Q-L-GNLLDKRIIVAVDSWDCQ-SRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARP 85 (575)
Q Consensus 11 ~~~~~~P~d~r~p-~i~i~~~-~-~-~~~~~~~~~v~i~~w~~~-~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~ 85 (575)
+..+++|.|.+++ .|.|+.. . . ....|++|+|+|++||.. ...|.|+|+++||..+++++++++++++|+|+. .
T Consensus 95 ~~~~~~p~d~~~~~~i~i~~~~~~~~~~~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~-~ 173 (644)
T PRK05054 95 DRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLER-E 173 (644)
T ss_pred ceEEEEECCCCCCccEEeccccccccCCCCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCC-C
Confidence 4678999999998 5888532 2 2 334689999999999986 456999999999999999999999999999998 5
Q ss_pred CcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHH
Q 008167 86 FSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDD 165 (575)
Q Consensus 86 f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~ 165 (575)
||+++++. .+.+++ . +|+|||++++|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+
T Consensus 174 f~~~~~~~------~~~~~~-~--~R~Dlr~~~~~TID~~~akD~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~ 244 (644)
T PRK05054 174 APAGGVAW------EMLDEG-L--EREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDK 244 (644)
T ss_pred CCchhhhc------cCChhc-c--CcccccCCcEEEECCCCCCcccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHH
Confidence 99987542 222222 2 79999999999999999999999999999988899999999999999999999999
Q ss_pred HHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEE-EEEEEEEEeecceeCHHHHHHHhcCC
Q 008167 166 EASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS-TRYTKSVIKSCAALSYVEAQARMDDS 244 (575)
Q Consensus 166 eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~-~~~~~s~I~s~~~ltY~~v~~~l~~~ 244 (575)
||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+++
T Consensus 245 eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~~~R~als~~~~id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~ 324 (644)
T PRK05054 245 AARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENG 324 (644)
T ss_pred HHHHhCceEeCCCCcccCCChHHhcCccccCCCCCceEEEEEEEEeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999999999999999998 89999999999999999999999875
Q ss_pred CC----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHH
Q 008167 245 RL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAE 320 (575)
Q Consensus 245 ~~----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~ 320 (575)
.. ..++.+.|..|.++++.|+++|.++|+++|+.||+++.+|++ |.+..+...++.+||.|||||||+||++||+
T Consensus 325 ~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~i~~d~~e~~i~ld~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~ 403 (644)
T PRK05054 325 GDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEK-GEVLDIVAEPRRIANRIVEESMIAANICAAR 403 (644)
T ss_pred CccccchhHHHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEECCC-CCEEEEEEecCcHHHHHHHHHHHHHHHHHHH
Confidence 32 245778899999999999999999999999999999999976 6788999999999999999999999999999
Q ss_pred HHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCC---HHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167 321 QILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS---SKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF 397 (575)
Q Consensus 321 ~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~---~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~ 397 (575)
++.++ +.|++||+|+.|++++++++.+++..+|+.++..+ ...+++.++...+ .+. . .+..+++|+|++|.|
T Consensus 404 ~l~~~-~~p~iyRvH~~P~~~~l~~l~~~~~~~g~~~~~~~~~~l~~~~~~~~~l~~-~~~-~-~l~~~llr~~~~a~y- 478 (644)
T PRK05054 404 VLRDK-LGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDA-QPT-G-YLDSRIRRFQSFAEI- 478 (644)
T ss_pred HHHHc-CCCEEEECCCCCCHHHHHHHHHHHHHCCCCcCCCcccChHHHHHHHHHHhc-chH-H-HHHHHHHHHHhceec-
Confidence 99987 78999999999999999999999999999886543 2334444443322 221 2 233446899999999
Q ss_pred ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167 398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSV 477 (575)
Q Consensus 398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~ 477 (575)
++.|.+|||||++.|||||||||||+||+|||||+++|.+++.+ ..++.+|.+||.++++|++|+|++.
T Consensus 479 -----s~~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~a~l~~~~~~------~~~~~~~~~~s~~er~a~~aer~~~ 547 (644)
T PRK05054 479 -----STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAE------RPQDEITVQLAERRRLNRMAERDVG 547 (644)
T ss_pred -----CCCCcCccccccccccccCChhhhhHHHHHHHHHHHHHcCCCCC------ccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999999999999876532 2378899999999999999999999
Q ss_pred HHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceec--CCcEEEEeeCCCeEEeeCc
Q 008167 478 ELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVD--EQQQKIVKMDGNLSYSVLQ 552 (575)
Q Consensus 478 ~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d--~~~~~l~g~~~~~~~~lGD 552 (575)
++|.+.||++++ ++|+|+|++|+++|+||.|+++|++|+||++.+.++| ..|.|+ +..+.+ +++++|++||
T Consensus 548 ~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~-~~y~~~~~~~~~~~---~~~~~~~lGd 623 (644)
T PRK05054 548 DWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVR-DELVCNQENGTVQI---KGETVYKLGD 623 (644)
T ss_pred HHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCc-cceEEccccceEEE---eCCEEEcCCC
Confidence 999999999986 3899999999999999999999999999999998875 124444 444444 3458999999
Q ss_pred EEEEEEEEecCCCCCCceEEEeC
Q 008167 553 TVNIHMEVVEPQPNRPKLQLTLI 575 (575)
Q Consensus 553 ~V~V~V~~vd~~~~~~~i~l~l~ 575 (575)
+|+|+|.+||.. +++|.|+++
T Consensus 624 ~V~V~v~~vd~~--~~~i~~~~~ 644 (644)
T PRK05054 624 VIDVTLAEVRME--TRSIIARPV 644 (644)
T ss_pred EEEEEEEEEccc--cCeEEEEEC
Confidence 999999999976 999999875
No 6
>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=100.00 E-value=1.1e-111 Score=942.35 Aligned_cols=529 Identities=21% Similarity=0.275 Sum_probs=465.0
Q ss_pred cEEEEEeCCCCCCc-eEecCC-cc--CcCCCCEEEEEEeecCCCC-CCcceEEEEeecCCCChhhHHHHHHhhCCCCCCC
Q 008167 11 AHALFVPKDRRIPK-IRIQTR-QL--GNLLDKRIIVAVDSWDCQS-RYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARP 85 (575)
Q Consensus 11 ~~~~~~P~d~r~p~-i~i~~~-~~--~~~~~~~~~v~i~~w~~~~-~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~ 85 (575)
+..+++|.|.+++. |.+... .. ....|+.|+|+|++||... ..|.|+|+++||..+++++++++++.+|+|+. .
T Consensus 92 ~~~~v~p~d~~~~~~i~~~~~~~~~~~~~~gd~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~-~ 170 (639)
T TIGR02062 92 DKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLER-E 170 (639)
T ss_pred CeEEEEECCCCCCccEEecCccccccCCCCCCEEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCC-C
Confidence 46789999988875 555322 21 2236889999999999865 55899999999999999999999999999998 5
Q ss_pred CcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHH
Q 008167 86 FSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDD 165 (575)
Q Consensus 86 f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~ 165 (575)
||+++++++.. +.. +|+|||++++|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+
T Consensus 171 f~~~v~~ea~~--------~~~--~R~DLr~~~~~TID~~~akD~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~ 240 (639)
T TIGR02062 171 EPDGVADEMLL--------DGL--VREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDK 240 (639)
T ss_pred CCHHHHHhhhh--------ccc--cCcccccCCEEEECCCCCCcccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHH
Confidence 99999988731 113 79999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEE-EEEEEEEEeecceeCHHHHHHHhcCC
Q 008167 166 EASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS-TRYTKSVIKSCAALSYVEAQARMDDS 244 (575)
Q Consensus 166 eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~-~~~~~s~I~s~~~ltY~~v~~~l~~~ 244 (575)
||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+++
T Consensus 241 eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e~R~als~~~~ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~ 320 (639)
T TIGR02062 241 AAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENT 320 (639)
T ss_pred HHHHhCCcEeCCCceecCCCHHHhcCccccCCCCCeeEEEEEEEEcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999999999999999999 79999999999999999999999875
Q ss_pred CC----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHH
Q 008167 245 RL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAE 320 (575)
Q Consensus 245 ~~----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~ 320 (575)
.. ..++.++|..|.++|+.|+++|.++|++.|+.||+++.+|++ |.+..+...++.+||.|||||||+||++||+
T Consensus 321 ~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i~ld~pE~~~~ld~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~ 399 (639)
T TIGR02062 321 SDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEK-GEVLDIVAEPRRIANRIVEEAMIIANICAAR 399 (639)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHHhCCcccccCCceEEEECCC-CCEEEEEEecCCHHHHHHHHHHHHHHHHHHH
Confidence 42 234667899999999999999999999999999999999976 6788888889999999999999999999999
Q ss_pred HHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC---CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167 321 QILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF 397 (575)
Q Consensus 321 ~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~ 397 (575)
|+.++ ..|++||+|+.|+++++++|.++++.+|+.++.. +...+...++.+.+ .+ ...+..+++|+|++|.|
T Consensus 400 ~l~~~-~~p~iyR~H~~P~~~~l~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~l~~~~~r~~~~a~y- 474 (639)
T TIGR02062 400 FLRDK-LGFGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDA-QE--TGYLDSRIRRYQSFAEI- 474 (639)
T ss_pred HHHHh-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCCCcccccCHHHHHHHHHHhhc-ch--HHHHHHHHHHHhhhccc-
Confidence 99987 5689999999999999999999999999987543 23444444443332 22 13466778899999999
Q ss_pred ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167 398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSV 477 (575)
Q Consensus 398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~ 477 (575)
++++.+|||||++.|||||||||||+||+|||||+++|.+++.+. .++.+|.+||.+++.|++|+|++.
T Consensus 475 -----s~~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~~~l~~~~~~~------~~~~~~~~~s~~er~a~~aeR~~~ 543 (639)
T TIGR02062 475 -----STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR------PQEDITVQLAERRRLNRIAERDVA 543 (639)
T ss_pred -----CCCCcCcchhccccccccCChhhhhHHHHHHHHHHHHHcCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999999999999999998764321 367889999999999999999999
Q ss_pred HHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCc
Q 008167 478 ELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQ 552 (575)
Q Consensus 478 ~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD 552 (575)
++|++.||++++ ++|+|+|+++.++|++|.|++.|++|+||++.+.+++ ..|.|++ ..+.++|+ ++|++||
T Consensus 544 ~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~-~~~~~~~~~~~~~l~g~---~~~~lgd 619 (639)
T TIGR02062 544 DWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANR-EELVCNQENGTVQIKGE---TVYKIGD 619 (639)
T ss_pred HHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCC-cceEEcccccEEEEecc---EEEecCC
Confidence 999999999986 3799999999999999999999999999999998731 1255655 44677654 5999999
Q ss_pred EEEEEEEEecCCCCCCceEEE
Q 008167 553 TVNIHMEVVEPQPNRPKLQLT 573 (575)
Q Consensus 553 ~V~V~V~~vd~~~~~~~i~l~ 573 (575)
+|+|+|.+||.+ +++|.|+
T Consensus 620 ~v~V~v~~vd~~--~~~i~~~ 638 (639)
T TIGR02062 620 VIDVVLTEVRME--TRSIIAR 638 (639)
T ss_pred EEEEEEEEeccc--cCcEeee
Confidence 999999999976 8999886
No 7
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.1e-105 Score=908.82 Aligned_cols=555 Identities=51% Similarity=0.858 Sum_probs=508.5
Q ss_pred CCCCCccEEEEEeCCCCCCceEecCC-ccCcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCC
Q 008167 5 AGSGSVAHALFVPKDRRIPKIRIQTR-QLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDA 83 (575)
Q Consensus 5 ~~~~~~~~~~~~P~d~r~p~i~i~~~-~~~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~ 83 (575)
..+....++||+|.|+|+|+|.|+++ +..++.++++++.|++||.++.||.|++++.||..++.++++++||.+++++.
T Consensus 366 ~~~~~~~~~~~~p~DkRvP~i~i~t~~~~~~~~~~~~~~~I~~W~~ts~~p~g~~v~~lG~i~~~~~e~~aLL~en~v~~ 445 (941)
T KOG2102|consen 366 LKGSSALIVLFIPSDKRVPLIRILTDDQAQDLIDKRIVAAIDRWPRTSLYPFGHLVRELGTIGDTETETEALLLENGVPH 445 (941)
T ss_pred ccccccceeeeccccCCCCeeeccccccccchhceeEEEEecccccCCcccCceehhhccCcCCccchhhhhhhcCCCcc
Confidence 34678899999999999999999999 88899999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHhcCCC-CCCCCCccccCCCC-CccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCC
Q 008167 84 RPFSTQVLACLPP-LPWSVSSEDLANPI-RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGT 161 (575)
Q Consensus 84 ~~f~~~v~~~~~~-~~~~~~~~~~~~~~-R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s 161 (575)
.+|+++++.+++. .+|.++.++.. . |.|||++.+|+|||++|.|||||+|+..++||+|+|||||||||+||+|||
T Consensus 446 ~~f~~~~~~~lp~~~~~~~~~~~~~--~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~fV~pgs 523 (941)
T KOG2102|consen 446 KPFSQALLDCLPRSHPWPITEEELQ--KLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTHFVKPGS 523 (941)
T ss_pred cccCHHHHhcCCccCCCCcChHHhh--hhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchhhcCCCC
Confidence 9999999999999 99999888887 6 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHh
Q 008167 162 PLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARM 241 (575)
Q Consensus 162 ~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l 241 (575)
+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+++.+|.|++.||++|+|+|+++|+|+++|++|
T Consensus 524 ~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye~Aq~~i 603 (941)
T KOG2102|consen 524 ALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYEEAQDIL 603 (941)
T ss_pred ccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHH
Q 008167 242 DDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQ 321 (575)
Q Consensus 242 ~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~ 321 (575)
+++...+++...|+.|.++|+.||++|+++|++.+..+|+.+.+|+++.+|.+++.++..+++.||||||++||..||++
T Consensus 604 d~~~~~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e~~~~~~~n~lveEfmllaN~~vA~~ 683 (941)
T KOG2102|consen 604 DTPNSSDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVEVKELTETNFLVEEFMLLANISVAEK 683 (941)
T ss_pred cCCcccchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCccccceeeeehhhhHHHHHHHHHhHHHHHH
Confidence 99887789999999999999999999999999999999999999999888999999899999999999999999999999
Q ss_pred HHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCCHHHHHHHHHHHhC-CChhHHHHHHHHHHhhccCceecccC
Q 008167 322 ILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSG 400 (575)
Q Consensus 322 l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~r~m~~a~Y~~~~ 400 (575)
+.+.|+.++++|+|+.|....++.+.+.+.++|.+++..+++.|.++++++.+ ..|++..+++.+.+|+|.+|+|||+|
T Consensus 684 I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p~~~~~l~~l~~r~m~~A~yf~sg 763 (941)
T KOG2102|consen 684 ILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKPYLNTLLRILATRSMTRAVYFCSG 763 (941)
T ss_pred HHHhCCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchHHHHHHHHHHHhhhhhceeEEeec
Confidence 99999999999999999999999999999999999999999999999999988 44688888999999999999999999
Q ss_pred CCCCCCCCccccCCCCccccccccccchhHHHHHHHHH-HhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167 401 DLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSA-SLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVEL 479 (575)
Q Consensus 401 ~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~-~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~ 479 (575)
....+.++|||||++.|||||||||||+|++|||||++ ++...+ ...+...+..+|.+||.+.+.++.|++++.++
T Consensus 764 ~~~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~---~~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l 840 (941)
T KOG2102|consen 764 SSDTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSP---TAPDRPNLSSLAANCNERKKAAKKAQEASTEL 840 (941)
T ss_pred ccCcchhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCc---cccccccHHHHHhhhhhhHHHHHHHHHhhHHH
Confidence 87888899999999999999999999999999999995 333322 22334589999999999999999999999999
Q ss_pred HHHHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEE
Q 008167 480 HTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME 559 (575)
Q Consensus 480 ~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~ 559 (575)
|.+.|++++....+|+|..|.++|+.|++|+||++|.|+++.+.... .+..++ .....+.+.|.|.+.+.
T Consensus 841 ~~~~~~k~~~~~~~a~v~~V~~~~~~v~ipe~G~e~~v~l~~~~~~~--~~~~~~--------~~~~~~~~~~~v~~~~~ 910 (941)
T KOG2102|consen 841 YLCEYLKDKQVLEEAVVLFVRPNGIDVVIPEYGLEGRVYLDLLKPSQ--TFFLDD--------EVSLRFEESDPVVVRIK 910 (941)
T ss_pred HHHHHHHhcccccceEEEEEecCceEEEEcccCceEEEEecccCCcc--ceeecc--------cccccccccCCceeeec
Confidence 99999999977889999999999999999999999999998333221 112111 11122677777777766
Q ss_pred EecCCCCCCceEEEe
Q 008167 560 VVEPQPNRPKLQLTL 574 (575)
Q Consensus 560 ~vd~~~~~~~i~l~l 574 (575)
.........+|.+.+
T Consensus 911 ~~~~~~~~~~l~~~~ 925 (941)
T KOG2102|consen 911 LDKLVPQPDRLRIEL 925 (941)
T ss_pred ccccccCcceEEEEe
Confidence 555445566666654
No 8
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=100.00 E-value=3.5e-79 Score=637.86 Aligned_cols=317 Identities=45% Similarity=0.727 Sum_probs=257.5
Q ss_pred CccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHhCCCceEcCCccccCCChhhhc
Q 008167 111 RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTE 190 (575)
Q Consensus 111 R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~ 190 (575)
|+|||++++|||||++|+|+||||||++.++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
T Consensus 1 R~Dl~~~~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~ 80 (325)
T PF00773_consen 1 RKDLRDLPVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSE 80 (325)
T ss_dssp SEECTTSEEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHC
T ss_pred CccCCCCCEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCCCCc---hHHHHHHHHHHHHHHHHH
Q 008167 191 DICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDP---LTTDLRNMNSLAKKMRQR 267 (575)
Q Consensus 191 ~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~---~~~~L~~L~~la~~lr~~ 267 (575)
++|||.||++|+|||+.+++|++|+|.+++|++|+|+|.++|||++|+++|++...... ..++|..|+++|+.|+++
T Consensus 81 ~~~SL~~~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~ 160 (325)
T PF00773_consen 81 DLCSLNPGKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKK 160 (325)
T ss_dssp TTSSTTBTSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999998654433 378999999999999999
Q ss_pred HHhcCCccc-cCcceEEEecCCCCCeeeEEEee---cchHHHHHHHHHHHHHHHHHHHHHHhCCCceeeeeCCCCChhhH
Q 008167 268 RIERGALTL-ASAEVKFQIDTETHDPLDIGMYQ---IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEML 343 (575)
Q Consensus 268 R~~~Gal~~-~~~e~~~~~d~~~~~~~~v~~~~---~~~s~~lVeE~MilAN~~vA~~l~~~~~~~~~~R~h~~P~~~~~ 343 (575)
|.++|++.+ +.|+..+.++++ +.+..+.... ...|+.||+||||+||++||+|+.++ +.|++||+|+.|+..++
T Consensus 161 R~~~Ga~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~-~ip~iyR~~~~p~~~~~ 238 (325)
T PF00773_consen 161 RLSRGAIELFNSPELKFSLDED-GPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSEN-GIPAIYRVQPEPDPERL 238 (325)
T ss_dssp HHHTTS-----SHCEEEEEETT-TTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHC-TTTSEEEEB-SSSCCCH
T ss_pred hhhccCccccCCCceEEEEecC-CCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHc-CCCceeeeCCCCCHHHH
Confidence 999999999 889999999875 5566666555 88999999999999999999999975 99999999999999998
Q ss_pred HHHHHHHHHcCCccCCCCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCCCccccCCCCccccccc
Q 008167 344 EPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSP 423 (575)
Q Consensus 344 ~~l~~~~~~~g~~~~~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSP 423 (575)
+++.+.+ +++++.....++++.+.. . ++.....++.++.++|.+|+| +..|.+|||||++.|||||||
T Consensus 239 ~~~~~~~---~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~l~~~l~~a~y------~~~p~~H~~L~l~~Yt~~TSP 306 (325)
T PF00773_consen 239 EELLKLL---KLDLDETKSLTLQNLLQA-E--NPPNSLALRYLLLKTLPPAEY------STEPSGHFGLGLPAYTHFTSP 306 (325)
T ss_dssp HHHHHHH---T---STCHHHCHHCHHCC-C--CTTSSHHHHHHHHCCC--EEE------ESSGC-BTTTTBSS-B--S-T
T ss_pred HHHHHHh---cCCCCCcchhhHHHHHHh-c--CChHHHHHHHHHHHhhccccc------ccCCCcceeeeccccccccCh
Confidence 8888777 444443333345555554 2 222334567788999999999 678889999999999999999
Q ss_pred cccchhHHHHHHHHHHhC
Q 008167 424 IRRYADVVVHRLLSASLG 441 (575)
Q Consensus 424 IRRY~DlvvHr~L~~~l~ 441 (575)
||||+||+|||||+++|.
T Consensus 307 lRRY~Dl~~hrql~~~L~ 324 (325)
T PF00773_consen 307 LRRYADLVVHRQLKAALR 324 (325)
T ss_dssp TTBHHHHHHHHHHHHHHH
T ss_pred hhhhHHHHHHHHHHHHhh
Confidence 999999999999999985
No 9
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=1.1e-75 Score=592.54 Aligned_cols=526 Identities=22% Similarity=0.315 Sum_probs=422.0
Q ss_pred CccEEEEEeCCCCCCceEecCCccC----c-CCCCEEEEEEeecCCCCC-CcceEEEEeecCCCChhhHHHHHHhhCCCC
Q 008167 9 SVAHALFVPKDRRIPKIRIQTRQLG----N-LLDKRIIVAVDSWDCQSR-YPFGHYVRVIGEIGDRDTESEMVLIDNDID 82 (575)
Q Consensus 9 ~~~~~~~~P~d~r~p~i~i~~~~~~----~-~~~~~~~v~i~~w~~~~~-~p~g~i~~~lG~~~~~~~~~~~il~~~~i~ 82 (575)
+.+...++|+.+-+-.. |+-.+.. . ..|+.+|+++.+-|-... .-.+.|.+.|...+|.-+-.=..|++|+++
T Consensus 93 kd~rL~i~pDhP~lk~~-i~~~~~k~l~~~fQeGDW~VA~lk~HpLkgDr~F~a~lt~~It~~dD~l~PWWVTLArh~l~ 171 (645)
T COG4776 93 KDDRLQIVPDHPLLKDA-IPCRAAKGLNEEFQEGDWAVAELKRHPLKGDRSFYAELTQKITFADDHLAPWWVTLARHNLE 171 (645)
T ss_pred cCCceEEcCCChhhhhh-cccccccchhhhhhcCceehhhhhcCCCCCchhHHHHHHHHhhccCCcccceeeehhhccCC
Confidence 34445566665444321 3322221 2 268899999998887653 335566666666666555555567778877
Q ss_pred CCCCcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCH
Q 008167 83 ARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTP 162 (575)
Q Consensus 83 ~~~f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~ 162 (575)
..+ |. ...++.+..+.+ .|+||+.++++|||+++++|+|||++++++++|.|.|-|+||||++||.+||.
T Consensus 172 r~~-p~------g~~d~~m~d~~l---~RedLTaL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~ 241 (645)
T COG4776 172 REA-PA------GIVDTEMLDEGL---VREDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSK 241 (645)
T ss_pred ccC-CC------cccchhhhhhhh---hhccccccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCcch
Confidence 531 11 112333322222 69999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEE-EEEEEEEEEeecceeCHHHHHHHh
Q 008167 163 LDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKSCAALSYVEAQARM 241 (575)
Q Consensus 163 LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~-~~~~~~s~I~s~~~ltY~~v~~~l 241 (575)
||++|+.|+.|.|||+..|||||++||+++|||.||+.|+++.|.++++++|+|. +.+|..+.|+|+++|.|++|..+|
T Consensus 242 ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwl 321 (645)
T COG4776 242 LDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSDWL 321 (645)
T ss_pred hhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhccccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHHHH
Confidence 9999999999999999999999999999999999999999999999999999997 589999999999999999999999
Q ss_pred cCCC----CCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHH
Q 008167 242 DDSR----LMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVS 317 (575)
Q Consensus 242 ~~~~----~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~ 317 (575)
++.. .+.++.+++..|+.++++.-++|..+.-+.-++|+++|.+.++ |.+.+|....++.|++||||+||+||.+
T Consensus 322 E~~~~WqPe~~~iAqqi~~L~~~~~aR~~WRk~hal~FkdrpdYrF~l~e~-g~V~~I~ae~RRiAnriVEE~MI~ANIc 400 (645)
T COG4776 322 ENTGDWQPESEAIAQQIRLLHQFCQARIEWRKTHALVFKDRPDYRFILGEK-GEVLDIVAEPRRIANRIVEESMIAANIC 400 (645)
T ss_pred hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhceeeccCCCceEEEecCC-CceEeeehhHHHHHHHHHHHHHHHHHHH
Confidence 9653 3567889999999999999999999877777899999999865 7888888888999999999999999999
Q ss_pred HHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCCHHHHHH------HHHHHhCCChhHHHHHHHHHHhhc
Q 008167 318 VAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD------SLDRAVGDDPYFNKLIRILATRCM 391 (575)
Q Consensus 318 vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~l~~------~l~~~~~~~~~~~~~l~~~~~r~m 391 (575)
+|.+|.++++ .++|.+|...++..++....++...|...+..+-.+|.. .|+.. ...+...-+ .|
T Consensus 401 Aa~~L~~~~g-fGI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr~l~~~--~t~yld~Ri----Rr-- 471 (645)
T COG4776 401 AARVLREKLG-FGIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTLEGFCKLRRELDAQ--PTGYLDSRI----RR-- 471 (645)
T ss_pred HHHHHHHhcC-cceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhhHHHHHHHHHhhcc--ccchHHHHH----HH--
Confidence 9999999865 689999999999999999999999998776543333322 23222 223333222 22
Q ss_pred cCceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 008167 392 TQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQM 471 (575)
Q Consensus 392 ~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~ 471 (575)
|.+.++++..|.+|||||++.|+.||||||+|+|+++||+|++++.+++.... =+.+..++.++.|.-+.
T Consensus 472 ----fqsfae~~t~p~PHFglGl~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~kP------qedi~v~lae~Rr~nrm 541 (645)
T COG4776 472 ----FQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAEKP------QEDITVQLAERRRLNRM 541 (645)
T ss_pred ----HHhHHhhccCcCccccccchheeeccchhhhhhhHHHHHHHHHHHcCCCcCCC------chHHHHHHHHHHHhhhh
Confidence 33445668899999999999999999999999999999999999998753221 13455678889999999
Q ss_pred HHHHHHHHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCe
Q 008167 472 ASRGSVELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNL 546 (575)
Q Consensus 472 a~r~~~~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~ 546 (575)
|||+.-+|..|+||+.+. ..|.|.|.+|...|+.|+|-+.|.-.+|+-.-+.+.. .+..++. .++.+ ++..
T Consensus 542 aERdv~DWLY~r~L~~k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~r-eei~~n~e~gtv~I---~ge~ 617 (645)
T COG4776 542 AERDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANR-EELVCNQENGTVQI---KGET 617 (645)
T ss_pred hhhhhHHHHHHHHhccccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccch-hheEecCCCceEEE---ccEE
Confidence 999999999999998876 5799999999999999999999999999987766542 2344444 33444 3568
Q ss_pred EEeeCcEEEEEEEEecCCCCCCceE
Q 008167 547 SYSVLQTVNIHMEVVEPQPNRPKLQ 571 (575)
Q Consensus 547 ~~~lGD~V~V~V~~vd~~~~~~~i~ 571 (575)
+|++||.|+|++..|..+ .|.|-
T Consensus 618 ~Yk~~D~i~V~l~eVr~e--tRsii 640 (645)
T COG4776 618 VYKVGDVIDVTLAEVRME--TRSII 640 (645)
T ss_pred EEeeccEEEEEeHHHHHh--hhhhh
Confidence 899999999999999865 56654
No 10
>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=99.22 E-value=1e-10 Score=96.89 Aligned_cols=81 Identities=20% Similarity=0.331 Sum_probs=73.7
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|+++.++|++|.++.+|++|++|++++++++ |.+|+..+.+.+++.++.|++||.|+|+|.++|.+ +++
T Consensus 3 ~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~---~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~--~~~ 77 (83)
T cd04471 3 EEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDY---YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD--RRK 77 (83)
T ss_pred CEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCc---EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc--cCE
Confidence 5789999999999999999999999999999998665 89999998888877789999999999999999974 899
Q ss_pred eEEEeC
Q 008167 570 LQLTLI 575 (575)
Q Consensus 570 i~l~l~ 575 (575)
|.|+|.
T Consensus 78 i~~~l~ 83 (83)
T cd04471 78 IDFELV 83 (83)
T ss_pred EEEEEC
Confidence 999874
No 11
>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=98.73 E-value=5.7e-08 Score=83.51 Aligned_cols=80 Identities=15% Similarity=0.202 Sum_probs=69.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC---
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN--- 566 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~--- 566 (575)
+.+.|.|+++.++|++|.+. +++|+++++++.+++ +.+++..+++.+.+.+..|++||.|+|+|.++|.+..
T Consensus 1 ~vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~---~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~ 75 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDY---ISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPR 75 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCc---eEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCC
Confidence 36899999999999999996 599999999998775 7888888999988888999999999999999997532
Q ss_pred CCceEEEe
Q 008167 567 RPKLQLTL 574 (575)
Q Consensus 567 ~~~i~l~l 574 (575)
..+|.||+
T Consensus 76 ~~~i~ls~ 83 (99)
T cd04460 76 ESKIGLTM 83 (99)
T ss_pred CceEEEEE
Confidence 25788875
No 12
>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=98.72 E-value=7.8e-08 Score=77.78 Aligned_cols=69 Identities=20% Similarity=0.176 Sum_probs=58.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|+++.++|+||.+++++.+|++|++++.++. ++ +.+..|++||+|+|+|.+++.+ + +
T Consensus 5 ~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~-----~~---------~~~~~~~~Gd~v~vkv~~vd~~--~-k 67 (73)
T cd05686 5 QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCR-----VD---------DPSEVVDVGEKVWVKVIGREMK--D-K 67 (73)
T ss_pred CEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCc-----cc---------CHhhEECCCCEEEEEEEEECCC--C-c
Confidence 6789999999999999999876689999999887542 11 3467799999999999999975 4 9
Q ss_pred eEEEeC
Q 008167 570 LQLTLI 575 (575)
Q Consensus 570 i~l~l~ 575 (575)
|.||+.
T Consensus 68 i~ls~~ 73 (73)
T cd05686 68 MKLSLS 73 (73)
T ss_pred EEEEeC
Confidence 999873
No 13
>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=98.63 E-value=9.4e-08 Score=76.31 Aligned_cols=68 Identities=25% Similarity=0.274 Sum_probs=58.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+.++|.|++|.++|++|.+++ |++|+||.+++.+++ + .+....|++||.|+|+|.++|.+ +++
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~~~~---~-----------~~~~~~~~~Gd~i~~~V~~id~~--~~~ 64 (69)
T cd05697 2 QVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADVR---L-----------KHPEKKFKPGLKVKCRVLSVEPE--RKR 64 (69)
T ss_pred CEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCcc---c-----------cCHHHcCCCCCEEEEEEEEEECC--CCE
Confidence 468999999999999999986 899999999987653 1 12356799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|+|
T Consensus 65 i~ls~ 69 (69)
T cd05697 65 LVLTL 69 (69)
T ss_pred EEEEC
Confidence 99986
No 14
>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=98.53 E-value=5.1e-07 Score=72.81 Aligned_cols=68 Identities=16% Similarity=0.188 Sum_probs=58.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.|+. +++|++|.+++.+++ .. +....|++||.|+++|.++|.. +++
T Consensus 5 ~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~~~~----~~----------~~~~~~~~Gd~v~~~V~~~d~~--~~~ 67 (73)
T cd05706 5 DILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDY----SE----------ALPYKFKKNDIVRACVLSVDVP--NKK 67 (73)
T ss_pred CEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCcc----cc----------ccccccCCCCEEEEEEEEEeCC--CCE
Confidence 678999999999999999987 899999999998653 11 2246799999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 68 i~ls~ 72 (73)
T cd05706 68 IALSL 72 (73)
T ss_pred EEEEE
Confidence 99986
No 15
>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=98.51 E-value=2.8e-07 Score=73.34 Aligned_cols=68 Identities=21% Similarity=0.199 Sum_probs=55.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.++. +++|++|.++++.. .. ..+....|++||+|+|+|.++|.+ +++
T Consensus 2 ~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~~-----~~--------~~~~~~~~~~G~~v~v~v~~id~~--~~~ 65 (69)
T cd05690 2 TVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWT-----QR--------VRHPSEIYKKGQEVEAVVLNIDVE--RER 65 (69)
T ss_pred CEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCCc-----cc--------cCChhhEECCCCEEEEEEEEEECC--cCE
Confidence 468999999999999999986 89999999988621 10 123457899999999999999975 888
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.|+
T Consensus 66 i~l~ 69 (69)
T cd05690 66 ISLG 69 (69)
T ss_pred EeCC
Confidence 8774
No 16
>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=98.47 E-value=6.1e-07 Score=72.15 Aligned_cols=68 Identities=16% Similarity=0.251 Sum_probs=55.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.+++ |++|++|.++++.+ ... .+....|++||+|+|+|.++|.+ +++
T Consensus 5 ~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~~-----~~~--------~~~~~~~~~Gd~v~v~v~~id~~--~~~ 68 (72)
T cd05689 5 TRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDWT-----NKN--------IHPSKVVSLGDEVEVMVLDIDEE--RRR 68 (72)
T ss_pred CEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccCc-----ccc--------cCcccEeCCCCEEEEEEEEeeCC--cCE
Confidence 579999999999999999987 89999999988521 010 13457899999999999999975 788
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.|+
T Consensus 69 i~~~ 72 (72)
T cd05689 69 ISLG 72 (72)
T ss_pred EeCC
Confidence 8763
No 17
>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=98.46 E-value=5.8e-07 Score=72.30 Aligned_cols=68 Identities=16% Similarity=0.182 Sum_probs=56.3
Q ss_pred ceeE-EEEEEE-ecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167 490 TDTE-ARIVKI-RSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR 567 (575)
Q Consensus 490 ~~~~-g~V~~v-~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~ 567 (575)
+.++ |.|+.+ .++|++|.|++ |++|++|.++++++. . ......|++||.|+++|.++|.. +
T Consensus 2 ~v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~----~----------~~~~~~~~vG~~v~~kV~~id~~--~ 64 (71)
T cd05696 2 AVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDK----V----------PSDTGPFKAGTTHKARIIGYSPM--D 64 (71)
T ss_pred cEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcch----h----------cCcccccCCCCEEEEEEEEEeCC--C
Confidence 3567 999998 69999999987 899999999987542 1 12346799999999999999976 8
Q ss_pred CceEEEe
Q 008167 568 PKLQLTL 574 (575)
Q Consensus 568 ~~i~l~l 574 (575)
++|.||+
T Consensus 65 ~~i~lS~ 71 (71)
T cd05696 65 GLLQLSL 71 (71)
T ss_pred CEEEEeC
Confidence 9999986
No 18
>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=98.46 E-value=5.1e-07 Score=73.01 Aligned_cols=70 Identities=10% Similarity=0.116 Sum_probs=57.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
....|.|..+.++|++|.|.+ +++|+|++++++++. ... ++....|++||.|+++|.++|.+ +++
T Consensus 2 ~~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~~----~~~--------~~~~~~~~vG~~v~~kV~~id~~--~~~ 66 (73)
T cd05703 2 QEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDV----SVL--------EHPEKKFPIGQALKAKVVGVDKE--HKL 66 (73)
T ss_pred CEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCcc----ccc--------cCHHHhCCCCCEEEEEEEEEeCC--CCE
Confidence 357899999999999999976 899999999987431 000 13457799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 67 i~Ls~ 71 (73)
T cd05703 67 LRLSA 71 (73)
T ss_pred EEEEe
Confidence 99986
No 19
>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=98.45 E-value=4.6e-07 Score=72.07 Aligned_cols=67 Identities=18% Similarity=0.287 Sum_probs=56.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+++ +++|++|.+++++++ . .+....|++||.|+|+|.++|.+ +++
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l~~~~----~----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~ 64 (68)
T cd05707 2 DVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSY----L----------KDWKKRFKVGQLVKGKIVSIDPD--NGR 64 (68)
T ss_pred CEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCchh----h----------cCHhhccCCCCEEEEEEEEEeCC--CCE
Confidence 368999999999999999986 799999999998653 1 13467799999999999999975 788
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.||
T Consensus 65 i~ls 68 (68)
T cd05707 65 IEMT 68 (68)
T ss_pred EecC
Confidence 8775
No 20
>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=98.44 E-value=1.1e-06 Score=71.40 Aligned_cols=69 Identities=10% Similarity=0.229 Sum_probs=59.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.+.+++|++|.+++.+++ .. +....|++||.|+|+|.+++.+ +++
T Consensus 4 ~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~----~~----------~~~~~~~~Gd~v~v~i~~vd~~--~~~ 67 (77)
T cd05708 4 QKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR----VA----------DASKLFRVGDKVRAKVLKIDAE--KKR 67 (77)
T ss_pred CEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc----cC----------CHhHeecCCCEEEEEEEEEeCC--CCE
Confidence 5789999999999999999877899999999987642 11 2457899999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 68 i~ls~ 72 (77)
T cd05708 68 ISLGL 72 (77)
T ss_pred EEEEE
Confidence 99886
No 21
>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=98.42 E-value=8e-07 Score=71.01 Aligned_cols=68 Identities=24% Similarity=0.315 Sum_probs=57.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.++. +++|++|.+++..++ .. +....|++||.|+|+|.++|.+ +++
T Consensus 2 ~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~~~~----~~----------~~~~~~~~G~~i~v~v~~~d~~--~~~ 64 (70)
T cd05698 2 LKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAF----IK----------DPEEHFRVGQVVKVKVLSCDPE--QQR 64 (70)
T ss_pred CEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChhh----cC----------CHHHcccCCCEEEEEEEEEcCC--CCE
Confidence 368999999999999999986 799999999997652 22 2246799999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||+
T Consensus 65 i~ls~ 69 (70)
T cd05698 65 LLLSC 69 (70)
T ss_pred EEEEe
Confidence 99986
No 22
>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=98.42 E-value=7.8e-07 Score=72.14 Aligned_cols=70 Identities=11% Similarity=0.049 Sum_probs=56.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
....|.|.++.++|+||.+.. |++|+||++++++++ +. +. .+..+.|++||.|+++|.++|.+ +++
T Consensus 5 ~~V~g~V~~i~~~G~fV~l~~-~v~G~v~~~~ls~~~---~~-~~-------~~~~~~~~~G~~v~~kVl~id~~--~~~ 70 (74)
T cd05705 5 QLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYF---VS-DP-------SLYNKYLPEGKLLTAKVLSVNSE--KNL 70 (74)
T ss_pred CEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCcc---cc-Ch-------hhHhcccCCCCEEEEEEEEEECC--CCE
Confidence 578999999999999999975 999999999998653 11 10 01247899999999999999976 788
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.||
T Consensus 71 i~LS 74 (74)
T cd05705 71 VELS 74 (74)
T ss_pred EecC
Confidence 8875
No 23
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.42 E-value=5.4e-07 Score=86.03 Aligned_cols=88 Identities=15% Similarity=0.233 Sum_probs=72.9
Q ss_pred HHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167 482 LIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 560 (575)
Q Consensus 482 ~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~ 560 (575)
+.+++... +.++|+|++++++|++|.+. .++|.++.+++.+++ +.||+....+.+++.+..|++||+|+|+|.+
T Consensus 74 ~i~f~p~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~---~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 148 (179)
T TIGR00448 74 ALVFKPELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDY---CYYDPKESALIGKETKKVLDEGDKVRARIVA 148 (179)
T ss_pred EEEEeccCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCc---eEEccccceEEEccCCeEEcCCCEEEEEEEE
Confidence 34455554 78999999999999999994 489999999988775 7788888888888888999999999999999
Q ss_pred ecCC---CCCCceEEEe
Q 008167 561 VEPQ---PNRPKLQLTL 574 (575)
Q Consensus 561 vd~~---~~~~~i~l~l 574 (575)
++.. +...+|.+++
T Consensus 149 v~~~~~~~~~~~I~lt~ 165 (179)
T TIGR00448 149 LSLKDRRPEGSKIGLTM 165 (179)
T ss_pred EEccCCCCCcceEEEEe
Confidence 9852 2356788775
No 24
>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=98.40 E-value=8.2e-07 Score=73.63 Aligned_cols=68 Identities=16% Similarity=0.201 Sum_probs=59.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.+.. |++|++|.++++.++ . .+....|++||.|+|+|.++|.+ +++
T Consensus 16 ~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~~----~----------~~~~~~~~~Gd~v~vkV~~id~~--~~~ 78 (83)
T cd04461 16 MVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEF----V----------TDPSFGFKKGQSVTAKVTSVDEE--KQR 78 (83)
T ss_pred CEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCccc----c----------cCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence 789999999999999999976 899999999987652 1 13467899999999999999975 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|||
T Consensus 79 i~lsl 83 (83)
T cd04461 79 FLLSL 83 (83)
T ss_pred EEEeC
Confidence 99986
No 25
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=2.8e-07 Score=79.93 Aligned_cols=67 Identities=19% Similarity=0.204 Sum_probs=58.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
...+|.|++|+++|+||.|+. |-.|+||+|++.+.| .- +-+..+++||.|.|+|.++|. +.+
T Consensus 7 ~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~f----Vk----------dI~d~L~vG~eV~vKVl~ide---~GK 68 (129)
T COG1098 7 SKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGF----VK----------DIHDHLKVGQEVKVKVLDIDE---NGK 68 (129)
T ss_pred ceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhh----HH----------hHHHHhcCCCEEEEEEEeecc---CCC
Confidence 578999999999999999986 899999999998763 32 346779999999999999996 688
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|+|||
T Consensus 69 isLSI 73 (129)
T COG1098 69 ISLSI 73 (129)
T ss_pred cceeh
Confidence 99886
No 26
>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=98.38 E-value=1.3e-06 Score=70.65 Aligned_cols=68 Identities=22% Similarity=0.334 Sum_probs=59.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+.++|.|.++.++|++|.+. .|++|+||.+++..++ . ......|++||+|+|+|.++|.+ +++
T Consensus 6 ~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~~~----~----------~~~~~~~~~G~~v~v~v~~vd~~--~~~ 68 (74)
T PF00575_consen 6 DIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSDDR----I----------DDPSEVYKIGQTVRVKVIKVDKE--KGR 68 (74)
T ss_dssp SEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSSSE----E----------SSSHGTCETTCEEEEEEEEEETT--TTE
T ss_pred CEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcCcc----c----------cccccccCCCCEEEEEEEEEECC--CCe
Confidence 68999999999999999998 6999999999998541 1 24567899999999999999976 889
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 69 i~lS~ 73 (74)
T PF00575_consen 69 IRLSL 73 (74)
T ss_dssp EEEES
T ss_pred EEEEE
Confidence 99985
No 27
>PRK07252 hypothetical protein; Provisional
Probab=98.38 E-value=1.5e-06 Score=77.20 Aligned_cols=68 Identities=16% Similarity=0.130 Sum_probs=58.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|++|.++|++|.++. +++|++|++++.+++ +. .....|++||.|+|+|.++|.+ +++
T Consensus 5 ~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~---~~-----------~~~~~~~vGD~V~VkI~~iD~~--~~r 67 (120)
T PRK07252 5 DKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGF---ID-----------NIHQLLKVGEEVLVQVVDFDEY--TGK 67 (120)
T ss_pred CEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCcc---cc-----------ChhhccCCCCEEEEEEEEEeCC--CCE
Confidence 678999999999999999976 799999999997653 21 2346799999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 68 i~lSl 72 (120)
T PRK07252 68 ASLSL 72 (120)
T ss_pred EEEEE
Confidence 99886
No 28
>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=98.37 E-value=2.1e-06 Score=70.49 Aligned_cols=68 Identities=18% Similarity=0.207 Sum_probs=56.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCC--ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKF--GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR 567 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~--gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~ 567 (575)
..++|.|+++.++|+||.+.+. +++|++|.++++.++ + . .+....|++||.|+|+|.++| +
T Consensus 2 ~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~---~---------~-~~~~~~~~~Gd~v~v~v~~vd----~ 64 (79)
T cd05684 2 KIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEG---R---------V-ANPSDVVKRGQKVKVKVISIQ----N 64 (79)
T ss_pred CEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCC---C---------c-CChhheeCCCCEEEEEEEEEe----C
Confidence 4689999999999999999864 799999999987553 2 1 134578999999999999998 5
Q ss_pred CceEEEe
Q 008167 568 PKLQLTL 574 (575)
Q Consensus 568 ~~i~l~l 574 (575)
+++.|++
T Consensus 65 ~~i~~s~ 71 (79)
T cd05684 65 GKISLSM 71 (79)
T ss_pred CEEEEEE
Confidence 7888876
No 29
>PRK08582 hypothetical protein; Provisional
Probab=98.37 E-value=1.9e-06 Score=78.55 Aligned_cols=67 Identities=22% Similarity=0.269 Sum_probs=57.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|+|++|.++|+||.|++ +++|+||++++.+++ .. +....|++||.|+|+|.+++. .++
T Consensus 7 ~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~~----v~----------~~~~~l~vGD~VkvkV~~id~---~gk 68 (139)
T PRK08582 7 SKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNY----VK----------DINDHLKVGDEVEVKVLNVED---DGK 68 (139)
T ss_pred CEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCccc----cc----------ccccccCCCCEEEEEEEEECC---CCc
Confidence 689999999999999999986 899999999997653 22 234679999999999999985 478
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 69 I~LSl 73 (139)
T PRK08582 69 IGLSI 73 (139)
T ss_pred EEEEE
Confidence 99986
No 30
>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=98.34 E-value=2.6e-06 Score=69.09 Aligned_cols=69 Identities=14% Similarity=0.131 Sum_probs=58.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
..+.|.|+++.++|++|.+.++ |++|++|.+++++++ +. +....|++||.|+|+|.+++.. ++
T Consensus 5 ~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~---~~-----------~~~~~~~~Gd~v~vkv~~~d~~--~~ 68 (76)
T cd04452 5 ELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRR---IR-----------SIRKLVKVGRKEVVKVIRVDKE--KG 68 (76)
T ss_pred CEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcc---cC-----------CHHHeeCCCCEEEEEEEEEECC--CC
Confidence 5789999999999999999765 699999999987653 11 2357799999999999999975 78
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
++.|++
T Consensus 69 ~i~ls~ 74 (76)
T cd04452 69 YIDLSK 74 (76)
T ss_pred EEEEEE
Confidence 899886
No 31
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.28 E-value=3.5e-06 Score=78.79 Aligned_cols=80 Identities=19% Similarity=0.205 Sum_probs=69.9
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC--
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR-- 567 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~-- 567 (575)
+..+|.|+.+.++|+||.+. .++|+||.+++.+|+ +.+|+..-.++|+.+++.++.||.|+++|.+++....+
T Consensus 83 EVV~GeVv~~~~~G~fV~ig--p~dglvh~sqi~dd~---~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~ 157 (183)
T COG1095 83 EVVEGEVVEVVEFGAFVRIG--PLDGLVHVSQIMDDY---IDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPR 157 (183)
T ss_pred cEEEEEEEEEeecceEEEec--cccccccHhhccCcc---cccCcccceeeecccceEEecCCEEEEEEEEEecccCccc
Confidence 67899999999999999997 589999999999986 89999999999999999999999999999999875322
Q ss_pred -CceEEEe
Q 008167 568 -PKLQLTL 574 (575)
Q Consensus 568 -~~i~l~l 574 (575)
-+|.+++
T Consensus 158 ~~~I~lTm 165 (183)
T COG1095 158 ESKIGLTM 165 (183)
T ss_pred cceEEEEe
Confidence 4555543
No 32
>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=98.28 E-value=2.8e-06 Score=67.28 Aligned_cols=64 Identities=23% Similarity=0.274 Sum_probs=54.1
Q ss_pred eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCce
Q 008167 491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 570 (575)
Q Consensus 491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i 570 (575)
..+|.|+.+.++|++|.|.+ +++|+++.+++..+. . . ...|++||+|+++|..+|++ +++|
T Consensus 3 ~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~----~-----------~-~~~~~~G~~i~~kVi~id~~--~~~i 63 (66)
T cd05695 3 LVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEK----S-----------S-KSTYKEGQKVRARILYVDPS--TKVV 63 (66)
T ss_pred EEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCcc----C-----------c-ccCcCCCCEEEEEEEEEeCC--CCEE
Confidence 57899999999999999987 899999999886442 0 1 46699999999999999976 7888
Q ss_pred EEE
Q 008167 571 QLT 573 (575)
Q Consensus 571 ~l~ 573 (575)
.||
T Consensus 64 ~LS 66 (66)
T cd05695 64 GLS 66 (66)
T ss_pred ecC
Confidence 775
No 33
>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=98.27 E-value=1.8e-06 Score=68.06 Aligned_cols=67 Identities=13% Similarity=0.147 Sum_probs=55.7
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.. +.+|++|.+++.+++ +. +....|++||.|+|+|.++|.+ +++
T Consensus 2 ~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~---~~-----------~~~~~~~~Gd~v~v~i~~vd~~--~~~ 64 (68)
T cd05685 2 MVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRF---VS-----------HPSDVVSVGDIVEVKVISIDEE--RGR 64 (68)
T ss_pred CEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCcc---cc-----------CHHHhcCCCCEEEEEEEEEECC--CCE
Confidence 468999999999999999975 799999999887653 11 2346799999999999999975 788
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
+.||
T Consensus 65 i~ls 68 (68)
T cd05685 65 ISLS 68 (68)
T ss_pred EecC
Confidence 8775
No 34
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.26 E-value=1.7e-06 Score=88.64 Aligned_cols=77 Identities=16% Similarity=0.219 Sum_probs=63.8
Q ss_pred HHHHhc-CC---ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167 482 LIYFRK-RP---TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556 (575)
Q Consensus 482 ~~~l~~-~~---~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V 556 (575)
|+|..+ .+ ..+.|.|+.|.++|+||.|.+| |++|+||+++++..+ . ++....+++||+|.|
T Consensus 7 cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~r----i----------~~i~d~vkvGd~v~v 72 (319)
T PTZ00248 7 CRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRR----I----------RSINKLIRVGRHEVV 72 (319)
T ss_pred ccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccc----c----------CCHHHhcCCCCEEEE
Confidence 555544 34 5789999999999999999888 999999999987542 1 234678999999999
Q ss_pred EEEEecCCCCCCceEEEe
Q 008167 557 HMEVVEPQPNRPKLQLTL 574 (575)
Q Consensus 557 ~V~~vd~~~~~~~i~l~l 574 (575)
+|..||.+ +++|.||+
T Consensus 73 kVl~VD~e--kg~IdLS~ 88 (319)
T PTZ00248 73 VVLRVDKE--KGYIDLSK 88 (319)
T ss_pred EEEEEeCC--CCEEEEEe
Confidence 99999976 89999986
No 35
>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=98.17 E-value=4.5e-06 Score=67.30 Aligned_cols=66 Identities=20% Similarity=0.146 Sum_probs=55.1
Q ss_pred ceeEEEEEEEec-CeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~-~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
..+.|.|.++.+ +|++|.++. |.+|++|++++.+++ . ......|++||.|+|+|.+++ +.
T Consensus 5 ~iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~~s~~~----~----------~~~~~~~~~Gd~v~~kV~~~~----~~ 65 (72)
T cd05704 5 AVTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFHLSDSY----T----------ENPLEGFKPGKIVRCCILSKK----DG 65 (72)
T ss_pred CEEEEEEEEeeCCcEEEEECCC-CCEEEEEHHHhcCcc----c----------CCHHHhCCCCCEEEEEEEEec----CC
Confidence 678999999986 899999986 999999999988653 1 122367899999999999987 48
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
+|+||+
T Consensus 66 ~i~LSl 71 (72)
T cd05704 66 KYQLSL 71 (72)
T ss_pred EEEEEe
Confidence 899987
No 36
>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=98.16 E-value=7.9e-06 Score=65.60 Aligned_cols=68 Identities=16% Similarity=0.286 Sum_probs=57.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.+ +++|++|.+++.+++ . .+....|++||.|+++|.++|.. +++
T Consensus 2 ~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~~~~~----~----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~ 64 (73)
T cd05691 2 SIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDR----V----------EDATERFKVGDEVEAKITNVDRK--NRK 64 (73)
T ss_pred CEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCcc----c----------cCHHHccCCCCEEEEEEEEEeCC--CCE
Confidence 367899999999999999976 799999999988653 1 13456799999999999999975 788
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 65 i~ls~ 69 (73)
T cd05691 65 ISLSI 69 (73)
T ss_pred EEEEE
Confidence 88876
No 37
>PHA02945 interferon resistance protein; Provisional
Probab=98.15 E-value=1.4e-05 Score=65.49 Aligned_cols=66 Identities=8% Similarity=0.066 Sum_probs=55.7
Q ss_pred ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCC--CCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPR--GQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN 566 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l--~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~ 566 (575)
+..-|+|.. .++|++|.|++| |+||+||++.. .+.| . +....+ .|++|.++|..+|..
T Consensus 13 elvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~w----v-----------K~rd~l-~GqkvV~KVirVd~~-- 73 (88)
T PHA02945 13 DVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRY----F-----------KYRDKL-VGKTVKVKVIRVDYT-- 73 (88)
T ss_pred cEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccce----E-----------eeeeEe-cCCEEEEEEEEECCC--
Confidence 567899999 999999999999 99999999955 5543 2 224566 999999999999976
Q ss_pred CCceEEEe
Q 008167 567 RPKLQLTL 574 (575)
Q Consensus 567 ~~~i~l~l 574 (575)
+..|++||
T Consensus 74 kg~IDlSl 81 (88)
T PHA02945 74 KGYIDVNY 81 (88)
T ss_pred CCEEEeEe
Confidence 89999987
No 38
>PRK05807 hypothetical protein; Provisional
Probab=98.09 E-value=1.7e-05 Score=72.05 Aligned_cols=66 Identities=20% Similarity=0.225 Sum_probs=55.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|+++.++|++|.| + +.+|+||++++.+++ .. +....|++||.|+|+|.+++. .++
T Consensus 7 ~vv~G~Vt~i~~~GafV~L-~-~~~Glvhiseis~~~----v~----------~~~~~~kvGd~V~VkV~~id~---~gk 67 (136)
T PRK05807 7 SILEGTVVNITNFGAFVEV-E-GKTGLVHISEVADTY----VK----------DIREHLKEQDKVKVKVISIDD---NGK 67 (136)
T ss_pred CEEEEEEEEEECCeEEEEE-C-CEEEEEEhhhccccc----cc----------CccccCCCCCEEEEEEEEECC---CCc
Confidence 6899999999999999999 4 789999999998653 22 224569999999999999985 588
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 68 I~LSl 72 (136)
T PRK05807 68 ISLSI 72 (136)
T ss_pred EEEEE
Confidence 99886
No 39
>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=98.08 E-value=1.4e-05 Score=63.05 Aligned_cols=67 Identities=21% Similarity=0.241 Sum_probs=55.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.++. +.+|++|.+++..++ . ......|++||.|+|+|.+++. +++
T Consensus 2 ~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~~~----~----------~~~~~~~~~Gd~v~v~v~~~d~---~~~ 63 (68)
T cd04472 2 KIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDER----V----------EKVEDVLKVGDEVKVKVIEVDD---RGR 63 (68)
T ss_pred CEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCcc----c----------cCHHHccCCCCEEEEEEEEECC---CCc
Confidence 468999999999999999985 799999999887542 1 1234689999999999999985 578
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||.
T Consensus 64 i~ls~ 68 (68)
T cd04472 64 ISLSR 68 (68)
T ss_pred EEeeC
Confidence 88773
No 40
>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=98.07 E-value=1.5e-05 Score=62.79 Aligned_cols=67 Identities=18% Similarity=0.275 Sum_probs=55.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.+ +.+|++|.+++.+++ .. .....|++||.|+|+|.+++. +++
T Consensus 2 ~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l~~~~----~~----------~~~~~~~~Gd~v~v~v~~~~~---~~~ 63 (69)
T cd05692 2 SVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKR----VK----------DVKDVLKEGDKVKVKVLSIDA---RGR 63 (69)
T ss_pred CEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCcc----cC----------CHHHccCCCCEEEEEEEEECC---CCc
Confidence 468999999999999999976 799999999887652 11 234679999999999999985 578
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 64 i~ls~ 68 (69)
T cd05692 64 ISLSI 68 (69)
T ss_pred EEEEE
Confidence 88876
No 41
>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=98.06 E-value=1.6e-05 Score=62.77 Aligned_cols=66 Identities=15% Similarity=0.202 Sum_probs=54.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+. +++|++|.+++...+ . ...+..|++||.|+|+|.+++.+ +++
T Consensus 3 ~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~~----~----------~~~~~~~~~Gd~v~v~i~~vd~~--~~~ 64 (68)
T cd05688 3 DVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWGR----V----------KHPSEVVNVGDEVEVKVLKIDKE--RKR 64 (68)
T ss_pred CEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCcc----c----------cCHhHEECCCCEEEEEEEEEECC--CCE
Confidence 46899999999999999995 699999999886321 1 13457799999999999999975 788
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
+.||
T Consensus 65 i~ls 68 (68)
T cd05688 65 ISLG 68 (68)
T ss_pred EecC
Confidence 8775
No 42
>PRK08059 general stress protein 13; Validated
Probab=98.05 E-value=1.5e-05 Score=71.34 Aligned_cols=68 Identities=18% Similarity=0.199 Sum_probs=57.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.. +++|++|+++++.++ .. +....|++||.|+|+|.+++.+ +++
T Consensus 9 ~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~~----~~----------~~~~~~~vGD~I~vkI~~id~~--~~~ 71 (123)
T PRK08059 9 SVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGF----VK----------DIHDFLSVGDEVKVKVLSVDEE--KGK 71 (123)
T ss_pred CEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCccc----cc----------CHHHcCCCCCEEEEEEEEEECC--CCe
Confidence 689999999999999999975 899999999987542 11 2346799999999999999865 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 72 i~lsl 76 (123)
T PRK08059 72 ISLSI 76 (123)
T ss_pred EEEEE
Confidence 99886
No 43
>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=98.03 E-value=2.7e-05 Score=63.57 Aligned_cols=60 Identities=13% Similarity=0.202 Sum_probs=52.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|.+++++|++|.+.+ +.+|++|.+++. ..|++||+|+|+|.++ .+ +++
T Consensus 18 ~~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se~~----------------------~~~~iGd~v~v~I~~i-~e--~~~ 71 (77)
T cd04473 18 KLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL----------------------RDYEVGDEVIVQVTDI-PE--NGN 71 (77)
T ss_pred CEEEEEEEeEecceEEEEECC-CcEEEEEchhcc----------------------CcCCCCCEEEEEEEEE-CC--CCc
Confidence 689999999999999999986 799999987542 3499999999999998 44 899
Q ss_pred eEEEeC
Q 008167 570 LQLTLI 575 (575)
Q Consensus 570 i~l~l~ 575 (575)
|.|+++
T Consensus 72 i~l~~~ 77 (77)
T cd04473 72 IDLIPV 77 (77)
T ss_pred EEEEEC
Confidence 999874
No 44
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.99 E-value=5.2e-05 Score=72.95 Aligned_cols=80 Identities=16% Similarity=0.217 Sum_probs=68.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC--
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR-- 567 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~-- 567 (575)
+.++|.|+++.++|++|.+. .++|+++.+.+..++ +.||+....+.+++....|++||.|+|+|.+++.+..+
T Consensus 83 EVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~l~~~~---~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~ 157 (187)
T PRK08563 83 EVVEGEVVEVVEFGAFVRIG--PVDGLLHISQIMDDY---ISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR 157 (187)
T ss_pred CEEEEEEEEEEccEEEEEEe--CceEEEEcHHcCCCc---eEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence 78999999999999999996 489999999998765 67888888888888889999999999999999875322
Q ss_pred -CceEEEe
Q 008167 568 -PKLQLTL 574 (575)
Q Consensus 568 -~~i~l~l 574 (575)
.+|.+|+
T Consensus 158 ~~~I~ls~ 165 (187)
T PRK08563 158 GSKIGLTM 165 (187)
T ss_pred CCEEEEEe
Confidence 3777765
No 45
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.96 E-value=2.8e-05 Score=89.42 Aligned_cols=78 Identities=14% Similarity=0.155 Sum_probs=61.2
Q ss_pred HHHHHHHhcCC-ceeE-EEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167 479 LHTLIYFRKRP-TDTE-ARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556 (575)
Q Consensus 479 ~~~~~~l~~~~-~~~~-g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V 556 (575)
+....|+.... ..|+ |.|++|.++|+||.|.. |++|+||++++.+++ +. +....|++||.|+|
T Consensus 743 ~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~r---v~-----------~~~dv~kvGD~V~V 807 (891)
T PLN00207 743 IISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNW---LA-----------KPEDAFKVGDRIDV 807 (891)
T ss_pred HHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCcc---cc-----------CHHHhcCCCCEEEE
Confidence 33344444444 6785 69999999999999975 899999999998653 22 22467999999999
Q ss_pred EEEEecCCCCCCceEEEe
Q 008167 557 HMEVVEPQPNRPKLQLTL 574 (575)
Q Consensus 557 ~V~~vd~~~~~~~i~l~l 574 (575)
+|.++|. ++||.|++
T Consensus 808 kVi~ID~---~grI~LSl 822 (891)
T PLN00207 808 KLIEVND---KGQLRLSR 822 (891)
T ss_pred EEEEECC---CCcEEEEE
Confidence 9999995 57999986
No 46
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.94 E-value=4e-05 Score=60.48 Aligned_cols=68 Identities=21% Similarity=0.288 Sum_probs=57.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.+.. +++|+++.+++.+.+ ..+....|++||.|+|+|..++.+ +++
T Consensus 4 ~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~~--------------~~~~~~~~~~G~~v~~~V~~~~~~--~~~ 66 (72)
T smart00316 4 DVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKR--------------VKDPEEVLKVGDEVKVKVLSVDEE--KGR 66 (72)
T ss_pred CEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCccc--------------cCCHHHeecCCCEEEEEEEEEeCC--CCE
Confidence 578999999999999999975 899999999887542 123456799999999999999965 699
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 67 i~ls~ 71 (72)
T smart00316 67 IILSL 71 (72)
T ss_pred EEEEe
Confidence 99886
No 47
>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=97.93 E-value=5.3e-05 Score=61.41 Aligned_cols=63 Identities=16% Similarity=0.124 Sum_probs=54.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.+|.++|++|.+..-|++|+++.++++.+ ..+++||.|.++|.+++.+ +++
T Consensus 6 ~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--------------------~~~~~Gq~v~~~V~~vd~~--~~~ 63 (74)
T cd05694 6 MVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--------------------SKLKVGQLLLCVVEKVKDD--GRV 63 (74)
T ss_pred CEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--------------------cccCCCCEEEEEEEEEECC--CCE
Confidence 568999999999999999953489999999877521 5689999999999999975 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||+
T Consensus 64 v~ls~ 68 (74)
T cd05694 64 VSLSA 68 (74)
T ss_pred EEEEE
Confidence 99986
No 48
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.92 E-value=2.6e-05 Score=78.56 Aligned_cols=69 Identities=16% Similarity=0.173 Sum_probs=59.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
..+.|.|.+|.++|++|.|.++ |++|+||++++..++ +. .....|++||.|.|+|.++|.+ ++
T Consensus 10 diV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~---i~-----------~i~~~~kvGd~V~vkVi~VD~~--k~ 73 (262)
T PRK03987 10 ELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGW---VK-----------NIRDHVKEGQKVVCKVIRVDPR--KG 73 (262)
T ss_pred CEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCccc---cc-----------CHHHhCCCCCEEEEEEEEEecc--cC
Confidence 6789999999999999999988 899999999987653 11 1246799999999999999976 78
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
+|.||+
T Consensus 74 ~I~LSl 79 (262)
T PRK03987 74 HIDLSL 79 (262)
T ss_pred eEEEEE
Confidence 999986
No 49
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.92 E-value=3.7e-05 Score=83.89 Aligned_cols=67 Identities=18% Similarity=0.235 Sum_probs=58.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+..+|+|.+++++|+||.|. |++|+||+++++... . ..+...+++||+|+|+|.++|.+ +.|
T Consensus 194 ~vV~G~V~~It~~GafVdig--GvdGLlHiseiS~~r----v----------~~P~~vvkvGd~VkvkVi~~D~e--~~R 255 (541)
T COG0539 194 EVVEGVVKNITDYGAFVDIG--GVDGLLHISEISWKR----V----------DHPSEVVKVGDEVKVKVISLDEE--RGR 255 (541)
T ss_pred ceEEEEEEEeecCcEEEEec--CeeeEEehhhccccc----c----------CCHHHhcccCCEEEEEEEEEccC--CCe
Confidence 78999999999999999996 799999999997442 1 14568899999999999999976 999
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|||
T Consensus 256 VsLSl 260 (541)
T COG0539 256 VSLSL 260 (541)
T ss_pred EEEEe
Confidence 99987
No 50
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.86 E-value=2.9e-05 Score=84.66 Aligned_cols=68 Identities=21% Similarity=0.314 Sum_probs=59.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
....|+|+.+.++|+||.+.+ |+||++|+|+++.. .. ..+...+++||.|+|+|..+|++ +||
T Consensus 279 ~~v~G~Vt~i~~~GafVei~~-GvEGlvhvSEisw~------~~--------~~P~evv~~Gq~V~V~Vl~id~e--~rR 341 (541)
T COG0539 279 DKVEGKVTNLTDYGAFVEIEE-GVEGLVHVSEISWT------KK--------NVPSEVVKVGQEVEVKVLDIDPE--RRR 341 (541)
T ss_pred CEEEEEEEEeecCcEEEEecC-Cccceeechhhccc------cc--------CCHHHhcccCCEEEEEEEeeCch--hce
Confidence 689999999999999999976 99999999988733 21 12567899999999999999986 999
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|+|+|
T Consensus 342 IsL~i 346 (541)
T COG0539 342 ISLGL 346 (541)
T ss_pred EEeee
Confidence 99987
No 51
>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=97.86 E-value=6e-05 Score=60.12 Aligned_cols=68 Identities=15% Similarity=0.154 Sum_probs=55.9
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.|.. +.+|++|.+++...+ . .+....|++||.|+++|.+++.+ ..+
T Consensus 2 ~iv~g~V~~i~~~~~~v~l~~-~~~g~l~~~e~~~~~----~----------~~~~~~~~~Gd~i~~~i~~~~~~--~~~ 64 (70)
T cd05687 2 DIVKGTVVSVDDDEVLVDIGY-KSEGIIPISEFSDDP----I----------ENGEDEVKVGDEVEVYVLRVEDE--EGN 64 (70)
T ss_pred CEEEEEEEEEeCCEEEEEeCC-CceEEEEHHHhCccc----c----------CCHhHcCCCCCEEEEEEEEEECC--CCe
Confidence 357899999999999999964 899999999886542 1 12356799999999999999964 688
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 65 i~lS~ 69 (70)
T cd05687 65 VVLSK 69 (70)
T ss_pred EEEEe
Confidence 99886
No 52
>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=97.84 E-value=5.3e-05 Score=58.55 Aligned_cols=65 Identities=23% Similarity=0.376 Sum_probs=53.1
Q ss_pred eEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCceE
Q 008167 492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQ 571 (575)
Q Consensus 492 ~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i~ 571 (575)
+.|.|.++.++|++|.+.. +.+|+++.+++.+++ + .+....|++||.|+|+|.++|.. ++++.
T Consensus 1 v~g~V~~v~~~g~~v~l~~-~~~g~~~~~~~~~~~---~-----------~~~~~~~~~G~~v~~~v~~~d~~--~~~i~ 63 (65)
T cd00164 1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKF---V-----------KDPSEVFKVGDEVEVKVLEVDPE--KGRIS 63 (65)
T ss_pred CEEEEEEEEeeeEEEEecC-CCEEEEEHHHCCCcc---c-----------cCHhhEeCCCCEEEEEEEEEcCC--cCEEe
Confidence 3799999999999999975 799999999887542 1 13457799999999999999964 67776
Q ss_pred EE
Q 008167 572 LT 573 (575)
Q Consensus 572 l~ 573 (575)
||
T Consensus 64 ls 65 (65)
T cd00164 64 LS 65 (65)
T ss_pred cC
Confidence 64
No 53
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.80 E-value=7e-05 Score=81.91 Aligned_cols=68 Identities=21% Similarity=0.243 Sum_probs=58.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.|++ |++|++|++++..+. +. .....|++||+|+|+|..+|.+ ++|
T Consensus 295 ~vv~G~V~~I~~fGvFVeL~~-gieGLvh~SeLs~~~---v~-----------~~~~~~kvGd~V~VkIi~ID~e--~rr 357 (486)
T PRK07899 295 QIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERH---VE-----------VPEQVVQVGDEVFVKVIDIDLE--RRR 357 (486)
T ss_pred CEEEEEEEEEeccEEEEEeCC-CcEEEEEHHHcCccc---cc-----------CccceeCCCCEEEEEEEEEECC--CCE
Confidence 789999999999999999986 899999999987542 11 2346799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 358 I~LSl 362 (486)
T PRK07899 358 ISLSL 362 (486)
T ss_pred EEEEE
Confidence 99987
No 54
>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=97.68 E-value=0.00018 Score=56.85 Aligned_cols=65 Identities=14% Similarity=0.185 Sum_probs=51.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|..+.++|++|.+ + |++|++|.+++...+ .. +... .+||.++|+|..+|.+ +++
T Consensus 2 ~iv~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~~~~----~~----------~~~~--~vG~~i~~~i~~vd~~--~~~ 61 (67)
T cd04465 2 EIVEGKVTEKVKGGLIVDI-E-GVRAFLPASQVDLRP----VE----------DLDE--YVGKELKFKIIEIDRE--RNN 61 (67)
T ss_pred CEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcc----cC----------ChHH--hCCCEEEEEEEEEeCC--CCE
Confidence 3679999999999999999 4 899999999886432 10 1111 3899999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||.
T Consensus 62 i~lS~ 66 (67)
T cd04465 62 IVLSR 66 (67)
T ss_pred EEEEc
Confidence 99885
No 55
>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=97.65 E-value=6.7e-05 Score=64.52 Aligned_cols=84 Identities=17% Similarity=0.205 Sum_probs=59.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcce-----ecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWY-----VDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~-----~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
..+.|.|..+.++|++|.||. |++|+++++++.+++..+.. ...........+....|++||.|+++|.+++..
T Consensus 5 ~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~ 83 (100)
T cd05693 5 MLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS 83 (100)
T ss_pred CEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCC
Confidence 578999999999999999996 99999999998754200000 000001111123357799999999999999963
Q ss_pred C-CCCceEEEe
Q 008167 565 P-NRPKLQLTL 574 (575)
Q Consensus 565 ~-~~~~i~l~l 574 (575)
. .+++|.|||
T Consensus 84 ~~~~~~i~LSl 94 (100)
T cd05693 84 KSGKKRIELSL 94 (100)
T ss_pred cCCCcEEEEEe
Confidence 1 268999987
No 56
>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=97.59 E-value=0.0002 Score=57.15 Aligned_cols=62 Identities=6% Similarity=0.033 Sum_probs=50.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
....|.|+.+.++|++|.++. |++|++|.+++.++| .. .......|++||.|+++|.+++.+
T Consensus 2 ~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~----~~--------~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 2 DLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEW----PD--------GKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred CEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhcccc----cc--------ccChhHhCCCCCEEEEEEEEEeCc
Confidence 357899999999999999986 999999999887542 10 112346799999999999999875
No 57
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.58 E-value=0.0002 Score=83.40 Aligned_cols=71 Identities=20% Similarity=0.245 Sum_probs=59.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|+++.++|+||.|++ |++|+||++++++++ ..+ .+ ..++.|++||.|+|+|.++|.+ +++
T Consensus 754 ~iV~GkV~~v~~~GvFVeL~~-gVeGlI~~s~lsdd~----~~~------~~-~~~~~f~vGD~V~v~Vl~iD~~--~rk 819 (863)
T PRK12269 754 STVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENR----DGD------PG-EALRKYAVGDRVKAVIVDMNVK--DRK 819 (863)
T ss_pred CEEEEEEEEEecCeEEEEcCC-CeEEEEEHHHcCCcc----ccc------ch-hhccccCCCCEEEEEEEEEEcC--CCE
Confidence 789999999999999999987 899999999998652 211 01 1246799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 820 I~LSl 824 (863)
T PRK12269 820 VAFSV 824 (863)
T ss_pred EEEEE
Confidence 99987
No 58
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.58 E-value=0.00021 Score=74.33 Aligned_cols=67 Identities=10% Similarity=0.224 Sum_probs=57.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.+. |++|+||.++++.++ . .+....|++||.|+|+|.++|.+ +++
T Consensus 198 ~vv~G~V~~I~~~G~fV~i~--gv~Gllhisels~~~----~----------~~~~~~~~vGd~VkvkVl~iD~e--~~r 259 (318)
T PRK07400 198 EVVVGTVRGIKPYGAFIDIG--GVSGLLHISEISHEH----I----------ETPHSVFNVNDEMKVMIIDLDAE--RGR 259 (318)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHccccc----c----------cChhhccCCCCEEEEEEEEEeCC--CCE
Confidence 78999999999999999994 899999999987542 1 13457799999999999999975 799
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 260 I~LS~ 264 (318)
T PRK07400 260 ISLST 264 (318)
T ss_pred EEEEE
Confidence 99886
No 59
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.55 E-value=0.0004 Score=76.06 Aligned_cols=67 Identities=21% Similarity=0.202 Sum_probs=56.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|+|+++.++|+||.|. |++|+||.++++..+ . .+....|++||.|+|+|..+|.+ +++
T Consensus 210 ~iv~G~V~~i~~~G~FVdlg--gv~Glv~~Sels~~~----v----------~~~~~~~kvGd~V~vkVl~iD~e--~~r 271 (486)
T PRK07899 210 QVRKGVVSSIVNFGAFVDLG--GVDGLVHVSELSWKH----I----------DHPSEVVEVGQEVTVEVLDVDMD--RER 271 (486)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHCCCcc----c----------CCHHHhcCCCCEEEEEEEEEECC--CCE
Confidence 78999999999999999995 899999999987431 1 12346799999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 272 I~LSl 276 (486)
T PRK07899 272 VSLSL 276 (486)
T ss_pred EEEEE
Confidence 99886
No 60
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.52 E-value=0.00019 Score=79.29 Aligned_cols=68 Identities=16% Similarity=0.196 Sum_probs=58.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|+++.++|+||.+.+ |++|+||.+++..+. . .+....+++||+|+|+|..+|.+ ++|
T Consensus 381 ~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se~s~~~----~----------~~~~~~~~~Gd~v~~~V~~id~e--~~r 443 (491)
T PRK13806 381 TTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISRAG----K----------PATYEKLKPGDSVTLVVEEIDTA--KRK 443 (491)
T ss_pred CEEEEEEEEEecCceEEEcCC-CcEEEEEHHHcCccc----c----------cchhhcCCCCCEEEEEEEEEeCC--CCE
Confidence 689999999999999999976 999999999887542 1 13457799999999999999976 889
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 444 i~Ls~ 448 (491)
T PRK13806 444 ISLAP 448 (491)
T ss_pred EEEEe
Confidence 99986
No 61
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.48 E-value=0.00071 Score=77.64 Aligned_cols=67 Identities=15% Similarity=0.177 Sum_probs=56.9
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|++|.++|+||.|.. |.+|+||++++.+++ . .+....|++||.|+|+|.++|.+ ++
T Consensus 623 ~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~----v----------~~~~~v~kvGD~V~VkV~~iD~~---gr 684 (693)
T PRK11824 623 EIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADER----V----------EKVEDVLKEGDEVKVKVLEIDKR---GR 684 (693)
T ss_pred eEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCcc----c----------cCccceeCCCCEEEEEEEEECCC---Cc
Confidence 789999999999999999975 899999999987542 1 13457899999999999999953 78
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 685 I~LS~ 689 (693)
T PRK11824 685 IRLSR 689 (693)
T ss_pred EEEEE
Confidence 88875
No 62
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.38 E-value=0.00037 Score=76.98 Aligned_cols=69 Identities=17% Similarity=0.273 Sum_probs=57.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.+.. |++|+||+++++.. .. ..+....|++||.|+|+|..+|.+ +++
T Consensus 294 ~~v~G~V~~v~~~G~fV~l~~-gv~Glvh~sels~~-----~~--------~~~~~~~~~~Gd~v~vkVl~iD~e--~~r 357 (491)
T PRK13806 294 DKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMSWT-----RR--------VNKPEDVVAPGDAVAVKIKDIDPA--KRR 357 (491)
T ss_pred CEEEEEEEEEeCceEEEEeCC-CcEEEEEHHHcCcc-----cc--------cCCHHHcCCCCCEEEEEEEEEEcc--CCE
Confidence 789999999999999999965 89999999988621 10 013456799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 358 i~Ls~ 362 (491)
T PRK13806 358 ISLSL 362 (491)
T ss_pred EEEEE
Confidence 99986
No 63
>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=97.37 E-value=0.00052 Score=57.10 Aligned_cols=71 Identities=8% Similarity=0.031 Sum_probs=55.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+.. +.+|++|.+++..+. +... ..+....+++||.|+++|.+++.+ ++
T Consensus 8 diV~g~V~~i~~~g~~v~i~~-~~~G~l~~se~~~~~---~~~~-------~~~~~~~l~vGd~i~~~V~~~~~~---~~ 73 (86)
T cd05789 8 DVVIGRVTEVGFKRWKVDINS-PYDAVLPLSEVNLPR---TDED-------ELNMRSYLDEGDLIVAEVQSVDSD---GS 73 (86)
T ss_pred CEEEEEEEEECCCEEEEECCC-CeEEEEEHHHccCCC---Cccc-------hHHHHhhCCCCCEEEEEEEEECCC---CC
Confidence 678999999999999999975 899999999886321 1000 012345699999999999999753 78
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||+
T Consensus 74 i~LS~ 78 (86)
T cd05789 74 VSLHT 78 (86)
T ss_pred EEEEe
Confidence 88885
No 64
>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=97.31 E-value=0.00047 Score=77.91 Aligned_cols=69 Identities=20% Similarity=0.179 Sum_probs=55.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCC-CCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQK-GSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d-~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
..++|.|++|.++|+||.|.. |++|+||++++.+- | +... .+....+++||+|+|+|.++|. ++
T Consensus 649 ~i~~GkV~~I~dfGaFVel~~-G~eGLvHISeisdls~---~~rv--------~~~~dv~kvGd~V~VKVl~ID~---~g 713 (719)
T TIGR02696 649 ERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQIRKLAG---GKRV--------ENVEDVLSVGQKIQVEIADIDD---RG 713 (719)
T ss_pred CEEEEEEEEEECceEEEEecC-CceEEEEhhhcccccc---ccCc--------CCHHHcCCCCCEEEEEEEEECC---CC
Confidence 789999999999999999974 89999999988531 1 1110 1345779999999999999994 67
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
||.|+
T Consensus 714 KI~L~ 718 (719)
T TIGR02696 714 KLSLV 718 (719)
T ss_pred Ceeec
Confidence 88875
No 65
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.30 E-value=0.00051 Score=80.01 Aligned_cols=69 Identities=17% Similarity=0.258 Sum_probs=57.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|.++.++|+||.+.+ |++|+||.++++. .... ......|++||.|+|+|..+|.+ +++
T Consensus 667 ~~v~G~V~~i~~~G~fV~l~~-gV~GlIh~sels~------~~~~-------~~~~~~~kvGq~VkvkVl~ID~e--~rr 730 (863)
T PRK12269 667 ARFTRRIVKVTNAGAFIEMEE-GIDGFLHVDDLSW------VKRT-------RPADHELEVGKEIECMVIECDPQ--ARR 730 (863)
T ss_pred CEEEEEEEEEecceEEEEeCC-CcEEEEEhHHhhc------cccc-------cchhhccCCCCEEEEEEEEEecc--CCE
Confidence 789999999999999999976 9999999988752 2111 12235699999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 731 I~LS~ 735 (863)
T PRK12269 731 IRLGV 735 (863)
T ss_pred EEEEe
Confidence 99986
No 66
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.30 E-value=0.0016 Score=61.88 Aligned_cols=70 Identities=13% Similarity=0.153 Sum_probs=58.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCcEEEEEEEEecCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQP 565 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~ 565 (575)
+..+|.|+++.++|++|.+. -++++||.+.++++ +.||+ ....|.++++...++.||.|+++|.++..+.
T Consensus 83 EVv~g~V~~v~~~G~~v~~G--p~~ifI~~~~l~~~----~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 83 EVLDAIVTDVNKLGFFAQAG--PLKAFVSRSAIPPD----FVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred CEEEEEEEEEecceEEEEee--CeEEEEcHHHCCCc----cEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 78999999999999999996 35699999999876 45655 4446666667899999999999999998753
No 67
>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=97.29 E-value=0.00063 Score=75.81 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=59.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..++|.|++++++|+||.+++ |++|++|.+++++++ . .+....|++||.|+|+|..+|.+ +++
T Consensus 448 ~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~l~~~~----~----------~~~~~~~~~Gd~v~~~V~~id~~--~~~ 510 (516)
T TIGR00717 448 SVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENR----D----------EDKTDEIKVGDEVEAKVVDIDKK--NRK 510 (516)
T ss_pred eEEEEEEEEEecceEEEEcCC-CeEEEEEHHHcCccc----c----------ccccccCCCCCEEEEEEEEEeCC--CCE
Confidence 689999999999999999987 899999999998652 1 13467899999999999999975 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 511 i~ls~ 515 (516)
T TIGR00717 511 VSLSV 515 (516)
T ss_pred EEEEE
Confidence 99987
No 68
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.27 E-value=0.00053 Score=77.30 Aligned_cols=69 Identities=19% Similarity=0.200 Sum_probs=58.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.|++ |++|++|++++..++ . +.+....|++||.|+|+|..+|.+ +++
T Consensus 375 ~~v~g~V~~v~~~G~fV~l~~-~v~g~i~~s~l~~~~----~---------~~~~~~~~~~Gd~v~v~Il~vd~~--~~~ 438 (565)
T PRK06299 375 DVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWDK----K---------GEEAVELYKKGDEVEAVVLKVDVE--KER 438 (565)
T ss_pred CEEEEEEEEEecceEEEECCC-CCEEEEEHHHcCccc----c---------ccChHhhCCCCCEEEEEEEEEeCC--CCE
Confidence 789999999999999999976 899999999987431 1 123457899999999999999975 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 439 i~ls~ 443 (565)
T PRK06299 439 ISLGI 443 (565)
T ss_pred EEEEE
Confidence 99986
No 69
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.26 E-value=0.00025 Score=69.72 Aligned_cols=69 Identities=16% Similarity=0.125 Sum_probs=59.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCc-eEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFG-IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~g-leg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
+.+-|.|..|.++|++|.|.+|+ +||+||+|.+...| . ++-...++.|++|-++|.+||+. +.
T Consensus 13 EiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~w----V----------knIrd~vkegqkvV~kVlrVd~~--rg 76 (269)
T COG1093 13 EIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGW----V----------KNIRDYVKEGQKVVAKVLRVDPK--RG 76 (269)
T ss_pred cEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHH----H----------HHHHHHhhcCCeEEEEEEEEcCC--CC
Confidence 46789999999999999999998 99999999988764 2 12356789999999999999986 89
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
.|+|||
T Consensus 77 ~IDLSl 82 (269)
T COG1093 77 HIDLSL 82 (269)
T ss_pred eEeeeh
Confidence 999997
No 70
>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=97.21 E-value=0.0014 Score=54.90 Aligned_cols=63 Identities=13% Similarity=-0.054 Sum_probs=49.1
Q ss_pred ceeEEEEEEEecC--eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~--g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
..+.|.|+.+.++ |+||.|.+ |.+|++|+++++... | +. . .+....+++||.|.|+|......
T Consensus 9 ~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~---~--~~----v--~~~~~~~~~Gd~v~VqV~~~~~~ 73 (88)
T cd04453 9 NIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAY---F--KK----H--KKIAKLLKEGQEILVQVVKEPIG 73 (88)
T ss_pred CEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchh---c--cc----c--CCHHHcCCCCCEEEEEEEEecCC
Confidence 6899999999996 99999987 899999999885321 1 10 0 12346799999999999987654
No 71
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.20 E-value=0.0029 Score=53.02 Aligned_cols=68 Identities=9% Similarity=0.034 Sum_probs=55.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
++.+|+|+++.+.|++|.+. .++++++-..++++ +.|+. ..-.+.+ +....++.|+.|+++|.++..+
T Consensus 3 EVi~g~V~~v~~~G~~v~~G--pl~~f~~~~~ip~~----~~~~~~~~~~~~~~-~~~~~i~~g~~VR~rV~~v~~~ 72 (88)
T cd04462 3 EVVDAIVTSVNKTGFFAEVG--PLSIFISRHLIPSD----MEFDPNASPPCFTS-NEDIVIKKDTEVRLKIIGTRVD 72 (88)
T ss_pred cEEEEEEEEEeccEEEEEEc--CceEEEEeeecCcc----ceECCcCCCCeEeC-CCcEEECCCCEEEEEEEEEEEc
Confidence 67899999999999999996 57899999999876 46654 2225553 3578999999999999999875
No 72
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.20 E-value=0.00098 Score=71.60 Aligned_cols=68 Identities=19% Similarity=0.239 Sum_probs=57.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.+++ |++|++|.+.+.... . .+....|++||+|+|+|..+|.+ +++
T Consensus 279 ~~v~g~V~~i~~~G~fV~l~~-gi~Glv~~se~~~~~----~----------~~~~~~~~~Gd~v~v~V~~id~e--~~~ 341 (390)
T PRK06676 279 DVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISHKH----I----------ATPSEVLEEGQEVKVKVLEVNEE--EKR 341 (390)
T ss_pred cEEEEEEEEEeCceEEEEECC-CCeEEEEhHHcCccc----c----------CChhhccCCCCEEEEEEEEEECC--CCE
Confidence 689999999999999999975 899999999886431 0 12346799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 342 i~ls~ 346 (390)
T PRK06676 342 ISLSI 346 (390)
T ss_pred EEEEE
Confidence 99986
No 73
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.16 E-value=0.00098 Score=76.19 Aligned_cols=68 Identities=19% Similarity=0.266 Sum_probs=58.3
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|+||.+.+ |++|++|.+++.++. . .+....|++||.|+|+|.++|.+ +++
T Consensus 564 ~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~sel~~~~----~----------~~~~~~~kvGd~V~vkV~~id~e--~~r 626 (647)
T PRK00087 564 SIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISWKR----I----------DKPEDVLSEGEEVKAKILEVDPE--EKR 626 (647)
T ss_pred eEEEEEEEEEECCeEEEEECC-CCEEEEEhhhcCccc----c----------CCHhhcCCCCCEEEEEEEEEeCC--CCE
Confidence 689999999999999999975 899999999887542 1 23456799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 627 I~lsl 631 (647)
T PRK00087 627 IRLSI 631 (647)
T ss_pred EEEEE
Confidence 99986
No 74
>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=97.09 E-value=0.0024 Score=50.53 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=49.9
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
...+|.|.++.++|++|.+. +.+|+++.+++.. +..|++||+|+|.|.+++.+....+
T Consensus 5 ~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~--------------------~~~~~~Gd~v~v~v~~v~~~~~~~~ 62 (67)
T cd04455 5 EIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP--------------------GESYRPGDRIKAYVLEVRKTSKGPQ 62 (67)
T ss_pred CEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC--------------------CCcCCCCCEEEEEEEEEecCCCCCE
Confidence 57899999999999999995 4899999876531 2358999999999999987544456
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.+|
T Consensus 63 i~lS 66 (67)
T cd04455 63 IILS 66 (67)
T ss_pred EEEe
Confidence 7665
No 75
>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=97.08 E-value=0.0019 Score=73.96 Aligned_cols=65 Identities=15% Similarity=0.179 Sum_probs=54.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|++|.++|+||.+.. |.+|++|++++.+.+ + .+....|++||+|+|+|.++|. +.+
T Consensus 620 ~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~---v-----------~~~~~~~kvGD~V~VkVi~id~---~gk 681 (684)
T TIGR03591 620 KIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANER---V-----------EKVEDVLKEGDEVKVKVLEIDK---QGR 681 (684)
T ss_pred cEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCc---c-----------cChhhccCCCCEEEEEEEEECC---CCC
Confidence 789999999999999999975 899999999997542 1 1346789999999999999995 456
Q ss_pred eEE
Q 008167 570 LQL 572 (575)
Q Consensus 570 i~l 572 (575)
|.|
T Consensus 682 i~L 684 (684)
T TIGR03591 682 IKL 684 (684)
T ss_pred ccC
Confidence 543
No 76
>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=97.03 E-value=0.0021 Score=52.91 Aligned_cols=67 Identities=9% Similarity=-0.078 Sum_probs=55.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
....|.|+++.+++++|.+.. +.+|.++.+++..++ . .+....+++||.|+++|.+++.. ++
T Consensus 8 diV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~~~~~~----~----------~~~~~~~~~GD~i~~~V~~~~~~---~~ 69 (82)
T cd04454 8 DIVIGIVTEVNSRFWKVDILS-RGTARLEDSSATEKD----K----------KEIRKSLQPGDLILAKVISLGDD---MN 69 (82)
T ss_pred CEEEEEEEEEcCCEEEEEeCC-CceEEeechhccCcc----h----------HHHHhcCCCCCEEEEEEEEeCCC---CC
Confidence 678999999999999999964 899999999886542 1 12346699999999999999852 78
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||+
T Consensus 70 i~LS~ 74 (82)
T cd04454 70 VLLTT 74 (82)
T ss_pred EEEEE
Confidence 88886
No 77
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.97 E-value=0.0032 Score=67.60 Aligned_cols=67 Identities=18% Similarity=0.262 Sum_probs=56.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|.++.++|++|.+. |++|+||.++++..+ . .+....|++||.|+|+|..+|.+ +++
T Consensus 194 ~~v~g~V~~v~~~G~fV~l~--~v~g~v~~sels~~~----~----------~~~~~~~~vGd~i~~~Vl~vd~~--~~~ 255 (390)
T PRK06676 194 DVVEGTVARLTDFGAFVDIG--GVDGLVHISELSHER----V----------EKPSEVVSVGQEVEVKVLSIDWE--TER 255 (390)
T ss_pred CEEEEEEEEEecceEEEEeC--CeEEEEEHHHcCccc----c----------CCHHHhcCCCCEEEEEEEEEeCC--CCE
Confidence 78999999999999999995 799999999887432 1 12346699999999999999975 788
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 256 i~lS~ 260 (390)
T PRK06676 256 ISLSL 260 (390)
T ss_pred EEEEE
Confidence 88875
No 78
>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=96.95 E-value=0.0017 Score=72.39 Aligned_cols=69 Identities=17% Similarity=0.236 Sum_probs=57.6
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|+||.++. |++|+||+++++.++ .. ......|++||.|+|+|..+|.+ +++
T Consensus 361 ~~v~g~V~~v~~~G~fV~l~~-~v~glv~~s~ls~~~----~~---------~~~~~~~~~G~~V~~~Vl~vd~~--~~~ 424 (516)
T TIGR00717 361 DRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWDK----DG---------READHLYKKGDEIEAVVLAVDKE--KKR 424 (516)
T ss_pred CEEEEEEEEEecceEEEECCC-CCEEEEEHHHCcCcc----cC---------CCHhHccCCCCEEEEEEEEEeCc--CCE
Confidence 789999999999999999985 999999999987431 11 12347799999999999999975 788
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 425 i~ls~ 429 (516)
T TIGR00717 425 ISLGV 429 (516)
T ss_pred EEEee
Confidence 98876
No 79
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.82 E-value=0.0015 Score=73.55 Aligned_cols=68 Identities=19% Similarity=0.230 Sum_probs=59.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
...+|+|.+|..||.||.|. ...+|+||++.+.+. |..+ +...+++||.|+|+|..+|.. +++
T Consensus 660 m~leg~Vrnv~~fgafVdIg-v~qDglvHis~ls~~----fv~~----------P~~vv~vGdiV~v~V~~vD~~--r~r 722 (780)
T COG2183 660 MILEGTVRNVVDFGAFVDIG-VHQDGLVHISQLSDK----FVKD----------PNEVVKVGDIVKVKVIEVDTA--RKR 722 (780)
T ss_pred CEEEEEEEEeeeccceEEec-cccceeeeHHHhhhh----hcCC----------hHHhcccCCEEEEEEEEEecc--cCe
Confidence 57899999999999999996 488999999999876 4433 467899999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.|++
T Consensus 723 I~Lsm 727 (780)
T COG2183 723 IALSM 727 (780)
T ss_pred eeeEe
Confidence 99986
No 80
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=96.80 E-value=0.0066 Score=63.29 Aligned_cols=64 Identities=14% Similarity=0.186 Sum_probs=52.8
Q ss_pred CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
...++|.|+++.++|++|.+. |++|+||.+.++.. + ... ..+|+.|+++|..+|.+ ++
T Consensus 119 ~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~~------~-----------~~~-~~vG~~i~~kVl~id~~--~~ 176 (318)
T PRK07400 119 DATVRSEVFATNRGGALVRIE--GLRGFIPGSHISTR------K-----------PKE-ELVGEELPLKFLEVDEE--RN 176 (318)
T ss_pred CCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCcc------C-----------Ccc-ccCCCEEEEEEEEEEcc--cC
Confidence 478999999999999999994 99999999988631 1 112 34999999999999976 78
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
+|.||+
T Consensus 177 ~i~lS~ 182 (318)
T PRK07400 177 RLVLSH 182 (318)
T ss_pred EEEEEh
Confidence 998875
No 81
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=96.78 E-value=0.0025 Score=71.94 Aligned_cols=69 Identities=20% Similarity=0.299 Sum_probs=56.8
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.++|++|.++. |++|+||+++++.+. . ..+....|++||.|+|+|..+|.+ +++
T Consensus 288 ~~v~g~V~~i~~~G~fV~l~~-~v~Glv~~sel~~~~------~-------~~~~~~~~~~G~~v~v~V~~id~~--~~~ 351 (565)
T PRK06299 288 SKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWTK------K-------NKHPSKVVSVGQEVEVMVLEIDEE--KRR 351 (565)
T ss_pred CEEEEEEEEEeCCeEEEEeCC-CCEEEEEHHHcCccc------c-------ccCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence 789999999999999999975 899999999886321 0 012345689999999999999975 789
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 352 i~ls~ 356 (565)
T PRK06299 352 ISLGL 356 (565)
T ss_pred EEEeh
Confidence 99875
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.27 E-value=0.038 Score=60.46 Aligned_cols=63 Identities=11% Similarity=0.062 Sum_probs=52.5
Q ss_pred CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
.....|+|.++.++|++|.|. |++|++|.++.. .+..|++||+|+|.|..|+.+....
T Consensus 135 GeIV~G~V~ri~~~giiVDLg--gvea~LP~sE~i--------------------p~E~~~~GdrIka~I~~Vd~~~kg~ 192 (470)
T PRK09202 135 GEIITGVVKRVERGNIIVDLG--RAEAILPRKEQI--------------------PRENFRPGDRVRAYVYEVRKEARGP 192 (470)
T ss_pred CCEEEEEEEEEecCCEEEEEC--CeEEEecHHHcC--------------------CCccCCCCCEEEEEEEEEecCCCCC
Confidence 478999999999999999994 899999977542 3466999999999999999764445
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
+|.||
T Consensus 193 qIilS 197 (470)
T PRK09202 193 QIILS 197 (470)
T ss_pred eEEEE
Confidence 88776
No 83
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.13 E-value=0.021 Score=65.49 Aligned_cols=68 Identities=15% Similarity=0.195 Sum_probs=56.4
Q ss_pred CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
...+.|.|.++.++|++|.+ . |++|++|.+++...+ . .+....|++||.|+|+|.++|.+ ++
T Consensus 478 G~iV~g~V~~v~~~G~fV~l-~-gv~Gll~~sels~~~----~----------~~~~~~~~vGd~V~vkV~~id~~--~~ 539 (647)
T PRK00087 478 GDVVEGEVKRLTDFGAFVDI-G-GVDGLLHVSEISWGR----V----------EKPSDVLKVGDEIKVYILDIDKE--NK 539 (647)
T ss_pred CCEEEEEEEEEeCCcEEEEE-C-CEEEEEEHHHcCccc----c----------CCHHHhcCCCCEEEEEEEEEECC--CC
Confidence 37899999999999999999 3 899999999886431 1 12456799999999999999975 78
Q ss_pred ceEEEe
Q 008167 569 KLQLTL 574 (575)
Q Consensus 569 ~i~l~l 574 (575)
+|.||+
T Consensus 540 ~I~lS~ 545 (647)
T PRK00087 540 KLSLSL 545 (647)
T ss_pred EEEEEe
Confidence 888875
No 84
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.02 E-value=0.013 Score=65.12 Aligned_cols=67 Identities=15% Similarity=0.212 Sum_probs=55.9
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+.+.|.|+.+.+||+||.+.. |-+|++|++.+.... + ++....+++||.|.|+|..+|. +-|
T Consensus 621 ~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~~~~~r------------v--~kv~dvlk~Gd~v~Vkv~~iD~---~Gr 682 (692)
T COG1185 621 EVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKER------------V--EKVEDVLKEGDEVKVKVIEIDK---QGR 682 (692)
T ss_pred cEEEEEEEEEeecceEEEecC-CcceeEEehhhhhhh------------h--hcccceeecCceEEEEEeeecc---cCC
Confidence 689999999999999999986 889999999987541 1 2345889999999999999996 466
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.|++
T Consensus 683 i~ls~ 687 (692)
T COG1185 683 IRLSI 687 (692)
T ss_pred cccee
Confidence 76664
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.71 E-value=0.093 Score=55.48 Aligned_cols=70 Identities=10% Similarity=0.053 Sum_probs=54.5
Q ss_pred HHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 482 LIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 482 ~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
..|..+..+...|+|..+.++|++|.+. |++|+++.++.. .+..|+.||+|+|.|..|
T Consensus 128 ~ef~~k~GeiV~G~V~~~~~~~~~Vdlg--~vEa~LP~~E~i--------------------p~e~~~~Gd~Ika~V~~V 185 (362)
T PRK12327 128 NEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPAEQI--------------------PGETYKHGDRIKVYVVKV 185 (362)
T ss_pred HHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHHHcC--------------------CCCCCCCCCEEEEEEEEE
Confidence 3344444478899999999999999985 699999965432 245699999999999999
Q ss_pred cCCCCCCceEEE
Q 008167 562 EPQPNRPKLQLT 573 (575)
Q Consensus 562 d~~~~~~~i~l~ 573 (575)
+.+....+|.+|
T Consensus 186 ~~~~kgp~IivS 197 (362)
T PRK12327 186 EKTTKGPQIFVS 197 (362)
T ss_pred ecCCCCCeEEEE
Confidence 977556677776
No 86
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=95.47 E-value=0.032 Score=53.76 Aligned_cols=66 Identities=11% Similarity=0.043 Sum_probs=52.1
Q ss_pred ceeEEEEEEEecCeEEEEEcC---------CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167 490 TDTEARIVKIRSNGFIVFVPK---------FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 560 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~---------~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~ 560 (575)
..+.|.|+++.++|++|.|.. .+++|++|.+++...+ . .+....|++||.|+++|.+
T Consensus 66 diV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~----~----------~~~~~~~~~GD~V~akV~~ 131 (189)
T PRK09521 66 DIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGY----V----------ESLTDAFKIGDIVRAKVIS 131 (189)
T ss_pred CEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhh----h----------hhHHhccCCCCEEEEEEEe
Confidence 688999999999999999953 3689999999876432 1 1234679999999999998
Q ss_pred ecCCCCCCceEEEe
Q 008167 561 VEPQPNRPKLQLTL 574 (575)
Q Consensus 561 vd~~~~~~~i~l~l 574 (575)
++ +++.||+
T Consensus 132 i~-----~~i~LS~ 140 (189)
T PRK09521 132 YT-----DPLQLST 140 (189)
T ss_pred cC-----CcEEEEE
Confidence 87 4677664
No 87
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.21 E-value=0.058 Score=53.78 Aligned_cols=71 Identities=11% Similarity=0.061 Sum_probs=55.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|+++.+++++|.|.. +.+|++|++++...+ ...|+ .+....|++||.|.++|.+++.+ ++
T Consensus 65 DiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~~---~~~d~-------~~~~~~~~~GDlV~akV~~i~~~---~~ 130 (235)
T PRK04163 65 DLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGRP---VNVEG-------TDLRKYLDIGDYIIAKVKDVDRT---RD 130 (235)
T ss_pred CEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCCc---cccch-------hhhHhhCCCCCEEEEEEEEECCC---Cc
Confidence 688999999999999999975 689999999886542 11222 23456799999999999999864 45
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
+.||+
T Consensus 131 ~~LS~ 135 (235)
T PRK04163 131 VVLTL 135 (235)
T ss_pred EEEEE
Confidence 77764
No 88
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.12 E-value=0.2 Score=52.56 Aligned_cols=70 Identities=11% Similarity=0.120 Sum_probs=53.8
Q ss_pred HHHHhcCCceeEEEEEEEecCe-EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167 482 LIYFRKRPTDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 560 (575)
Q Consensus 482 ~~~l~~~~~~~~g~V~~v~~~g-~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~ 560 (575)
..|-....+...|+|.++.+.| ++|.+. |++|+++.++.. .+..|++||+|+|.|..
T Consensus 125 ~ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP~~E~i--------------------p~E~~~~Gd~ik~~V~~ 182 (341)
T TIGR01953 125 DEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILPKKEQI--------------------PGEKFRIGDRIKAYVYE 182 (341)
T ss_pred HHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEecHHHcC--------------------CCcCCCCCCEEEEEEEE
Confidence 3444334478899999999988 588884 899999977543 12449999999999999
Q ss_pred ecCCCCCCceEEE
Q 008167 561 VEPQPNRPKLQLT 573 (575)
Q Consensus 561 vd~~~~~~~i~l~ 573 (575)
|+......+|.||
T Consensus 183 V~~~~kg~qIivS 195 (341)
T TIGR01953 183 VRKTAKGPQIILS 195 (341)
T ss_pred EEcCCCCCeEEEE
Confidence 9976556677776
No 89
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=94.80 E-value=0.042 Score=44.86 Aligned_cols=64 Identities=16% Similarity=0.209 Sum_probs=50.1
Q ss_pred EEEEEecCeEEEEEcCCceEEEEE-ccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCceEEE
Q 008167 495 RIVKIRSNGFIVFVPKFGIEGPVY-LTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 573 (575)
Q Consensus 495 ~V~~v~~~g~~V~l~~~gleg~v~-~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i~l~ 573 (575)
-|..+.+.|+.|.|.+||+||.|- .+++.-+. . +.-++.+ +|-.+.|+|..+|.+ +.=|+||
T Consensus 22 ~Vv~i~d~~~YV~LleY~iegmIl~~selsr~r----------i----rsi~kll-VGk~e~v~ViRVDk~--KGYIDLs 84 (86)
T PHA02858 22 GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADR----------A----EKLKKKL-VGKTINVQVIRTDKL--KGYIDVR 84 (86)
T ss_pred EEEEEeccEEEEEEecCccceEEecHHHHhHHH----------H----Hhhhhhh-cCCeeEEEEEEECCC--CCEEEeE
Confidence 677889999999999999999987 66554331 1 1224567 999999999999976 8888888
Q ss_pred eC
Q 008167 574 LI 575 (575)
Q Consensus 574 l~ 575 (575)
.+
T Consensus 85 ~~ 86 (86)
T PHA02858 85 HV 86 (86)
T ss_pred cC
Confidence 64
No 90
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: 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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.54 E-value=0.093 Score=41.97 Aligned_cols=67 Identities=16% Similarity=-0.011 Sum_probs=52.9
Q ss_pred eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEE-EEEEEEecCCCCCCc
Q 008167 491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTV-NIHMEVVEPQPNRPK 569 (575)
Q Consensus 491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V-~V~V~~vd~~~~~~~ 569 (575)
..+|.|..-+++++.|.+.+.|+.|+++...++|. +.-. +..-+.+++||++ ++.|. +. .+|.
T Consensus 3 lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~----~~k~--------~~~~~klrvG~~L~~~lvL--~~--~~r~ 66 (72)
T cd05699 3 LVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH----VSNC--------PLLWHCLQEGDTIPNLMCL--SN--YKGR 66 (72)
T ss_pred eEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc----hhhC--------HHHHhhhhcCCCccceEEE--ec--cccE
Confidence 57899999999999999999999999999988873 2211 1124779999999 88888 43 3777
Q ss_pred eEEE
Q 008167 570 LQLT 573 (575)
Q Consensus 570 i~l~ 573 (575)
|.++
T Consensus 67 i~lt 70 (72)
T cd05699 67 IILT 70 (72)
T ss_pred EEEe
Confidence 7776
No 91
>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=93.24 E-value=0.093 Score=40.24 Aligned_cols=52 Identities=21% Similarity=0.379 Sum_probs=38.1
Q ss_pred CCccEEEEEeCCCCCCceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEe
Q 008167 8 GSVAHALFVPKDRRIPKIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRV 61 (575)
Q Consensus 8 ~~~~~~~~~P~d~r~p~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~ 61 (575)
..+.+.+++|.| .-..|.|+.+.... ..|++|+|++.. +.....|.|+|+++
T Consensus 6 ~~~GfGFv~~~~-~~~DifIp~~~l~~A~~gD~V~v~i~~-~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 6 HPKGFGFVIPDD-GGEDIFIPPRNLNGAMDGDKVLVRITP-PSRGKRPEGEVVEV 58 (58)
T ss_dssp -SSS-EEEEECT--TEEEEE-HHHHTTS-TT-EEEEEEEE-SSSEEEEEEEEEE-
T ss_pred EcCCCEEEEECC-CCCCEEECHHHHCCCCCCCEEEEEEec-CCCCCCCCEEEEeC
Confidence 356789999999 33469999887654 578999999999 88888999999975
No 92
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.16 E-value=0.47 Score=43.65 Aligned_cols=70 Identities=9% Similarity=-0.002 Sum_probs=48.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
+..+|+|+.|.+.|+|+.... ++.++.--..+.|+ +|+..+..-.+.+++.. +++.|++|+++|.....+
T Consensus 83 EVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~--~f~p~~n~P~f~~~d~s-~I~~~~~VR~kiigtr~~ 152 (170)
T KOG3298|consen 83 EVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDY--EFDPGENPPNFQTEDES-VIQKGVEVRLKIIGTRVD 152 (170)
T ss_pred cEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCc--ccCCCCCCCcccccccc-eeeeCcEEEEEEEEEEEe
Confidence 788999999999999999974 55555433445443 24433332334333333 899999999999988764
No 93
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=91.71 E-value=0.41 Score=52.16 Aligned_cols=60 Identities=18% Similarity=0.134 Sum_probs=51.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
..+.|.|+.+++.|++|.++. +.+|++|.++++..| . .+....+.+||.|.|+....|+.
T Consensus 670 ~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e~----i----------akpsd~levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 670 GVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQEK----I----------AKPSDLLEVGQEIQVKYIERDPR 729 (760)
T ss_pred eEEEEEEeeecccceEEEecC-Cchhhccchhccccc----c----------cChHHHHhhcceeEEEEEeecCc
Confidence 457999999999999999987 999999999998664 1 13445699999999999999985
No 94
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=91.46 E-value=1.2 Score=35.25 Aligned_cols=62 Identities=11% Similarity=0.123 Sum_probs=45.9
Q ss_pred ceeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
-+++|+|+..-+++. .|.+++ |.+-..|++...- ...-.+..||.|.|.+..-|++ +.
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr------------------~~rI~I~~GD~V~Ve~spyd~t--kg 63 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIR------------------MHYIRILPGDKVKVELSPYDLT--RG 63 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECC-CCEEEEEecCcch------------------hccEEECCCCEEEEEECcccCC--cE
Confidence 367999999988775 578875 8888888764321 2345689999999999887754 77
Q ss_pred ceEE
Q 008167 569 KLQL 572 (575)
Q Consensus 569 ~i~l 572 (575)
+|.+
T Consensus 64 rIi~ 67 (68)
T TIGR00008 64 RITY 67 (68)
T ss_pred eEEe
Confidence 7654
No 95
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=91.26 E-value=0.18 Score=60.09 Aligned_cols=68 Identities=21% Similarity=0.286 Sum_probs=58.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|.|..+.++|.+|.++. |++|+.+.+...+++ .- +....|.+||+|+++|..+|.+ +++
T Consensus 601 ~~~~G~l~~~~~~g~~V~F~g-~lsGf~p~s~~sd~~----v~----------~~~ehf~vGqTv~~~i~nvd~e--k~r 663 (1710)
T KOG1070|consen 601 KITKGTLCAIKENGAFVTFTG-GLSGFAPVSEMSDDF----VL----------SDSEHFPVGQTVRAKIVNVDDE--KRR 663 (1710)
T ss_pred ceEEEEEeeeccCCeEEEecC-ccccccchhhhhhhh----hc----------ChhhhcccccEEEEEEEecCch--hce
Confidence 578999999999999999997 999999999988874 32 3456799999999999999976 899
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.+++
T Consensus 664 m~l~~ 668 (1710)
T KOG1070|consen 664 MPLGL 668 (1710)
T ss_pred eehhh
Confidence 88764
No 96
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=91.03 E-value=0.58 Score=46.79 Aligned_cols=59 Identities=19% Similarity=0.218 Sum_probs=50.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+..+|+|-.+...|.||.+ +.+.-|+||-++.- ...++|++++++|..+.. .++
T Consensus 157 q~v~~tVYr~~~~G~fv~~-e~~~~GfIh~sEr~----------------------~~prlG~~l~~rVi~~re---Dg~ 210 (287)
T COG2996 157 QEVDATVYRLLESGTFVIT-ENGYLGFIHKSERF----------------------AEPRLGERLTARVIGVRE---DGK 210 (287)
T ss_pred CeeeeEEEEEeccceEEEE-cCCeEEEEcchhhc----------------------ccccCCceEEEEEEEEcc---CCe
Confidence 6889999999999999999 55999999965432 347999999999999996 589
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.||+
T Consensus 211 lnLSl 215 (287)
T COG2996 211 LNLSL 215 (287)
T ss_pred eeccc
Confidence 99886
No 97
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=90.21 E-value=2 Score=35.56 Aligned_cols=63 Identities=10% Similarity=0.165 Sum_probs=47.5
Q ss_pred ceeEEEEEEEecCeEE-EEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFI-VFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~-V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
-+++|+|+.+.+++.| |.|. .|.+-..|++..- +...-.+.+||+|.|.+.--|++ +.
T Consensus 7 ie~~G~V~e~Lp~~~frV~Le-nG~~vla~isGKm------------------R~~rIrIl~GD~V~VE~spYDlt--kG 65 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLE-NGVEVGAYASGRM------------------RKHRIRILAGDRVTLELSPYDLT--KG 65 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeC-CCCEEEEEeccce------------------eeeeEEecCCCEEEEEECcccCC--ce
Confidence 4689999999887754 7775 4888888876432 12245689999999999988865 88
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
+|.+.
T Consensus 66 RIiyR 70 (87)
T PRK12442 66 RINFR 70 (87)
T ss_pred eEEEE
Confidence 88765
No 98
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=89.76 E-value=3.4 Score=43.76 Aligned_cols=70 Identities=14% Similarity=0.138 Sum_probs=52.3
Q ss_pred HHHHhcCCceeEEEEEEEecC-eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167 482 LIYFRKRPTDTEARIVKIRSN-GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 560 (575)
Q Consensus 482 ~~~l~~~~~~~~g~V~~v~~~-g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~ 560 (575)
-.|.....+...|+|..+... +++|.|. +.+|.++-++. -.+..|+.||+|+|.|..
T Consensus 132 ~ey~~~~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eq--------------------ip~E~~~~Gdrik~~i~~ 189 (374)
T PRK12328 132 EKYKKKVGKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNR--------------------IKGEKFKVGDVVKAVLKR 189 (374)
T ss_pred HHHHHhcCcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHc--------------------CCCCcCCCCCEEEEEEEE
Confidence 344444458899999999864 5788885 68998876532 135679999999999999
Q ss_pred ecCCCC-CCceEEE
Q 008167 561 VEPQPN-RPKLQLT 573 (575)
Q Consensus 561 vd~~~~-~~~i~l~ 573 (575)
|+.... ..+|.||
T Consensus 190 V~~~~k~gp~IilS 203 (374)
T PRK12328 190 VKIDKNNGILIELS 203 (374)
T ss_pred EecCCCCCCEEEEE
Confidence 998654 4677776
No 99
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=89.47 E-value=3.7 Score=44.34 Aligned_cols=71 Identities=21% Similarity=0.316 Sum_probs=51.7
Q ss_pred HHHhcCCceeEEEEEEEecCeEEEEEc-CCc---eEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEE
Q 008167 483 IYFRKRPTDTEARIVKIRSNGFIVFVP-KFG---IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM 558 (575)
Q Consensus 483 ~~l~~~~~~~~g~V~~v~~~g~~V~l~-~~g---leg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V 558 (575)
.|-....+...|+|..+...++.|.+. .+| ++|.++.++. -.+..|+.||+|+|.|
T Consensus 147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq--------------------ip~E~y~~Gdrika~i 206 (449)
T PRK12329 147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ--------------------LPNDNYRANATFKVFL 206 (449)
T ss_pred HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc--------------------CCCCcCCCCCEEEEEE
Confidence 343334478999999998888888873 233 7888876532 1356799999999999
Q ss_pred EEecCCC-CCCceEEE
Q 008167 559 EVVEPQP-NRPKLQLT 573 (575)
Q Consensus 559 ~~vd~~~-~~~~i~l~ 573 (575)
..|+... ...+|.||
T Consensus 207 ~~V~~~~~kGpqIilS 222 (449)
T PRK12329 207 KEVSEGPRRGPQLFVS 222 (449)
T ss_pred EEeecCCCCCCEEEEE
Confidence 9998752 44667665
No 100
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=88.23 E-value=1.2 Score=37.47 Aligned_cols=69 Identities=12% Similarity=0.042 Sum_probs=50.4
Q ss_pred ceeEEEEEEEecCeEEEEE--------cCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 490 TDTEARIVKIRSNGFIVFV--------PKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l--------~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
..+-|.|++++...+.|.| +. ...|.+|.++....+ .++. +....|++||-|+.+|.+.
T Consensus 8 DiVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~dv~~~~-----~d~~-------~~~~~f~~GDiV~AkVis~ 74 (92)
T cd05791 8 SIVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKEDIRATE-----KDKV-------EMYKCFRPGDIVRAKVISL 74 (92)
T ss_pred CEEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHHccccc-----cchH-------HHHhhcCCCCEEEEEEEEc
Confidence 5788999999999999988 54 568889988765431 1111 1346799999999999998
Q ss_pred cCCCCCCceEEEe
Q 008167 562 EPQPNRPKLQLTL 574 (575)
Q Consensus 562 d~~~~~~~i~l~l 574 (575)
.. .+.+.||+
T Consensus 75 ~~---~~~~~Lst 84 (92)
T cd05791 75 GD---ASSYYLST 84 (92)
T ss_pred CC---CCCcEEEe
Confidence 74 25566654
No 101
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=87.21 E-value=1.8 Score=52.28 Aligned_cols=68 Identities=13% Similarity=0.121 Sum_probs=57.0
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
....|.|..+.+.|+|+.+- .+++++++++++.+.+ .- ...+.|..|+.|.++|.+++.. .++
T Consensus 1164 ~iv~G~V~nv~~~glfi~ls-~~v~a~v~is~~~ds~----~k----------~w~k~~~~gklv~~rv~~ve~~--s~r 1226 (1710)
T KOG1070|consen 1164 DIVRGFVKNVETKGLFIALS-RKVEAFVPISGLSDSF----EK----------EWEKHLPVGKLVTGRVLSVEED--SKR 1226 (1710)
T ss_pred ceeEEEEEEecCCcEEEEEc-cceEEEEEccccccch----hh----------hhhccCCccceeeeEEEEeecc--Cce
Confidence 57899999999999999996 5999999999887753 11 2246799999999999999975 778
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|.++|
T Consensus 1227 iel~L 1231 (1710)
T KOG1070|consen 1227 IELSL 1231 (1710)
T ss_pred EEEEE
Confidence 88876
No 102
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=84.79 E-value=9.9 Score=33.85 Aligned_cols=69 Identities=14% Similarity=0.050 Sum_probs=50.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe---eCCCeEEeeCcEEEEEEEEecC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK---MDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g---~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
++..|.|.+....|+.|.| .|--+-+|+-..|... -.||+.+..++. ......+..|+.|+.+|.++..
T Consensus 5 Evl~g~I~~~~~~Gi~vsl-gFFddI~IP~~~L~~p----s~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 5 EVLTGKIKSSTAEGIRVSL-GFFDDIFIPPSLLPEP----SRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp -EEEEEEEEEETTEEEEEE-CCEEEEEEECCCC-TT----EEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CEEEEEEEecCCCcEEEEe-cccccEEECHHHCCCC----CccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 5789999999999999999 4667888998888865 345555555543 3345667999999999998875
No 103
>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=84.36 E-value=2 Score=49.88 Aligned_cols=60 Identities=15% Similarity=0.238 Sum_probs=46.9
Q ss_pred CccEEEEEeCCCCCCceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCCh
Q 008167 9 SVAHALFVPKDRRIPKIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDR 68 (575)
Q Consensus 9 ~~~~~~~~P~d~r~p~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~ 68 (575)
.+++++++|.|..-..|.|+..+.. ...|++|+|+|..|+.....|.|+|+++||...+.
T Consensus 77 ~~g~gFv~~~~~~~~di~I~~~~~~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~ 137 (709)
T TIGR02063 77 RDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQ 137 (709)
T ss_pred CCccEEEEECCCCCCcEEEChHHhCcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCCE
Confidence 4567888998722236999877664 45799999999999876667899999999998773
No 104
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=82.27 E-value=10 Score=30.65 Aligned_cols=63 Identities=13% Similarity=0.219 Sum_probs=46.1
Q ss_pred ceeEEEEEEEecCe-EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g-~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
..+.|+|..+-+++ |.|.+.+ |.+-.-|++...- ...-.+..||.|.|.+...+.+ +-
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr------------------~~~i~I~~GD~V~Ve~~~~d~~--kg 65 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMR------------------KNRIRILPGDVVLVELSPYDLT--KG 65 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcch------------------heeEEeCCCCEEEEEecccccc--cc
Confidence 46789999988776 5588765 8888888765431 2245689999999999887754 66
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
+|...
T Consensus 66 ~I~~R 70 (75)
T COG0361 66 RIVYR 70 (75)
T ss_pred cEEEE
Confidence 66543
No 105
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=82.16 E-value=1 Score=49.55 Aligned_cols=62 Identities=13% Similarity=0.255 Sum_probs=52.1
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
..+.|+|.+|.++|+||.|.+ .+.|++|-+++.++ ..+.+||.+-|++..+.++ ++.
T Consensus 124 ~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~--------------------~~~~vgdeiiV~v~~vr~~--~ge 180 (715)
T COG1107 124 KYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD--------------------PDYAVGDEIIVQVSDVRPE--KGE 180 (715)
T ss_pred eeeeccccchhhhcceeecCh-hhhccccccccCCC--------------------CCCCCCCeEEEEeeccCCC--CCc
Confidence 568999999999999999987 78898887766542 4589999999999999875 788
Q ss_pred eEEEe
Q 008167 570 LQLTL 574 (575)
Q Consensus 570 i~l~l 574 (575)
|+|..
T Consensus 181 idf~~ 185 (715)
T COG1107 181 IDFEP 185 (715)
T ss_pred cceee
Confidence 88864
No 106
>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=80.43 E-value=4.4 Score=43.90 Aligned_cols=69 Identities=10% Similarity=0.001 Sum_probs=46.8
Q ss_pred ceeEEEEEEEecC--eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 490 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 490 ~~~~g~V~~v~~~--g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
..+.|.|.++.++ |+||.+.. |-.|++|++++.... .+.+......-...+....++.||.|.|+|..-
T Consensus 27 nIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~--~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke 97 (414)
T TIGR00757 27 NIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNY--ECLAPAEAKREAGPSISELLRPGQSVLVQVVKE 97 (414)
T ss_pred CEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchh--hccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence 6799999999997 99999975 889999999886432 011111000000011234689999999999873
No 107
>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=79.21 E-value=6.5 Score=29.73 Aligned_cols=51 Identities=16% Similarity=0.113 Sum_probs=36.5
Q ss_pred ccEEEEEeCCCCCCceEecCCc----cCc-CCCCEEEEEEeecCCCCCCcceEEEEee
Q 008167 10 VAHALFVPKDRRIPKIRIQTRQ----LGN-LLDKRIIVAVDSWDCQSRYPFGHYVRVI 62 (575)
Q Consensus 10 ~~~~~~~P~d~r~p~i~i~~~~----~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~l 62 (575)
+.+.++.|.+.. +.|.++.+. ... ..|++|++++..|. ....+.|.+++++
T Consensus 9 ~g~gfv~~~~~~-~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~-~~~~~~a~~v~~~ 64 (64)
T smart00357 9 KGFGFIRPDDGG-KDVFVHPSQIQGGLKSLREGDEVEFKVVSPR-GGGKPEAENVVKL 64 (64)
T ss_pred CCeeEEecCCCC-ccEEEEhHHhhcCCCcCCCCCEEEEEEEEcc-CCCCcEEEEEEeC
Confidence 457788887654 568887655 333 46999999999883 4455788988874
No 108
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=74.70 E-value=14 Score=30.75 Aligned_cols=59 Identities=8% Similarity=-0.052 Sum_probs=45.5
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
..+-|+|+++...++.|.|.. ...+.++...+.+- .++....++.||-|-.+|..++..
T Consensus 8 D~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga---------------tk~~rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 8 DHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA---------------TKRNRPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred CEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc---------------cccccccCCCCCEEEEEEEecCCC
Confidence 567899999999999999976 45788887544321 023457799999999999999864
No 109
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=74.51 E-value=20 Score=27.62 Aligned_cols=48 Identities=13% Similarity=0.080 Sum_probs=28.4
Q ss_pred eEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 492 ~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
....|+.+.++|+++...+ +-+-+++.++.+ ..+++||.|+|-|....
T Consensus 5 ~~L~V~~~~~~g~fL~~~~-~~~vlLp~~e~~----------------------~~~~~Gd~v~VFvY~D~ 52 (61)
T PF13509_consen 5 NTLKVVDKNEFGYFLDDGE-GKEVLLPKSEVP----------------------EPLKVGDEVEVFVYLDK 52 (61)
T ss_dssp ----EEEE-SSEEEEEETT--EEEEEEGGG----------------------------TTSEEEEEEEE-T
T ss_pred cceEEEEEeCCEEEEECCC-CCEEEechHHcC----------------------CCCCCCCEEEEEEEECC
Confidence 4578999999999988654 456677665432 45899999999998754
No 110
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=63.75 E-value=21 Score=35.37 Aligned_cols=64 Identities=14% Similarity=0.082 Sum_probs=49.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
..+=|.|.+|...+..|.|-. ...+.+++++.... +++-++ .+....|++||-|-.+|..++.+
T Consensus 66 D~VIG~I~~v~~~~W~VDI~s-p~~A~L~ls~~~~r---~~~~~~-------~~~r~~l~vGD~v~AkV~~vd~~ 129 (239)
T COG1097 66 DVVIGKIIEVGPSGWKVDIGS-PYPALLSLSDFLRR---KFENAE-------KDLRPFLNVGDLVYAKVVDVDRD 129 (239)
T ss_pred CEEEEEEEEEcccceEEEcCC-ccceEeehhhhhcc---cccccc-------cccccccccCCEEEEEEEEccCC
Confidence 567899999999999999975 46789999876322 122222 24467899999999999999975
No 111
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=58.64 E-value=51 Score=28.27 Aligned_cols=62 Identities=6% Similarity=-0.025 Sum_probs=44.0
Q ss_pred ceeEEEEEEEecCeEE-EEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGFI-VFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~-V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
....|.|+....++.+ |.+++ |.+-+++++..- +..-.+..||.|.|.+..-+. .+-
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~-------------------Rk~IwI~~GD~VlVe~~~~~~--~kg 78 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGKM-------------------KKRMWIREGDVVIVAPWDFQD--EKA 78 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhh-------------------cccEEecCCCEEEEEecccCC--CEE
Confidence 5688999999887755 77775 888888775321 124568999999999876663 366
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
+|...
T Consensus 79 ~Iv~r 83 (100)
T PRK04012 79 DIIWR 83 (100)
T ss_pred EEEEE
Confidence 66544
No 112
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=56.70 E-value=53 Score=26.71 Aligned_cols=60 Identities=10% Similarity=-0.003 Sum_probs=40.6
Q ss_pred eEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCce
Q 008167 492 TEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 570 (575)
Q Consensus 492 ~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i 570 (575)
..|.|+....++. .|.+++ |.+-+.+++..- +..-.++.||.|.|.+..-+. .+-+|
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~-g~~~la~i~gK~-------------------rk~iwI~~GD~V~Ve~~~~d~--~kg~I 59 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD-GKKRLCRIRGKM-------------------RKRVWINEGDIVLVAPWDFQD--DKADI 59 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-CCEEEEEEchhh-------------------cccEEEcCCCEEEEEeccccC--CEEEE
Confidence 4688998887775 477775 888777765321 124568999999999776543 35555
Q ss_pred EEE
Q 008167 571 QLT 573 (575)
Q Consensus 571 ~l~ 573 (575)
...
T Consensus 60 v~r 62 (77)
T cd05793 60 IYK 62 (77)
T ss_pred EEE
Confidence 443
No 113
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=52.44 E-value=21 Score=29.38 Aligned_cols=59 Identities=10% Similarity=-0.006 Sum_probs=33.4
Q ss_pred ceeEEEEEEEecCeEEEEEcCC-----------------ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCc
Q 008167 490 TDTEARIVKIRSNGFIVFVPKF-----------------GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQ 552 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~-----------------gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD 552 (575)
..+-|.|+.+++..+.|.|-.. .+.|.|+.++.... +.|+ -...+.|+.||
T Consensus 6 diV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~t-----e~Dk-------v~~~~~FrpGD 73 (82)
T PF10447_consen 6 DIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRAT-----EKDK-------VKMYDCFRPGD 73 (82)
T ss_dssp -EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT------SS-----------GGGT--SSS
T ss_pred CEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeeccc-----ccch-------hhHHhccCCCC
Confidence 4678999999999888887533 33455555443221 1111 02356799999
Q ss_pred EEEEEEEE
Q 008167 553 TVNIHMEV 560 (575)
Q Consensus 553 ~V~V~V~~ 560 (575)
-|+.+|.+
T Consensus 74 IVrA~ViS 81 (82)
T PF10447_consen 74 IVRARVIS 81 (82)
T ss_dssp EEEEEEEE
T ss_pred EEEEEEee
Confidence 99999986
No 114
>PRK10811 rne ribonuclease E; Reviewed
Probab=51.65 E-value=42 Score=39.88 Aligned_cols=67 Identities=12% Similarity=-0.005 Sum_probs=46.3
Q ss_pred ceeEEEEEEEec--CeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEee-CCCeEEeeCcEEEEEEEEecC
Q 008167 490 TDTEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKM-DGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 490 ~~~~g~V~~v~~--~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~-~~~~~~~lGD~V~V~V~~vd~ 563 (575)
.+|.|.|.+|-+ .++||.|.. |-.|++++++....+ |. .. ....+. ..+..++.||.|-|.|..--.
T Consensus 40 nIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~---f~--~~-~~~~~~~~i~~~Lk~GqeILVQV~KEa~ 109 (1068)
T PRK10811 40 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREY---FP--AN-YSAHGRPNIKDVLREGQEVIVQIDKEER 109 (1068)
T ss_pred ceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccc---cc--cc-cccccccccccccCCCCEEEEEEeeccc
Confidence 679999999865 689999986 999999999885432 11 10 000001 124568999999999987543
No 115
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=46.25 E-value=24 Score=42.30 Aligned_cols=59 Identities=14% Similarity=0.103 Sum_probs=44.1
Q ss_pred eeEEEEEEEecCe---EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167 491 DTEARIVKIRSNG---FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 564 (575)
Q Consensus 491 ~~~g~V~~v~~~g---~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~ 564 (575)
.+.+.|.+|+... +.|.+. .|+.|+|+.+++++.. + .+....+++|+.|.++|.++|.+
T Consensus 988 iV~~~V~~vt~rr~~Cv~v~ld-~G~~g~i~~~~~Sd~~---v-----------~~p~~~v~vgq~v~~kvi~id~e 1049 (1299)
T KOG1856|consen 988 IVPVTVTKVTHRRGICVRVRLD-CGVTGFILAKNLSDRD---V-----------RRPENRVKVGQTVYCKVIKIDKE 1049 (1299)
T ss_pred eEEEeeeEEEecccceeEEEec-CCCceeeeccccChhh---c-----------cCHHHhhccCceEEEEeeeeeHh
Confidence 3566777887655 566775 5999999998887621 1 24556788999999999999854
No 116
>PRK15464 cold shock-like protein CspH; Provisional
Probab=43.68 E-value=64 Score=25.68 Aligned_cols=53 Identities=8% Similarity=-0.111 Sum_probs=37.4
Q ss_pred eEEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 492 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 492 ~~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
..|+|.-... .|+ |+.-++-+-+.++|++.+... +.+.++.||+|+..|..-.
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~------------------g~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR------------------DAEVLIPGLRVEFCRVNGL 59 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc------------------CCCCCCCCCEEEEEEEECC
Confidence 4688887754 455 455556567999999887532 2356899999999987643
No 117
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=43.47 E-value=66 Score=24.30 Aligned_cols=23 Identities=9% Similarity=-0.003 Sum_probs=19.3
Q ss_pred eeCCCeEEeeCcEEEEEEEEecC
Q 008167 541 KMDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 541 g~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
.++.+..+.+||.|+|+|.+++.
T Consensus 5 sRk~gE~I~Ig~~I~I~Vl~i~~ 27 (54)
T PF02599_consen 5 SRKVGESIVIGDDIEITVLEISG 27 (54)
T ss_dssp EEETT-EEEETTTEEEEEEEEET
T ss_pred EccCCCEEEECCCEEEEEEEEcC
Confidence 46788999999999999999983
No 118
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=43.08 E-value=1.6e+02 Score=23.42 Aligned_cols=62 Identities=15% Similarity=0.158 Sum_probs=35.6
Q ss_pred ceeEEEEEEEecC-eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSN-GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~-g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
-+..|.|+....+ -+.|.+.+ |..-..+++. . +. .......+||.|.|.+...+.+ +.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~G---k----lr-----------~~~i~i~vGD~V~ve~~~~~~~--~g 65 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELEN-GHEVLAHISG---K----MR-----------KNYIRILPGDKVTVELSPYDLT--KG 65 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEcc---c----ee-----------eCCcccCCCCEEEEEEcccCCC--eE
Confidence 4568999988766 45565543 4333333221 1 00 1233478999999998665543 45
Q ss_pred ceEE
Q 008167 569 KLQL 572 (575)
Q Consensus 569 ~i~l 572 (575)
.|..
T Consensus 66 ~Iv~ 69 (72)
T PRK00276 66 RITY 69 (72)
T ss_pred EEEE
Confidence 5544
No 119
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=39.94 E-value=1.6e+02 Score=24.33 Aligned_cols=61 Identities=15% Similarity=0.091 Sum_probs=40.8
Q ss_pred ceeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
....|.|+....++. .|.+++ |.+-++++... | +..-.++.||.|.|.+..-+. .+-
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK-------~------------Rk~iwI~~GD~VlVe~~~~~~--~kg 62 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-GKERLARIPGK-------M------------RKKVWIRRGDIVLVDPWDFQD--VKA 62 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEchh-------h------------cccEEEcCCCEEEEEecCCCC--CEE
Confidence 457899999887765 477775 88888777532 1 124568999999998765442 244
Q ss_pred ceEE
Q 008167 569 KLQL 572 (575)
Q Consensus 569 ~i~l 572 (575)
+|..
T Consensus 63 ~Iv~ 66 (83)
T smart00652 63 DIIY 66 (83)
T ss_pred EEEE
Confidence 4544
No 120
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=39.65 E-value=1.5e+02 Score=24.13 Aligned_cols=49 Identities=12% Similarity=-0.004 Sum_probs=34.1
Q ss_pred EEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 493 EARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 493 ~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
-|.|+....++. .|.+++ |.+-++++...- +..-.++.||.|.|....-
T Consensus 3 i~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~-------------------Rk~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 3 IVRVLRMLGNNRHEVECAD-GQRRLVSIPGKL-------------------RKNIWIKRGDFLIVDPIEE 52 (78)
T ss_pred EEEEEEECCCCEEEEEECC-CCEEEEEEchhh-------------------ccCEEEcCCCEEEEEeccc
Confidence 477888877665 588876 888877765321 1235688999999987654
No 121
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=38.87 E-value=85 Score=30.02 Aligned_cols=57 Identities=9% Similarity=0.083 Sum_probs=41.2
Q ss_pred ceeEEEEEEEecCeEEEEEcCCce-----------EEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEE
Q 008167 490 TDTEARIVKIRSNGFIVFVPKFGI-----------EGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM 558 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~V~l~~~gl-----------eg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V 558 (575)
..+-|.|+++....+.|.+- ++ .|-+|+++..+.+ . ++-...|++||-|+.+|
T Consensus 66 diV~grV~~v~~~~a~V~i~--~ve~~~r~~~~~~~~~ihvs~~~~~~----~----------~~~~d~f~~GDivrA~V 129 (188)
T COG1096 66 DIVYGRVTDVREQRALVRIV--GVEGKERELATSGAADIHVSQVRDGY----V----------EKLSDAFRIGDIVRARV 129 (188)
T ss_pred CEEEEEEeeccceEEEEEEE--EEecccccCCCCceeeEEEEeccccc----c----------cccccccccccEEEEEE
Confidence 57889999999988887773 33 3456666665542 1 12347799999999999
Q ss_pred EEec
Q 008167 559 EVVE 562 (575)
Q Consensus 559 ~~vd 562 (575)
.+.-
T Consensus 130 is~~ 133 (188)
T COG1096 130 ISTG 133 (188)
T ss_pred EecC
Confidence 9863
No 122
>PRK15463 cold shock-like protein CspF; Provisional
Probab=38.56 E-value=84 Score=24.96 Aligned_cols=52 Identities=6% Similarity=-0.064 Sum_probs=36.4
Q ss_pred eEEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 492 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 492 ~~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
..|+|..... .|+ |+.-++-+-+.++|++.+... +.+.++.||+|...+..-
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~------------------g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR------------------DAEELTTGLRVEFCRING 58 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc------------------CCCCCCCCCEEEEEEEEC
Confidence 3688887755 555 344445467899999987642 245688999999987653
No 123
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=37.23 E-value=98 Score=24.92 Aligned_cols=52 Identities=12% Similarity=0.075 Sum_probs=34.9
Q ss_pred EEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 493 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 493 ~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
.|+|.-... .|+ |+.-++-|-+.++|++.+..+ +.+.++.||+|+..+..-.
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~------------------g~~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------------------GYRTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc------------------CCCCCCCCCEEEEEEEECC
Confidence 467776644 455 455555578999999887542 2356888888888876543
No 124
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=36.96 E-value=51 Score=26.28 Aligned_cols=23 Identities=9% Similarity=0.019 Sum_probs=20.3
Q ss_pred eeCCCeEEeeCcEEEEEEEEecC
Q 008167 541 KMDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 541 g~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
.++.+..+.+||.|+|+|.+++-
T Consensus 5 sRk~~Esi~IgddI~itVl~i~g 27 (73)
T COG1551 5 SRKVGESIMIGDDIEITVLSIKG 27 (73)
T ss_pred EeecCceEEecCCeEEEEEEEcC
Confidence 36778999999999999999984
No 125
>PRK11712 ribonuclease G; Provisional
Probab=35.82 E-value=88 Score=34.75 Aligned_cols=71 Identities=10% Similarity=-0.021 Sum_probs=45.4
Q ss_pred ceeEEEEEEEec--CeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecC
Q 008167 490 TDTEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 490 ~~~~g~V~~v~~--~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
..+.|.|.+|-+ +++||.|.. +-.|++|++++.... .+..+.........+-...++.||.|-|+|..-..
T Consensus 40 nIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~--~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~ 112 (489)
T PRK11712 40 NIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHT--ECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPL 112 (489)
T ss_pred cEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchh--hhcccccccccccccHHHhccCCCEEEEEEEeCCc
Confidence 579999999966 679999984 999999999874321 01111100000000113458999999999987543
No 126
>PRK01712 carbon storage regulator; Provisional
Probab=34.94 E-value=88 Score=24.54 Aligned_cols=22 Identities=9% Similarity=-0.015 Sum_probs=19.5
Q ss_pred eCCCeEEeeCcEEEEEEEEecC
Q 008167 542 MDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 542 ~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
++.+..+.+||.++|+|..+..
T Consensus 6 Rk~gE~I~Igd~I~I~V~~i~~ 27 (64)
T PRK01712 6 RKVGESLMIGDDIEVTVLGVKG 27 (64)
T ss_pred ccCCCEEEeCCCEEEEEEEEeC
Confidence 6778899999999999999884
No 127
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=34.86 E-value=68 Score=25.23 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=17.9
Q ss_pred EEEEEEEEcCCCcEEEEEEEEE
Q 008167 203 AFSVIWELTPEAEIISTRYTKS 224 (575)
Q Consensus 203 a~s~~~~i~~~G~i~~~~~~~s 224 (575)
.+.+.+.||++|++.+.++..|
T Consensus 17 ~v~v~~~I~~~G~v~~~~v~~s 38 (79)
T PF03544_consen 17 TVVVEFTIDPDGRVSDVRVIQS 38 (79)
T ss_dssp EEEEEEEEETTTEEEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEEEEEc
Confidence 4677889999999999876554
No 128
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=32.99 E-value=1.4e+02 Score=23.55 Aligned_cols=54 Identities=11% Similarity=0.062 Sum_probs=36.7
Q ss_pred eeEEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 491 DTEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 491 ~~~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
...|+|.-... .|+ |+.-++-|-+-++|++.+... +.+.++.||+|...+..-+
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN------------------GFKTLAEGQRVEFEITNGA 58 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc------------------CCCCCCCCCEEEEEEEECC
Confidence 35688877653 454 355555567899999877532 2366889999999887644
No 129
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=32.79 E-value=1.3e+02 Score=27.88 Aligned_cols=62 Identities=8% Similarity=0.166 Sum_probs=41.9
Q ss_pred ceeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
...-|.|+....++. .|.+.+ |...+.|++..- +..-.+..||.|.|.+..-+. .+-
T Consensus 32 gq~~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GKm-------------------RK~IWI~~GD~VlVel~~yd~--~Kg 89 (155)
T PTZ00329 32 GQEYAQVLRMLGNGRLEAYCFD-GVKRLCHIRGKM-------------------RKRVWINIGDIILVSLRDFQD--SKA 89 (155)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEeeccc-------------------eeeEEecCCCEEEEeccCCCC--CEE
Confidence 456788988887775 477765 888888876431 113568999999998755443 355
Q ss_pred ceEEE
Q 008167 569 KLQLT 573 (575)
Q Consensus 569 ~i~l~ 573 (575)
+|.+.
T Consensus 90 dIi~R 94 (155)
T PTZ00329 90 DVILK 94 (155)
T ss_pred EEEEE
Confidence 66554
No 130
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=32.38 E-value=64 Score=26.04 Aligned_cols=25 Identities=32% Similarity=0.490 Sum_probs=16.8
Q ss_pred eeeEEEEEEEEcCCCcEEEEEEEEE
Q 008167 200 ERLAFSVIWELTPEAEIISTRYTKS 224 (575)
Q Consensus 200 ~r~a~s~~~~i~~~G~i~~~~~~~s 224 (575)
......|.++|+++|+|.++++.++
T Consensus 24 ~~~~~~V~i~i~~dG~v~~~~i~~s 48 (85)
T PF13103_consen 24 GGLSVTVRITIDPDGRVISVRIVKS 48 (85)
T ss_dssp TT--EEEEEEE-TTSBEEEEEEEE-
T ss_pred CCcEEEEEEEECCCCCEEEEEEecC
Confidence 3455778889999999998876543
No 131
>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=31.38 E-value=98 Score=24.25 Aligned_cols=58 Identities=14% Similarity=0.032 Sum_probs=38.6
Q ss_pred eEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecC
Q 008167 492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 492 ~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
+.|+|-.+.+.-..|.|.+-|--..++++.--.+- |.++ ..++++|+.+.|++...+.
T Consensus 4 htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdt---frf~-----------seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 4 HTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDT---FRFD-----------SEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred cchhhhhhhhceEEEEeeccccEEEEEchhhcccc---cccc-----------ceeeeccceEEEEEecCcc
Confidence 45666667666677777776666666665422221 4443 4789999999999987654
No 132
>PRK00568 carbon storage regulator; Provisional
Probab=30.85 E-value=79 Score=25.68 Aligned_cols=22 Identities=9% Similarity=0.114 Sum_probs=19.4
Q ss_pred eCCCeEEeeCcEEEEEEEEecC
Q 008167 542 MDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 542 ~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
++.+..+.+||.++|+|..+.-
T Consensus 6 RK~gEsI~Igd~I~I~Vl~i~g 27 (76)
T PRK00568 6 RKVNEGIVIDDNIHIKVISIDR 27 (76)
T ss_pred eeCCCeEEeCCCeEEEEEEEcC
Confidence 6778899999999999998884
No 133
>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=30.22 E-value=1.2e+02 Score=35.06 Aligned_cols=58 Identities=10% Similarity=0.012 Sum_probs=40.9
Q ss_pred CccEEEEEeCCCCCCceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEeecCCCC
Q 008167 9 SVAHALFVPKDRRIPKIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGD 67 (575)
Q Consensus 9 ~~~~~~~~P~d~r~p~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~ 67 (575)
.+++++++|.+..-..|.|+...... ..|++|.|+|..-.... .|.|+|+++|-...+
T Consensus 25 ~~gfgFv~~~~~~~~difI~~~~~~~a~~GD~V~v~i~~~~~~~-~~~g~v~~il~r~~~ 83 (654)
T TIGR00358 25 NKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRG-RFEAEVERILEPALT 83 (654)
T ss_pred CCccEEEEeCCCCCCcEEEchHHhCcCCCCCEEEEEEeecCCCC-CceEEEEEEeccCCC
Confidence 45678888876332378998876644 57999999986422222 389999999977644
No 134
>CHL00010 infA translation initiation factor 1
Probab=29.49 E-value=3.1e+02 Score=22.22 Aligned_cols=61 Identities=15% Similarity=0.215 Sum_probs=33.7
Q ss_pred eeEEEEEEEecCe-EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167 491 DTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 569 (575)
Q Consensus 491 ~~~g~V~~v~~~g-~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~ 569 (575)
+..|.|+.+..+| +.|.+.+ |..-..+++ +. +. .......+||.|.|.+...+.+ +..
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~-g~~~~c~~r---Gk----lr-----------~~~i~~~vGD~V~ve~~~~~~~--~g~ 66 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDN-GCQVLGYIS---GK----IR-----------RNSIRILPGDRVKVELSPYDLT--KGR 66 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-CCEEEEEec---cc----ee-----------cCCcccCCCCEEEEEEcccCCC--eEE
Confidence 4689999988544 5565543 433333322 11 11 1133468899999997655532 444
Q ss_pred eEE
Q 008167 570 LQL 572 (575)
Q Consensus 570 i~l 572 (575)
|..
T Consensus 67 Ii~ 69 (78)
T CHL00010 67 IIY 69 (78)
T ss_pred EEE
Confidence 443
No 135
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=28.04 E-value=1.8e+02 Score=22.89 Aligned_cols=52 Identities=15% Similarity=0.087 Sum_probs=35.5
Q ss_pred EEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 493 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 493 ~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
.|+|.-... .|+ |+.-++-|-+-++|++.+... +.+.++.||+|+..+..-+
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK10354 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND------------------GYKSLDEGQKVSFTIESGA 59 (70)
T ss_pred eEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc------------------CCCCCCCCCEEEEEEEECC
Confidence 688877643 444 355555557899999887542 2356899999999887643
No 136
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=27.97 E-value=85 Score=22.20 Aligned_cols=33 Identities=24% Similarity=0.203 Sum_probs=27.1
Q ss_pred ceeEEEEEEEe-cCeEEEEEcCCceEEEEEccCC
Q 008167 490 TDTEARIVKIR-SNGFIVFVPKFGIEGPVYLTPR 522 (575)
Q Consensus 490 ~~~~g~V~~v~-~~g~~V~l~~~gleg~v~~~~l 522 (575)
..+.|.|.++. +..+.|.+.+||-...|+.+++
T Consensus 13 ~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 13 KWYRAKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred eEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 46799999998 5668899999999888877654
No 137
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=27.94 E-value=23 Score=35.55 Aligned_cols=77 Identities=14% Similarity=0.199 Sum_probs=54.5
Q ss_pred HHHHHhcC-C---ceeEEEEEEEecCeEEEEEcCCc-eEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEE
Q 008167 481 TLIYFRKR-P---TDTEARIVKIRSNGFIVFVPKFG-IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVN 555 (575)
Q Consensus 481 ~~~~l~~~-~---~~~~g~V~~v~~~g~~V~l~~~g-leg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~ 555 (575)
.|+|.+++ | ..+-+-|..|..-|+.|.|-+|+ +||+|-++.|+--. . +..++.+++|-.=-
T Consensus 5 ~cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRR----------I----RSI~klirVGr~E~ 70 (304)
T KOG2916|consen 5 ECRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRR----------I----RSIQKLIRVGRNEP 70 (304)
T ss_pred eeehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHH----------H----HHHHHHHhcCCcce
Confidence 35555554 4 34556666778899999997765 89999998886421 1 12356678898888
Q ss_pred EEEEEecCCCCCCceEEE
Q 008167 556 IHMEVVEPQPNRPKLQLT 573 (575)
Q Consensus 556 V~V~~vd~~~~~~~i~l~ 573 (575)
|.|..||.+ +.=|+||
T Consensus 71 vvVlrVDke--kGYIDLS 86 (304)
T KOG2916|consen 71 VVVLRVDKE--KGYIDLS 86 (304)
T ss_pred EEEEEEcCC--CCceech
Confidence 899999975 7777765
No 138
>PRK10943 cold shock-like protein CspC; Provisional
Probab=27.61 E-value=1.7e+02 Score=23.02 Aligned_cols=54 Identities=11% Similarity=0.090 Sum_probs=36.5
Q ss_pred eeEEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 491 DTEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 491 ~~~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
...|+|..... .|+ |+.-++-|-+-++|++.+... +.+.+..||+|+..+..-+
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN------------------GFKTLAEGQNVEFEIQDGQ 58 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc------------------CCCCCCCCCEEEEEEEECC
Confidence 35688887654 455 344445567899999887642 2356889999999887543
No 139
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=27.55 E-value=1e+02 Score=23.78 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=16.5
Q ss_pred EEEEEEEcCCCcEEEEEEEE
Q 008167 204 FSVIWELTPEAEIISTRYTK 223 (575)
Q Consensus 204 ~s~~~~i~~~G~i~~~~~~~ 223 (575)
+.+.+.|+++|++.+.++.+
T Consensus 12 v~v~~~i~~~G~v~~~~i~~ 31 (74)
T TIGR01352 12 VVVRFTVDADGRVTSVSVLK 31 (74)
T ss_pred EEEEEEECCCCCEEEEEEEE
Confidence 66778999999999987754
No 140
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=26.31 E-value=1.7e+02 Score=22.67 Aligned_cols=52 Identities=12% Similarity=0.098 Sum_probs=34.0
Q ss_pred eeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 491 DTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 491 ~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
...|.|+....++. .|.+++ |.+-+++++.. + +..-.++.||.|.|.+..-+
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK-------~------------r~~iwI~~GD~V~V~~~~~d 56 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGK-------F------------RKRIWIKRGDFVLVEPSPYD 56 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HH-------H------------HTCC---TTEEEEEEESTTC
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccc-------e------------eeeEecCCCCEEEEEecccC
Confidence 56789999887765 588876 88888877532 1 23456899999999884333
No 141
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.16 E-value=1.3e+02 Score=28.03 Aligned_cols=50 Identities=20% Similarity=0.151 Sum_probs=37.0
Q ss_pred cCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHH
Q 008167 271 RGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQ 321 (575)
Q Consensus 271 ~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~ 321 (575)
.+.+.|...+.-+.+-.. |.+.--.++...+|..+.+|+|-.+|+++|.-
T Consensus 64 k~~l~~~kgerIitiy~s-GkVsm~~ikdedEAkeilgel~d~ineA~~kg 113 (193)
T COG4871 64 KNILILQKGERIITIYGS-GKVSMTMIKDEDEAKEILGELMDIINEAIAKG 113 (193)
T ss_pred cceEEEeeccEEEEEccC-CeEEeeeecCHHHHHHHHHHHHHHHHHHHHcc
Confidence 467777777766666543 44443445677899999999999999998863
No 142
>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=25.97 E-value=1.8e+02 Score=22.24 Aligned_cols=51 Identities=16% Similarity=0.102 Sum_probs=34.6
Q ss_pred EEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167 493 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 561 (575)
Q Consensus 493 ~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v 561 (575)
.|+|..... .|+ |+.-++.|-+-++|.+.+... +...++.||.|+..+...
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~------------------~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD------------------GFRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc------------------CCCcCCCCCEEEEEEEEC
Confidence 467776655 444 344455577888888776532 236689999999998765
No 143
>PRK14998 cold shock-like protein CspD; Provisional
Probab=25.78 E-value=2e+02 Score=23.00 Aligned_cols=52 Identities=12% Similarity=0.064 Sum_probs=34.7
Q ss_pred EEEEEEEec-CeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167 493 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 562 (575)
Q Consensus 493 ~g~V~~v~~-~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd 562 (575)
.|+|.-... .|+ |+.-++-|-+-++|++.+... +.+.++.|++|+..+..-+
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------------------GYRTLKAGQSVRFDVHQGP 56 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc------------------CCCCCCCCCEEEEEEEECC
Confidence 467776644 455 355555567999999877532 2366888999888886533
No 144
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=25.68 E-value=4.2e+02 Score=22.61 Aligned_cols=49 Identities=10% Similarity=-0.025 Sum_probs=34.8
Q ss_pred ceeEEEEEEEecCeEE-EEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEE
Q 008167 490 TDTEARIVKIRSNGFI-VFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM 558 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~~-V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V 558 (575)
....|.|+....++.+ |.+++ |.+-+++++..- +..-.+..||.|.|..
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~-------------------Rk~iwI~~GD~VlVsp 68 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCLD-GKTRLGRIPGKL-------------------KKRIWIREGDVVIVKP 68 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhh-------------------cccEEecCCCEEEEEE
Confidence 5678999999877754 77765 888777765321 1245689999999943
No 145
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=25.46 E-value=1.3e+02 Score=24.00 Aligned_cols=22 Identities=14% Similarity=0.098 Sum_probs=19.4
Q ss_pred eCCCeEEeeCcEEEEEEEEecC
Q 008167 542 MDGNLSYSVLQTVNIHMEVVEP 563 (575)
Q Consensus 542 ~~~~~~~~lGD~V~V~V~~vd~ 563 (575)
++.+..+.+||.++|+|..+..
T Consensus 6 Rk~gE~I~Igd~I~I~Vl~i~g 27 (69)
T TIGR00202 6 RKVNESIQIGDDIEVKVLSVKG 27 (69)
T ss_pred ccCCCEEEeCCCEEEEEEEEcC
Confidence 6778899999999999999873
No 146
>PLN00208 translation initiation factor (eIF); Provisional
Probab=24.31 E-value=2.3e+02 Score=26.00 Aligned_cols=61 Identities=8% Similarity=0.113 Sum_probs=40.8
Q ss_pred ceeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167 490 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 568 (575)
Q Consensus 490 ~~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~ 568 (575)
...-|.|+....++. .|.+.+ |...+++++..- +..-.++.||.|.|.+..-+.. +-
T Consensus 32 gq~~g~V~~~lGn~~~~V~c~d-G~~rLa~IpGKm-------------------RKrIWI~~GD~VlVel~~~d~~--Kg 89 (145)
T PLN00208 32 GQEYAQVLRMLGNGRCEALCID-GTKRLCHIRGKM-------------------RKKVWIAAGDIILVGLRDYQDD--KA 89 (145)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEeccc-------------------eeeEEecCCCEEEEEccCCCCC--EE
Confidence 456788888877765 477765 888888775321 1135578999999987655532 55
Q ss_pred ceEE
Q 008167 569 KLQL 572 (575)
Q Consensus 569 ~i~l 572 (575)
.|..
T Consensus 90 dIv~ 93 (145)
T PLN00208 90 DVIL 93 (145)
T ss_pred EEEE
Confidence 5544
No 147
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=23.07 E-value=4.1e+02 Score=21.49 Aligned_cols=61 Identities=21% Similarity=0.267 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCC
Q 008167 453 PQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPR 522 (575)
Q Consensus 453 ~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l 522 (575)
+.-..+|.|+|.-... +...+...|. +.....++.+++|...|+.+.. +-+...+|++..-
T Consensus 8 ~~~~~ii~HMN~DH~d-------~l~~~~~~~~-~~~~~~~a~m~~id~~G~~l~~-~~~~~~ripF~~p 68 (83)
T PF10615_consen 8 EAAARIIEHMNDDHAD-------DLLLYARHYG-GVPDAASARMTDIDRDGFDLRV-GGDQDVRIPFPPP 68 (83)
T ss_dssp HHHHHHHHHHHHH-HH-------HHHHHHHHHH-T-SSSSS-EEEEEETTEEEEEE-TTTEEEEEE-SS-
T ss_pred HHHHHHHHHHHHhHHH-------HHHHHHHhcC-CCCCCCCEEEEEEeccccEEEE-eCCcceEcCCCCC
Confidence 4778999999976532 3333333333 3333478899999999999988 3356777777643
No 148
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=22.41 E-value=2.3e+02 Score=27.39 Aligned_cols=34 Identities=15% Similarity=0.307 Sum_probs=25.9
Q ss_pred hcCCceeEEEEEEEecCeEEEEEcCCceEEEEEc
Q 008167 486 RKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519 (575)
Q Consensus 486 ~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~ 519 (575)
+....+.+|.|+.|.+.-|.+...+|+=.-.|++
T Consensus 36 e~n~~tiEGrVvEV~~~~i~iesk~yn~~v~i~~ 69 (213)
T PRK06763 36 ESNFSTIEGRVVEVDNGVIVIKSKQYEEPVSVYI 69 (213)
T ss_pred hcccceeeeEEEEEeCCEEEEEeccCCCceEEEe
Confidence 3444688999999999999999887765555543
No 149
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=21.95 E-value=1.4e+02 Score=21.93 Aligned_cols=33 Identities=27% Similarity=0.278 Sum_probs=27.7
Q ss_pred ceeEEEEEEEec-CeEEEEEcCCceEEEEEccCC
Q 008167 490 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPR 522 (575)
Q Consensus 490 ~~~~g~V~~v~~-~g~~V~l~~~gleg~v~~~~l 522 (575)
..+.|.|+++.+ ..+.|.+.++|-...|...++
T Consensus 17 ~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l 50 (57)
T smart00333 17 EWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDL 50 (57)
T ss_pred CEEEEEEEEECCCCEEEEEEECCCccEEEeHHHe
Confidence 568999999988 778899999998888876654
No 150
>PRK11642 exoribonuclease R; Provisional
Probab=20.94 E-value=2e+02 Score=34.11 Aligned_cols=58 Identities=10% Similarity=0.099 Sum_probs=41.4
Q ss_pred CCccEEEEEeCCCCCCceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEeecCCCC
Q 008167 8 GSVAHALFVPKDRRIPKIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGD 67 (575)
Q Consensus 8 ~~~~~~~~~P~d~r~p~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~ 67 (575)
..+++++++|.+.. ..|+|+..+... ..|++|+|+|..-.. ...|.|+|+++|....+
T Consensus 92 ~~~GfgFv~~e~~~-~difI~~~~l~~A~~GD~V~v~i~~~~~-~~r~eg~Vv~IleR~~~ 150 (813)
T PRK11642 92 HRDGYGFLRVEGRK-DDLYLSSEQMKTCIHGDQVLAQPLGADR-KGRREARIVRVLVPKTS 150 (813)
T ss_pred CCCccEEEEECCCC-CCEEEChHHHccCCCCCEEEEEEccCCC-CCCcEEEEEEEEecCCC
Confidence 35678888896532 379998877654 579999999763211 23489999999988755
Done!