Query 029485
Match_columns 192
No_of_seqs 137 out of 1109
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 13:40:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029485.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029485hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3297 DNA-directed RNA polym 100.0 3.2E-56 6.9E-61 346.7 18.1 187 1-192 1-199 (202)
2 PTZ00162 DNA-directed RNA poly 100.0 5.1E-52 1.1E-56 329.6 20.5 172 1-190 1-172 (176)
3 TIGR00448 rpoE DNA-directed RN 100.0 6.6E-51 1.4E-55 324.6 21.0 176 1-192 1-176 (179)
4 COG1095 RPB7 DNA-directed RNA 100.0 3E-50 6.6E-55 316.1 20.2 176 1-192 1-176 (183)
5 PRK08563 DNA-directed RNA poly 100.0 2.8E-48 6.1E-53 311.2 19.9 176 1-192 1-176 (187)
6 KOG3298 DNA-directed RNA polym 100.0 1.2E-40 2.6E-45 255.1 18.9 170 1-189 1-170 (170)
7 PF08292 RNA_pol_Rbc25: RNA po 100.0 3.2E-32 7E-37 203.9 12.1 109 79-192 1-122 (122)
8 cd04330 RNAP_III_Rpc25_N RNAP_ 99.9 1.4E-26 3E-31 161.7 10.1 80 2-81 1-80 (80)
9 cd00655 RNAP_Rpb7_N_like RNAP_ 99.9 4.4E-26 9.5E-31 159.2 10.1 80 2-81 1-80 (80)
10 cd04329 RNAP_II_Rpb7_N RNAP_II 99.9 3.9E-26 8.4E-31 159.5 9.4 80 2-81 1-80 (80)
11 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.9 8.5E-26 1.8E-30 157.7 9.5 79 2-80 1-79 (80)
12 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.8 6.7E-20 1.5E-24 130.2 11.3 88 81-187 1-88 (88)
13 PF03876 SHS2_Rpb7-N: SHS2 dom 99.8 7.3E-19 1.6E-23 119.5 9.3 70 8-77 1-70 (70)
14 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.7 2.9E-16 6.2E-21 111.7 9.2 79 1-81 8-89 (89)
15 cd04460 S1_RpoE S1_RpoE: RpoE, 99.5 1.4E-13 3E-18 99.5 8.4 94 83-192 1-94 (99)
16 cd04471 S1_RNase_R S1_RNase_R: 99.1 5.2E-10 1.1E-14 77.4 9.8 73 81-160 1-75 (83)
17 PRK11642 exoribonuclease R; Pr 99.1 1.7E-10 3.6E-15 110.3 7.2 85 71-162 633-719 (813)
18 KOG4134 DNA-dependent RNA poly 99.1 1.7E-09 3.6E-14 87.7 10.6 115 5-121 30-147 (253)
19 TIGR00358 3_prime_RNase VacB a 98.9 2.5E-09 5.3E-14 100.5 7.4 83 72-161 563-647 (654)
20 TIGR02063 RNase_R ribonuclease 98.9 3.9E-09 8.4E-14 100.0 8.2 86 69-161 615-702 (709)
21 PF00575 S1: S1 RNA binding do 98.9 1.2E-08 2.5E-13 69.3 8.1 66 78-161 1-67 (74)
22 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.8 1.6E-08 3.4E-13 70.8 7.3 84 77-189 2-86 (86)
23 cd05686 S1_pNO40 S1_pNO40: pNO 98.7 1.3E-07 2.9E-12 64.3 8.0 63 79-159 1-65 (73)
24 cd05708 S1_Rrp5_repeat_sc12 S1 98.7 2.1E-07 4.5E-12 63.2 9.0 62 81-160 2-65 (77)
25 cd05706 S1_Rrp5_repeat_sc10 S1 98.7 3.3E-07 7.1E-12 62.0 9.7 63 80-160 2-65 (73)
26 cd04454 S1_Rrp4_like S1_Rrp4_l 98.7 1.4E-07 3E-12 65.5 8.0 80 77-189 2-82 (82)
27 PRK08582 hypothetical protein; 98.5 6.7E-07 1.5E-11 68.6 9.2 64 77-158 1-65 (139)
28 cd05689 S1_RPS1_repeat_ec4 S1_ 98.5 8.7E-07 1.9E-11 59.7 8.5 64 81-161 3-67 (72)
29 cd04461 S1_Rrp5_repeat_hs8_sc7 98.5 5.3E-07 1.1E-11 62.7 7.5 65 79-161 12-77 (83)
30 PRK05054 exoribonuclease II; P 98.5 2.5E-07 5.5E-12 86.9 7.3 85 71-161 549-637 (644)
31 cd04452 S1_IF2_alpha S1_IF2_al 98.5 1.7E-06 3.7E-11 58.7 9.4 64 79-160 1-67 (76)
32 PRK04163 exosome complex RNA-b 98.5 1.3E-06 2.9E-11 72.5 10.5 85 77-190 59-144 (235)
33 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.5 8.4E-07 1.8E-11 59.4 7.6 62 82-161 1-63 (69)
34 cd05698 S1_Rrp5_repeat_hs6_sc5 98.5 9.2E-07 2E-11 59.2 7.3 61 82-160 1-62 (70)
35 COG0557 VacB Exoribonuclease R 98.5 1.8E-07 3.8E-12 88.8 5.0 87 68-161 609-697 (706)
36 PRK05807 hypothetical protein; 98.4 1.6E-06 3.4E-11 66.3 8.8 63 78-158 2-64 (136)
37 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.4 1.7E-06 3.7E-11 58.6 8.0 62 82-161 1-65 (71)
38 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 1.2E-06 2.5E-11 60.1 7.0 67 80-161 2-69 (74)
39 cd05690 S1_RPS1_repeat_ec5 S1_ 98.4 1.6E-06 3.4E-11 57.8 7.5 63 82-161 1-64 (69)
40 COG1098 VacB Predicted RNA bin 98.4 2.5E-07 5.4E-12 68.9 3.6 64 77-158 1-65 (129)
41 PRK07252 hypothetical protein; 98.4 2.8E-06 6E-11 63.6 9.2 65 80-162 2-67 (120)
42 smart00316 S1 Ribosomal protei 98.4 3.5E-06 7.7E-11 55.4 8.4 62 81-160 2-64 (72)
43 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 1.4E-06 3.1E-11 58.1 6.5 61 82-160 1-62 (68)
44 cd05688 S1_RPS1_repeat_ec3 S1_ 98.4 2.5E-06 5.5E-11 56.2 7.5 62 81-160 1-62 (68)
45 cd05691 S1_RPS1_repeat_ec6 S1_ 98.4 3.3E-06 7.3E-11 56.7 8.0 61 82-160 1-62 (73)
46 COG0539 RpsA Ribosomal protein 98.3 1.5E-06 3.3E-11 79.5 7.7 103 41-161 118-254 (541)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 98.3 3.3E-06 7.1E-11 55.6 7.4 59 82-158 1-60 (69)
48 cd05684 S1_DHX8_helicase S1_DH 98.3 6.2E-06 1.4E-10 56.7 9.0 59 82-157 1-63 (79)
49 TIGR02062 RNase_B exoribonucle 98.3 8.1E-07 1.7E-11 83.4 5.7 83 71-161 545-633 (639)
50 cd05703 S1_Rrp5_repeat_hs12_sc 98.3 5.1E-06 1.1E-10 56.6 7.7 64 82-161 1-65 (73)
51 cd05685 S1_Tex S1_Tex: The C-t 98.3 3E-06 6.4E-11 55.7 6.3 62 82-161 1-63 (68)
52 cd05704 S1_Rrp5_repeat_hs13 S1 98.2 3.1E-06 6.7E-11 57.5 5.6 60 80-157 2-63 (72)
53 PRK08059 general stress protei 98.2 9.9E-06 2.1E-10 60.8 8.6 65 79-161 5-70 (123)
54 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.2 1.1E-05 2.4E-10 53.9 7.2 60 82-161 1-61 (66)
55 cd05687 S1_RPS1_repeat_ec1_hs1 98.2 1.5E-05 3.4E-10 53.2 8.0 59 82-158 1-60 (70)
56 PRK09521 exosome complex RNA-b 98.1 2.4E-05 5.3E-10 62.8 9.3 80 76-190 59-149 (189)
57 cd04472 S1_PNPase S1_PNPase: P 98.1 1.5E-05 3.2E-10 52.6 6.7 59 82-158 1-60 (68)
58 cd05694 S1_Rrp5_repeat_hs2_sc2 98.1 3.7E-05 8E-10 52.6 8.7 57 80-160 3-61 (74)
59 PTZ00248 eukaryotic translatio 98.1 1.4E-05 3E-10 69.0 7.8 66 79-162 15-83 (319)
60 PRK07400 30S ribosomal protein 98.0 3.1E-05 6.8E-10 67.0 9.3 65 79-161 194-258 (318)
61 PRK03987 translation initiatio 98.0 3.4E-05 7.4E-10 65.1 7.9 65 79-161 6-73 (262)
62 cd05702 S1_Rrp5_repeat_hs11_sc 97.9 6.7E-05 1.4E-09 50.4 7.0 63 82-160 1-64 (70)
63 PLN00207 polyribonucleotide nu 97.9 2.7E-05 5.7E-10 75.1 6.8 66 75-158 747-814 (891)
64 COG2183 Tex Transcriptional ac 97.9 2.9E-05 6.3E-10 73.3 6.5 77 68-162 637-722 (780)
65 cd05693 S1_Rrp5_repeat_hs1_sc1 97.9 3.1E-05 6.6E-10 56.1 5.1 73 80-159 2-83 (100)
66 TIGR03591 polynuc_phos polyrib 97.8 1.8E-05 3.9E-10 75.0 4.7 85 56-158 591-678 (684)
67 cd04465 S1_RPS1_repeat_ec2_hs2 97.8 0.00013 2.8E-09 48.4 7.6 58 82-159 1-58 (67)
68 cd04453 S1_RNase_E S1_RNase_E: 97.8 8.2E-05 1.8E-09 52.6 6.7 66 79-159 5-73 (88)
69 PHA02945 interferon resistance 97.8 0.00025 5.5E-09 49.9 8.9 65 79-162 9-76 (88)
70 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.8 9.4E-05 2E-09 52.7 6.8 82 77-189 2-92 (92)
71 cd04473 S1_RecJ_like S1_RecJ_l 97.8 0.00013 2.8E-09 50.1 7.2 56 78-160 13-69 (77)
72 PRK07899 rpsA 30S ribosomal pr 97.8 0.0001 2.2E-09 67.3 8.4 63 81-161 208-270 (486)
73 PRK11824 polynucleotide phosph 97.7 0.00022 4.9E-09 67.7 9.3 63 78-158 618-681 (693)
74 cd04455 S1_NusA S1_NusA: N-uti 97.7 0.00021 4.5E-09 47.7 6.6 55 80-158 2-56 (67)
75 cd00164 S1_like S1_like: Ribos 97.6 0.00019 4.2E-09 46.0 6.1 58 85-160 1-59 (65)
76 TIGR02696 pppGpp_PNP guanosine 97.6 0.00013 2.9E-09 69.0 7.0 66 78-158 644-711 (719)
77 PRK12269 bifunctional cytidyla 97.6 0.00026 5.6E-09 68.6 9.0 68 80-162 751-819 (863)
78 PRK06676 rpsA 30S ribosomal pr 97.6 0.00031 6.7E-09 62.2 8.5 65 79-161 190-254 (390)
79 PRK13806 rpsA 30S ribosomal pr 97.6 0.00031 6.6E-09 64.3 8.7 66 80-162 291-357 (491)
80 COG1097 RRP4 RNA-binding prote 97.6 0.0011 2.5E-08 54.8 11.0 86 76-190 59-145 (239)
81 PRK07899 rpsA 30S ribosomal pr 97.6 0.00037 8.1E-09 63.6 8.9 64 81-162 293-357 (486)
82 PRK13806 rpsA 30S ribosomal pr 97.5 0.00034 7.5E-09 63.9 8.4 64 81-162 379-443 (491)
83 PRK06299 rpsA 30S ribosomal pr 97.5 0.00035 7.5E-09 64.7 7.8 66 80-162 372-438 (565)
84 PF03293 Pox_RNA_pol: Poxvirus 97.5 0.016 3.4E-07 44.2 14.8 134 6-157 7-145 (160)
85 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.5 0.0011 2.5E-08 46.7 8.1 63 77-158 2-65 (86)
86 TIGR00717 rpsA ribosomal prote 97.4 0.00076 1.7E-08 61.7 8.4 64 80-161 445-509 (516)
87 COG0539 RpsA Ribosomal protein 97.4 0.00061 1.3E-08 62.7 7.4 64 81-162 277-341 (541)
88 PRK07400 30S ribosomal protein 97.3 0.0008 1.7E-08 58.3 7.6 65 79-161 29-94 (318)
89 PRK09202 nusA transcription el 97.3 0.00054 1.2E-08 62.3 6.5 60 78-161 131-190 (470)
90 PRK12269 bifunctional cytidyla 97.3 0.0012 2.6E-08 64.1 9.2 63 81-161 493-555 (863)
91 TIGR00717 rpsA ribosomal prote 97.3 0.0011 2.3E-08 60.8 8.3 64 81-161 359-423 (516)
92 PRK06676 rpsA 30S ribosomal pr 97.3 0.0016 3.4E-08 57.7 9.0 64 81-162 277-341 (390)
93 PRK06299 rpsA 30S ribosomal pr 97.2 0.0014 3E-08 60.8 8.6 65 79-161 199-263 (565)
94 PRK00087 4-hydroxy-3-methylbut 97.2 0.002 4.2E-08 60.9 8.9 64 80-161 561-625 (647)
95 PRK00087 4-hydroxy-3-methylbut 97.1 0.0016 3.5E-08 61.5 7.9 64 80-161 476-539 (647)
96 PRK12327 nusA transcription el 97.0 0.0017 3.7E-08 57.2 6.4 61 77-161 130-190 (362)
97 COG1093 SUI2 Translation initi 97.0 0.00043 9.3E-09 57.9 2.3 66 79-162 9-77 (269)
98 TIGR01953 NusA transcription t 96.7 0.0043 9.4E-08 54.3 6.6 60 77-160 127-187 (341)
99 COG1185 Pnp Polyribonucleotide 95.8 0.022 4.7E-07 53.7 6.4 64 77-158 615-679 (692)
100 COG1096 Predicted RNA-binding 95.7 0.089 1.9E-06 42.1 8.7 98 57-189 39-148 (188)
101 PRK12328 nusA transcription el 95.6 0.036 7.9E-07 49.0 6.7 61 77-161 134-195 (374)
102 PF13509 S1_2: S1 domain; PDB: 94.9 0.14 2.9E-06 33.5 6.3 34 81-114 1-34 (61)
103 PF10447 EXOSC1: Exosome compo 94.9 0.1 2.2E-06 36.4 5.9 24 79-102 2-25 (82)
104 PRK12329 nusA transcription el 93.9 0.17 3.7E-06 45.7 6.5 59 77-159 148-212 (449)
105 TIGR00757 RNaseEG ribonuclease 93.1 0.26 5.6E-06 44.4 6.2 73 78-156 22-97 (414)
106 PHA02858 EIF2a-like PKR inhibi 92.0 0.38 8.3E-06 33.7 4.6 64 78-161 13-79 (86)
107 KOG3409 Exosomal 3'-5' exoribo 91.7 1 2.2E-05 35.8 7.2 65 78-158 65-138 (193)
108 COG4776 Rnb Exoribonuclease II 89.0 0.25 5.3E-06 45.0 2.0 74 78-161 558-637 (645)
109 KOG1004 Exosomal 3'-5' exoribo 87.9 8.6 0.00019 31.6 10.0 94 67-189 51-145 (230)
110 cd05699 S1_Rrp5_repeat_hs7 S1_ 85.3 1.4 3.1E-05 29.9 3.6 58 82-154 1-60 (72)
111 COG1107 Archaea-specific RecJ- 85.1 0.92 2E-05 42.5 3.4 58 81-162 122-180 (715)
112 KOG1067 Predicted RNA-binding 84.5 1.7 3.7E-05 40.6 4.8 63 81-161 668-731 (760)
113 PF10246 MRP-S35: Mitochondria 84.1 5.1 0.00011 29.1 6.2 59 77-160 19-78 (104)
114 KOG1070 rRNA processing protei 81.8 6.4 0.00014 40.6 7.8 84 81-182 509-608 (1710)
115 KOG1070 rRNA processing protei 78.4 13 0.00027 38.6 8.6 63 81-161 1162-1225(1710)
116 PRK11712 ribonuclease G; Provi 76.7 6.4 0.00014 36.3 5.8 75 78-158 35-112 (489)
117 PRK10811 rne ribonuclease E; R 71.3 27 0.00059 35.0 8.8 71 79-158 36-109 (1068)
118 COG2996 Predicted RNA-bindinin 67.0 25 0.00053 30.1 6.7 52 81-158 155-207 (287)
119 cd04486 YhcR_OBF_like YhcR_OBF 64.3 40 0.00088 22.9 6.3 25 134-158 36-60 (78)
120 KOG2916 Translation initiation 54.7 11 0.00025 32.0 2.6 66 79-162 14-82 (304)
121 KOG4078 Putative mitochondrial 46.2 34 0.00074 26.4 3.8 72 64-160 65-137 (173)
122 PRK09838 periplasmic copper-bi 45.4 58 0.0013 24.0 4.9 55 85-155 45-101 (115)
123 PF11604 CusF_Ec: Copper bindi 43.7 27 0.0006 23.2 2.7 54 87-156 1-56 (70)
124 PF07238 PilZ: PilZ domain; I 43.0 92 0.002 20.7 5.5 35 68-102 8-42 (102)
125 PF03504 Chlam_OMP6: Chlamydia 40.0 47 0.001 23.3 3.4 36 112-153 51-91 (95)
126 PF07076 DUF1344: Protein of u 39.0 80 0.0017 20.7 4.2 19 83-101 3-21 (61)
127 PF01938 TRAM: TRAM domain; I 37.3 1.1E+02 0.0023 19.3 6.5 24 78-101 37-60 (61)
128 TIGR02866 CoxB cytochrome c ox 33.7 74 0.0016 25.4 4.3 22 139-160 117-138 (201)
129 PF01629 DUF22: Domain of unkn 33.3 1.8E+02 0.0039 21.4 5.8 32 131-162 37-68 (112)
130 COG2996 Predicted RNA-bindinin 31.4 69 0.0015 27.5 3.8 37 80-116 72-109 (287)
131 PRK12442 translation initiatio 26.3 2.4E+02 0.0051 19.9 7.2 57 84-161 8-65 (87)
132 PF02237 BPL_C: Biotin protein 26.0 1.2E+02 0.0026 18.3 3.4 19 81-99 11-29 (48)
133 PF01835 A2M_N: MG2 domain; I 24.6 96 0.0021 21.3 3.1 20 140-159 8-27 (99)
134 TIGR01433 CyoA cytochrome o ub 21.7 1.5E+02 0.0032 24.4 4.1 22 139-160 139-160 (226)
135 COG1622 CyoA Heme/copper-type 21.1 1.7E+02 0.0037 24.5 4.3 30 130-159 122-157 (247)
136 PF00394 Cu-oxidase: Multicopp 20.3 2.3E+02 0.0049 21.4 4.7 22 139-160 60-81 (159)
137 PF06995 Phage_P2_GpU: Phage P 20.1 3.5E+02 0.0075 19.6 6.8 69 6-74 44-113 (121)
No 1
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=3.2e-56 Score=346.70 Aligned_cols=187 Identities=49% Similarity=0.948 Sum_probs=178.7
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||++.+++|+|+|+|++|.++++++|+++|++||+||+++|.|+|||++||.++++|.|.||||+.+.+|.|++++||||
T Consensus 1 MF~Lsel~D~VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF 80 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPF 80 (202)
T ss_pred CeeehhcccceecChHHhCchHHHHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeC-----CceeEEcCCCEEEEEEEE
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFG-----DTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~-----~~~~~i~~G~~VrvrV~~ 155 (192)
+||++.|+|+++++.|+.|+||||+++++|.++||+++.| +++++. |+|.|+ .+++++..|..|||||.+
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f--~~~e~v---WVWey~~Edg~~~~Ly~D~~e~IRFRV~~ 155 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVF--EPDEQV---WVWEYEQEDGPGTKLYFDVGEEIRFRVED 155 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCccc--ccccEE---EEEEecccCCCCceeEecCCCeEEEEEee
Confidence 9999999999999999999999999999999999999999 888887 999997 578999999999999999
Q ss_pred EecCCCcccc-------cCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 156 VNYPSIPIEQ-------AEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 156 v~~~~~~~~~-------~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
..|.+.+.++ .+..++.+||.++|||+++|||++|||
T Consensus 156 e~f~d~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GLG~lsWW 199 (202)
T KOG3297|consen 156 ESFVDVSPEGNSTAITGAEDPEKESPYTLLGSMNEDGLGPLSWW 199 (202)
T ss_pred ecccccCccccccccccccccccCCCeEEEEEecCCCCccchhh
Confidence 9998876543 445567889999999999999999999
No 2
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=5.1e-52 Score=329.61 Aligned_cols=172 Identities=23% Similarity=0.371 Sum_probs=165.2
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||++++++|+|+|||++||++++++|+++|+++|+|||.+++|+||+++|+.++++|+|.+|||+++|+|+|+|++||||
T Consensus 1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf 80 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80 (176)
T ss_pred CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+||+++|+|++++++|+|+++||++ +++|++++|+++.| |++++. |+|..++++.++++|+.||+||.+++++.
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~f--d~~~~~---~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVY--DSDSAY---PCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEE--CCCCCc---ceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 9999999999999999999999998 99999999999999 998888 99998888999999999999999999865
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCcccc
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLGPVS 190 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~is 190 (192)
+ .+.++|||++||||+++
T Consensus 155 ~------------~~~~i~T~~~~~LG~~~ 172 (176)
T PTZ00162 155 S------------NLFAIATINSDYLGPIE 172 (176)
T ss_pred C------------CcEEEEEecCCCcCccc
Confidence 3 16999999999999974
No 3
>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=100.00 E-value=6.6e-51 Score=324.55 Aligned_cols=176 Identities=34% Similarity=0.550 Sum_probs=166.4
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||++++++|+|+|||++|+++++++|+++|+++|+|||++++|+||+++||.++++|+|.||||+++|+|+|+|++|+|+
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~ 80 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPE 80 (179)
T ss_pred CeEEEEEeeEEEECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+||+++|+|++++++|+|+++||+++++++++++++++.| |++++. |.| ++++.+|++||.|||||.++++++
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~--d~~~~~---~~~--~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYY--DPKESA---LIG--KETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEE--ccccce---EEE--ccCCeEEcCCCEEEEEEEEEEccC
Confidence 9999999999999999999999999999999999999999 999888 555 677899999999999999999976
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
...+ ..+|.+||+++|||+++|+
T Consensus 154 ~~~~---------~~~I~lt~k~~~LG~~~w~ 176 (179)
T TIGR00448 154 RRPE---------GSKIGLTMRQPLLGKLEWI 176 (179)
T ss_pred CCCC---------cceEEEEeccCcCCccccc
Confidence 5221 2488999999999999996
No 4
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=3e-50 Score=316.06 Aligned_cols=176 Identities=30% Similarity=0.508 Sum_probs=166.6
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||++.+++|+|+|||++||++++++++++|+++|+||+.++.|+||+++++.++++|+|.+|||++|++|+|+|++|+|+
T Consensus 1 My~l~~~~d~VripP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~ 80 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPF 80 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
.||+++|.|++++++|+||.+||+++++|.++.+++++.| |++. |.|.++++++++++||.||+||+++++.+
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~--d~~~-----~~~~g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDY--DEKN-----KVLIGEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred cccEEEEEEEEEeecceEEEeccccccccHhhccCccccc--Cccc-----ceeeecccceEEecCCEEEEEEEEEeccc
Confidence 9999999999999999999999999999999998887777 7765 66999999999999999999999999987
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
+.+ .+ .+|.+||+++|||+++||
T Consensus 154 ~~~--~~-------~~I~lTmrq~~LGklew~ 176 (183)
T COG1095 154 RRP--RE-------SKIGLTMRQPGLGKLEWI 176 (183)
T ss_pred Ccc--cc-------ceEEEEeccccCCcchhh
Confidence 632 11 599999999999999998
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=2.8e-48 Score=311.23 Aligned_cols=176 Identities=25% Similarity=0.417 Sum_probs=165.0
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||++++++|+|+|||++|+++++++|.++|+++|+|||++++||||+++|+.++++|+|.+|||+++++|+|+|++|+|+
T Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~ 80 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPE 80 (187)
T ss_pred CeEEEEEeEEEEECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+||+++|+|++++++|+||++|++++++++++++++++.| |++++. |..++.+.+|++||.|||||.++++.+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~--d~~~~~-----~~~~~~~~~i~~Gd~VrvrV~~v~~~~ 153 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISY--DPKNGR-----LIGKESKRVLKVGDVVRARIVAVSLKE 153 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEE--ccccce-----EEEccCCeEEcCCCEEEEEEEEEEccc
Confidence 9999999999999999999999999999999999988899 999888 555677889999999999999999865
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
... . ...|.+||+++|||+++||
T Consensus 154 ~~~--~-------~~~I~ls~~~~~LG~~~w~ 176 (187)
T PRK08563 154 RRP--R-------GSKIGLTMRQPGLGKLEWI 176 (187)
T ss_pred CCC--C-------CCEEEEEecCCCCCcHHHH
Confidence 311 0 1489999999999999999
No 6
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.2e-40 Score=255.10 Aligned_cols=170 Identities=24% Similarity=0.426 Sum_probs=158.1
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
||+...++..+.++|+++|.++++.|++.|.+..+|||..++|++|+++++++|++|+|.+++|.+.|.|+|+|++|+||
T Consensus 1 mff~~~l~~~i~l~p~~~gp~~~~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~Fkpf 80 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGPNLQAILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPF 80 (170)
T ss_pred CcceeeeeeeeeecccccCchHHHHHHHHHHHHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+||+++|+|++|++.|+|++.||+ .+++.+++.|++++| ++.++. +.+..++.. .|++|+.||++|+++++..
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl-~~f~sshl~ppd~~f--~p~~n~---P~f~~~d~s-~I~~~~~VR~kiigtr~~~ 153 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPL-EVFYSSHLKPPDYEF--DPGENP---PNFQTEDES-VIQKGVEVRLKIIGTRVDE 153 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccce-EeeeecccCCCCccc--CCCCCC---Ccccccccc-eeeeCcEEEEEEEEEEEee
Confidence 999999999999999999999999 589999999999999 877665 445544444 9999999999999999965
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccc
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLGPV 189 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 189 (192)
. ++.++||+++|+||++
T Consensus 154 ~------------~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 154 T------------EIFALGTLKGDYLGPI 170 (170)
T ss_pred e------------eEEEEEEecCcccccC
Confidence 3 2899999999999986
No 7
>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=99.98 E-value=3.2e-32 Score=203.89 Aligned_cols=109 Identities=49% Similarity=0.965 Sum_probs=84.8
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEe-CCceeEEcCCCEEEEEEEEEe
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEF-GDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~-~~~~~~i~~G~~VrvrV~~v~ 157 (192)
||+||++.|+|+++++.||+|+||||++++||.++|++++.| |++++. |+|.+ +++.+++..|+.|||||.++.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~f--d~~~~~---W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRF--DEEEQA---WVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEE--ECCCTE---EEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCcc--CccCCE---EEEECCCCceeEccCCCEEEEEEeEEE
Confidence 899999999999999999999999999999999999999999 999998 99999 899999999999999999999
Q ss_pred cCCCccc------------ccCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 158 YPSIPIE------------QAEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 158 ~~~~~~~------------~~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
|.+.+.. ..+.+..+|||.|+|||+++|||+++||
T Consensus 76 f~d~~p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~~sWW 122 (122)
T PF08292_consen 76 FPDVPPTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGLVSWW 122 (122)
T ss_dssp E---------------------------SEEEEEEB-STT-EEGGGC
T ss_pred EecCCCCCcccccccccccccccccCCCCeEEEEEecCCCCcccccC
Confidence 9765421 1234457999999999999999999999
No 8
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.94 E-value=1.4e-26 Score=161.70 Aligned_cols=80 Identities=56% Similarity=1.027 Sum_probs=78.7
Q ss_pred eEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecCC
Q 029485 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (192)
Q Consensus 2 F~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~~ 81 (192)
|++++++|+|+|||++||++++++|+++|++||+||++++.|+||+++|+.++++|+|.+|||+++++|+|+|++|+|++
T Consensus 1 F~~~~l~d~v~i~P~~fg~~~~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CEEEEEEEEEEECHHHcCcCHHHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999985
No 9
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.93 E-value=4.4e-26 Score=159.22 Aligned_cols=80 Identities=29% Similarity=0.479 Sum_probs=78.6
Q ss_pred eEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecCC
Q 029485 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (192)
Q Consensus 2 F~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~~ 81 (192)
|++++++|+|+|||++||++++++|.++|+++|+||+++++|+||+++|+.++++|+|.+|||+++++|+|+|++|+|+.
T Consensus 1 f~l~~l~d~v~i~P~~f~~~~~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.93 E-value=3.9e-26 Score=159.48 Aligned_cols=80 Identities=29% Similarity=0.568 Sum_probs=78.7
Q ss_pred eEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecCC
Q 029485 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (192)
Q Consensus 2 F~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~~ 81 (192)
|++++++|+|+|||++||++++++|.++|+++|+||+.+++|+||+++|+.++++|+|.+|||+++++|+|+|++|+|++
T Consensus 1 F~~~~l~d~v~i~P~~fg~~l~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999985
No 11
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.93 E-value=8.5e-26 Score=157.66 Aligned_cols=79 Identities=32% Similarity=0.599 Sum_probs=77.9
Q ss_pred eEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEEecC
Q 029485 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 2 F~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
|++++++|+|+|||++||++++++|+++|+++|+|||.+++|+||+++|+.++++|+|.+|||+++++|+|+|++|+|.
T Consensus 1 f~~~~l~d~vri~P~~fg~~~~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~ 79 (80)
T cd04331 1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE 79 (80)
T ss_pred CEEEEEEEeEEECHHHcCcCHHHHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999999999996
No 12
>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=99.83 E-value=6.7e-20 Score=130.20 Aligned_cols=88 Identities=22% Similarity=0.338 Sum_probs=74.2
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+||+++|+|++++++|+|+++||++++++ ..++|+++.| |++++. |+|.. ++++++++|+.|||||.+++++.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~-~~~ip~~~~~--~~~~~~---~~~~~-~~~~~i~~g~~VR~rV~~v~~~~ 73 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFIS-RHLIPSDMEF--DPNASP---PCFTS-NEDIVIKKDTEVRLKIIGTRVDA 73 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEE-eeecCccceE--CCcCCC---CeEeC-CCcEEECCCCEEEEEEEEEEEcc
Confidence 59999999999999999999999975444 4455666888 886666 88874 47899999999999999999853
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCc
Q 029485 161 IPIEQAEGSKPFAPMVINGSIDYDGLG 187 (192)
Q Consensus 161 ~~~~~~~~~~~~~~~~i~gs~~~~gLG 187 (192)
+ .+.++|||++||||
T Consensus 74 ~------------~~~~igt~~~~~LG 88 (88)
T cd04462 74 T------------DIFAIGTIKDDYLG 88 (88)
T ss_pred C------------ceEEEEEccCCCCC
Confidence 2 28999999999998
No 13
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.79 E-value=7.3e-19 Score=119.47 Aligned_cols=70 Identities=43% Similarity=0.692 Sum_probs=66.6
Q ss_pred eeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEEEEE
Q 029485 8 EHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVF 77 (192)
Q Consensus 8 ~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~~vf 77 (192)
+|+|+|+|++|+++++++|+++|.++|+||+.+++|+||+++++..+++|+|.+++|+++++|+|+|++|
T Consensus 1 e~~v~l~P~~l~~~~~~~i~~~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 1 EDTVRLPPSYLGPDLKDGIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTSTHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCcCHHHHHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 6899999999998999999999999999999999999999999999999999999999999999999998
No 14
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.68 E-value=2.9e-16 Score=111.71 Aligned_cols=79 Identities=28% Similarity=0.379 Sum_probs=74.4
Q ss_pred CeEEEEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccc-cEEEEEeeeccccc--ceeecCCCceeeEEEEEEEEE
Q 029485 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANL-GLCISIYDIKEIEG--GFVYPGEGASTHTVKFRLVVF 77 (192)
Q Consensus 1 MF~~~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~-G~~i~i~~i~~i~~--g~I~~~~g~~~~~V~f~~~vf 77 (192)
||.++++++.|+|+|++++++. ++|+++|++++. |+.++. |+|++.+|+..+++ |+|.+++|.++++|+|++++|
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~~~-~~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVF 85 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGNPL-TGIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVF 85 (89)
T ss_pred cEEEEEEEEEEEECchhhcCHh-HHHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEE
Confidence 8999999999999999997554 599999999999 999999 99999999998866 999999999999999999999
Q ss_pred ecCC
Q 029485 78 RPFV 81 (192)
Q Consensus 78 ~p~~ 81 (192)
+|++
T Consensus 86 rP~~ 89 (89)
T cd04328 86 RPKI 89 (89)
T ss_pred ecCC
Confidence 9985
No 15
>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=99.49 E-value=1.4e-13 Score=99.48 Aligned_cols=94 Identities=20% Similarity=0.281 Sum_probs=79.1
Q ss_pred cEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCCCc
Q 029485 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPSIP 162 (192)
Q Consensus 83 Ev~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~~~ 162 (192)
+++.|+|++++++|+||+++..+++++.+++.++++.| ++.... |.+++.+..|++||.|+++|.+++..++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~--~~~~~~-----~~~~~~~~~~~~Gd~v~vkI~~vd~~~~- 72 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISY--DPKNKR-----LIGEETKRVLKVGDVVRARIVAVSLKER- 72 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEe--chhhee-----ecccCcCCEECCCCEEEEEEEEEeHHHC-
Confidence 58999999999999999998788999888888888888 877766 7888888899999999999999986432
Q ss_pred ccccCCCCCCCCeEEEEEecCCCCccccCC
Q 029485 163 IEQAEGSKPFAPMVINGSIDYDGLGPVSWW 192 (192)
Q Consensus 163 ~~~~~~~~~~~~~~i~gs~~~~gLG~isWw 192 (192)
.+.. -.+..|+++++||++.|.
T Consensus 73 -~~~~-------~~i~ls~k~~~~g~~~~~ 94 (99)
T cd04460 73 -RPRE-------SKIGLTMRQPGLGKLEWI 94 (99)
T ss_pred -cCCC-------ceEEEEEecCCCCcHHHh
Confidence 0001 267889999999999993
No 16
>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=99.14 E-value=5.2e-10 Score=77.41 Aligned_cols=73 Identities=23% Similarity=0.131 Sum_probs=62.6
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCc--cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 81 VGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~--~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.|++++|+|++++++|+||+++. .+++++.+++.++.+.| |+.... +..+.....|++||.|+++|.+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~--d~~~~~-----~~~~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEF--DEENHA-----LVGERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEE--cccceE-----EEeccCCCEEcCCCEEEEEEEEecc
Confidence 48999999999999999999985 78999998887777777 877654 7777777899999999999999986
Q ss_pred CC
Q 029485 159 PS 160 (192)
Q Consensus 159 ~~ 160 (192)
..
T Consensus 74 ~~ 75 (83)
T cd04471 74 DR 75 (83)
T ss_pred cc
Confidence 43
No 17
>PRK11642 exoribonuclease R; Provisional
Probab=99.09 E-value=1.7e-10 Score=110.32 Aligned_cols=85 Identities=18% Similarity=0.133 Sum_probs=76.7
Q ss_pred EEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCE
Q 029485 71 KFRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDE 148 (192)
Q Consensus 71 ~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~ 148 (192)
.++|.+++.++|++++|+|++++++|+||+|. .++|+++.+++-+++|.| |+..+. +.+++++..|++||.
T Consensus 633 ~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~--d~~~~~-----L~g~~~~~~~~lGD~ 705 (813)
T PRK11642 633 WLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRF--DQVGQR-----LIGESSGQTYRLGDR 705 (813)
T ss_pred HHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEe--cchheE-----EecccCCcEECCCCE
Confidence 35677789999999999999999999999996 489999999998888899 998887 888888999999999
Q ss_pred EEEEEEEEecCCCc
Q 029485 149 IKFRVLSVNYPSIP 162 (192)
Q Consensus 149 VrvrV~~v~~~~~~ 162 (192)
|+|+|.+++..++.
T Consensus 706 V~VkV~~vD~~~rk 719 (813)
T PRK11642 706 VEVRVEAVNMDERK 719 (813)
T ss_pred EEEEEEEeecCCCe
Confidence 99999999987764
No 18
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=99.06 E-value=1.7e-09 Score=87.67 Aligned_cols=115 Identities=21% Similarity=0.324 Sum_probs=95.9
Q ss_pred EEEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccc-cEEEEEeeeccc-ccceeecCCCceeeEEEEEEEEEecCCC
Q 029485 5 SKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANL-GLCISIYDIKEI-EGGFVYPGEGASTHTVKFRLVVFRPFVG 82 (192)
Q Consensus 5 ~~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~-G~~i~i~~i~~i-~~g~I~~~~g~~~~~V~f~~~vf~p~~g 82 (192)
.+...-+.+.|.++..+++..|++.|..++. +..... |++++..+|.-+ ..++|++++++.+..++-..++|+|..|
T Consensus 30 ~t~dlhlalaP~yl~npl~~~i~ehld~~vl-~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~G 108 (253)
T KOG4134|consen 30 ITTDLHLALAPYYLANPLHALIEEHLDTKVL-FYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAG 108 (253)
T ss_pred eeeheeeeecchhhcchhHHHHHHHhhHHHh-hhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCC
Confidence 3456678999999987787789999998875 444444 888888888766 4689999999999999999999999999
Q ss_pred cEEEEEEEEEeCCeeEEEe-CccceEEecCCCCCCCCCcC
Q 029485 83 EIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSE 121 (192)
Q Consensus 83 Ev~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~f~ 121 (192)
++++|.|-.|++.+|-+-+ |.| +.-||....|.+++|+
T Consensus 109 d~LeG~Vn~vS~sHIglLIhg~F-NASIpk~nip~dw~fI 147 (253)
T KOG4134|consen 109 DILEGVVNHVSRSHIGLLIHGVF-NASIPKTNIPADWEFI 147 (253)
T ss_pred Ceeeeeeeecchhhhceeehhhh-hccCCCCCCccceeee
Confidence 9999999999999998665 677 5778887777777664
No 19
>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=98.91 E-value=2.5e-09 Score=100.47 Aligned_cols=83 Identities=14% Similarity=0.021 Sum_probs=75.3
Q ss_pred EEEEEEecCCCcEEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEE
Q 029485 72 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI 149 (192)
Q Consensus 72 f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~V 149 (192)
++|.+|+.+.|++++|+|++++++|+||+|. .++|+++.+++-+++|.| |+.... +.+++++..|++||+|
T Consensus 563 ~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~--d~~~~~-----l~g~~~~~~~~lGD~V 635 (654)
T TIGR00358 563 LKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVF--DQEKMA-----LIGKGTGKVYRIGDRV 635 (654)
T ss_pred HHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEE--eccccE-----EEeccCCcEECCCCEE
Confidence 5577789999999999999999999999996 589999999998888889 999888 8888888999999999
Q ss_pred EEEEEEEecCCC
Q 029485 150 KFRVLSVNYPSI 161 (192)
Q Consensus 150 rvrV~~v~~~~~ 161 (192)
+|+|.+++..++
T Consensus 636 ~Vki~~vd~~~~ 647 (654)
T TIGR00358 636 TVKLTEVNMETR 647 (654)
T ss_pred EEEEEEEecccC
Confidence 999999998665
No 20
>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=98.90 E-value=3.9e-09 Score=99.98 Aligned_cols=86 Identities=19% Similarity=0.051 Sum_probs=75.9
Q ss_pred EEEEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCC
Q 029485 69 TVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGL 146 (192)
Q Consensus 69 ~V~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G 146 (192)
.-.++|.++++++|++++|+|++++++|+||++. ..+|+++.+++.++++.| |+.... +.+++.+..|++|
T Consensus 615 ~~~~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~--d~~~~~-----l~g~~~~~~~~lG 687 (709)
T TIGR02063 615 NDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVF--DEKGLA-----LVGERTGKVFRLG 687 (709)
T ss_pred HHHHHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEE--cccceE-----EEeccCCcEECCC
Confidence 3446677789999999999999999999999996 489999999998888888 988877 8888888899999
Q ss_pred CEEEEEEEEEecCCC
Q 029485 147 DEIKFRVLSVNYPSI 161 (192)
Q Consensus 147 ~~VrvrV~~v~~~~~ 161 (192)
|.|+|+|.+++..++
T Consensus 688 d~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 688 DRVKVRVVKADLDTG 702 (709)
T ss_pred CEEEEEEEEEecccC
Confidence 999999999997654
No 21
>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=98.89 E-value=1.2e-08 Score=69.27 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=50.4
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
++..|++++|+|++++++|+||+++ ..+++++.+++.++ + .+ +....+++|+.|+++|.++
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~---~--~~-------------~~~~~~~~G~~v~v~v~~v 62 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD---R--ID-------------DPSEVYKIGQTVRVKVIKV 62 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS---E--ES-------------SSHGTCETTCEEEEEEEEE
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc---c--cc-------------ccccccCCCCEEEEEEEEE
Confidence 5789999999999999999999998 77665555544332 2 12 2223789999999999999
Q ss_pred ecCCC
Q 029485 157 NYPSI 161 (192)
Q Consensus 157 ~~~~~ 161 (192)
+...+
T Consensus 63 d~~~~ 67 (74)
T PF00575_consen 63 DKEKG 67 (74)
T ss_dssp ETTTT
T ss_pred ECCCC
Confidence 97654
No 22
>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=98.83 E-value=1.6e-08 Score=70.82 Aligned_cols=84 Identities=15% Similarity=0.177 Sum_probs=64.9
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|.|.+|++++|+|++++++|++|.++ .++++++.+++..+. + +... ++....+++||.|+++|.+
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~--~--~~~~----------~~~~~~l~vGd~i~~~V~~ 67 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR--T--DEDE----------LNMRSYLDEGDLIVAEVQS 67 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC--C--ccch----------HHHHhhCCCCCEEEEEEEE
Confidence 56899999999999999999999996 788888888764321 1 1100 1223479999999999999
Q ss_pred EecCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 029485 156 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 189 (192)
Q Consensus 156 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 189 (192)
++-. .++..|+++++||.+
T Consensus 68 ~~~~---------------~~i~LS~~~~~~g~~ 86 (86)
T cd05789 68 VDSD---------------GSVSLHTRSLKYGKL 86 (86)
T ss_pred ECCC---------------CCEEEEeCcccccCC
Confidence 8531 278899999999975
No 23
>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=98.68 E-value=1.3e-07 Score=64.29 Aligned_cols=63 Identities=17% Similarity=0.250 Sum_probs=50.3
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC-c-cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG-F-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg-~-~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
|..|++++|+|++++++|+||++. . .++++|.+++.++ .+ + +.+..|++||.|+++|.++
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~--~~--~--------------~~~~~~~~Gd~v~vkv~~v 62 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RV--D--------------DPSEVVDVGEKVWVKVIGR 62 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC--cc--c--------------CHhhEECCCCEEEEEEEEE
Confidence 458999999999999999999994 3 6888888866443 23 2 2333799999999999999
Q ss_pred ecC
Q 029485 157 NYP 159 (192)
Q Consensus 157 ~~~ 159 (192)
+..
T Consensus 63 d~~ 65 (73)
T cd05686 63 EMK 65 (73)
T ss_pred CCC
Confidence 863
No 24
>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=98.68 E-value=2.1e-07 Score=63.22 Aligned_cols=62 Identities=15% Similarity=0.267 Sum_probs=49.3
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 81 VGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
+|+++.|+|++++++|+||++. ..+++++.+++.+++ .. +....|++||.|+++|.+++.
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~-~~-----------------~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR-VA-----------------DASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc-cC-----------------CHhHeecCCCEEEEEEEEEeC
Confidence 6999999999999999999996 578888877665432 11 122389999999999999986
Q ss_pred CC
Q 029485 159 PS 160 (192)
Q Consensus 159 ~~ 160 (192)
+.
T Consensus 64 ~~ 65 (77)
T cd05708 64 EK 65 (77)
T ss_pred CC
Confidence 54
No 25
>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=98.67 E-value=3.3e-07 Score=61.99 Aligned_cols=63 Identities=21% Similarity=0.249 Sum_probs=50.3
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|+++.|+|++++++|+||+|+ .++++++.+++.++ | +.+. ...|++||.|+++|.+++.
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~---~--~~~~-------------~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD---Y--SEAL-------------PYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc---c--cccc-------------ccccCCCCEEEEEEEEEeC
Confidence 47999999999999999999996 67888888876543 2 2111 2378999999999999986
Q ss_pred CC
Q 029485 159 PS 160 (192)
Q Consensus 159 ~~ 160 (192)
..
T Consensus 64 ~~ 65 (73)
T cd05706 64 PN 65 (73)
T ss_pred CC
Confidence 54
No 26
>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=98.67 E-value=1.4e-07 Score=65.51 Aligned_cols=80 Identities=16% Similarity=0.143 Sum_probs=61.3
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|.|.+|+++.|+|++++..|++|.++ .++++++.+++..+ + . ++....+++||.++++|.+
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~---~--~-------------~~~~~~~~~GD~i~~~V~~ 63 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK---D--K-------------KEIRKSLQPGDLILAKVIS 63 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc---c--h-------------HHHHhcCCCCCEEEEEEEE
Confidence 56999999999999999999999996 66665555544322 1 1 1122268999999999999
Q ss_pred EecCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 029485 156 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 189 (192)
Q Consensus 156 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 189 (192)
++-. ..+..|++++.||.+
T Consensus 64 ~~~~---------------~~i~LS~~~~~~Gvi 82 (82)
T cd04454 64 LGDD---------------MNVLLTTADNELGVI 82 (82)
T ss_pred eCCC---------------CCEEEEECCCCCccC
Confidence 8632 278999999999975
No 27
>PRK08582 hypothetical protein; Provisional
Probab=98.54 E-value=6.7e-07 Score=68.60 Aligned_cols=64 Identities=19% Similarity=0.110 Sum_probs=51.6
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|+..+|++++|+|++++++|+||.|+ ..+++++.+++.+++. . + ....|++||.|+|+|.+
T Consensus 1 m~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v-~--~---------------~~~~l~vGD~VkvkV~~ 62 (139)
T PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV-K--D---------------INDHLKVGDEVEVKVLN 62 (139)
T ss_pred CCCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccc-c--c---------------cccccCCCCEEEEEEEE
Confidence 45678999999999999999999996 6789999887754421 1 2 12379999999999999
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
++.
T Consensus 63 id~ 65 (139)
T PRK08582 63 VED 65 (139)
T ss_pred ECC
Confidence 985
No 28
>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=98.52 E-value=8.7e-07 Score=59.73 Aligned_cols=64 Identities=17% Similarity=0.088 Sum_probs=49.0
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|+++.|+|++++++|+||++. ..+++++.+++-.+ .. . .+....|++||.|+++|.+++..
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~--~~-------~--------~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT--NK-------N--------IHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc--cc-------c--------cCcccEeCCCCEEEEEEEEeeCC
Confidence 6999999999999999999995 57888887765211 01 0 12235899999999999999865
Q ss_pred CC
Q 029485 160 SI 161 (192)
Q Consensus 160 ~~ 161 (192)
++
T Consensus 66 ~~ 67 (72)
T cd05689 66 RR 67 (72)
T ss_pred cC
Confidence 43
No 29
>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=98.52 E-value=5.3e-07 Score=62.71 Aligned_cols=65 Identities=11% Similarity=0.053 Sum_probs=50.3
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
...|+++.|+|++++++|+||+++ ..+++++.+++..++ + .+....|++||.|+++|.+++
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~--~----------------~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEF--V----------------TDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccc--c----------------cCHHHhcCCCCEEEEEEEEEc
Confidence 678999999999999999999994 677766666553321 1 122348999999999999998
Q ss_pred cCCC
Q 029485 158 YPSI 161 (192)
Q Consensus 158 ~~~~ 161 (192)
...+
T Consensus 74 ~~~~ 77 (83)
T cd04461 74 EEKQ 77 (83)
T ss_pred CCCC
Confidence 7543
No 30
>PRK05054 exoribonuclease II; Provisional
Probab=98.50 E-value=2.5e-07 Score=86.86 Aligned_cols=85 Identities=14% Similarity=0.009 Sum_probs=65.1
Q ss_pred EEEEEEEecCCCc--EEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCC
Q 029485 71 KFRLVVFRPFVGE--IIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGL 146 (192)
Q Consensus 71 ~f~~~vf~p~~gE--v~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G 146 (192)
.++|.+++.++|+ .++|.|++++++|+||+|. .++++++.+++.++.+.|.++.++.. .. ..+++.|++|
T Consensus 549 ~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~-----~~-~~~~~~~~lG 622 (644)
T PRK05054 549 WLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGT-----VQ-IKGETVYKLG 622 (644)
T ss_pred HHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccce-----EE-EeCCEEEcCC
Confidence 3556678899975 9999999999999999994 57899999888765333322655443 22 2344799999
Q ss_pred CEEEEEEEEEecCCC
Q 029485 147 DEIKFRVLSVNYPSI 161 (192)
Q Consensus 147 ~~VrvrV~~v~~~~~ 161 (192)
|.|+|+|.+++..++
T Consensus 623 d~V~V~v~~vd~~~~ 637 (644)
T PRK05054 623 DVIDVTLAEVRMETR 637 (644)
T ss_pred CEEEEEEEEEccccC
Confidence 999999999998665
No 31
>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=98.49 E-value=1.7e-06 Score=58.72 Aligned_cols=64 Identities=20% Similarity=0.215 Sum_probs=49.8
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC---ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg---~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|..|+++.|+|+++.++|+||++. ..+++++.+++.+++.. +-...|++||.|+++|.+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~------------------~~~~~~~~Gd~v~vkv~~ 62 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR------------------SIRKLVKVGRKEVVKVIR 62 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC------------------CHHHeeCCCCEEEEEEEE
Confidence 568999999999999999999995 26787777765443211 113378999999999999
Q ss_pred EecCC
Q 029485 156 VNYPS 160 (192)
Q Consensus 156 v~~~~ 160 (192)
++..+
T Consensus 63 ~d~~~ 67 (76)
T cd04452 63 VDKEK 67 (76)
T ss_pred EECCC
Confidence 98654
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.49 E-value=1.3e-06 Score=72.49 Aligned_cols=85 Identities=20% Similarity=0.305 Sum_probs=65.4
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
+.|.+|+++.|+|++++++|++++++ .++++++.++......+. |. .+....|++||.|+.||.+
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~--d~------------~~~~~~~~~GDlV~akV~~ 124 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNV--EG------------TDLRKYLDIGDYIIAKVKD 124 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcccc--ch------------hhhHhhCCCCCEEEEEEEE
Confidence 88999999999999999999999997 778877776654321111 21 2234479999999999999
Q ss_pred EecCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 029485 156 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 190 (192)
Q Consensus 156 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~is 190 (192)
++-. ..+..|+++++||.+.
T Consensus 125 i~~~---------------~~~~LS~k~~~lG~L~ 144 (235)
T PRK04163 125 VDRT---------------RDVVLTLKGKGLGKIE 144 (235)
T ss_pred ECCC---------------CcEEEEEcCCCCCccC
Confidence 8631 2478889999999874
No 33
>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=98.49 E-value=8.4e-07 Score=59.41 Aligned_cols=62 Identities=19% Similarity=0.285 Sum_probs=47.7
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|++++|+|++++++|+||+++ .++++++.+++.+++ + ++....|++||.+++||.+++..+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~--~----------------~~~~~~~~~Gd~i~~~V~~id~~~ 62 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVR--L----------------KHPEKKFKPGLKVKCRVLSVEPER 62 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcc--c----------------cCHHHcCCCCCEEEEEEEEEECCC
Confidence 789999999999999999994 577777666553331 1 122337999999999999998754
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 63 ~ 63 (69)
T cd05697 63 K 63 (69)
T ss_pred C
Confidence 3
No 34
>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=98.46 E-value=9.2e-07 Score=59.21 Aligned_cols=61 Identities=20% Similarity=0.148 Sum_probs=46.5
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|++++++|+||+++ .++++++.+++..+ +.+ ++ ...+++||.++++|.+++...
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~-~~~--~~---------------~~~~~~G~~i~v~v~~~d~~~ 62 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA-FIK--DP---------------EEHFRVGQVVKVKVLSCDPEQ 62 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh-hcC--CH---------------HHcccCCCEEEEEEEEEcCCC
Confidence 789999999999999999995 57776666655332 222 32 126899999999999998644
No 35
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.46 E-value=1.8e-07 Score=88.79 Aligned_cols=87 Identities=20% Similarity=0.114 Sum_probs=77.4
Q ss_pred eEEEEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC-c-cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcC
Q 029485 68 HTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLG-F-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDG 145 (192)
Q Consensus 68 ~~V~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg-~-~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~ 145 (192)
+.-..+|.+++-++|++++|+|++++.+|+||.+. + ++++++++.+.+++|.| ++.... +.++.++..++.
T Consensus 609 ~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~--~~~~~~-----l~~~~~~~~~~l 681 (706)
T COG0557 609 VIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHF--DERGQA-----LVGEKSGKVYRL 681 (706)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeee--ccccce-----eecccccccccc
Confidence 44456677788999999999999999999999995 4 79999999999999999 988877 888999999999
Q ss_pred CCEEEEEEEEEecCCC
Q 029485 146 LDEIKFRVLSVNYPSI 161 (192)
Q Consensus 146 G~~VrvrV~~v~~~~~ 161 (192)
||.|+|||.+++...+
T Consensus 682 gd~v~v~v~~v~~~~~ 697 (706)
T COG0557 682 GDEVKVKVTSVDLDER 697 (706)
T ss_pred CCEEEEEEEEEccccc
Confidence 9999999999998654
No 36
>PRK05807 hypothetical protein; Provisional
Probab=98.43 E-value=1.6e-06 Score=66.30 Aligned_cols=63 Identities=14% Similarity=0.129 Sum_probs=50.4
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
+..+|++++|+|++++++|+||.|+-.+++++.+++.+++ .. +. ...+++||.|+|+|.+++
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~-v~--~~---------------~~~~kvGd~V~VkV~~id 63 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTY-VK--DI---------------REHLKEQDKVKVKVISID 63 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhccccc-cc--Cc---------------cccCCCCCEEEEEEEEEC
Confidence 4567999999999999999999997667888888775532 11 21 126899999999999998
Q ss_pred c
Q 029485 158 Y 158 (192)
Q Consensus 158 ~ 158 (192)
.
T Consensus 64 ~ 64 (136)
T PRK05807 64 D 64 (136)
T ss_pred C
Confidence 6
No 37
>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=98.43 E-value=1.7e-06 Score=58.60 Aligned_cols=62 Identities=16% Similarity=0.110 Sum_probs=47.3
Q ss_pred CcEEE-EEEEEE-eCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 82 GEIIA-AKLKES-DANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 82 gEv~~-g~V~~v-~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
|++++ |+|+++ .++|+||++. -++++++.+++.++.. + .....+++||.+++||.+++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~-----~-------------~~~~~~~vG~~v~~kV~~id~ 62 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKV-----P-------------SDTGPFKAGTTHKARIIGYSP 62 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchh-----c-------------CcccccCCCCEEEEEEEEEeC
Confidence 78999 999999 6999999995 4788888876643311 1 112269999999999999986
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
.++
T Consensus 63 ~~~ 65 (71)
T cd05696 63 MDG 65 (71)
T ss_pred CCC
Confidence 543
No 38
>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=1.2e-06 Score=60.06 Aligned_cols=67 Identities=15% Similarity=0.086 Sum_probs=50.3
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|+++.|+|++++++|+||+++ -++++++.+++..+.. .++. +-...|++||.|+++|.+++.
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~---~~~~------------~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFV---SDPS------------LYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccc---cChh------------hHhcccCCCCEEEEEEEEEEC
Confidence 47999999999999999999996 5778888776644321 0111 112389999999999999987
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
+.+
T Consensus 67 ~~~ 69 (74)
T cd05705 67 EKN 69 (74)
T ss_pred CCC
Confidence 543
No 39
>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=98.41 E-value=1.6e-06 Score=57.75 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=48.4
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|++++++|+||+++ ..+++++.+++. + .. ..++....|++||.|+++|.+++.++
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~-----~--~~----------~~~~~~~~~~~G~~v~v~v~~id~~~ 63 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS-----W--TQ----------RVRHPSEIYKKGQEVEAVVLNIDVER 63 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCC-----C--cc----------ccCChhhEECCCCEEEEEEEEEECCc
Confidence 789999999999999999995 578888777553 1 10 11233448999999999999999755
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 64 ~ 64 (69)
T cd05690 64 E 64 (69)
T ss_pred C
Confidence 4
No 40
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.41 E-value=2.5e-07 Score=68.88 Aligned_cols=64 Identities=17% Similarity=0.114 Sum_probs=52.4
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
+++.+|+++.|+|++++++|+||++. --.|++|+++.... ||.|-++ .+++||.|.|+|++
T Consensus 1 ~~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~---fVkdI~d---------------~L~vG~eV~vKVl~ 62 (129)
T COG1098 1 MSMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADG---FVKDIHD---------------HLKVGQEVKVKVLD 62 (129)
T ss_pred CCccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhh---hHHhHHH---------------HhcCCCEEEEEEEe
Confidence 35678999999999999999999993 45689999987765 4333322 67899999999999
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
++-
T Consensus 63 ide 65 (129)
T COG1098 63 IDE 65 (129)
T ss_pred ecc
Confidence 986
No 41
>PRK07252 hypothetical protein; Provisional
Probab=98.40 E-value=2.8e-06 Score=63.62 Aligned_cols=65 Identities=11% Similarity=0.086 Sum_probs=50.9
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|+++.|+|++++++|+||+++ ..+++++.+++.+++ + + +....|++||.|+++|.+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~--~--~--------------~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF--I--D--------------NIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc--c--c--------------ChhhccCCCCEEEEEEEEEeC
Confidence 36999999999999999999995 678888887764432 1 1 112378999999999999997
Q ss_pred CCCc
Q 029485 159 PSIP 162 (192)
Q Consensus 159 ~~~~ 162 (192)
..+.
T Consensus 64 ~~~r 67 (120)
T PRK07252 64 YTGK 67 (120)
T ss_pred CCCE
Confidence 6553
No 42
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.37 E-value=3.5e-06 Score=55.37 Aligned_cols=62 Identities=29% Similarity=0.342 Sum_probs=47.6
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|+++.|+|.+++++|+|+.++ .++++++.+++.++ + . .+....|++||.++++|.+++..
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~---~--~-------------~~~~~~~~~G~~v~~~V~~~~~~ 63 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK---R--V-------------KDPEEVLKVGDEVKVKVLSVDEE 63 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc---c--c-------------CCHHHeecCCCEEEEEEEEEeCC
Confidence 6999999999999999999998 66666665554432 1 1 12234799999999999999864
Q ss_pred C
Q 029485 160 S 160 (192)
Q Consensus 160 ~ 160 (192)
+
T Consensus 64 ~ 64 (72)
T smart00316 64 K 64 (72)
T ss_pred C
Confidence 3
No 43
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.37 E-value=1.4e-06 Score=58.12 Aligned_cols=61 Identities=21% Similarity=0.185 Sum_probs=47.5
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|+++.++|+||+++ .++++++.+++.++ + .. +....|++||.|+++|.+++...
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~---~--~~-------------~~~~~~~~Gd~v~~~v~~~d~~~ 62 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDS---Y--LK-------------DWKKRFKVGQLVKGKIVSIDPDN 62 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCch---h--hc-------------CHhhccCCCCEEEEEEEEEeCCC
Confidence 789999999999999999995 57788877765433 1 11 12237899999999999998644
No 44
>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=98.36 E-value=2.5e-06 Score=56.25 Aligned_cols=62 Identities=18% Similarity=0.238 Sum_probs=48.2
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+|+++.|+|++++++|+||+++..+++++.+++... + . ...+..|++||.|+++|.+++..+
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~---~--~-------------~~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWG---R--V-------------KHPSEVVNVGDEVEVKVLKIDKER 62 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCc---c--c-------------cCHhHEECCCCEEEEEEEEEECCC
Confidence 489999999999999999999878877777655311 1 1 112247999999999999998654
No 45
>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=98.35 E-value=3.3e-06 Score=56.65 Aligned_cols=61 Identities=25% Similarity=0.334 Sum_probs=48.0
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|+++.++|+||+++ .++++++.+++.+++ + ++....|++||.++++|.+++...
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~--~----------------~~~~~~~~~Gd~v~~~v~~~d~~~ 62 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDR--V----------------EDATERFKVGDEVEAKITNVDRKN 62 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcc--c----------------cCHHHccCCCCEEEEEEEEEeCCC
Confidence 789999999999999999994 678877777665432 1 122337899999999999998754
No 46
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.34 E-value=1.5e-06 Score=79.49 Aligned_cols=103 Identities=17% Similarity=0.212 Sum_probs=73.9
Q ss_pred cccEEEEEeeec------ccccceeecCCCceeeEEEEEEEEEecC----------------------------CCcEEE
Q 029485 41 NLGLCISIYDIK------EIEGGFVYPGEGASTHTVKFRLVVFRPF----------------------------VGEIIA 86 (192)
Q Consensus 41 ~~G~~i~i~~i~------~i~~g~I~~~~g~~~~~V~f~~~vf~p~----------------------------~gEv~~ 86 (192)
..|+.+.+..+. .++...|...+...--...|+.+-+.+. +|++++
T Consensus 118 KGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~ 197 (541)
T COG0539 118 KGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVE 197 (541)
T ss_pred cCcEEEEECCEEEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEE
Confidence 347877774332 1233344444455556667776666433 899999
Q ss_pred EEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCCC
Q 029485 87 AKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPSI 161 (192)
Q Consensus 87 g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~~ 161 (192)
|+|++++++|+||.||-++|++|++++....-.+ -..++++||+|.++|++++....
T Consensus 198 G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~------------------P~~vvkvGd~VkvkVi~~D~e~~ 254 (541)
T COG0539 198 GVVKNITDYGAFVDIGGVDGLLHISEISWKRVDH------------------PSEVVKVGDEVKVKVISLDEERG 254 (541)
T ss_pred EEEEEeecCcEEEEecCeeeEEehhhccccccCC------------------HHHhcccCCEEEEEEEEEccCCC
Confidence 9999999999999998899999999875442211 12389999999999999997665
No 47
>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=98.33 E-value=3.3e-06 Score=55.62 Aligned_cols=59 Identities=22% Similarity=0.306 Sum_probs=46.0
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
|+++.|+|++++++|+||.++ ..+++++.+++.++ +.. ++ ...+++||.|+++|.+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~-~~~--~~---------------~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK-RVK--DV---------------KDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc-ccC--CH---------------HHccCCCCEEEEEEEEECC
Confidence 789999999999999999997 67777777655433 111 11 2378999999999999875
No 48
>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=98.33 E-value=6.2e-06 Score=56.66 Aligned_cols=59 Identities=20% Similarity=0.198 Sum_probs=46.6
Q ss_pred CcEEEEEEEEEeCCeeEEEeC----ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 82 GEIIAAKLKESDANGLRLSLG----FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg----~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
|++++|+|+++.++|+||+++ ..+++++.+++.++.. .++....|++||.|+++|.+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~-----------------~~~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGR-----------------VANPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCC-----------------cCChhheeCCCCEEEEEEEEEe
Confidence 789999999999999999997 4678887776543311 0123347999999999999998
No 49
>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=98.31 E-value=8.1e-07 Score=83.41 Aligned_cols=83 Identities=12% Similarity=-0.043 Sum_probs=64.7
Q ss_pred EEEEEEEecCCCc--EEEEEEEEEeCCeeEEEeC--ccceEEecCCCCC--CCCCcCcCCCCCeeeeEEEEeCCceeEEc
Q 029485 71 KFRLVVFRPFVGE--IIAAKLKESDANGLRLSLG--FFEDIYVPSHLLP--SPSRSEPDPYGRYEVKWIWEFGDTKYVID 144 (192)
Q Consensus 71 ~f~~~vf~p~~gE--v~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~--~~~~f~~d~~~~~~~~w~~~~~~~~~~i~ 144 (192)
.++|.+|+.++|+ .++|+|++++++|+||+|. .++++++.+++.+ ++|.| |+++.. -.+.++ +.|+
T Consensus 545 ~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~--~~~~~~---~~l~g~---~~~~ 616 (639)
T TIGR02062 545 WLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVC--NQENGT---VQIKGE---TVYK 616 (639)
T ss_pred HHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEE--cccccE---EEEecc---EEEe
Confidence 3455678888865 9999999999999999993 5788888887766 56767 776653 114433 4999
Q ss_pred CCCEEEEEEEEEecCCC
Q 029485 145 GLDEIKFRVLSVNYPSI 161 (192)
Q Consensus 145 ~G~~VrvrV~~v~~~~~ 161 (192)
+||+|+|+|.+++..++
T Consensus 617 lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 617 IGDVIDVVLTEVRMETR 633 (639)
T ss_pred cCCEEEEEEEEeccccC
Confidence 99999999999998665
No 50
>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=98.28 E-value=5.1e-06 Score=56.63 Aligned_cols=64 Identities=9% Similarity=-0.005 Sum_probs=48.3
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|.++.|+|++++++|+||+|+ -++++++.+++..+. .. . ++-...|++||.|+++|.+++.+.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~-~~--~-------------~~~~~~~~vG~~v~~kV~~id~~~ 64 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV-SV--L-------------EHPEKKFPIGQALKAKVVGVDKEH 64 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc-cc--c-------------cCHHHhCCCCCEEEEEEEEEeCCC
Confidence 789999999999999999995 577877777664321 11 0 122237999999999999998765
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 65 ~ 65 (73)
T cd05703 65 K 65 (73)
T ss_pred C
Confidence 4
No 51
>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=98.28 E-value=3e-06 Score=55.74 Aligned_cols=62 Identities=13% Similarity=0.148 Sum_probs=47.2
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|++++++|+||+++ ..+++++.+++.+++ + . +....+++||.++++|.+++..+
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~--~--~--------------~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRF--V--S--------------HPSDVVSVGDIVEVKVISIDEER 62 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcc--c--c--------------CHHHhcCCCCEEEEEEEEEECCC
Confidence 789999999999999999996 567777766553321 1 1 22347899999999999998654
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 63 ~ 63 (68)
T cd05685 63 G 63 (68)
T ss_pred C
Confidence 3
No 52
>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=98.22 E-value=3.1e-06 Score=57.47 Aligned_cols=60 Identities=15% Similarity=0.027 Sum_probs=46.8
Q ss_pred CCCcEEEEEEEEEeC-CeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 80 FVGEIIAAKLKESDA-NGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~-~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
.+|+++.|+|+++.+ +|+|++++ -.++++|.+++.++ | ..+ -...|++||.||++|.+++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~---~--~~~-------------~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS---Y--TEN-------------PLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc---c--cCC-------------HHHhCCCCCEEEEEEEEec
Confidence 379999999999986 89999995 56789988866443 2 211 1127899999999999985
No 53
>PRK08059 general stress protein 13; Validated
Probab=98.21 E-value=9.9e-06 Score=60.76 Aligned_cols=65 Identities=22% Similarity=0.176 Sum_probs=50.7
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
..+|+++.|+|++++++|+||.++ ..+++++.+++.++ + . .+....|++||.|+++|.+++
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~---~--~-------------~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG---F--V-------------KDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc---c--c-------------cCHHHcCCCCCEEEEEEEEEE
Confidence 457999999999999999999996 57788877766433 2 1 112237899999999999998
Q ss_pred cCCC
Q 029485 158 YPSI 161 (192)
Q Consensus 158 ~~~~ 161 (192)
..++
T Consensus 67 ~~~~ 70 (123)
T PRK08059 67 EEKG 70 (123)
T ss_pred CCCC
Confidence 6554
No 54
>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=98.17 E-value=1.1e-05 Score=53.88 Aligned_cols=60 Identities=25% Similarity=0.328 Sum_probs=46.5
Q ss_pred CcEEEEEEEEEeCCeeEEEe-CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|++++|+|+++.++|++|++ +.++++++.+++.++ . .. ...|++|+.|++||.+++...
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~---~--~~---------------~~~~~~G~~i~~kVi~id~~~ 60 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE---K--SS---------------KSTYKEGQKVRARILYVDPST 60 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc---c--Cc---------------ccCcCCCCEEEEEEEEEeCCC
Confidence 78999999999999999999 567777776655221 1 11 226999999999999998754
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 61 ~ 61 (66)
T cd05695 61 K 61 (66)
T ss_pred C
Confidence 3
No 55
>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=98.16 E-value=1.5e-05 Score=53.23 Aligned_cols=59 Identities=20% Similarity=0.233 Sum_probs=45.3
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
|+++.|+|.+++++|++|+++ .++++++.+++.++ + .. +-...+++||.++++|.+++-
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~---~--~~-------------~~~~~~~~Gd~i~~~i~~~~~ 60 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD---P--IE-------------NGEDEVKVGDEVEVYVLRVED 60 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc---c--cC-------------CHhHcCCCCCEEEEEEEEEEC
Confidence 789999999999999999996 56777776655433 1 11 112268999999999999984
No 56
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.10 E-value=2.4e-05 Score=62.78 Aligned_cols=80 Identities=11% Similarity=-0.033 Sum_probs=58.1
Q ss_pred EEecCCCcEEEEEEEEEeCCeeEEEeCc-----------cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEc
Q 029485 76 VFRPFVGEIIAAKLKESDANGLRLSLGF-----------FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVID 144 (192)
Q Consensus 76 vf~p~~gEv~~g~V~~v~~~Gifv~lg~-----------~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~ 144 (192)
...|.+|+++.|+|++++.+|++|+++. ++++++.++..++ + . ++-...++
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~---~--~-------------~~~~~~~~ 120 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG---Y--V-------------ESLTDAFK 120 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh---h--h-------------hhHHhccC
Confidence 4668899999999999999999999953 3455555433221 1 0 11133789
Q ss_pred CCCEEEEEEEEEecCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 029485 145 GLDEIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 190 (192)
Q Consensus 145 ~G~~VrvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~is 190 (192)
+||.|++||.+++ + .+..|++++.||.+.
T Consensus 121 ~GD~V~akV~~i~---~--------------~i~LS~k~~~lGvv~ 149 (189)
T PRK09521 121 IGDIVRAKVISYT---D--------------PLQLSTKGKDLGVIY 149 (189)
T ss_pred CCCEEEEEEEecC---C--------------cEEEEEecCCceEEE
Confidence 9999999999986 2 577788888888764
No 57
>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=98.10 E-value=1.5e-05 Score=52.57 Aligned_cols=59 Identities=20% Similarity=0.178 Sum_probs=45.5
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
|+++.|+|+++.++|+||+++ ..+++++.+++.+++ + ......|++||.|+++|.+++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~--~----------------~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDER--V----------------EKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcc--c----------------cCHHHccCCCCEEEEEEEEECC
Confidence 689999999999999999996 466777776554331 1 1112379999999999999985
No 58
>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=98.09 E-value=3.7e-05 Score=52.61 Aligned_cols=57 Identities=11% Similarity=0.034 Sum_probs=44.2
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC--ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
..|+++.|.|+++.++|+|+++| -++++++.+++ .. + ..+++|+.+.++|.+++
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~-~~------~-----------------~~~~~Gq~v~~~V~~vd 58 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDA-GN------F-----------------SKLKVGQLLLCVVEKVK 58 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHC-Cc------c-----------------cccCCCCEEEEEEEEEE
Confidence 46899999999999999999997 46665554432 11 1 27899999999999998
Q ss_pred cCC
Q 029485 158 YPS 160 (192)
Q Consensus 158 ~~~ 160 (192)
.+.
T Consensus 59 ~~~ 61 (74)
T cd05694 59 DDG 61 (74)
T ss_pred CCC
Confidence 644
No 59
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.07 E-value=1.4e-05 Score=69.03 Aligned_cols=66 Identities=18% Similarity=0.050 Sum_probs=53.4
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC---ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg---~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|.+|+++.|+|++++++|+||+|+ -++|++|.+.+... +. ++-...+++|+.|.++|++
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~-----------------ri-~~i~d~vkvGd~v~vkVl~ 76 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR-----------------RI-RSINKLIRVGRHEVVVVLR 76 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc-----------------cc-CCHHHhcCCCCEEEEEEEE
Confidence 668999999999999999999993 68999999875322 21 2334489999999999999
Q ss_pred EecCCCc
Q 029485 156 VNYPSIP 162 (192)
Q Consensus 156 v~~~~~~ 162 (192)
++..++.
T Consensus 77 VD~ekg~ 83 (319)
T PTZ00248 77 VDKEKGY 83 (319)
T ss_pred EeCCCCE
Confidence 9876653
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.03 E-value=3.1e-05 Score=67.04 Aligned_cols=65 Identities=15% Similarity=0.182 Sum_probs=51.8
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
..+|+++.|+|++++++|+||+++.+++++|.+++..+. . .+....|++||.|+++|.+++.
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~-----~-------------~~~~~~~~vGd~VkvkVl~iD~ 255 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEH-----I-------------ETPHSVFNVNDEMKVMIIDLDA 255 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHccccc-----c-------------cChhhccCCCCEEEEEEEEEeC
Confidence 457999999999999999999998888888888664431 1 1122379999999999999987
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
..+
T Consensus 256 e~~ 258 (318)
T PRK07400 256 ERG 258 (318)
T ss_pred CCC
Confidence 554
No 61
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.96 E-value=3.4e-05 Score=65.11 Aligned_cols=65 Identities=17% Similarity=0.154 Sum_probs=52.0
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC---ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg---~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|.+|+++.|+|+++.++|+||+|. .++++++.+++.++...+ -...+++||.|+++|.+
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~------------------i~~~~kvGd~V~vkVi~ 67 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKN------------------IRDHVKEGQKVVCKVIR 67 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccC------------------HHHhCCCCCEEEEEEEE
Confidence 889999999999999999999994 478888888765432211 12378999999999999
Q ss_pred EecCCC
Q 029485 156 VNYPSI 161 (192)
Q Consensus 156 v~~~~~ 161 (192)
++...+
T Consensus 68 VD~~k~ 73 (262)
T PRK03987 68 VDPRKG 73 (262)
T ss_pred EecccC
Confidence 997654
No 62
>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=97.89 E-value=6.7e-05 Score=50.35 Aligned_cols=63 Identities=17% Similarity=0.128 Sum_probs=47.2
Q ss_pred CcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
|+++.|+|+++.++|++|+++ -++++++.+++.+++ ... ++-...|++||.|+++|.+++-..
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~-----~~~-----------~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW-----PDG-----------KNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcccc-----ccc-----------cChhHhCCCCCEEEEEEEEEeCcc
Confidence 789999999999999999995 677888777664331 011 111236899999999999987543
No 63
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.89 E-value=2.7e-05 Score=75.12 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=53.0
Q ss_pred EEEecCCCcEEE-EEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEE
Q 029485 75 VVFRPFVGEIIA-AKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFR 152 (192)
Q Consensus 75 ~vf~p~~gEv~~-g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~Vrvr 152 (192)
+++.|.+|++++ |+|+++.++|+||++. ..++++|.+++..+.+.+ ....|++||.|+|+
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~------------------~~dv~kvGD~V~Vk 808 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAK------------------PEDAFKVGDRIDVK 808 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccC------------------HHHhcCCCCEEEEE
Confidence 345689999996 6999999999999995 579999999775443222 12379999999999
Q ss_pred EEEEec
Q 029485 153 VLSVNY 158 (192)
Q Consensus 153 V~~v~~ 158 (192)
|.+++.
T Consensus 809 Vi~ID~ 814 (891)
T PLN00207 809 LIEVND 814 (891)
T ss_pred EEEECC
Confidence 999985
No 64
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.87 E-value=2.9e-05 Score=73.34 Aligned_cols=77 Identities=18% Similarity=0.200 Sum_probs=62.2
Q ss_pred eEEEEEEEEEec--------CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCC
Q 029485 68 HTVKFRLVVFRP--------FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGD 138 (192)
Q Consensus 68 ~~V~f~~~vf~p--------~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~ 138 (192)
.+-.|....|+- +.|++++|+|++|..||+||.+| --++++|.+.+.+. |++|+ +.
T Consensus 637 pR~~f~~~~~~~~v~~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~---fv~~P--~~---------- 701 (780)
T COG2183 637 PRDEFHTPTLDEGVESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDK---FVKDP--NE---------- 701 (780)
T ss_pred CcccccccchhhhhhhHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhh---hcCCh--HH----------
Confidence 666677666653 48999999999999999999999 44788999887665 33366 22
Q ss_pred ceeEEcCCCEEEEEEEEEecCCCc
Q 029485 139 TKYVIDGLDEIKFRVLSVNYPSIP 162 (192)
Q Consensus 139 ~~~~i~~G~~VrvrV~~v~~~~~~ 162 (192)
++++||.|.++|.+++.....
T Consensus 702 ---vv~vGdiV~v~V~~vD~~r~r 722 (780)
T COG2183 702 ---VVKVGDIVKVKVIEVDTARKR 722 (780)
T ss_pred ---hcccCCEEEEEEEEEecccCe
Confidence 789999999999999987764
No 65
>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=97.85 E-value=3.1e-05 Score=56.10 Aligned_cols=73 Identities=14% Similarity=0.094 Sum_probs=50.9
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCc--------CCCCCeeeeEEEEeCCceeEEcCCCEEE
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEP--------DPYGRYEVKWIWEFGDTKYVIDGLDEIK 150 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~--------d~~~~~~~~w~~~~~~~~~~i~~G~~Vr 150 (192)
.+|+++.|+|++++++|+|++|+ .++++++.+++.+++....+ +..+ ....+-...|++||.||
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~f~vGd~V~ 74 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDE-------EELPDLEDLFSVGQLVR 74 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccc-------cccCCHHHhccCCCEEE
Confidence 47999999999999999999995 56787777766543211100 1111 11123345799999999
Q ss_pred EEEEEEecC
Q 029485 151 FRVLSVNYP 159 (192)
Q Consensus 151 vrV~~v~~~ 159 (192)
++|++++..
T Consensus 75 ~kVi~~d~~ 83 (100)
T cd05693 75 CKVVSLDKS 83 (100)
T ss_pred EEEEEccCC
Confidence 999999864
No 66
>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=97.84 E-value=1.8e-05 Score=74.96 Aligned_cols=85 Identities=16% Similarity=0.156 Sum_probs=60.9
Q ss_pred cceeecCCCceeeEE--EEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeE
Q 029485 56 GGFVYPGEGASTHTV--KFRLVVFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKW 132 (192)
Q Consensus 56 ~g~I~~~~g~~~~~V--~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w 132 (192)
..+|...++..+-+. ..+.+...|.+|++++|+|+++.++|+||++. ..++++|.+++.++ + -
T Consensus 591 ~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~---~--v--------- 656 (684)
T TIGR03591 591 TVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE---R--V--------- 656 (684)
T ss_pred EEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC---c--c---------
Confidence 334444444333333 33444567899999999999999999999994 57899999876432 2 1
Q ss_pred EEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 133 IWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 133 ~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
++-...|++||.|+|||.+++.
T Consensus 657 ----~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 657 ----EKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred ----cChhhccCCCCEEEEEEEEECC
Confidence 1223379999999999999985
No 67
>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=97.83 E-value=0.00013 Score=48.39 Aligned_cols=58 Identities=19% Similarity=0.341 Sum_probs=41.2
Q ss_pred CcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
|++++|+|+++.++|++|+++-+++ |+|.+.+... + . ... .. .+|+.++++|.+++..
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~g-fip~s~~~~~--~--~--~~~----------~~---~vG~~i~~~i~~vd~~ 58 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRA-FLPASQVDLR--P--V--EDL----------DE---YVGKELKFKIIEIDRE 58 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEE-EEEHHHCCCc--c--c--CCh----------HH---hCCCEEEEEEEEEeCC
Confidence 7899999999999999999965654 4554444321 1 1 111 01 3899999999999854
No 68
>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=97.82 E-value=8.2e-05 Score=52.60 Aligned_cols=66 Identities=18% Similarity=0.202 Sum_probs=48.8
Q ss_pred cCCCcEEEEEEEEEeCC--eeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDAN--GLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~--Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
+..|+++.|+|+++.++ |+||+++ -.++++|.+++... .| +.. .+-...+++||.|.|+|..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~--~~--~~v-----------~~~~~~~~~Gd~v~VqV~~ 69 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPA--YF--KKH-----------KKIAKLLKEGQEILVQVVK 69 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCch--hc--ccc-----------CCHHHcCCCCCEEEEEEEE
Confidence 56899999999999997 9999997 46788888765321 11 111 1123379999999999999
Q ss_pred EecC
Q 029485 156 VNYP 159 (192)
Q Consensus 156 v~~~ 159 (192)
.-..
T Consensus 70 ~~~~ 73 (88)
T cd04453 70 EPIG 73 (88)
T ss_pred ecCC
Confidence 6553
No 69
>PHA02945 interferon resistance protein; Provisional
Probab=97.81 E-value=0.00025 Score=49.85 Aligned_cols=65 Identities=22% Similarity=0.225 Sum_probs=49.4
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEe---CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|-.||++.|+|+. ..+|+||+| |-.+++++.+.. +.... |. +. +..+ .|++|.+||+.
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev----------eva~~-----wv-K~-rd~l-~GqkvV~KVir 69 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ----------MHMNR-----YF-KY-RDKL-VGKTVKVKVIR 69 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh----------hhccc-----eE-ee-eeEe-cCCEEEEEEEE
Confidence 9999999999999 999999999 356777777633 11222 33 22 4466 99999999999
Q ss_pred EecCCCc
Q 029485 156 VNYPSIP 162 (192)
Q Consensus 156 v~~~~~~ 162 (192)
++..++.
T Consensus 70 Vd~~kg~ 76 (88)
T PHA02945 70 VDYTKGY 76 (88)
T ss_pred ECCCCCE
Confidence 9987663
No 70
>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=97.80 E-value=9.4e-05 Score=52.73 Aligned_cols=82 Identities=17% Similarity=0.204 Sum_probs=58.7
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEe--------C-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCC
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSL--------G-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLD 147 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~l--------g-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~ 147 (192)
+.|.+|.++.|+|+.++...+.|++ . ++.++++.++..+.+ . |.. +-...|++||
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~--~--d~~------------~~~~~f~~GD 65 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATE--K--DKV------------EMYKCFRPGD 65 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccc--c--chH------------HHHhhcCCCC
Confidence 4689999999999999999999998 3 445566655443221 1 110 1123789999
Q ss_pred EEEEEEEEEecCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 029485 148 EIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 189 (192)
Q Consensus 148 ~VrvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 189 (192)
.||.||.+..-. .....|++++.||.+
T Consensus 66 iV~AkVis~~~~---------------~~~~Lst~~~~lGVv 92 (92)
T cd05791 66 IVRAKVISLGDA---------------SSYYLSTAENELGVV 92 (92)
T ss_pred EEEEEEEEcCCC---------------CCcEEEecCCCCccC
Confidence 999999997421 246789999999964
No 71
>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=97.79 E-value=0.00013 Score=50.06 Aligned_cols=56 Identities=18% Similarity=0.175 Sum_probs=45.2
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
....|++++|+|++++++|+|+++. ..+++++.+++ . ..++.||.++++|.++
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-------------~-------------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-------------L-------------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-------------c-------------CcCCCCCEEEEEEEEE
Confidence 3668999999999999999999995 46777776542 0 1589999999999998
Q ss_pred ecCC
Q 029485 157 NYPS 160 (192)
Q Consensus 157 ~~~~ 160 (192)
.++
T Consensus 67 -~e~ 69 (77)
T cd04473 67 -PEN 69 (77)
T ss_pred -CCC
Confidence 544
No 72
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.78 E-value=0.0001 Score=67.26 Aligned_cols=63 Identities=17% Similarity=0.141 Sum_probs=49.8
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
.|+++.|+|++++++|+||.+|.++++++.+++... .. ++-...+++||.|+++|.+++..+
T Consensus 208 ~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~--~v----------------~~~~~~~kvGd~V~vkVl~iD~e~ 269 (486)
T PRK07899 208 KGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWK--HI----------------DHPSEVVEVGQEVTVEVLDVDMDR 269 (486)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc--cc----------------CCHHHhcCCCCEEEEEEEEEECCC
Confidence 799999999999999999999888888777655321 01 122237899999999999999765
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 270 ~ 270 (486)
T PRK07899 270 E 270 (486)
T ss_pred C
Confidence 4
No 73
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.68 E-value=0.00022 Score=67.72 Aligned_cols=63 Identities=22% Similarity=0.211 Sum_probs=50.9
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
.+.+|+++.|+|+++.++|+||+++ ..++++|.+++.++ + - ++....|++||.|+|+|.++
T Consensus 618 ~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~---~--v-------------~~~~~v~kvGD~V~VkV~~i 679 (693)
T PRK11824 618 EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADE---R--V-------------EKVEDVLKEGDEVKVKVLEI 679 (693)
T ss_pred cCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCc---c--c-------------cCccceeCCCCEEEEEEEEE
Confidence 4789999999999999999999995 57899999876432 2 1 11123899999999999999
Q ss_pred ec
Q 029485 157 NY 158 (192)
Q Consensus 157 ~~ 158 (192)
+.
T Consensus 680 D~ 681 (693)
T PRK11824 680 DK 681 (693)
T ss_pred CC
Confidence 74
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=97.67 E-value=0.00021 Score=47.68 Aligned_cols=55 Identities=29% Similarity=0.310 Sum_probs=42.1
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
..|++++|+|.++++.|+||.+|..++++..+++.+. . .+++||.|++.|.+++-
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~-----------~-------------~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG-----------E-------------SYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC-----------C-------------cCCCCCEEEEEEEEEec
Confidence 5799999999999999999999876554443322110 1 46899999999999974
No 75
>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=97.65 E-value=0.00019 Score=45.98 Aligned_cols=58 Identities=22% Similarity=0.175 Sum_probs=42.1
Q ss_pred EEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 85 IAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 85 ~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+.|+|++++++|+|+.++ ..+++++.+++.++ + . .+....|++||.|+++|.+++..+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~---~--~-------------~~~~~~~~~G~~v~~~v~~~d~~~ 59 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK---F--V-------------KDPSEVFKVGDEVEVKVLEVDPEK 59 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc---c--c-------------cCHhhEeCCCCEEEEEEEEEcCCc
Confidence 479999999999999997 56666655544322 1 1 122347999999999999998643
No 76
>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=97.63 E-value=0.00013 Score=68.96 Aligned_cols=66 Identities=17% Similarity=0.136 Sum_probs=51.4
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCC-CCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPS-PSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~-~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
.|.+|++++|+|+++.++|+||+++ -.+|++|.+++.+- .... . ++-...+++||.|+|||.+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~r--------------v-~~~~dv~kvGd~V~VKVl~ 708 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKR--------------V-ENVEDVLSVGQKIQVEIAD 708 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccC--------------c-CCHHHcCCCCCEEEEEEEE
Confidence 4889999999999999999999995 57999999866321 0011 0 2223489999999999999
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
++-
T Consensus 709 ID~ 711 (719)
T TIGR02696 709 IDD 711 (719)
T ss_pred ECC
Confidence 983
No 77
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.62 E-value=0.00026 Score=68.62 Aligned_cols=68 Identities=18% Similarity=0.226 Sum_probs=52.7
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|++++|+|++++++|+||+|+ .++++++.+++.+++ .. +. .+....|++||.|+++|.+++.
T Consensus 751 ~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~-~~--~~------------~~~~~~f~vGD~V~v~Vl~iD~ 815 (863)
T PRK12269 751 GVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENR-DG--DP------------GEALRKYAVGDRVKAVIVDMNV 815 (863)
T ss_pred CCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcc-cc--cc------------hhhccccCCCCEEEEEEEEEEc
Confidence 37999999999999999999994 688888888776542 11 11 1123479999999999999998
Q ss_pred CCCc
Q 029485 159 PSIP 162 (192)
Q Consensus 159 ~~~~ 162 (192)
..+.
T Consensus 816 ~~rk 819 (863)
T PRK12269 816 KDRK 819 (863)
T ss_pred CCCE
Confidence 6653
No 78
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.60 E-value=0.00031 Score=62.15 Aligned_cols=65 Identities=15% Similarity=0.204 Sum_probs=50.0
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
...|++++|+|++++++|+||.++.++++++.+++..+ + . ++-...+++||.|+++|.+++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~---~--~-------------~~~~~~~~vGd~i~~~Vl~vd~ 251 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHE---R--V-------------EKPSEVVSVGQEVEVKVLSIDW 251 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcc---c--c-------------CCHHHhcCCCCEEEEEEEEEeC
Confidence 45899999999999999999999878777666655321 2 1 1222368999999999999987
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
.++
T Consensus 252 ~~~ 254 (390)
T PRK06676 252 ETE 254 (390)
T ss_pred CCC
Confidence 554
No 79
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.59 E-value=0.00031 Score=64.27 Aligned_cols=66 Identities=12% Similarity=0.097 Sum_probs=50.6
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
..|+++.|+|++++++|+||+++ .+++++|.+++.. ... . .+-...+++||.|+++|.+++.
T Consensus 291 ~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~--~~~--~-------------~~~~~~~~~Gd~v~vkVl~iD~ 353 (491)
T PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSW--TRR--V-------------NKPEDVVAPGDAVAVKIKDIDP 353 (491)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCc--ccc--c-------------CCHHHcCCCCCEEEEEEEEEEc
Confidence 37999999999999999999996 6788888776531 111 0 1223379999999999999998
Q ss_pred CCCc
Q 029485 159 PSIP 162 (192)
Q Consensus 159 ~~~~ 162 (192)
..+.
T Consensus 354 e~~r 357 (491)
T PRK13806 354 AKRR 357 (491)
T ss_pred cCCE
Confidence 7653
No 80
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.58 E-value=0.0011 Score=54.82 Aligned_cols=86 Identities=19% Similarity=0.323 Sum_probs=65.4
Q ss_pred EEecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEE
Q 029485 76 VFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 154 (192)
Q Consensus 76 vf~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~ 154 (192)
-|.|.+|+++.|+|.++...+..|+++ +...+.+.++.+.. .+ +.. .++.+.++++||.|-.||.
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r--~~--~~~----------~~~~r~~l~vGD~v~AkV~ 124 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRR--KF--ENA----------EKDLRPFLNVGDLVYAKVV 124 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcc--cc--ccc----------ccccccccccCCEEEEEEE
Confidence 478999999999999999999999997 67655555544322 12 211 1345669999999999999
Q ss_pred EEecCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 029485 155 SVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 190 (192)
Q Consensus 155 ~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~is 190 (192)
+++-. +.+..++++.|||++.
T Consensus 125 ~vd~~---------------~~~~L~~k~~~~GkL~ 145 (239)
T COG1097 125 DVDRD---------------GEVELTLKDEGLGKLK 145 (239)
T ss_pred EccCC---------------CceEEEeecCCCcccc
Confidence 98642 4677778999999874
No 81
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.58 E-value=0.00037 Score=63.63 Aligned_cols=64 Identities=17% Similarity=0.191 Sum_probs=51.2
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|+++.|+|++++++|+||++. .++++++.+++.++. + +.....|++||.|+++|.+++..
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~--v----------------~~~~~~~kvGd~V~VkIi~ID~e 354 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH--V----------------EVPEQVVQVGDEVFVKVIDIDLE 354 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCccc--c----------------cCccceeCCCCEEEEEEEEEECC
Confidence 6999999999999999999994 688888887664332 1 11224799999999999999977
Q ss_pred CCc
Q 029485 160 SIP 162 (192)
Q Consensus 160 ~~~ 162 (192)
++.
T Consensus 355 ~rr 357 (486)
T PRK07899 355 RRR 357 (486)
T ss_pred CCE
Confidence 654
No 82
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.55 E-value=0.00034 Score=63.93 Aligned_cols=64 Identities=14% Similarity=0.158 Sum_probs=50.5
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|++++|+|++++++|+||++. -+++++|.+++.++. .+ +....+++||.|+++|.+++..
T Consensus 379 vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~-----~~-------------~~~~~~~~Gd~v~~~V~~id~e 440 (491)
T PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG-----KP-------------ATYEKLKPGDSVTLVVEEIDTA 440 (491)
T ss_pred CCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCccc-----cc-------------chhhcCCCCCEEEEEEEEEeCC
Confidence 7999999999999999999994 678888887664321 11 1122689999999999999986
Q ss_pred CCc
Q 029485 160 SIP 162 (192)
Q Consensus 160 ~~~ 162 (192)
++.
T Consensus 441 ~~r 443 (491)
T PRK13806 441 KRK 443 (491)
T ss_pred CCE
Confidence 653
No 83
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.50 E-value=0.00035 Score=64.74 Aligned_cols=66 Identities=18% Similarity=0.142 Sum_probs=51.5
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
..|+++.|+|++++++|+||+++ .++++++.+++..+ + . .++....|++||.|+++|.+++.
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~---~--~------------~~~~~~~~~~Gd~v~v~Il~vd~ 434 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD---K--K------------GEEAVELYKKGDEVEAVVLKVDV 434 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc---c--c------------ccChHhhCCCCCEEEEEEEEEeC
Confidence 36999999999999999999997 78888887766422 2 1 12223378999999999999997
Q ss_pred CCCc
Q 029485 159 PSIP 162 (192)
Q Consensus 159 ~~~~ 162 (192)
.+++
T Consensus 435 ~~~~ 438 (565)
T PRK06299 435 EKER 438 (565)
T ss_pred CCCE
Confidence 6553
No 84
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=97.46 E-value=0.016 Score=44.18 Aligned_cols=134 Identities=17% Similarity=0.168 Sum_probs=86.6
Q ss_pred EEeeEEEECCCCCCccHHHHHHHHHHhHhcceEeccccEEEEEeeeccc-----ccceeecCCCceeeEEEEEEEEEecC
Q 029485 6 KIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEI-----EGGFVYPGEGASTHTVKFRLVVFRPF 80 (192)
Q Consensus 6 ~l~d~v~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i-----~~g~I~~~~g~~~~~V~f~~~vf~p~ 80 (192)
.+--.|.++|++|+-|+++.|++...++|..|-.. |+. ..+|.-. .=|+|. ...+.++|-..+-+=.-+
T Consensus 7 ~vYLpV~l~PhELtLd~~~Ni~~aV~~eYLhkE~~--G~M--akkIei~~d~~lPLGeiv--NN~ivv~VPC~vtykyYk 80 (160)
T PF03293_consen 7 NVYLPVTLQPHELTLDIRKNIKDAVYREYLHKESG--GIM--AKKIEICEDKELPLGEIV--NNHIVVKVPCNVTYKYYK 80 (160)
T ss_pred eeEEEEecCcceeeehHHHhHHHHHHHHHhhhccc--Cce--eeeEEEEeccccchHhhc--ccEEEEEeeeEEEEEEEe
Confidence 45557889999999999999999999999876433 332 2333222 235555 344444444333333367
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
.|+++.|+..=-++.-++|.+|=+ +...+.- .....| +..... +. +++..|.-|+.|.+...+.+
T Consensus 81 ~GDvV~GtLnIedESni~V~CgDL--iCkl~rd-sGtVSf--~dsKYC-----fi--rNg~vY~ngs~Vsv~LkEaq 145 (160)
T PF03293_consen 81 VGDVVRGTLNIEDESNITVQCGDL--ICKLSRD-SGTVSF--NDSKYC-----FI--RNGVVYDNGSEVSVVLKEAQ 145 (160)
T ss_pred eCCEEEEEEEecccCceEEEcCcE--EEEeecc-CCeEEe--cCceEE-----EE--ECCEEecCCCEEEEEehhhh
Confidence 999999999999999999999822 1111111 112335 554433 44 56779999999998877643
No 85
>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=97.45 E-value=0.0011 Score=46.69 Aligned_cols=63 Identities=11% Similarity=0.088 Sum_probs=47.9
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|.|.+|+.+.|+|++++..+.+|+++ +..++. |. ..| ...+ ++++..+++||-|-.||.+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L-~~------~~f--~gat----------k~~rp~L~~GDlV~ArV~~ 62 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASL-SY------LAF--EGAT----------KRNRPNLNVGDLVYARVVK 62 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEe-ch------HHc--cccc----------ccccccCCCCCEEEEEEEe
Confidence 67999999999999999999999997 544333 32 224 2211 3456689999999999999
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
++.
T Consensus 63 ~~~ 65 (86)
T cd05790 63 ANR 65 (86)
T ss_pred cCC
Confidence 874
No 86
>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=97.38 E-value=0.00076 Score=61.70 Aligned_cols=64 Identities=23% Similarity=0.248 Sum_probs=50.4
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|+++.|+|++++++|+||.++ .++++++.+++.++ + .. +....|++||.|++||.+++.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~---~--~~-------------~~~~~~~~Gd~v~~~V~~id~ 506 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSEN---R--DE-------------DKTDEIKVGDEVEAKVVDIDK 506 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcc---c--cc-------------cccccCCCCCEEEEEEEEEeC
Confidence 37999999999999999999995 57888888776543 2 21 122379999999999999986
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
.++
T Consensus 507 ~~~ 509 (516)
T TIGR00717 507 KNR 509 (516)
T ss_pred CCC
Confidence 543
No 87
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.36 E-value=0.00061 Score=62.67 Aligned_cols=64 Identities=16% Similarity=0.157 Sum_probs=52.6
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|..+.|+|++++++|+||+++ .+++++|.+++... + .. . -...+++||.|.|+|.+++.+
T Consensus 277 ~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~---~--~~------------~-P~evv~~Gq~V~V~Vl~id~e 338 (541)
T COG0539 277 VGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWT---K--KN------------V-PSEVVKVGQEVEVKVLDIDPE 338 (541)
T ss_pred CCCEEEEEEEEeecCcEEEEecCCccceeechhhccc---c--cC------------C-HHHhcccCCEEEEEEEeeCch
Confidence 8999999999999999999995 78999999866322 1 11 1 233899999999999999998
Q ss_pred CCc
Q 029485 160 SIP 162 (192)
Q Consensus 160 ~~~ 162 (192)
.++
T Consensus 339 ~rR 341 (541)
T COG0539 339 RRR 341 (541)
T ss_pred hce
Confidence 875
No 88
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.34 E-value=0.0008 Score=58.33 Aligned_cols=65 Identities=14% Similarity=0.157 Sum_probs=46.9
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeCc-cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg~-~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
...|+++.|+|.++++.|++|.+|. .++ ++|.+-+.+. | ..+ ....+++|+.|+|+|++++
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g-~lp~sEis~~--~--~~~-------------~~~~~~~G~~v~~~Vi~~~ 90 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGAKTAA-FMPIQEMSIN--R--VEG-------------PEEVLQPNETREFFILSDE 90 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECCCeEE-EEEHHHhccc--c--ccC-------------HHHccCCCCEEEEEEEEEe
Confidence 5789999999999999999999985 455 4444333321 2 211 1126899999999999987
Q ss_pred cCCC
Q 029485 158 YPSI 161 (192)
Q Consensus 158 ~~~~ 161 (192)
-.++
T Consensus 91 ~~~~ 94 (318)
T PRK07400 91 NEDG 94 (318)
T ss_pred CCCC
Confidence 6543
No 89
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.31 E-value=0.00054 Score=62.30 Aligned_cols=60 Identities=23% Similarity=0.272 Sum_probs=47.3
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEe
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 157 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~ 157 (192)
++..|+++.|+|.++++.|++|.+|-.+++.+.+++.|. . .|++|+.||+.|..++
T Consensus 131 k~~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ip~-----------E-------------~~~~GdrIka~I~~Vd 186 (470)
T PRK09202 131 KDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPR-----------E-------------NFRPGDRVRAYVYEVR 186 (470)
T ss_pred HhhcCCEEEEEEEEEecCCEEEEECCeEEEecHHHcCCC-----------c-------------cCCCCCEEEEEEEEEe
Confidence 444899999999999999999999877665555444322 1 5789999999999998
Q ss_pred cCCC
Q 029485 158 YPSI 161 (192)
Q Consensus 158 ~~~~ 161 (192)
...+
T Consensus 187 ~~~k 190 (470)
T PRK09202 187 KEAR 190 (470)
T ss_pred cCCC
Confidence 7554
No 90
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.31 E-value=0.0012 Score=64.11 Aligned_cols=63 Identities=13% Similarity=0.239 Sum_probs=47.6
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+|++++|+|++++++|+||+++-++++++.+++..+ ++.++ ...+++|+.|++||++++.+.
T Consensus 493 ~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~---~v~~~---------------~~~~kvGq~v~vkVi~iD~e~ 554 (863)
T PRK12269 493 IEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWG---HVARP---------------REFVKKGQTIELKVIRLDQAE 554 (863)
T ss_pred CCCEEEEEEEEEeCCcEEEEECCEEEEEEchhcccc---ccCCH---------------HHhccCCCEEEEEEEEEecCC
Confidence 689999999999999999999877777776654322 10011 125799999999999998765
Q ss_pred C
Q 029485 161 I 161 (192)
Q Consensus 161 ~ 161 (192)
+
T Consensus 555 ~ 555 (863)
T PRK12269 555 K 555 (863)
T ss_pred C
Confidence 4
No 91
>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=0.0011 Score=60.78 Aligned_cols=64 Identities=22% Similarity=0.215 Sum_probs=49.9
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|+++.|+|++++++|+||+++ ..+++++.+++..+ + .. .+....+++|+.|.++|.+++..
T Consensus 359 ~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~---~--~~------------~~~~~~~~~G~~V~~~Vl~vd~~ 421 (516)
T TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWD---K--DG------------READHLYKKGDEIEAVVLAVDKE 421 (516)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCc---c--cC------------CCHhHccCCCCEEEEEEEEEeCc
Confidence 7999999999999999999997 77888877665321 1 11 12224799999999999999976
Q ss_pred CC
Q 029485 160 SI 161 (192)
Q Consensus 160 ~~ 161 (192)
++
T Consensus 422 ~~ 423 (516)
T TIGR00717 422 KK 423 (516)
T ss_pred CC
Confidence 54
No 92
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.28 E-value=0.0016 Score=57.68 Aligned_cols=64 Identities=20% Similarity=0.187 Sum_probs=49.7
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
+|+++.|+|++++++|+||++. .++++++.+++.++ . . .+....|++||.|+++|.+++.+
T Consensus 277 ~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~---~--~-------------~~~~~~~~~Gd~v~v~V~~id~e 338 (390)
T PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK---H--I-------------ATPSEVLEEGQEVKVKVLEVNEE 338 (390)
T ss_pred CCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc---c--c-------------CChhhccCCCCEEEEEEEEEECC
Confidence 7999999999999999999995 67888887765322 1 1 11223689999999999999976
Q ss_pred CCc
Q 029485 160 SIP 162 (192)
Q Consensus 160 ~~~ 162 (192)
++.
T Consensus 339 ~~~ 341 (390)
T PRK06676 339 EKR 341 (390)
T ss_pred CCE
Confidence 653
No 93
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.24 E-value=0.0014 Score=60.76 Aligned_cols=65 Identities=17% Similarity=0.188 Sum_probs=49.8
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
...|++++|+|++++++|+||.+|-++++++.+++..+ .. .+-...+++||.|+++|.+++.
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~-------~~-----------~~~~~~~kvG~~v~v~V~~~d~ 260 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWK-------RV-----------NHPSEVVNVGDEVKVKVLKFDK 260 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhccc-------cc-----------CCHhhcCCCCCEEEEEEEEEeC
Confidence 45899999999999999999999878887776654221 10 1112368999999999999987
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
+++
T Consensus 261 ~~~ 263 (565)
T PRK06299 261 EKK 263 (565)
T ss_pred CCC
Confidence 654
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.17 E-value=0.002 Score=60.92 Aligned_cols=64 Identities=19% Similarity=0.158 Sum_probs=50.0
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 80 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.+|+++.|+|++++++|+||+++ .++++++.+++.++ . . ++....|++||.|+++|.+++.
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~---~--~-------------~~~~~~~kvGd~V~vkV~~id~ 622 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK---R--I-------------DKPEDVLSEGEEVKAKILEVDP 622 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc---c--c-------------CCHhhcCCCCCEEEEEEEEEeC
Confidence 47999999999999999999994 67888887765432 1 1 1223378999999999999987
Q ss_pred CCC
Q 029485 159 PSI 161 (192)
Q Consensus 159 ~~~ 161 (192)
.++
T Consensus 623 e~~ 625 (647)
T PRK00087 623 EEK 625 (647)
T ss_pred CCC
Confidence 554
No 95
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.14 E-value=0.0016 Score=61.52 Aligned_cols=64 Identities=17% Similarity=0.192 Sum_probs=49.7
Q ss_pred CCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 80 ~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
..|+++.|+|++++++|+||.++..+++++.+++... + . ++-...|++||.|+++|.+++..
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~---~--~-------------~~~~~~~~vGd~V~vkV~~id~~ 537 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWG---R--V-------------EKPSDVLKVGDEIKVYILDIDKE 537 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcc---c--c-------------CCHHHhcCCCCEEEEEEEEEECC
Confidence 3799999999999999999999888877777655321 1 1 11223789999999999999876
Q ss_pred CC
Q 029485 160 SI 161 (192)
Q Consensus 160 ~~ 161 (192)
++
T Consensus 538 ~~ 539 (647)
T PRK00087 538 NK 539 (647)
T ss_pred CC
Confidence 54
No 96
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.01 E-value=0.0017 Score=57.22 Aligned_cols=61 Identities=23% Similarity=0.344 Sum_probs=46.6
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
|++..|+++.|+|.+.++.|++|.+|-.+++...+++.|. ..|++||.+++.|.++
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip~------------------------e~~~~Gd~Ika~V~~V 185 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIPG------------------------ETYKHGDRIKVYVVKV 185 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCCC------------------------CCCCCCCEEEEEEEEE
Confidence 3456999999999999999999999877653333433221 1578999999999999
Q ss_pred ecCCC
Q 029485 157 NYPSI 161 (192)
Q Consensus 157 ~~~~~ 161 (192)
+...+
T Consensus 186 ~~~~k 190 (362)
T PRK12327 186 EKTTK 190 (362)
T ss_pred ecCCC
Confidence 86553
No 97
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.98 E-value=0.00043 Score=57.89 Aligned_cols=66 Identities=20% Similarity=0.222 Sum_probs=53.5
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEe---CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|-.||++.|+|..|.++|+||.| |-.++++|.+..... |. ++-+.+++.|+++-++|++
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~-----------------wV-knIrd~vkegqkvV~kVlr 70 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASG-----------------WV-KNIRDYVKEGQKVVAKVLR 70 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHH-----------------HH-HHHHHHhhcCCeEEEEEEE
Confidence 88999999999999999999999 457888888754322 22 3445589999999999999
Q ss_pred EecCCCc
Q 029485 156 VNYPSIP 162 (192)
Q Consensus 156 v~~~~~~ 162 (192)
|+...+.
T Consensus 71 Vd~~rg~ 77 (269)
T COG1093 71 VDPKRGH 77 (269)
T ss_pred EcCCCCe
Confidence 9987764
No 98
>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=96.72 E-value=0.0043 Score=54.30 Aligned_cols=60 Identities=30% Similarity=0.341 Sum_probs=45.2
Q ss_pred EecCCCcEEEEEEEEEeCCe-eEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANG-LRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~G-ifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|+...|+++.|+|.++++.| ++|.+|-.+++...+++.|. . .|++||.+++.|.+
T Consensus 127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip~-----------E-------------~~~~Gd~ik~~V~~ 182 (341)
T TIGR01953 127 FSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPG-----------E-------------KFRIGDRIKAYVYE 182 (341)
T ss_pred HHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCCC-----------c-------------CCCCCCEEEEEEEE
Confidence 34459999999999999988 69999977654444333221 1 37899999999999
Q ss_pred EecCC
Q 029485 156 VNYPS 160 (192)
Q Consensus 156 v~~~~ 160 (192)
++-..
T Consensus 183 V~~~~ 187 (341)
T TIGR01953 183 VRKTA 187 (341)
T ss_pred EEcCC
Confidence 98654
No 99
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.85 E-value=0.022 Score=53.66 Aligned_cols=64 Identities=20% Similarity=0.168 Sum_probs=50.3
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
=.+.+||++.|+|+.+..||+||.+- --++++|.+.+..+ .- +.-..+.++||.|+|||..
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~--rv----------------~kv~dvlk~Gd~v~Vkv~~ 676 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE--RV----------------EKVEDVLKEGDEVKVKVIE 676 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh--hh----------------hcccceeecCceEEEEEee
Confidence 34779999999999999999999994 45788998866433 11 1122489999999999999
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
++-
T Consensus 677 iD~ 679 (692)
T COG1185 677 IDK 679 (692)
T ss_pred ecc
Confidence 874
No 100
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=95.75 E-value=0.089 Score=42.15 Aligned_cols=98 Identities=17% Similarity=0.076 Sum_probs=61.1
Q ss_pred ceeecCCCceeeEEEEEEE-EEecCCCcEEEEEEEEEeCCeeEEEeCccce-----------EEecCCCCCCCCCcCcCC
Q 029485 57 GFVYPGEGASTHTVKFRLV-VFRPFVGEIIAAKLKESDANGLRLSLGFFED-----------IYVPSHLLPSPSRSEPDP 124 (192)
Q Consensus 57 g~I~~~~g~~~~~V~f~~~-vf~p~~gEv~~g~V~~v~~~Gifv~lg~~~~-----------i~i~~~~~~~~~~f~~d~ 124 (192)
|.+..++-+..+.|+=.-- ...|..|.++-|+|+++....+-|++-.+++ -+|.++....+
T Consensus 39 G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~------- 111 (188)
T COG1096 39 GVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGY------- 111 (188)
T ss_pred ccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccc-------
Confidence 4444444444455443333 3458899999999999999999998843322 22222221111
Q ss_pred CCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 029485 125 YGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 189 (192)
Q Consensus 125 ~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 189 (192)
.++-.-.|++||.||.||++.-. -+..|.+++-||.+
T Consensus 112 -----------~~~~~d~f~~GDivrA~Vis~~~-----------------~~~Lst~~~dlGVI 148 (188)
T COG1096 112 -----------VEKLSDAFRIGDIVRARVISTGD-----------------PIQLSTKGNDLGVI 148 (188)
T ss_pred -----------ccccccccccccEEEEEEEecCC-----------------CeEEEecCCcceEE
Confidence 12233489999999999999741 34456666666654
No 101
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.63 E-value=0.036 Score=49.01 Aligned_cols=61 Identities=11% Similarity=0.104 Sum_probs=46.1
Q ss_pred EecCCCcEEEEEEEEEeCC-eeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDAN-GLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~-Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|++.+||++.|+|..++.. +++|.+|-.+++...++++|. . .|++||.+|+-|..
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~-----------E-------------~~~~Gdrik~~i~~ 189 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKG-----------E-------------KFKVGDVVKAVLKR 189 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCC-----------C-------------cCCCCCEEEEEEEE
Confidence 5677999999999999974 599999876544433333221 1 57899999999999
Q ss_pred EecCCC
Q 029485 156 VNYPSI 161 (192)
Q Consensus 156 v~~~~~ 161 (192)
|+....
T Consensus 190 V~~~~k 195 (374)
T PRK12328 190 VKIDKN 195 (374)
T ss_pred EecCCC
Confidence 987553
No 102
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.95 E-value=0.14 Score=33.51 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=19.4
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCccceEEecCCCC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLL 114 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~ 114 (192)
+|++-..+|...+++|+|++.|--..++.|.+..
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~ 34 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV 34 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHc
Confidence 4888899999999999999988656788876543
No 103
>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=94.94 E-value=0.1 Score=36.44 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=18.4
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEeC
Q 029485 79 PFVGEIIAAKLKESDANGLRLSLG 102 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~lg 102 (192)
|.+|.++.|+|+.+++.-+++++=
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il 25 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEIL 25 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEE
Confidence 889999999999999999998873
No 104
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.92 E-value=0.17 Score=45.75 Aligned_cols=59 Identities=14% Similarity=0.175 Sum_probs=44.4
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEe----Cc--cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSL----GF--FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIK 150 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~l----g~--~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~Vr 150 (192)
|++.+|+++.|+|..+...+++|.+ |- .+++...++++|. -.|+.||.||
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~------------------------E~y~~Gdrik 203 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPN------------------------DNYRANATFK 203 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCC------------------------CcCCCCCEEE
Confidence 5777999999999999999999998 42 4433333333221 1578999999
Q ss_pred EEEEEEecC
Q 029485 151 FRVLSVNYP 159 (192)
Q Consensus 151 vrV~~v~~~ 159 (192)
+-|..|+..
T Consensus 204 a~i~~V~~~ 212 (449)
T PRK12329 204 VFLKEVSEG 212 (449)
T ss_pred EEEEEeecC
Confidence 999999865
No 105
>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=93.07 E-value=0.26 Score=44.38 Aligned_cols=73 Identities=11% Similarity=0.079 Sum_probs=48.1
Q ss_pred ecCCCcEEEEEEEEEeCC--eeEEEeCc-cceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDAN--GLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 154 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~ 154 (192)
++.+|.++.|+|.++.+. |+||.+|. -+++++.++..++.+.+ ...... - -...+-...++.||.|.|+|.
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~--~~~~~~---~-~~~~~i~~~l~~G~~IlVQV~ 95 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECL--APAEAK---R-EAGPSISELLRPGQSVLVQVV 95 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhcc--cccccc---c-cccCCHHHhCcCCCEEEEEEe
Confidence 356899999999999999 99999984 35667766665543222 111100 0 000112235899999999999
Q ss_pred EE
Q 029485 155 SV 156 (192)
Q Consensus 155 ~v 156 (192)
.-
T Consensus 96 Ke 97 (414)
T TIGR00757 96 KE 97 (414)
T ss_pred eC
Confidence 84
No 106
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=92.03 E-value=0.38 Score=33.67 Aligned_cols=64 Identities=16% Similarity=0.080 Sum_probs=45.6
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEe---CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 154 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~ 154 (192)
-|.+|++.. .|..+.+.|++|+| | +++++.+.+.+. ... .++=++.+ +|-.+.++|+
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~sels--------r~r---------irsi~kll-VGk~e~v~Vi 72 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVN--------ADR---------AEKLKKKL-VGKTINVQVI 72 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHHHHh--------HHH---------HHhhhhhh-cCCeeEEEEE
Confidence 499999999 78899999999999 5 777766332211 100 11222355 9999999999
Q ss_pred EEecCCC
Q 029485 155 SVNYPSI 161 (192)
Q Consensus 155 ~v~~~~~ 161 (192)
.++..++
T Consensus 73 RVDk~KG 79 (86)
T PHA02858 73 RTDKLKG 79 (86)
T ss_pred EECCCCC
Confidence 9998765
No 107
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=91.72 E-value=1 Score=35.85 Aligned_cols=65 Identities=14% Similarity=0.137 Sum_probs=40.3
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEeCcc---------ceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSLGFF---------EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDE 148 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~lg~~---------~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~ 148 (192)
-|+.|.++.++|+.++..=+-|.+--+ .++++..+.-+- +.+.-. . -..|++||.
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t------Ekdrv~------v----~ksFrPgDi 128 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT------EKDRVK------V----YKSFRPGDI 128 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc------ccchhh------h----hhccCCCcE
Confidence 499999999999999998776665222 222222211110 111000 1 137899999
Q ss_pred EEEEEEEEec
Q 029485 149 IKFRVLSVNY 158 (192)
Q Consensus 149 VrvrV~~v~~ 158 (192)
|+.+|++..-
T Consensus 129 VlAkVis~~~ 138 (193)
T KOG3409|consen 129 VLAKVISLGD 138 (193)
T ss_pred EEEEEeecCC
Confidence 9999999543
No 108
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=89.02 E-value=0.25 Score=44.96 Aligned_cols=74 Identities=16% Similarity=0.179 Sum_probs=55.5
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEe---CccceEEecCCCCCCCC---CcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEE
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPS---RSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKF 151 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~---~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~Vrv 151 (192)
++..+..|.+.|..++..|+.|.| |- .+|||..++-++- .+ +.++.+ .+=++...|++||.|.|
T Consensus 558 k~~~~~~F~AEI~Di~R~G~RvrLleNGA--~~FIPa~lih~~reei~~--n~e~gt------v~I~ge~~Yk~~D~i~V 627 (645)
T COG4776 558 KAGTNTRFAAEIQDISRGGMRVRLLENGA--IAFIPAPLIHANREELVC--NQENGT------VQIKGETVYKVGDVIDV 627 (645)
T ss_pred ccccCchhhhhhhhhccCceEEEeccCCc--ceecchhhhccchhheEe--cCCCce------EEEccEEEEeeccEEEE
Confidence 455678899999999999999998 43 3788988876542 23 444444 22356679999999999
Q ss_pred EEEEEecCCC
Q 029485 152 RVLSVNYPSI 161 (192)
Q Consensus 152 rV~~v~~~~~ 161 (192)
++..|+.+.+
T Consensus 628 ~l~eVr~etR 637 (645)
T COG4776 628 TLAEVRMETR 637 (645)
T ss_pred EeHHHHHhhh
Confidence 9999987654
No 109
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=87.94 E-value=8.6 Score=31.59 Aligned_cols=94 Identities=13% Similarity=0.070 Sum_probs=66.1
Q ss_pred eeEEEEEEEEEecCCCcEEEEEEEEEeCCeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCC
Q 029485 67 THTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGL 146 (192)
Q Consensus 67 ~~~V~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G 146 (192)
.+.+..+-.-|.|.+|+.+.|+|++.......|++|--+-.-.| +..| ...+ ++++-.+++|
T Consensus 51 v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~------~laF--e~At----------krNrPnl~vG 112 (230)
T KOG1004|consen 51 VYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLS------YLAF--EGAT----------KRNRPNLQVG 112 (230)
T ss_pred eEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCCeeeee------eccc--cCcc----------ccCCCccccc
Confidence 56888888999999999999999999999999999853222222 2335 3222 4556689999
Q ss_pred CEEEEEEEEEecCCCcccccCCCCCCCCeEEEEEe-cCCCCccc
Q 029485 147 DEIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSI-DYDGLGPV 189 (192)
Q Consensus 147 ~~VrvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~-~~~gLG~i 189 (192)
|.|-.||...+.+.. |-+.++.+. +..|.|++
T Consensus 113 dliyakv~~a~~~~E-----------pel~Cids~graaGfG~L 145 (230)
T KOG1004|consen 113 DLIYAKVVDANKDME-----------PELTCIDSTGRAAGFGVL 145 (230)
T ss_pred cEEEEEEEecCCCcC-----------cceEEEcccCcccCcccc
Confidence 999999998764321 115566553 23577765
No 110
>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=85.28 E-value=1.4 Score=29.92 Aligned_cols=58 Identities=21% Similarity=0.381 Sum_probs=40.9
Q ss_pred CcEEEEEEEEEeCCeeEEEeCccc-eEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEE-EEEEE
Q 029485 82 GEIIAAKLKESDANGLRLSLGFFE-DIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI-KFRVL 154 (192)
Q Consensus 82 gEv~~g~V~~v~~~Gifv~lg~~~-~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~V-rvrV~ 154 (192)
|.+++|+|..-++.++.|+++..+ ..++|...+.| .+ ...... | ..+++||++ ++-|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD--~~--~k~~~~-----~------~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD--HV--SNCPLL-----W------HCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC--ch--hhCHHH-----H------hhhhcCCCccceEEE
Confidence 688999999999999999996431 24666655555 23 222222 2 289999999 88888
No 111
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=85.14 E-value=0.92 Score=42.45 Aligned_cols=58 Identities=16% Similarity=0.064 Sum_probs=45.0
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
.|+...|+|+++.++|+|++|. -..++.+.+++..+ . .+.+|+.+-|+|.+++.+
T Consensus 122 ~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~-----------~-------------~~~vgdeiiV~v~~vr~~ 177 (715)
T COG1107 122 AGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-----------P-------------DYAVGDEIIVQVSDVRPE 177 (715)
T ss_pred cceeeeccccchhhhcceeecChhhhccccccccCCC-----------C-------------CCCCCCeEEEEeeccCCC
Confidence 7899999999999999999996 45577777765432 1 356788888888888876
Q ss_pred CCc
Q 029485 160 SIP 162 (192)
Q Consensus 160 ~~~ 162 (192)
++.
T Consensus 178 ~ge 180 (715)
T COG1107 178 KGE 180 (715)
T ss_pred CCc
Confidence 553
No 112
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=84.51 E-value=1.7 Score=40.58 Aligned_cols=63 Identities=16% Similarity=0.159 Sum_probs=46.9
Q ss_pred CCcEEEEEEEEEeCCeeEEEeCcc-ceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLGFF-EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg~~-~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
.|-++.|+|+++.+.|+||++-+. .++.|.+++ |+ . |..+-+.. +++||.|.++-.+.+..
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL---------~~---e-----~iakpsd~-levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNSQL---------DQ---E-----KIAKPSDL-LEVGQEIQVKYIERDPR 729 (760)
T ss_pred eeeEEEEEEeeecccceEEEecCCchhhccchhc---------cc---c-----cccChHHH-HhhcceeEEEEEeecCc
Confidence 466779999999999999999644 556666654 22 2 33344444 99999999999999876
Q ss_pred CC
Q 029485 160 SI 161 (192)
Q Consensus 160 ~~ 161 (192)
.+
T Consensus 730 g~ 731 (760)
T KOG1067|consen 730 GG 731 (760)
T ss_pred cc
Confidence 54
No 113
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=84.15 E-value=5.1 Score=29.09 Aligned_cols=59 Identities=14% Similarity=0.180 Sum_probs=41.6
Q ss_pred EecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 77 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
+-+..|-++.|+|..+...-+|+..| -|. .+-++ +.. +...|..|+.||+|+.+
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~KFh-cVc~r------------p~~------------~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGGKFH-CVCKR------------PAV------------NGEKYVRGSRVRLRLKD 73 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCCcee-EEEec------------ccc------------cccccccCCEEEEEECC
Confidence 45678999999999999999999998 332 22221 100 11156779999999997
Q ss_pred EecCC
Q 029485 156 VNYPS 160 (192)
Q Consensus 156 v~~~~ 160 (192)
.....
T Consensus 74 lELs~ 78 (104)
T PF10246_consen 74 LELSA 78 (104)
T ss_pred Hhhhh
Confidence 66543
No 114
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=81.75 E-value=6.4 Score=40.58 Aligned_cols=84 Identities=17% Similarity=0.268 Sum_probs=50.7
Q ss_pred CCcEEEEEEEEEeCCeeEEEe--CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 81 VGEIIAAKLKESDANGLRLSL--GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~l--g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
+|+.++|+|..+++.|+-|.+ |-+.+++.+.++.+-.-.| ... .+.+|..++.||..++.
T Consensus 509 iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~----------------p~~--~f~v~~~~k~RVl~~~~ 570 (1710)
T KOG1070|consen 509 IGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQP----------------PLR--DFKVGSGVKLRVLSVNR 570 (1710)
T ss_pred ccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhccccc----------------ccc--eeeeccccEEEEEEEEc
Confidence 899999999999999999887 4354544444443322222 222 33344444447777776
Q ss_pred CCCc--------------ccccCCCCCCCCeEEEEEec
Q 029485 159 PSIP--------------IEQAEGSKPFAPMVINGSID 182 (192)
Q Consensus 159 ~~~~--------------~~~~~~~~~~~~~~i~gs~~ 182 (192)
..++ ......+...|++...||+.
T Consensus 571 ~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~ 608 (1710)
T KOG1070|consen 571 DRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLC 608 (1710)
T ss_pred cCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEe
Confidence 5544 01112223577888888864
No 115
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=78.40 E-value=13 Score=38.60 Aligned_cols=63 Identities=27% Similarity=0.346 Sum_probs=46.2
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecC
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~ 159 (192)
.|+++.|.|.++...|+|+.++ -+++++..+.+. |.-... | +..+.+|+.|..||.+++-.
T Consensus 1162 ~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~--------ds~~k~-----w-----~k~~~~gklv~~rv~~ve~~ 1223 (1710)
T KOG1070|consen 1162 IGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS--------DSFEKE-----W-----EKHLPVGKLVTGRVLSVEED 1223 (1710)
T ss_pred cCceeEEEEEEecCCcEEEEEccceEEEEEccccc--------cchhhh-----h-----hccCCccceeeeEEEEeecc
Confidence 7999999999999999999998 455444434332 222222 2 23788999999999999876
Q ss_pred CC
Q 029485 160 SI 161 (192)
Q Consensus 160 ~~ 161 (192)
.+
T Consensus 1224 s~ 1225 (1710)
T KOG1070|consen 1224 SK 1225 (1710)
T ss_pred Cc
Confidence 54
No 116
>PRK11712 ribonuclease G; Provisional
Probab=76.73 E-value=6.4 Score=36.30 Aligned_cols=75 Identities=13% Similarity=0.193 Sum_probs=47.4
Q ss_pred ecCCCcEEEEEEEEEeCC--eeEEEeCcc-ceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEE
Q 029485 78 RPFVGEIIAAKLKESDAN--GLRLSLGFF-EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 154 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~--Gifv~lg~~-~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~ 154 (192)
+..+|.++.|+|.++.+. ++||.+|.= +++.+..+..|....+ .+..... .....-...++.||.|-|+|.
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~-~~~~~~~-----~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECV-AGEEQKQ-----FVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhc-ccccccc-----cccccHHHhccCCCEEEEEEE
Confidence 356899999999999997 899999843 4555556555542222 0111110 000111235899999999999
Q ss_pred EEec
Q 029485 155 SVNY 158 (192)
Q Consensus 155 ~v~~ 158 (192)
.--.
T Consensus 109 Ke~~ 112 (489)
T PRK11712 109 KDPL 112 (489)
T ss_pred eCCc
Confidence 8543
No 117
>PRK10811 rne ribonuclease E; Reviewed
Probab=71.32 E-value=27 Score=34.97 Aligned_cols=71 Identities=8% Similarity=-0.037 Sum_probs=44.7
Q ss_pred cCCCcEEEEEEEEEeCC--eeEEEeCcc-ceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDAN--GLRLSLGFF-EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~--Gifv~lg~~-~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
+.+|.++.|+|.++.+. ++||.+|.= .+++...+..... | ...... -.....+..++.||.|-|.|..
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~--f--~~~~~~-----~~~~~i~~~Lk~GqeILVQV~K 106 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREY--F--PANYSA-----HGRPNIKDVLREGQEVIVQIDK 106 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccc--c--cccccc-----ccccccccccCCCCEEEEEEee
Confidence 45799999999999998 999999843 4444444442222 2 111000 0000123368899999999998
Q ss_pred Eec
Q 029485 156 VNY 158 (192)
Q Consensus 156 v~~ 158 (192)
--.
T Consensus 107 Ea~ 109 (1068)
T PRK10811 107 EER 109 (1068)
T ss_pred ccc
Confidence 543
No 118
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=67.04 E-value=25 Score=30.08 Aligned_cols=52 Identities=12% Similarity=-0.058 Sum_probs=40.2
Q ss_pred CCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEec
Q 029485 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
.++.++|+|-...+.|.||-+. ..-+++|+++. | + ..+.|+.+..||++++.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------~-------~-------------~prlG~~l~~rVi~~re 207 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSER------F-------A-------------EPRLGERLTARVIGVRE 207 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------c-------c-------------cccCCceEEEEEEEEcc
Confidence 4899999999999999998872 33356666532 2 1 46789999999999987
No 119
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=64.29 E-value=40 Score=22.85 Aligned_cols=25 Identities=8% Similarity=0.094 Sum_probs=15.7
Q ss_pred EEeCCceeEEcCCCEEEEEEEEEec
Q 029485 134 WEFGDTKYVIDGLDEIKFRVLSVNY 158 (192)
Q Consensus 134 ~~~~~~~~~i~~G~~VrvrV~~v~~ 158 (192)
+.+......+++||.|++.=.--.+
T Consensus 36 fV~~~~~~~~~~Gd~V~vtG~v~ey 60 (78)
T cd04486 36 FVYTGSGADVAVGDLVRVTGTVTEY 60 (78)
T ss_pred EEecCCCCCCCCCCEEEEEEEEEee
Confidence 4443335678999999987443333
No 120
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=54.65 E-value=11 Score=31.96 Aligned_cols=66 Identities=20% Similarity=0.130 Sum_probs=46.2
Q ss_pred cCCCcEEEEEEEEEeCCeeEEEe---CccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 79 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 79 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
|-++|++-+.|.++...|++|.| +=++|++..+.+..--- +.-...+++|-.=-+-|..
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRI------------------RSI~klirVGr~E~vvVlr 75 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRI------------------RSIQKLIRVGRNEPVVVLR 75 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHH------------------HHHHHHHhcCCcceEEEEE
Confidence 88999999999999999999998 45667776665532210 1123356777666667777
Q ss_pred EecCCCc
Q 029485 156 VNYPSIP 162 (192)
Q Consensus 156 v~~~~~~ 162 (192)
|+-.++-
T Consensus 76 VDkekGY 82 (304)
T KOG2916|consen 76 VDKEKGY 82 (304)
T ss_pred EcCCCCc
Confidence 7765553
No 121
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=46.24 E-value=34 Score=26.38 Aligned_cols=72 Identities=11% Similarity=0.194 Sum_probs=48.2
Q ss_pred CceeeEEEEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC-ccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeE
Q 029485 64 GASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYV 142 (192)
Q Consensus 64 g~~~~~V~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~ 142 (192)
.++..-=.-++.-+-|+.|..+.|+|-.+.+.-+|+..| -|..+.- -+ .-+...
T Consensus 65 sFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~-------------rP------------~~n~e~ 119 (173)
T KOG4078|consen 65 SFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCK-------------RP------------ALNGEA 119 (173)
T ss_pred hHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEc-------------Cc------------CcCHHH
Confidence 333333344556677999999999999999999999987 3321111 11 112226
Q ss_pred EcCCCEEEEEEEEEecCC
Q 029485 143 IDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 143 i~~G~~VrvrV~~v~~~~ 160 (192)
|+.|..||.|+++....+
T Consensus 120 Y~~GaRVrlRl~DlELs~ 137 (173)
T KOG4078|consen 120 YQKGARVRLRLIDLELSE 137 (173)
T ss_pred hhcCceEEEEEcChhHhh
Confidence 788999999998876543
No 122
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=45.36 E-value=58 Score=24.02 Aligned_cols=55 Identities=13% Similarity=0.070 Sum_probs=34.7
Q ss_pred EEEEEEEEeCCe--eEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEE
Q 029485 85 IAAKLKESDANG--LRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 155 (192)
Q Consensus 85 ~~g~V~~v~~~G--ifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~ 155 (192)
.+|+|.+++... +-++-+++..+=-|.-- ..| .-.... .-..+++|+.|+|.+..
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMT----M~F--~v~~~~----------~l~~lk~G~~V~F~~~~ 101 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMT----MRF--TITPQT----------KMSEIKTGDKVAFNFVQ 101 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCcc----ccc--cCCChh----------hhccCCCCCEEEEEEEE
Confidence 489999998877 77777888644222211 224 322211 11268999999999875
No 123
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=43.71 E-value=27 Score=23.17 Aligned_cols=54 Identities=11% Similarity=0.041 Sum_probs=27.9
Q ss_pred EEEEEEeC--CeeEEEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEE
Q 029485 87 AKLKESDA--NGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 156 (192)
Q Consensus 87 g~V~~v~~--~Gifv~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v 156 (192)
|+|.+++. .-+-++-+++.++--|.-- ..| .-... ..-..++.||.|+|.+...
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMT----M~F--~v~~~----------~~l~~l~~Gd~V~F~~~~~ 56 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMT----MDF--PVADP----------VDLAGLKPGDKVRFTFERT 56 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEE----EEE--E--TT----------SEESS-STT-EEEEEEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeE----EEE--EcCCh----------hhhhcCCCCCEEEEEEEEC
Confidence 78999994 4555666777543323222 123 21111 1223789999999999874
No 124
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=43.04 E-value=92 Score=20.67 Aligned_cols=35 Identities=11% Similarity=0.102 Sum_probs=27.0
Q ss_pred eEEEEEEEEEecCCCcEEEEEEEEEeCCeeEEEeC
Q 029485 68 HTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLG 102 (192)
Q Consensus 68 ~~V~f~~~vf~p~~gEv~~g~V~~v~~~Gifv~lg 102 (192)
+.+...+.......+..+.|.+.+++..|+.+.+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEEC
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEEC
Confidence 34444454477788999999999999999998873
No 125
>PF03504 Chlam_OMP6: Chlamydia cysteine-rich outer membrane protein 6; InterPro: IPR003506 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=39.95 E-value=47 Score=23.32 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=19.6
Q ss_pred CCCCCCCCcC-cCCCCC----eeeeEEEEeCCceeEEcCCCEEEEEE
Q 029485 112 HLLPSPSRSE-PDPYGR----YEVKWIWEFGDTKYVIDGLDEIKFRV 153 (192)
Q Consensus 112 ~~~~~~~~f~-~d~~~~----~~~~w~~~~~~~~~~i~~G~~VrvrV 153 (192)
+.+|...+|| ||++.. ..+.|.+. .+..|++..+.|
T Consensus 51 qqLPce~eFV~SdPettp~~D~kLVW~Ig------~l~~G~k~kItV 91 (95)
T PF03504_consen 51 QQLPCEVEFVRSDPETTPTPDGKLVWKIG------RLGQGEKCKITV 91 (95)
T ss_pred ecCCcceEEEecCCccccCCCCEEEEEec------cccCCceeEEEE
Confidence 3445555565 455543 13455543 667788776655
No 126
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=39.03 E-value=80 Score=20.73 Aligned_cols=19 Identities=16% Similarity=0.352 Sum_probs=16.5
Q ss_pred cEEEEEEEEEeCCeeEEEe
Q 029485 83 EIIAAKLKESDANGLRLSL 101 (192)
Q Consensus 83 Ev~~g~V~~v~~~Gifv~l 101 (192)
...+|+|+++++...-+.|
T Consensus 3 ~~veG~I~~id~~~~titL 21 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITL 21 (61)
T ss_pred ccceEEEEEEcCCceEEEe
Confidence 3578999999999998888
No 127
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=37.33 E-value=1.1e+02 Score=19.27 Aligned_cols=24 Identities=25% Similarity=0.458 Sum_probs=17.5
Q ss_pred ecCCCcEEEEEEEEEeCCeeEEEe
Q 029485 78 RPFVGEIIAAKLKESDANGLRLSL 101 (192)
Q Consensus 78 ~p~~gEv~~g~V~~v~~~Gifv~l 101 (192)
.|.+|+.+..+|++..++-++.++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 466799999999999999887653
No 128
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=33.66 E-value=74 Score=25.43 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=18.7
Q ss_pred ceeEEcCCCEEEEEEEEEecCC
Q 029485 139 TKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 139 ~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
+...+..|+.||+++.+.+...
T Consensus 117 ~~l~vp~g~~v~~~~ts~DV~H 138 (201)
T TIGR02866 117 NELVVPAGTPVRLQVTSKDVIH 138 (201)
T ss_pred CEEEEEcCCEEEEEEEeCchhh
Confidence 4789999999999999977643
No 129
>PF01629 DUF22: Domain of unknown function DUF22; InterPro: IPR002572 This region is found in 1 to 3 copies in archaeal proteins whose function is unknown. It only appears in multiple copies in proteins from Archaeoglobus fulgidus.
Probab=33.25 E-value=1.8e+02 Score=21.40 Aligned_cols=32 Identities=13% Similarity=0.197 Sum_probs=27.4
Q ss_pred eEEEEeCCceeEEcCCCEEEEEEEEEecCCCc
Q 029485 131 KWIWEFGDTKYVIDGLDEIKFRVLSVNYPSIP 162 (192)
Q Consensus 131 ~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~~~ 162 (192)
.|...--+....++.|+..+++|..+.+..+.
T Consensus 37 ~wepiIAdEdvevk~Ge~~~IkIk~I~iP~~t 68 (112)
T PF01629_consen 37 KWEPIIADEDVEVKKGEVKIIKIKKIEIPPNT 68 (112)
T ss_pred eEEEEEEcCeeEEecCCEEEEEEEEEecCCCC
Confidence 37766678888999999999999999997764
No 130
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=31.42 E-value=69 Score=27.45 Aligned_cols=37 Identities=35% Similarity=0.409 Sum_probs=32.0
Q ss_pred CCCcEEEEEEEEEe-CCeeEEEeCccceEEecCCCCCC
Q 029485 80 FVGEIIAAKLKESD-ANGLRLSLGFFEDIYVPSHLLPS 116 (192)
Q Consensus 80 ~~gEv~~g~V~~v~-~~Gifv~lg~~~~i~i~~~~~~~ 116 (192)
.+|+---++|+.++ ..|+|+..|.=.++++|.+-+|.
T Consensus 72 tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~ 109 (287)
T COG2996 72 TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPT 109 (287)
T ss_pred eecceeEEEEEEEcCCcceEEecCCCcceeeehhhccc
Confidence 37888899999999 88999999955789999887775
No 131
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=26.27 E-value=2.4e+02 Score=19.88 Aligned_cols=57 Identities=9% Similarity=0.058 Sum_probs=33.6
Q ss_pred EEEEEEEEEeCCeeE-EEeCccceEEecCCCCCCCCCcCcCCCCCeeeeEEEEeCCceeEEcCCCEEEEEEEEEecCCC
Q 029485 84 IIAAKLKESDANGLR-LSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPSI 161 (192)
Q Consensus 84 v~~g~V~~v~~~Gif-v~lg~~~~i~i~~~~~~~~~~f~~d~~~~~~~~w~~~~~~~~~~i~~G~~VrvrV~~v~~~~~ 161 (192)
.++|+|+.+.+++.| |.|. ++..+.. ++|.- .+.+...+.+||.|.|.+..-+....
T Consensus 8 e~~G~V~e~Lp~~~frV~Le--nG~~vla--------~isGK-----------mR~~rIrIl~GD~V~VE~spYDltkG 65 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLE--NGVEVGA--------YASGR-----------MRKHRIRILAGDRVTLELSPYDLTKG 65 (87)
T ss_pred EEEEEEEEECCCCEEEEEeC--CCCEEEE--------Eeccc-----------eeeeeEEecCCCEEEEEECcccCCce
Confidence 578999999998888 5662 1111111 10010 02334477889999998886655443
No 132
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=26.01 E-value=1.2e+02 Score=18.29 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=16.6
Q ss_pred CCcEEEEEEEEEeCCeeEE
Q 029485 81 VGEIIAAKLKESDANGLRL 99 (192)
Q Consensus 81 ~gEv~~g~V~~v~~~Gifv 99 (192)
.++.++|++.++++.|..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 5888999999999998863
No 133
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=24.58 E-value=96 Score=21.26 Aligned_cols=20 Identities=10% Similarity=0.253 Sum_probs=15.2
Q ss_pred eeEEcCCCEEEEEEEEEecC
Q 029485 140 KYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 140 ~~~i~~G~~VrvrV~~v~~~ 159 (192)
+-.|++||.|.+|+.-.+..
T Consensus 8 r~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEEC
T ss_pred ccCcCCCCEEEEEEEEeccc
Confidence 34899999999999965554
No 134
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=21.68 E-value=1.5e+02 Score=24.38 Aligned_cols=22 Identities=14% Similarity=0.141 Sum_probs=19.3
Q ss_pred ceeEEcCCCEEEEEEEEEecCC
Q 029485 139 TKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 139 ~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
++..+-.|..||+++.+.+...
T Consensus 139 nel~lP~g~pV~~~ltS~DViH 160 (226)
T TIGR01433 139 NEIAFPVNTPINFKITSNSVMN 160 (226)
T ss_pred ceEEEECCCEEEEEEEECchhh
Confidence 6899999999999999988653
No 135
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=21.12 E-value=1.7e+02 Score=24.51 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=23.5
Q ss_pred eeEEEEeCC------ceeEEcCCCEEEEEEEEEecC
Q 029485 130 VKWIWEFGD------TKYVIDGLDEIKFRVLSVNYP 159 (192)
Q Consensus 130 ~~w~~~~~~------~~~~i~~G~~VrvrV~~v~~~ 159 (192)
-.|.+.|-+ +...+-.|..|+|++.+.+.-
T Consensus 122 w~W~f~Yp~~~~~t~n~l~lPv~~~V~f~ltS~DVi 157 (247)
T COG1622 122 WKWLFIYPDYGIATVNELVLPVGRPVRFKLTSADVI 157 (247)
T ss_pred EEEEEEccCcCccccceEEEeCCCeEEEEEEechhc
Confidence 335555655 789999999999999998754
No 136
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=20.32 E-value=2.3e+02 Score=21.43 Aligned_cols=22 Identities=5% Similarity=0.170 Sum_probs=17.3
Q ss_pred ceeEEcCCCEEEEEEEEEecCC
Q 029485 139 TKYVIDGLDEIKFRVLSVNYPS 160 (192)
Q Consensus 139 ~~~~i~~G~~VrvrV~~v~~~~ 160 (192)
....++.|+++|+|+++.....
T Consensus 60 ~~~~v~~g~~~rlRliNa~~~~ 81 (159)
T PF00394_consen 60 PVIKVKPGERYRLRLINAGAST 81 (159)
T ss_dssp GEEEEETTTEEEEEEEEESSS-
T ss_pred ceEEEcCCcEEEEEEEeccCCe
Confidence 3568999999999999876544
No 137
>PF06995 Phage_P2_GpU: Phage P2 GpU; InterPro: IPR009734 This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (O64315 from SWISSPROT) which is thought to be involved in tail assembly [].
Probab=20.12 E-value=3.5e+02 Score=19.56 Aligned_cols=69 Identities=14% Similarity=0.089 Sum_probs=38.3
Q ss_pred EEeeEEEECCCCCCcc-HHHHHHHHHHhHhcceEeccccEEEEEeeecccccceeecCCCceeeEEEEEE
Q 029485 6 KIEHTLRLPPHLLRLP-LNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRL 74 (192)
Q Consensus 6 ~l~d~v~I~P~~~~~~-~~~~i~~~L~~k~~gk~~~~~G~~i~i~~i~~i~~g~I~~~~g~~~~~V~f~~ 74 (192)
+++-...+.|...+.. --+.|++...+--.-..+...|.+..-+-|.++++..-.-.......++.|.+
T Consensus 44 ~itl~g~l~~~~~~~~~~l~~Lr~~~~~g~p~~Lv~G~G~~~G~~vI~si~e~~~~~~~~G~~~~~~~~l 113 (121)
T PF06995_consen 44 TITLSGVLFPEFGGGRKELDKLRAMAESGEPLPLVIGSGKVLGKWVITSISETQSYFDPDGNPRKIEFTL 113 (121)
T ss_pred eEEEEEEEehHHCCCHHHHHHHHHHHHcCCceEEEECCCceeEEEEEEEEechheEecCCCCEEEEEEEE
Confidence 5666788899776521 12233333332222234556677777788888877654444444445666554
Done!