Query 034902
Match_columns 79
No_of_seqs 100 out of 188
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:31:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034902.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034902hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3298 DNA-directed RNA polym 99.9 3.6E-27 7.8E-32 168.1 7.7 73 6-79 32-112 (170)
2 PTZ00162 DNA-directed RNA poly 99.9 8.7E-26 1.9E-30 160.0 8.6 75 3-78 29-111 (176)
3 COG1095 RPB7 DNA-directed RNA 99.9 1.1E-25 2.4E-30 162.1 8.4 75 3-78 29-111 (183)
4 TIGR00448 rpoE DNA-directed RN 99.9 1.5E-23 3.2E-28 147.1 9.4 76 3-78 29-112 (179)
5 PRK08563 DNA-directed RNA poly 99.9 2.8E-21 6E-26 135.5 8.8 75 2-77 28-110 (187)
6 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.5 1E-14 2.2E-19 92.5 4.9 45 3-47 28-72 (80)
7 cd04329 RNAP_II_Rpb7_N RNAP_II 99.5 1.5E-14 3.2E-19 91.5 5.2 46 2-47 27-72 (80)
8 cd00655 RNAP_Rpb7_N_like RNAP_ 99.5 3.7E-14 8E-19 89.6 5.3 45 3-47 28-72 (80)
9 cd04330 RNAP_III_Rpc25_N RNAP_ 99.5 4.5E-14 9.7E-19 89.3 4.8 46 2-47 27-72 (80)
10 PF03876 SHS2_Rpb7-N: SHS2 dom 99.2 4E-11 8.7E-16 72.4 4.9 45 3-47 22-66 (70)
11 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.0 1E-09 2.2E-14 70.2 4.5 30 48-78 2-31 (88)
12 KOG3297 DNA-directed RNA polym 98.9 4.8E-09 1E-13 76.8 6.3 73 6-78 32-112 (202)
13 PF00575 S1: S1 RNA binding do 97.7 9.3E-05 2E-09 43.9 4.7 30 48-78 5-35 (74)
14 cd04471 S1_RNase_R S1_RNase_R: 97.5 0.00025 5.5E-09 42.5 4.4 23 48-70 2-24 (83)
15 cd05692 S1_RPS1_repeat_hs4 S1_ 97.0 0.0027 5.9E-08 36.1 4.9 30 48-77 1-30 (69)
16 cd05686 S1_pNO40 S1_pNO40: pNO 96.9 0.0029 6.3E-08 38.1 4.8 29 48-77 4-34 (73)
17 cd05690 S1_RPS1_repeat_ec5 S1_ 96.9 0.003 6.4E-08 36.7 4.7 29 48-76 1-29 (69)
18 cd04472 S1_PNPase S1_PNPase: P 96.9 0.0037 8.1E-08 35.8 5.0 30 48-77 1-30 (68)
19 cd05684 S1_DHX8_helicase S1_DH 96.8 0.0027 5.9E-08 38.4 4.5 29 48-77 1-33 (79)
20 cd05688 S1_RPS1_repeat_ec3 S1_ 96.8 0.0029 6.2E-08 36.2 4.3 29 48-77 2-30 (68)
21 PF08292 RNA_pol_Rbc25: RNA po 96.8 0.0028 6.2E-08 43.0 4.9 34 46-79 2-35 (122)
22 cd05694 S1_Rrp5_repeat_hs2_sc2 96.8 0.0025 5.4E-08 39.2 4.2 30 48-78 5-36 (74)
23 cd05696 S1_Rrp5_repeat_hs4 S1_ 96.8 0.0022 4.8E-08 38.6 3.9 29 48-77 1-32 (71)
24 smart00316 S1 Ribosomal protei 96.7 0.0048 1E-07 34.7 4.6 30 48-77 3-32 (72)
25 cd04460 S1_RpoE S1_RpoE: RpoE, 96.7 0.0029 6.4E-08 40.1 4.1 27 49-76 1-27 (99)
26 cd05685 S1_Tex S1_Tex: The C-t 96.7 0.0045 9.7E-08 35.2 4.4 30 48-77 1-30 (68)
27 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.7 0.0047 1E-07 36.3 4.5 28 48-76 1-29 (69)
28 cd05689 S1_RPS1_repeat_ec4 S1_ 96.6 0.0062 1.4E-07 35.9 4.9 28 48-76 4-32 (72)
29 cd04465 S1_RPS1_repeat_ec2_hs2 96.6 0.0048 1E-07 36.2 4.0 29 48-77 1-29 (67)
30 cd04455 S1_NusA S1_NusA: N-uti 96.6 0.0038 8.2E-08 37.1 3.6 30 48-78 4-33 (67)
31 cd05705 S1_Rrp5_repeat_hs14 S1 96.5 0.0056 1.2E-07 37.4 4.3 29 48-76 4-32 (74)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 96.5 0.0069 1.5E-07 35.4 4.4 30 48-78 1-31 (70)
33 cd04328 RNAP_I_Rpa43_N RNAP_I_ 96.4 0.0062 1.3E-07 38.4 4.1 37 11-47 42-81 (89)
34 PRK08582 hypothetical protein; 96.4 0.0082 1.8E-07 41.2 5.0 29 48-76 6-34 (139)
35 cd05708 S1_Rrp5_repeat_sc12 S1 96.4 0.0069 1.5E-07 35.6 4.1 28 48-76 3-32 (77)
36 cd05707 S1_Rrp5_repeat_sc11 S1 96.4 0.0087 1.9E-07 35.1 4.4 29 48-76 1-29 (68)
37 cd04461 S1_Rrp5_repeat_hs8_sc7 96.3 0.009 2E-07 36.5 4.4 29 48-77 15-44 (83)
38 cd05706 S1_Rrp5_repeat_sc10 S1 96.3 0.013 2.8E-07 34.6 4.8 30 48-77 4-33 (73)
39 cd05691 S1_RPS1_repeat_ec6 S1_ 95.9 0.023 4.9E-07 33.1 4.5 29 48-77 1-30 (73)
40 cd04473 S1_RecJ_like S1_RecJ_l 95.9 0.027 5.8E-07 34.3 4.9 30 48-77 17-46 (77)
41 cd04453 S1_RNase_E S1_RNase_E: 95.8 0.022 4.8E-07 36.0 4.5 30 48-77 8-39 (88)
42 cd05687 S1_RPS1_repeat_ec1_hs1 95.8 0.026 5.5E-07 33.1 4.5 29 48-77 1-30 (70)
43 cd05695 S1_Rrp5_repeat_hs3 S1_ 95.8 0.02 4.4E-07 34.0 4.0 28 48-76 1-29 (66)
44 PRK07252 hypothetical protein; 95.7 0.028 6.1E-07 37.7 4.8 29 48-77 4-33 (120)
45 cd05704 S1_Rrp5_repeat_hs13 S1 95.6 0.03 6.4E-07 33.7 4.4 29 48-76 4-33 (72)
46 cd05703 S1_Rrp5_repeat_hs12_sc 95.6 0.023 5.1E-07 34.4 3.8 28 48-76 1-29 (73)
47 cd04452 S1_IF2_alpha S1_IF2_al 95.6 0.035 7.5E-07 32.7 4.4 29 48-77 4-35 (76)
48 COG0539 RpsA Ribosomal protein 95.4 0.018 4E-07 47.6 3.8 26 48-73 193-218 (541)
49 PRK07899 rpsA 30S ribosomal pr 95.3 0.024 5.3E-07 46.0 4.2 30 48-78 209-238 (486)
50 PRK05807 hypothetical protein; 95.3 0.037 7.9E-07 37.8 4.3 29 48-77 6-34 (136)
51 TIGR03591 polynuc_phos polyrib 95.0 0.013 2.9E-07 49.0 1.8 54 23-77 584-648 (684)
52 PRK08059 general stress protei 94.9 0.065 1.4E-06 35.6 4.7 29 48-76 8-36 (123)
53 COG1098 VacB Predicted RNA bin 94.8 0.035 7.5E-07 38.7 3.3 20 48-67 6-25 (129)
54 cd00164 S1_like S1_like: Ribos 94.8 0.065 1.4E-06 29.4 3.8 27 51-77 1-27 (65)
55 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 94.7 0.078 1.7E-06 32.3 4.3 28 48-76 7-35 (86)
56 PRK13806 rpsA 30S ribosomal pr 94.6 0.15 3.2E-06 41.0 6.7 29 48-77 293-322 (491)
57 PRK07400 30S ribosomal protein 94.4 0.065 1.4E-06 41.0 4.1 28 48-76 197-224 (318)
58 PRK06676 rpsA 30S ribosomal pr 94.2 0.074 1.6E-06 40.7 4.2 29 48-77 193-221 (390)
59 cd05702 S1_Rrp5_repeat_hs11_sc 94.2 0.086 1.9E-06 31.2 3.6 28 48-76 1-29 (70)
60 PTZ00248 eukaryotic translatio 94.1 0.084 1.8E-06 41.2 4.2 28 48-76 18-48 (319)
61 PRK06299 rpsA 30S ribosomal pr 94.1 0.077 1.7E-06 42.6 4.1 29 48-77 374-403 (565)
62 PRK06299 rpsA 30S ribosomal pr 93.9 0.091 2E-06 42.2 4.2 29 48-77 202-230 (565)
63 TIGR00717 rpsA ribosomal prote 93.7 0.097 2.1E-06 41.3 4.1 28 48-76 360-388 (516)
64 TIGR00717 rpsA ribosomal prote 92.9 0.15 3.2E-06 40.3 4.0 30 48-78 188-217 (516)
65 PF13509 S1_2: S1 domain; PDB: 92.6 0.21 4.4E-06 29.6 3.4 31 48-78 2-32 (61)
66 TIGR02063 RNase_R ribonuclease 92.6 0.16 3.5E-06 42.3 3.9 22 48-69 628-649 (709)
67 PRK09521 exosome complex RNA-b 92.6 0.57 1.2E-05 33.0 6.2 51 18-68 33-85 (189)
68 TIGR02696 pppGpp_PNP guanosine 92.4 0.24 5.3E-06 42.4 4.8 29 48-77 648-677 (719)
69 PRK13806 rpsA 30S ribosomal pr 92.3 0.23 5E-06 39.9 4.4 30 48-78 203-233 (491)
70 PRK11824 polynucleotide phosph 92.3 0.28 6.1E-06 41.3 5.0 30 48-77 622-651 (693)
71 PRK12269 bifunctional cytidyla 91.8 0.25 5.4E-06 42.9 4.2 30 48-78 494-523 (863)
72 PRK11642 exoribonuclease R; Pr 91.1 0.28 6E-06 42.2 3.8 22 48-69 644-665 (813)
73 PRK07400 30S ribosomal protein 90.8 0.47 1E-05 36.3 4.5 30 48-77 32-61 (318)
74 PRK04163 exosome complex RNA-b 90.8 0.43 9.4E-06 35.0 4.1 30 48-78 64-94 (235)
75 cd04454 S1_Rrp4_like S1_Rrp4_l 90.6 0.77 1.7E-05 27.7 4.5 29 48-77 7-36 (82)
76 PRK00087 4-hydroxy-3-methylbut 89.9 0.44 9.5E-06 39.5 3.9 29 48-77 478-506 (647)
77 PRK00087 4-hydroxy-3-methylbut 89.4 0.54 1.2E-05 39.0 4.0 30 48-78 390-419 (647)
78 PRK12269 bifunctional cytidyla 89.2 0.46 1E-05 41.3 3.7 28 48-76 579-607 (863)
79 PRK03987 translation initiatio 89.2 0.68 1.5E-05 34.9 4.2 28 48-76 9-39 (262)
80 PRK09202 nusA transcription el 88.1 0.67 1.5E-05 37.7 3.7 30 48-78 135-164 (470)
81 PLN00207 polyribonucleotide nu 88.0 0.87 1.9E-05 40.0 4.5 30 48-77 754-784 (891)
82 cd05693 S1_Rrp5_repeat_hs1_sc1 87.9 1.1 2.4E-05 28.8 4.0 28 48-76 4-32 (100)
83 COG0539 RpsA Ribosomal protein 86.9 0.77 1.7E-05 38.3 3.4 30 48-77 278-307 (541)
84 TIGR00358 3_prime_RNase VacB a 86.2 1.3 2.9E-05 36.8 4.6 21 48-68 573-593 (654)
85 COG2183 Tex Transcriptional ac 86.0 0.93 2E-05 39.4 3.6 30 48-77 659-688 (780)
86 PRK07899 rpsA 30S ribosomal pr 85.6 1.5 3.2E-05 35.8 4.4 32 46-77 33-65 (486)
87 PRK06676 rpsA 30S ribosomal pr 85.4 1.7 3.8E-05 33.2 4.5 30 48-77 18-48 (390)
88 PHA02945 interferon resistance 85.0 1.3 2.8E-05 29.1 3.2 19 48-67 12-30 (88)
89 TIGR00757 RNaseEG ribonuclease 83.5 2 4.3E-05 34.4 4.2 31 48-78 26-58 (414)
90 COG1185 Pnp Polyribonucleotide 83.0 2.1 4.6E-05 36.8 4.4 31 48-78 620-650 (692)
91 PRK12327 nusA transcription el 82.4 1.9 4.2E-05 34.0 3.7 29 48-77 135-163 (362)
92 COG1093 SUI2 Translation initi 78.6 2.4 5.3E-05 32.7 3.1 23 48-70 12-34 (269)
93 TIGR01953 NusA transcription t 78.4 3 6.4E-05 32.6 3.6 29 48-77 132-161 (341)
94 PRK05054 exoribonuclease II; P 77.0 2.9 6.4E-05 34.9 3.4 21 49-69 563-583 (644)
95 cd04486 YhcR_OBF_like YhcR_OBF 76.0 7.6 0.00016 24.0 4.3 29 50-78 1-40 (78)
96 COG0557 VacB Exoribonuclease R 66.0 7.6 0.00016 32.7 3.4 22 48-69 623-644 (706)
97 COG2996 Predicted RNA-bindinin 64.6 8.1 0.00018 30.1 3.1 31 48-78 74-105 (287)
98 TIGR02062 RNase_B exoribonucle 62.4 9.1 0.0002 32.1 3.2 19 49-67 559-577 (639)
99 PF02237 BPL_C: Biotin protein 53.2 34 0.00074 19.0 3.7 18 48-65 12-29 (48)
100 cd05699 S1_Rrp5_repeat_hs7 S1_ 52.7 25 0.00054 22.0 3.4 23 48-70 1-23 (72)
101 KOG4134 DNA-dependent RNA poly 46.5 61 0.0013 24.9 5.2 48 13-60 64-120 (253)
102 PF08729 HUN: HPC2 and ubinucl 45.8 11 0.00023 22.1 0.8 16 56-71 39-54 (55)
103 PHA02858 EIF2a-like PKR inhibi 44.7 39 0.00084 22.1 3.4 19 48-67 17-35 (86)
104 cd05790 S1_Rrp40 S1_Rrp40: Rrp 41.9 51 0.0011 21.0 3.6 30 48-77 7-36 (86)
105 PF07497 Rho_RNA_bind: Rho ter 35.7 80 0.0017 19.9 3.8 27 51-79 3-37 (78)
106 PF08634 Pet127: Mitochondrial 32.7 15 0.00032 28.5 0.0 14 65-78 216-229 (274)
107 COG1107 Archaea-specific RecJ- 28.4 25 0.00055 30.5 0.7 22 48-69 123-144 (715)
108 PRK12328 nusA transcription el 27.7 90 0.002 25.1 3.7 28 48-76 139-167 (374)
109 COG2996 Predicted RNA-bindinin 27.4 1.3E+02 0.0029 23.6 4.4 31 48-78 6-37 (287)
110 KOG2916 Translation initiation 24.6 61 0.0013 25.5 2.1 20 48-67 17-36 (304)
111 PF07364 DUF1485: Protein of u 23.1 45 0.00096 25.5 1.1 12 67-78 94-105 (292)
112 PF05899 Cupin_3: Protein of u 22.5 1.8E+02 0.004 17.2 3.9 30 48-77 29-58 (74)
113 PF12857 TOBE_3: TOBE-like dom 22.5 1.3E+02 0.0027 17.2 2.8 18 50-67 6-23 (58)
114 KOG1070 rRNA processing protei 22.1 1.4E+02 0.003 28.7 4.1 29 48-76 1163-1191(1710)
115 TIGR00638 Mop molybdenum-pteri 21.6 1.5E+02 0.0032 16.6 3.0 17 50-66 8-24 (69)
116 cd05791 S1_CSL4 S1_CSL4: CSL4, 20.5 1.8E+02 0.0039 18.2 3.4 20 48-67 7-26 (92)
No 1
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=99.94 E-value=3.6e-27 Score=168.09 Aligned_cols=73 Identities=32% Similarity=0.556 Sum_probs=69.9
Q ss_pred heeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 6 LTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 6 ~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
..-+|+|++++||+||||++++|++|+|+|++|.+.|||+|+ ||||||+|++|+|+|+|+++|||+ +|+|+
T Consensus 32 ~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~-~f~ss 110 (170)
T KOG3298|consen 32 AEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSGPLE-VFYSS 110 (170)
T ss_pred HHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEeccceE-eeeec
Confidence 356899999999999999999999999999999999999999 999999999999999999999995 99999
Q ss_pred CC
Q 034902 78 NA 79 (79)
Q Consensus 78 ~~ 79 (79)
|+
T Consensus 111 hl 112 (170)
T KOG3298|consen 111 HL 112 (170)
T ss_pred cc
Confidence 85
No 2
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=99.93 E-value=8.7e-26 Score=159.99 Aligned_cols=75 Identities=16% Similarity=0.340 Sum_probs=72.3
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceEE
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMSY 74 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~vF 74 (79)
+-+..|+|||.+++|++|||+++.++++|+|.||||++||+|+|+ |||+||+|++++++|+|+++||+| +|
T Consensus 29 ~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~-if 107 (176)
T PTZ00162 29 MLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AF 107 (176)
T ss_pred HHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEeeCeE-EE
Confidence 456789999999999999999999999999999999999999999 999999999999999999999999 99
Q ss_pred EecC
Q 034902 75 LHEN 78 (79)
Q Consensus 75 vS~~ 78 (79)
||.|
T Consensus 108 I~~~ 111 (176)
T PTZ00162 108 VSRS 111 (176)
T ss_pred EcHH
Confidence 9986
No 3
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=99.93 E-value=1.1e-25 Score=162.15 Aligned_cols=75 Identities=21% Similarity=0.397 Sum_probs=71.9
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceEE
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMSY 74 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~vF 74 (79)
+-|..|+|||+++.|++|+|.+++++++|+|.||||++||+|+|+ +|||||+|+++++||+|+++||+| .|
T Consensus 29 ~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~d-gl 107 (183)
T COG1095 29 ELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLD-GL 107 (183)
T ss_pred HHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEecccc-cc
Confidence 446789999999999999999999999999999999999999999 999999999999999999999998 89
Q ss_pred EecC
Q 034902 75 LHEN 78 (79)
Q Consensus 75 vS~~ 78 (79)
++.|
T Consensus 108 vh~s 111 (183)
T COG1095 108 VHVS 111 (183)
T ss_pred ccHh
Confidence 9876
No 4
>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=99.90 E-value=1.5e-23 Score=147.06 Aligned_cols=76 Identities=24% Similarity=0.397 Sum_probs=72.4
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceEE
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMSY 74 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~vF 74 (79)
+-|+.|+|||.+++|++|||++++++++|+|.||||++||+|+|+ +|+++|+|++++++|+|+++||++++|
T Consensus 29 ~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~ 108 (179)
T TIGR00448 29 QLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLF 108 (179)
T ss_pred HHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEEEEeCCceEEE
Confidence 457789999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred EecC
Q 034902 75 LHEN 78 (79)
Q Consensus 75 vS~~ 78 (79)
.+++
T Consensus 109 ~~~~ 112 (179)
T TIGR00448 109 HVSQ 112 (179)
T ss_pred EcHH
Confidence 8764
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=99.85 E-value=2.8e-21 Score=135.51 Aligned_cols=75 Identities=25% Similarity=0.418 Sum_probs=69.8
Q ss_pred hhhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceE
Q 034902 2 QQERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMS 73 (79)
Q Consensus 2 ~~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~v 73 (79)
++-|..|+|||.+++|++|+|+|++++++|+|.||||+++|+|+|+ +||++|.|++++++|+|+++||++ .
T Consensus 28 ~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~lg~~~-g 106 (187)
T PRK08563 28 EVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRIGPVD-G 106 (187)
T ss_pred HHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEEEEEeCce-E
Confidence 3557889999999999999999999999999999999999999999 999999999999999999999998 4
Q ss_pred EEec
Q 034902 74 YLHE 77 (79)
Q Consensus 74 FvS~ 77 (79)
|++.
T Consensus 107 ~v~~ 110 (187)
T PRK08563 107 LLHI 110 (187)
T ss_pred EEEc
Confidence 5544
No 6
>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=99.54 E-value=1e-14 Score=92.46 Aligned_cols=45 Identities=27% Similarity=0.421 Sum_probs=42.7
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI 47 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~ 47 (79)
+-|+.|+|||++++|++|||++++++++|+|.||||++||+|+|+
T Consensus 28 ~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~ 72 (80)
T cd04331 28 ILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFD 72 (80)
T ss_pred HHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEE
Confidence 447789999999999999999999999999999999999999997
No 7
>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=99.53 E-value=1.5e-14 Score=91.46 Aligned_cols=46 Identities=33% Similarity=0.491 Sum_probs=43.2
Q ss_pred hhhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec
Q 034902 2 QQERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI 47 (79)
Q Consensus 2 ~~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~ 47 (79)
++-++.|+|||.+++|++|||++++++++|+|.||||++||+|+|+
T Consensus 27 ~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~ 72 (80)
T cd04329 27 QKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYK 72 (80)
T ss_pred HHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEE
Confidence 3457789999999999999999999999999999999999999997
No 8
>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=99.50 E-value=3.7e-14 Score=89.55 Aligned_cols=45 Identities=22% Similarity=0.246 Sum_probs=42.7
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI 47 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~ 47 (79)
+-|+.|+|||++++|++|||++++++++|+|.||||++||+|+|+
T Consensus 28 ~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~ 72 (80)
T cd00655 28 LLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFR 72 (80)
T ss_pred HHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEE
Confidence 457789999999999999999999999999999999999999997
No 9
>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=99.48 E-value=4.5e-14 Score=89.29 Aligned_cols=46 Identities=13% Similarity=0.289 Sum_probs=43.4
Q ss_pred hhhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec
Q 034902 2 QQERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI 47 (79)
Q Consensus 2 ~~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~ 47 (79)
++-|+.|+||+.+++|++|||+++.++++|+|.||||++||+|+|+
T Consensus 27 ~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr 72 (80)
T cd04330 27 DELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFR 72 (80)
T ss_pred HHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEE
Confidence 3557889999999999999999999999999999999999999997
No 10
>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=99.18 E-value=4e-11 Score=72.36 Aligned_cols=45 Identities=31% Similarity=0.424 Sum_probs=41.0
Q ss_pred hhhheeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec
Q 034902 3 QERLTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI 47 (79)
Q Consensus 3 ~~~~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~ 47 (79)
|-+..|.||+.+++|++||++++..+++|+|.+|||+++|+|+|+
T Consensus 22 ~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~ 66 (70)
T PF03876_consen 22 QLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFR 66 (70)
T ss_dssp HHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEE
T ss_pred HHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEE
Confidence 445778999999999999999999999999999999999999996
No 11
>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=98.96 E-value=1e-09 Score=70.20 Aligned_cols=30 Identities=17% Similarity=0.404 Sum_probs=28.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
+||+||+|++++++|+|+++|||+ .|+|.+
T Consensus 2 gEVi~g~V~~v~~~G~~v~~Gpl~-~f~~~~ 31 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEVGPLS-IFISRH 31 (88)
T ss_pred CcEEEEEEEEEeccEEEEEEcCce-EEEEee
Confidence 799999999999999999999998 788875
No 12
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=98.88 E-value=4.8e-09 Score=76.83 Aligned_cols=73 Identities=18% Similarity=0.254 Sum_probs=68.2
Q ss_pred heeeeeeccceeEEEEEeEeeeeCCceEEcCCCceEEEEEec--------CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 6 LTWRRKSTKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 6 ~~~~~~~~~~~G~iv~V~~i~~i~~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
..|-+|+-.+.|.-|+|-||..+++|.|.||||+.|.+|.|+ +||+.|.+.+..+-|+-+.+|=+|-+||.+
T Consensus 32 ~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~ 111 (202)
T KOG3297|consen 32 RKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPK 111 (202)
T ss_pred HHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEEeeeceeech
Confidence 345667889999999999999999999999999999999999 999999999999999999999999999976
Q ss_pred C
Q 034902 78 N 78 (79)
Q Consensus 78 ~ 78 (79)
.
T Consensus 112 ~ 112 (202)
T KOG3297|consen 112 E 112 (202)
T ss_pred h
Confidence 4
No 13
>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=97.71 E-value=9.3e-05 Score=43.86 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=27.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~~ 78 (79)
|++++|.|++++++|+|+++| +++ .|++.+
T Consensus 5 G~iv~g~V~~v~~~g~~V~l~~~~~-g~ip~~ 35 (74)
T PF00575_consen 5 GDIVEGKVTSVEDFGVFVDLGNGIE-GFIPIS 35 (74)
T ss_dssp TSEEEEEEEEEETTEEEEEESTSSE-EEEEGG
T ss_pred CCEEEEEEEEEECCEEEEEECCcEE-EEEEee
Confidence 899999999999999999999 886 888754
No 14
>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=97.47 E-value=0.00025 Score=42.49 Aligned_cols=23 Identities=17% Similarity=0.515 Sum_probs=21.6
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSI 70 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPl 70 (79)
+++++|.|++|+++|+|++++|+
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~ 24 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNL 24 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCC
Confidence 68999999999999999999984
No 15
>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=96.95 E-value=0.0027 Score=36.07 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+++.|.|++++++|+|+++++-...|++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~ 30 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHI 30 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEh
Confidence 689999999999999999999433467764
No 16
>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=96.89 E-value=0.0029 Score=38.06 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=23.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC--CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS--IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP--ld~vFvS~ 77 (79)
|++++|.|+++.+||+|+++.. .+ -|++.
T Consensus 4 g~~~~g~V~~i~~fG~fv~l~~~~~e-Glvh~ 34 (73)
T cd05686 4 YQIFKGEVASVTEYGAFVKIPGCRKQ-GLVHK 34 (73)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCeE-EEEEc
Confidence 7899999999999999999944 45 55554
No 17
>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=96.89 E-value=0.003 Score=36.75 Aligned_cols=29 Identities=14% Similarity=0.290 Sum_probs=23.7
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|+++.|.|++++++|+|+++.|----+++
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~ 29 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVH 29 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEE
Confidence 57899999999999999999764335554
No 18
>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=96.87 E-value=0.0037 Score=35.83 Aligned_cols=30 Identities=27% Similarity=0.443 Sum_probs=25.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
++++.|.|+++.++|+|+++++-...|++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~ 30 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHI 30 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEh
Confidence 578999999999999999998754577664
No 19
>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=96.85 E-value=0.0027 Score=38.36 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=24.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC----CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS----IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP----ld~vFvS~ 77 (79)
+++++|.|+++..+|+|++++| .+ -|++.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~-gll~~ 33 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKE-GLVHI 33 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcE-EEEEh
Confidence 5789999999999999999994 54 56654
No 20
>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=96.84 E-value=0.0029 Score=36.20 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=25.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
++++.|.|++++++|+|+++++.+ .|++.
T Consensus 2 g~~~~g~V~~v~~~g~~v~l~~~~-g~l~~ 30 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDLGGVD-GLLHI 30 (68)
T ss_pred CCEEEEEEEEEEeeeEEEEECCeE-EEEEh
Confidence 689999999999999999999875 66653
No 21
>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=96.83 E-value=0.0028 Score=42.99 Aligned_cols=34 Identities=15% Similarity=0.358 Sum_probs=30.2
Q ss_pred ecCeEEEEEEEEEeeeeEEEEeCCCceEEEecCC
Q 034902 46 FIGKIFQGIVHKMLKHGVLFNCVSIDMSYLHENA 79 (79)
Q Consensus 46 f~~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~~ 79 (79)
|.+||+.|.|.+.++-|+.+.+|-+|-|||..++
T Consensus 2 F~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~ 35 (122)
T PF08292_consen 2 FVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSL 35 (122)
T ss_dssp -TT-EEEEEEEEEETTEEEEEECCEEEEEEECCC
T ss_pred CCCCEEEEEEEecCCCcEEEEecccccEEECHHH
Confidence 5689999999999999999999999999998764
No 22
>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=96.82 E-value=0.0025 Score=39.16 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=25.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC--CceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS--IDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP--ld~vFvS~~ 78 (79)
|.++.|.|.+|.++|+|+++|+ ++ -|++++
T Consensus 5 G~~v~g~V~si~d~G~~v~~g~~gv~-Gfl~~~ 36 (74)
T cd05694 5 GMVLSGCVSSVEDHGYILDIGIPGTT-GFLPKK 36 (74)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCCcE-EEEEHH
Confidence 6899999999999999999983 65 787753
No 23
>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=96.81 E-value=0.0022 Score=38.62 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=24.6
Q ss_pred CeEEE-EEEEEE-eeeeEEEEeCC-CceEEEec
Q 034902 48 GKIFQ-GIVHKM-LKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 48 ~EVvd-G~V~~V-~~~G~Fv~~GP-ld~vFvS~ 77 (79)
||+++ |.|+++ .++|+|+++.| ++ -|++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~-G~i~~ 32 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLL-GFVHI 32 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCE-EEEEH
Confidence 68999 999999 69999999987 64 67764
No 24
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.73 E-value=0.0048 Score=34.69 Aligned_cols=30 Identities=13% Similarity=0.223 Sum_probs=25.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|++++++|+|+++++--..|++.
T Consensus 3 G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~ 32 (72)
T smart00316 3 GDVVEGTVTEITPFGAFVDLGNGVEGLIPI 32 (72)
T ss_pred CCEEEEEEEEEEccEEEEEeCCCCEEEEEH
Confidence 789999999999999999999433477764
No 25
>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=96.73 E-value=0.0029 Score=40.07 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=24.1
Q ss_pred eEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 49 KIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 49 EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|+++|.|++++++|+|+++.|++ .|++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~-G~v~ 27 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVD-GLLH 27 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeE-EEEE
Confidence 68999999999999999999986 5664
No 26
>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=96.69 E-value=0.0045 Score=35.18 Aligned_cols=30 Identities=17% Similarity=0.381 Sum_probs=25.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
++++.|.|++++++|+|+++++-.--|++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~ 30 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHI 30 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEH
Confidence 578999999999999999999765566653
No 27
>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=96.67 E-value=0.0047 Score=36.32 Aligned_cols=28 Identities=18% Similarity=0.497 Sum_probs=23.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS 76 (79)
|++++|.|++|+++|+|+++++ ++ -|++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~-g~i~ 29 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIK-GLVP 29 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcE-EEEE
Confidence 6899999999999999999965 54 6664
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=96.65 E-value=0.0062 Score=35.90 Aligned_cols=28 Identities=18% Similarity=0.386 Sum_probs=23.7
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS 76 (79)
|++++|.|++++++|+|+++.| .+ -|++
T Consensus 4 g~~~~g~V~~i~~~G~fv~l~~~~~-Gl~~ 32 (72)
T cd05689 4 GTRLFGKVTNLTDYGCFVELEEGVE-GLVH 32 (72)
T ss_pred CCEEEEEEEEEEeeEEEEEcCCCCE-EEEE
Confidence 7899999999999999999986 44 4544
No 29
>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=96.56 E-value=0.0048 Score=36.18 Aligned_cols=29 Identities=24% Similarity=0.546 Sum_probs=25.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|++++++|+|++++-++ .|+..
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~-gfip~ 29 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVR-AFLPA 29 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEEH
Confidence 689999999999999999996564 78764
No 30
>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=96.55 E-value=0.0038 Score=37.14 Aligned_cols=30 Identities=23% Similarity=0.483 Sum_probs=26.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|++++|.|.++++.|+|+++|..+ .|++.+
T Consensus 4 g~iV~G~V~~~~~~~~~vdig~~e-g~lp~~ 33 (67)
T cd04455 4 GEIVTGIVKRVDRGNVIVDLGKVE-AILPKK 33 (67)
T ss_pred CCEEEEEEEEEcCCCEEEEcCCeE-EEeeHH
Confidence 789999999999999999999876 677653
No 31
>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=96.54 E-value=0.0056 Score=37.42 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=24.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|.+|.|.|.+++++|+|++++|----||+
T Consensus 4 G~~V~g~V~~i~~~G~fV~l~~~v~G~v~ 32 (74)
T cd05705 4 GQLLRGYVSSVTKQGVFFRLSSSIVGRVL 32 (74)
T ss_pred CCEEEEEEEEEeCCcEEEEeCCCCEEEEE
Confidence 78999999999999999999984346665
No 32
>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=96.50 E-value=0.0069 Score=35.42 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=24.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~~ 78 (79)
|+++.|.|+++.++|+|+++++ ++ .|++.+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~-gli~~s 31 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVK-GFLPKS 31 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCE-EEEEHH
Confidence 6789999999999999999975 54 676643
No 33
>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=96.42 E-value=0.0062 Score=38.44 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=33.7
Q ss_pred eeccce-eEEEEEeEeeeeCC--ceEEcCCCceEEEEEec
Q 034902 11 KSTKDL-GCYLAVTTLESTGE--GKVRENAGEMLFPVVFI 47 (79)
Q Consensus 11 ~~~~~~-G~iv~V~~i~~i~~--G~I~~gdG~~~~~V~f~ 47 (79)
|...++ |+++|.-|+..+++ |+|.+++|.++++|+|+
T Consensus 42 ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~ 81 (89)
T cd04328 42 KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISAD 81 (89)
T ss_pred hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEE
Confidence 566788 99999999999866 99999999999999997
No 34
>PRK08582 hypothetical protein; Provisional
Probab=96.42 E-value=0.0082 Score=41.16 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=24.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|++++|.|++|+++|+||+++|----+|+
T Consensus 6 G~iv~G~V~~I~~fG~fV~L~~~~~GlVh 34 (139)
T PRK08582 6 GSKLQGKVTGITNFGAFVELPEGKTGLVH 34 (139)
T ss_pred CCEEEEEEEEEECCeEEEEECCCCEEEEE
Confidence 89999999999999999999874334554
No 35
>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=96.41 E-value=0.0069 Score=35.58 Aligned_cols=28 Identities=21% Similarity=0.457 Sum_probs=23.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeC--CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV--SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G--Pld~vFvS 76 (79)
++++.|.|++++++|+|+++. +++ -++.
T Consensus 3 g~~v~g~V~~i~~~g~~v~l~~~~~~-g~i~ 32 (77)
T cd05708 3 GQKIDGTVRRVEDYGVFIDIDGTNVS-GLCH 32 (77)
T ss_pred CCEEEEEEEEEEcceEEEEECCCCeE-EEEE
Confidence 689999999999999999998 465 3443
No 36
>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=96.39 E-value=0.0087 Score=35.08 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=23.7
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|+++.|.|++|.++|+|+++++----|++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~ 29 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVR 29 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEE
Confidence 57999999999999999999863235554
No 37
>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=96.34 E-value=0.009 Score=36.45 Aligned_cols=29 Identities=17% Similarity=0.406 Sum_probs=24.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~ 77 (79)
|++++|.|++|+++|+|++++ +++ .|+..
T Consensus 15 G~i~~g~V~~v~~~G~fv~l~~~~~-g~v~~ 44 (83)
T cd04461 15 GMVVHGYVRNITPYGVFVEFLGGLT-GLAPK 44 (83)
T ss_pred CCEEEEEEEEEeeceEEEEcCCCCE-EEEEH
Confidence 899999999999999999995 564 67654
No 38
>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=96.31 E-value=0.013 Score=34.64 Aligned_cols=30 Identities=23% Similarity=0.115 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+++.|.|++++++|+|+++++--..|++.
T Consensus 4 G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~ 33 (73)
T cd05706 4 GDILPGRVTKVNDRYVLVQLGNKVTGPSFI 33 (73)
T ss_pred CCEEEEEEEEEeCCeEEEEeCCCcEEEEEh
Confidence 789999999999999999998643466654
No 39
>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=95.92 E-value=0.023 Score=33.09 Aligned_cols=29 Identities=21% Similarity=0.406 Sum_probs=24.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~ 77 (79)
|+++.|.|++|..+|+|++++ +++ -|++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~-g~i~~ 30 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVE-GFLRA 30 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCE-EEEEH
Confidence 679999999999999999995 454 56653
No 40
>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=95.89 E-value=0.027 Score=34.26 Aligned_cols=30 Identities=27% Similarity=0.473 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+.++|.|++++++|+|+++.|-..-|+..
T Consensus 17 G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~ 46 (77)
T cd04473 17 GKLYKGKVNGVAKYGVFVDLNDHVRGLIHR 46 (77)
T ss_pred CCEEEEEEEeEecceEEEEECCCcEEEEEc
Confidence 889999999999999999998733456554
No 41
>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=95.83 E-value=0.022 Score=36.04 Aligned_cols=30 Identities=23% Similarity=0.373 Sum_probs=25.7
Q ss_pred CeEEEEEEEEEeee--eEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKH--GVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~--G~Fv~~GPld~vFvS~ 77 (79)
|+++.|.|+++.++ |+|++++|=.--||+.
T Consensus 8 G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~ 39 (88)
T cd04453 8 GNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHL 39 (88)
T ss_pred CCEEEEEEEEeccCCcEEEEEeCCCCEEEEEh
Confidence 88999999999997 9999999833477764
No 42
>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=95.80 E-value=0.026 Score=33.05 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=24.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~ 77 (79)
|+++.|.|+++.++|+|+++|+ .+ .|++.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~-g~l~~ 30 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSE-GIIPI 30 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCce-EEEEH
Confidence 6899999999999999999984 54 56653
No 43
>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=95.78 E-value=0.02 Score=33.99 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=23.3
Q ss_pred CeEEEEEEEEEeeeeEEEEe-CCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC-VSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~-GPld~vFvS 76 (79)
|.+++|.|+++.++|+|+++ +-++ -|+.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~-g~v~ 29 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFT-GTVD 29 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCce-EEEE
Confidence 57899999999999999998 4476 5664
No 44
>PRK07252 hypothetical protein; Provisional
Probab=95.67 E-value=0.028 Score=37.69 Aligned_cols=29 Identities=14% Similarity=0.297 Sum_probs=24.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~ 77 (79)
|+++.|.|++|+++|+|+++.+ .+ -|++.
T Consensus 4 G~iv~G~V~~V~~~G~fVei~~~~~-Gllhi 33 (120)
T PRK07252 4 GDKLKGTITGIKPYGAFVALENGTT-GLIHI 33 (120)
T ss_pred CCEEEEEEEEEeCcEEEEEECCCCE-EEEEH
Confidence 7899999999999999999964 54 56553
No 45
>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=95.65 E-value=0.03 Score=33.73 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=24.1
Q ss_pred CeEEEEEEEEEee-eeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLK-HGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~-~G~Fv~~GPld~vFvS 76 (79)
|++++|.|+++.+ +|+|++++|=-.-+++
T Consensus 4 G~iv~G~V~~i~~~~g~~v~l~~~~~Glvh 33 (72)
T cd05704 4 GAVTLGMVTKVIPHSGLTVQLPFGKTGLVS 33 (72)
T ss_pred CCEEEEEEEEeeCCcEEEEECCCCCEEEEE
Confidence 7899999999986 9999999875445554
No 46
>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=95.57 E-value=0.023 Score=34.42 Aligned_cols=28 Identities=18% Similarity=0.285 Sum_probs=23.5
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS 76 (79)
|.++.|.|++++++|+|++++| ++ -|++
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~-G~i~ 29 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVK-GRIP 29 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcE-EEEE
Confidence 4689999999999999999987 54 5554
No 47
>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=95.56 E-value=0.035 Score=32.70 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=23.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC---CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS---IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP---ld~vFvS~ 77 (79)
|+++.|.|+++.++|+|+++.+ ++ .|++.
T Consensus 4 G~~~~g~V~~v~~~g~~v~l~~~~~~~-gll~~ 35 (76)
T cd04452 4 GELVVVTVKSIADMGAYVSLLEYGNIE-GMILL 35 (76)
T ss_pred CCEEEEEEEEEEccEEEEEEcCCCCeE-EEEEh
Confidence 6899999999999999999963 55 56553
No 48
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.40 E-value=0.018 Score=47.62 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=24.6
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceE
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMS 73 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~v 73 (79)
|++++|+|.+++.||+|+.+|=+||+
T Consensus 193 G~vV~G~V~~It~~GafVdigGvdGL 218 (541)
T COG0539 193 GEVVEGVVKNITDYGAFVDIGGVDGL 218 (541)
T ss_pred CceEEEEEEEeecCcEEEEecCeeeE
Confidence 99999999999999999999999854
No 49
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=95.32 E-value=0.024 Score=45.97 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=27.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|+++.|.|++++++|+|+++|.++ .||+.+
T Consensus 209 G~iv~G~V~~i~~~G~FVdlggv~-Glv~~S 238 (486)
T PRK07899 209 GQVRKGVVSSIVNFGAFVDLGGVD-GLVHVS 238 (486)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEEHH
Confidence 999999999999999999999987 677643
No 50
>PRK05807 hypothetical protein; Provisional
Probab=95.27 E-value=0.037 Score=37.75 Aligned_cols=29 Identities=21% Similarity=0.416 Sum_probs=24.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|+.++++|+||++...+ -+|+.
T Consensus 6 G~vv~G~Vt~i~~~GafV~L~~~~-Glvhi 34 (136)
T PRK05807 6 GSILEGTVVNITNFGAFVEVEGKT-GLVHI 34 (136)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEEh
Confidence 899999999999999999996553 55553
No 51
>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=94.98 E-value=0.013 Score=48.98 Aligned_cols=54 Identities=24% Similarity=0.409 Sum_probs=40.5
Q ss_pred eEeeeeCCceEEcCCCceEEEE---------Eec-CeEEEEEEEEEeeeeEEEEeCC-CceEEEec
Q 034902 23 TTLESTGEGKVRENAGEMLFPV---------VFI-GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 23 ~~i~~i~~G~I~~gdG~~~~~V---------~f~-~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~ 77 (79)
++|++.|..+|...++..+..+ .++ |++++|.|++|.+||+|+++.| .+ -|++.
T Consensus 584 I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~-GllHi 648 (684)
T TIGR03591 584 IDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKD-GLVHI 648 (684)
T ss_pred EEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcE-EEEEH
Confidence 4566677777777777765544 112 9999999999999999999977 54 56654
No 52
>PRK08059 general stress protein 13; Validated
Probab=94.93 E-value=0.065 Score=35.59 Aligned_cols=29 Identities=17% Similarity=0.269 Sum_probs=24.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|+++.|.|+++.++|+|+++++--.-|+.
T Consensus 8 G~iv~G~V~~i~~~G~fV~i~~~~~Gli~ 36 (123)
T PRK08059 8 GSVVTGKVTGIQPYGAFVALDEETQGLVH 36 (123)
T ss_pred CCEEEEEEEEEecceEEEEECCCCEEEEE
Confidence 89999999999999999999863234554
No 53
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=94.84 E-value=0.035 Score=38.70 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=19.1
Q ss_pred CeEEEEEEEEEeeeeEEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~ 67 (79)
|++++|.|+.+++|||||++
T Consensus 6 G~~l~GkItgI~~yGAFV~l 25 (129)
T COG1098 6 GSKLKGKITGITPYGAFVEL 25 (129)
T ss_pred cceEEEEEEeeEecceEEEe
Confidence 89999999999999999986
No 54
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=94.80 E-value=0.065 Score=29.41 Aligned_cols=27 Identities=22% Similarity=0.207 Sum_probs=22.2
Q ss_pred EEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 51 FQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 51 vdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
++|.|++++++|+|+++++-...|++.
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~ 27 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHI 27 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEH
Confidence 479999999999999999544577764
No 55
>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=94.69 E-value=0.078 Score=32.30 Aligned_cols=28 Identities=18% Similarity=0.145 Sum_probs=24.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS 76 (79)
|++|+|.|+++.++|+|++++ +++ -|++
T Consensus 7 GdiV~g~V~~i~~~g~~v~i~~~~~-G~l~ 35 (86)
T cd05789 7 GDVVIGRVTEVGFKRWKVDINSPYD-AVLP 35 (86)
T ss_pred CCEEEEEEEEECCCEEEEECCCCeE-EEEE
Confidence 899999999999999999998 454 4554
No 56
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=94.58 E-value=0.15 Score=40.99 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=25.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~ 77 (79)
|+++.|.|++++++|+|++++| ++ .|++.
T Consensus 293 G~~v~G~V~~v~~~G~fV~l~~gv~-Glvh~ 322 (491)
T PRK13806 293 GDKVTGKVVRLAPFGAFVEILPGIE-GLVHV 322 (491)
T ss_pred CCEEEEEEEEEeCceEEEEeCCCcE-EEEEH
Confidence 9999999999999999999986 54 56664
No 57
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=94.38 E-value=0.065 Score=41.01 Aligned_cols=28 Identities=21% Similarity=0.452 Sum_probs=25.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
|++++|.|++++++|+|++++.++ -|++
T Consensus 197 G~vv~G~V~~I~~~G~fV~i~gv~-Gllh 224 (318)
T PRK07400 197 GEVVVGTVRGIKPYGAFIDIGGVS-GLLH 224 (318)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEE
Confidence 999999999999999999999886 5554
No 58
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=94.24 E-value=0.074 Score=40.72 Aligned_cols=29 Identities=21% Similarity=0.524 Sum_probs=26.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|++++++|+|++++.++ .|++.
T Consensus 193 G~~v~g~V~~v~~~G~fV~l~~v~-g~v~~ 221 (390)
T PRK06676 193 GDVVEGTVARLTDFGAFVDIGGVD-GLVHI 221 (390)
T ss_pred CCEEEEEEEEEecceEEEEeCCeE-EEEEH
Confidence 999999999999999999999886 67764
No 59
>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=94.22 E-value=0.086 Score=31.16 Aligned_cols=28 Identities=11% Similarity=0.259 Sum_probs=22.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS 76 (79)
|.++.|.|+++.++|+|++++ .++ -+++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~-g~i~ 29 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVH-GRIH 29 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcE-EEEE
Confidence 579999999999999999997 343 4443
No 60
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=94.05 E-value=0.084 Score=41.17 Aligned_cols=28 Identities=11% Similarity=0.223 Sum_probs=24.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeC---CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV---SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G---Pld~vFvS 76 (79)
|++|.|.|++|.+||+||.++ -++ -||+
T Consensus 18 GdvV~g~V~~I~d~GafV~L~EY~gvE-GlIh 48 (319)
T PTZ00248 18 DDLVMVKVVRITEMGAYVSLLEYDDIE-GMIL 48 (319)
T ss_pred CCEEEEEEEEEeCCeEEEEecCCCCcE-EEEE
Confidence 999999999999999999994 577 4444
No 61
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=94.05 E-value=0.077 Score=42.60 Aligned_cols=29 Identities=24% Similarity=0.497 Sum_probs=25.5
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~ 77 (79)
|++++|.|++++++|+|++++ .++ .|++.
T Consensus 374 G~~v~g~V~~v~~~G~fV~l~~~v~-g~i~~ 403 (565)
T PRK06299 374 GDVVEGKVKNITDFGAFVGLEGGID-GLVHL 403 (565)
T ss_pred CCEEEEEEEEEecceEEEECCCCCE-EEEEH
Confidence 999999999999999999998 675 56654
No 62
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=93.85 E-value=0.091 Score=42.17 Aligned_cols=29 Identities=24% Similarity=0.565 Sum_probs=26.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|+++.++|+|+++|.++ .|++.
T Consensus 202 G~iv~g~V~~v~~~G~~V~i~g~~-glv~~ 230 (565)
T PRK06299 202 GQVVEGVVKNITDYGAFVDLGGVD-GLLHI 230 (565)
T ss_pred CCEEEEEEEEEeCCeEEEEECCEE-EEEEH
Confidence 999999999999999999999887 66654
No 63
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=93.74 E-value=0.097 Score=41.34 Aligned_cols=28 Identities=25% Similarity=0.506 Sum_probs=25.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS 76 (79)
|+++.|.|++++++|+|+++| .++ .|++
T Consensus 360 G~~v~g~V~~v~~~G~fV~l~~~v~-glv~ 388 (516)
T TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGID-GLIH 388 (516)
T ss_pred CCEEEEEEEEEecceEEEECCCCCE-EEEE
Confidence 999999999999999999999 565 6665
No 64
>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=92.94 E-value=0.15 Score=40.29 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=26.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|++++|.|.++.++|+|+++|.++ .|++.+
T Consensus 188 G~~v~g~V~~i~~~G~~V~l~g~~-g~lp~~ 217 (516)
T TIGR00717 188 GDVVKGVVKNITDFGAFVDLGGVD-GLLHIT 217 (516)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEEHH
Confidence 899999999999999999999886 677653
No 65
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=92.63 E-value=0.21 Score=29.60 Aligned_cols=31 Identities=16% Similarity=0.051 Sum_probs=19.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|++....|++.+++|+|+..|...-+|+.++
T Consensus 2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~ 32 (61)
T PF13509_consen 2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKS 32 (61)
T ss_dssp -------EEEE-SSEEEEEETT-EEEEEEGG
T ss_pred CCCcceEEEEEeCCEEEEECCCCCEEEechH
Confidence 5677889999999999999999777998764
No 66
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=92.58 E-value=0.16 Score=42.30 Aligned_cols=22 Identities=18% Similarity=0.523 Sum_probs=21.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS 69 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP 69 (79)
|++++|.|++|+++|+||++.|
T Consensus 628 G~~~~g~V~~v~~fGifV~L~~ 649 (709)
T TIGR02063 628 GEEFEGVISGVTSFGLFVELEN 649 (709)
T ss_pred CcEEEEEEEEEEeCCEEEEecC
Confidence 8999999999999999999987
No 67
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=92.58 E-value=0.57 Score=33.03 Aligned_cols=51 Identities=18% Similarity=0.105 Sum_probs=31.5
Q ss_pred EEEEEeEeeeeC-CceEEcCCCceEEEEEec-CeEEEEEEEEEeeeeEEEEeC
Q 034902 18 CYLAVTTLESTG-EGKVRENAGEMLFPVVFI-GKIFQGIVHKMLKHGVLFNCV 68 (79)
Q Consensus 18 ~iv~V~~i~~i~-~G~I~~gdG~~~~~V~f~-~EVvdG~V~~V~~~G~Fv~~G 68 (79)
++-++..+.++. +.+.+.=++...+.-.++ |++|.|.|+++..+|+|++++
T Consensus 33 i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~ 85 (189)
T PRK09521 33 VYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIV 85 (189)
T ss_pred EEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEE
Confidence 344555665543 232221122222233333 999999999999999999997
No 68
>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=92.39 E-value=0.24 Score=42.38 Aligned_cols=29 Identities=31% Similarity=0.457 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~ 77 (79)
|++++|.|++|.+||+|++++| .+ -+|+.
T Consensus 648 G~i~~GkV~~I~dfGaFVel~~G~e-GLvHI 677 (719)
T TIGR02696 648 GERFLGTVVKTTAFGAFVSLLPGKD-GLLHI 677 (719)
T ss_pred CCEEEEEEEEEECceEEEEecCCce-EEEEh
Confidence 9999999999999999999987 55 55543
No 69
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=92.33 E-value=0.23 Score=39.88 Aligned_cols=30 Identities=17% Similarity=0.505 Sum_probs=25.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS~~ 78 (79)
|++++|.|+++.++|+|++++| ++ .||+.+
T Consensus 203 G~iv~G~V~~v~~~G~fV~l~~gv~-g~v~~s 233 (491)
T PRK13806 203 GDVVEGTVTRLAPFGAFVELAPGVE-GMVHIS 233 (491)
T ss_pred CCEEEEEEEEEeCCeEEEEcCCCcE-EEEEHH
Confidence 9999999999999999999975 65 687643
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=92.29 E-value=0.28 Score=41.25 Aligned_cols=30 Identities=20% Similarity=0.459 Sum_probs=25.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|++|.+||+|+++.|-.--+|+.
T Consensus 622 G~v~~G~V~~I~~fGafVei~~~~~Gllhi 651 (693)
T PRK11824 622 GEIYEGKVVRIVDFGAFVEILPGKDGLVHI 651 (693)
T ss_pred CeEEEEEEEEEECCeEEEEECCCCEEEEEe
Confidence 999999999999999999998743456554
No 71
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=91.81 E-value=0.25 Score=42.85 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=26.5
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|++++|.|.+++++|+|+++|-++ -|++.|
T Consensus 494 G~~V~G~Vk~i~~~G~fVdl~Gv~-Gfvp~S 523 (863)
T PRK12269 494 EDSVSGVVKSFTSFGAFIDLGGFD-GLLHVN 523 (863)
T ss_pred CCEEEEEEEEEeCCcEEEEECCEE-EEEEch
Confidence 689999999999999999998886 787654
No 72
>PRK11642 exoribonuclease R; Provisional
Probab=91.11 E-value=0.28 Score=42.17 Aligned_cols=22 Identities=18% Similarity=0.546 Sum_probs=21.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS 69 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP 69 (79)
|++++|+|++|+++|+||++.+
T Consensus 644 Ge~f~G~Is~V~~fGifVeL~~ 665 (813)
T PRK11642 644 GNVFKGVISSVTGFGFFVRLDD 665 (813)
T ss_pred CcEEEEEEEEeecCceEEEECC
Confidence 9999999999999999999986
No 73
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.78 E-value=0.47 Score=36.32 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=25.9
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++|.|+++.+.|+|+.+|.-..-|++.
T Consensus 32 G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~ 61 (318)
T PRK07400 32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPI 61 (318)
T ss_pred CCEEEEEEEEEECCEEEEEECCCeEEEEEH
Confidence 999999999999999999999843467764
No 74
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=90.76 E-value=0.43 Score=35.02 Aligned_cols=30 Identities=20% Similarity=0.271 Sum_probs=26.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~~ 78 (79)
|++|.|.|++++..|+|++++ |++ .|++.+
T Consensus 64 GDiViG~V~~i~~~~~~vdI~~~~~-g~L~~s 94 (235)
T PRK04163 64 GDLVIGKVTDVTFSGWEVDINSPYK-AYLPVS 94 (235)
T ss_pred CCEEEEEEEEEeCceEEEEeCCCce-eEEEHH
Confidence 999999999999999999999 676 566643
No 75
>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=90.63 E-value=0.77 Score=27.71 Aligned_cols=29 Identities=21% Similarity=0.212 Sum_probs=24.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS~ 77 (79)
|.+|.|.|+++...++++++| +.+ .|++.
T Consensus 7 GdiV~G~V~~v~~~~~~V~i~~~~~-g~l~~ 36 (82)
T cd04454 7 GDIVIGIVTEVNSRFWKVDILSRGT-ARLED 36 (82)
T ss_pred CCEEEEEEEEEcCCEEEEEeCCCce-EEeec
Confidence 889999999999999999997 443 55554
No 76
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=89.89 E-value=0.44 Score=39.49 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=26.2
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+++.|.|++++++|+|++++.++ .|++.
T Consensus 478 G~iV~g~V~~v~~~G~fV~l~gv~-Gll~~ 506 (647)
T PRK00087 478 GDVVEGEVKRLTDFGAFVDIGGVD-GLLHV 506 (647)
T ss_pred CCEEEEEEEEEeCCcEEEEECCEE-EEEEH
Confidence 999999999999999999998886 67754
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=89.38 E-value=0.54 Score=38.99 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=27.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
|+++.|.|+++++.|+|+++|-++ .|++.+
T Consensus 390 G~iv~g~V~~v~~~G~~V~lggi~-gfiP~s 419 (647)
T PRK00087 390 GEPVKGKVKEVVKGGLLVDYGGVR-AFLPAS 419 (647)
T ss_pred CCEEEEEEEEEECCeEEEEECCEE-EEEEHH
Confidence 899999999999999999999886 888653
No 78
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=89.25 E-value=0.46 Score=41.25 Aligned_cols=28 Identities=21% Similarity=0.420 Sum_probs=24.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC-CceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS-IDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP-ld~vFvS 76 (79)
|++++|.|+++.+||+|++++| ++| +|+
T Consensus 579 G~iV~G~V~~I~~fG~fVeL~~gveG-Lvh 607 (863)
T PRK12269 579 NDVVKGRVTKIADFGAFIELAEGIEG-LAH 607 (863)
T ss_pred CCEEEEEEEEEeCCeEEEEecCCcee-eeE
Confidence 8999999999999999999986 653 454
No 79
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=89.23 E-value=0.68 Score=34.86 Aligned_cols=28 Identities=18% Similarity=0.483 Sum_probs=23.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeC---CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV---SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G---Pld~vFvS 76 (79)
|+++.|.|++|.++|+|+++. .++ -|++
T Consensus 9 GdiV~G~V~~I~~~G~fV~L~e~~gie-GlI~ 39 (262)
T PRK03987 9 GELVVGTVKEVKDFGAFVTLDEYPGKE-GFIH 39 (262)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCcE-EEEE
Confidence 899999999999999999995 355 4554
No 80
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=88.12 E-value=0.67 Score=37.68 Aligned_cols=30 Identities=17% Similarity=0.438 Sum_probs=26.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
||+|.|+|.++++.|+|+++|-.+ .|+.++
T Consensus 135 GeIV~G~V~ri~~~giiVDLggve-a~LP~s 164 (470)
T PRK09202 135 GEIITGVVKRVERGNIIVDLGRAE-AILPRK 164 (470)
T ss_pred CCEEEEEEEEEecCCEEEEECCeE-EEecHH
Confidence 899999999999999999999886 677643
No 81
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=87.97 E-value=0.87 Score=39.97 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=24.9
Q ss_pred CeEEE-EEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQ-GIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvd-G~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|++++ |.|++|.+||+||++.|----+|+.
T Consensus 754 G~iy~~g~V~~I~~FGaFVeL~~g~EGLVHI 784 (891)
T PLN00207 754 GDIYRNCEIKSIAPYGAFVEIAPGREGLCHI 784 (891)
T ss_pred CcEEECcEEEEEeccEEEEEeCCCCEEEEEh
Confidence 99996 6999999999999998854466654
No 82
>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=87.89 E-value=1.1 Score=28.83 Aligned_cols=28 Identities=18% Similarity=0.398 Sum_probs=23.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeC-CCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV-SIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G-Pld~vFvS 76 (79)
|.+|.|.|++|.++|+|+.+. .++ -|++
T Consensus 4 G~vV~G~V~~v~~~gl~v~L~~g~~-G~v~ 32 (100)
T cd05693 4 GMLVLGQVKEITKLDLVISLPNGLT-GYVP 32 (100)
T ss_pred CCEEEEEEEEEcCCCEEEECCCCcE-EEEE
Confidence 679999999999999999995 454 5554
No 83
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=86.86 E-value=0.77 Score=38.26 Aligned_cols=30 Identities=17% Similarity=0.211 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
+.++.|.|++++.+|+|++++|==--||+-
T Consensus 278 g~~v~G~Vt~i~~~GafVei~~GvEGlvhv 307 (541)
T COG0539 278 GDKVEGKVTNLTDYGAFVEIEEGVEGLVHV 307 (541)
T ss_pred CCEEEEEEEEeecCcEEEEecCCccceeec
Confidence 999999999999999999999843345543
No 84
>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=86.24 E-value=1.3 Score=36.84 Aligned_cols=21 Identities=19% Similarity=0.433 Sum_probs=20.4
Q ss_pred CeEEEEEEEEEeeeeEEEEeC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCV 68 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~G 68 (79)
|++++|.|++|+++|+||++.
T Consensus 573 G~~~~g~I~~v~~~GifV~L~ 593 (654)
T TIGR00358 573 GTEFSGEISSVTRFGMFVRLD 593 (654)
T ss_pred CcEEEEEEEeEEcCcEEEEec
Confidence 899999999999999999997
No 85
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=86.05 E-value=0.93 Score=39.36 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=26.7
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|-+++|.|.+|.+||+||.+|--+...|+-
T Consensus 659 Gm~leg~Vrnv~~fgafVdIgv~qDglvHi 688 (780)
T COG2183 659 GMILEGTVRNVVDFGAFVDIGVHQDGLVHI 688 (780)
T ss_pred CCEEEEEEEEeeeccceEEeccccceeeeH
Confidence 889999999999999999999877776654
No 86
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.61 E-value=1.5 Score=35.81 Aligned_cols=32 Identities=25% Similarity=0.314 Sum_probs=26.0
Q ss_pred ec-CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 46 FI-GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 46 f~-~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+ |++|+|.|++|.+.|+|+++|+----||+.
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~ 65 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPS 65 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEH
Confidence 45 999999999999999999999632356653
No 87
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.39 E-value=1.7 Score=33.24 Aligned_cols=30 Identities=20% Similarity=0.137 Sum_probs=25.0
Q ss_pred CeEEEEEEEEEeeeeEEEEe-CCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNC-VSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~-GPld~vFvS~ 77 (79)
|+++.|.|+++++.|+|+++ |+---.|++.
T Consensus 18 G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~ 48 (390)
T PRK06676 18 GDVVTGEVLKVEDKQVFVNIEGYKVEGVIPI 48 (390)
T ss_pred CCEEEEEEEEEECCeEEEEEecCCcEEEEEH
Confidence 89999999999999999999 7433367764
No 88
>PHA02945 interferon resistance protein; Provisional
Probab=85.05 E-value=1.3 Score=29.08 Aligned_cols=19 Identities=16% Similarity=0.322 Sum_probs=18.2
Q ss_pred CeEEEEEEEEEeeeeEEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~ 67 (79)
||++-|.|.+ ..+|||+.+
T Consensus 12 GelvigtV~~-~d~ga~v~L 30 (88)
T PHA02945 12 GDVLKGKVYE-NGYALYIDL 30 (88)
T ss_pred CcEEEEEEEe-cCceEEEEe
Confidence 9999999999 999999986
No 89
>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=83.50 E-value=2 Score=34.37 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=28.5
Q ss_pred CeEEEEEEEEEeee--eEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKH--GVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~--G~Fv~~GPld~vFvS~~ 78 (79)
|.+..|.|.+|.+. ||||++|+=...|++-+
T Consensus 26 GnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~ 58 (414)
T TIGR00757 26 GNIYKGRVTRILPSLQAAFVDIGLEKNGFLHAS 58 (414)
T ss_pred CCEEEEEEeeecCCCceEEEEcCCCceEEEEHH
Confidence 89999999999999 99999999888998754
No 90
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=82.98 E-value=2.1 Score=36.78 Aligned_cols=31 Identities=16% Similarity=0.456 Sum_probs=26.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~~ 78 (79)
||+.+|.|+.+.+||+|+++-|=.--.+|.|
T Consensus 620 g~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS 650 (692)
T COG1185 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHIS 650 (692)
T ss_pred ccEEEEEEEEEeecceEEEecCCcceeEEeh
Confidence 9999999999999999999999765565543
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=82.36 E-value=1.9 Score=34.01 Aligned_cols=29 Identities=28% Similarity=0.351 Sum_probs=26.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
|+++.|.|.++++.|+|+++|-.+ .|+.+
T Consensus 135 GeiV~G~V~~~~~~~~~Vdlg~vE-a~LP~ 163 (362)
T PRK12327 135 GDIVTGVVQRRDNRFVYVNLGKIE-AVLPP 163 (362)
T ss_pred CCEEEEEEEEEeCCcEEEEeCCeE-EEecH
Confidence 999999999999999999999887 57653
No 92
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=78.60 E-value=2.4 Score=32.71 Aligned_cols=23 Identities=22% Similarity=0.340 Sum_probs=20.6
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSI 70 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPl 70 (79)
||+|=|.|.+|.+||+|+.+=-.
T Consensus 12 GEiVv~tV~~V~~~GAyv~L~EY 34 (269)
T COG1093 12 GEIVVGTVKQVADYGAYVELDEY 34 (269)
T ss_pred CcEEEEEEEEeeccccEEEeecc
Confidence 99999999999999999987443
No 93
>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=78.45 E-value=3 Score=32.64 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=25.2
Q ss_pred CeEEEEEEEEEeeeeE-EEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGV-LFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~-Fv~~GPld~vFvS~ 77 (79)
||+|.|.|.++++.|+ |+++|-.+ .|+++
T Consensus 132 GeiV~G~V~~v~~~g~v~VdiG~~e-a~LP~ 161 (341)
T TIGR01953 132 GEIISGTVKRVNRRGNLYVELGKTE-GILPK 161 (341)
T ss_pred CCEEEEEEEEEecCCcEEEEECCeE-EEecH
Confidence 9999999999999994 99999776 66654
No 94
>PRK05054 exoribonuclease II; Provisional
Probab=76.97 E-value=2.9 Score=34.93 Aligned_cols=21 Identities=10% Similarity=0.197 Sum_probs=19.1
Q ss_pred eEEEEEEEEEeeeeEEEEeCC
Q 034902 49 KIFQGIVHKMLKHGVLFNCVS 69 (79)
Q Consensus 49 EVvdG~V~~V~~~G~Fv~~GP 69 (79)
+..+|.|+.|+++|+||++-.
T Consensus 563 ~~f~g~I~~v~~~G~fV~l~~ 583 (644)
T PRK05054 563 TRFAAEIIDISRGGMRVRLLE 583 (644)
T ss_pred eEEEEEEEeeecCcEEEEEeC
Confidence 599999999999999999954
No 95
>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=75.97 E-value=7.6 Score=23.99 Aligned_cols=29 Identities=10% Similarity=0.246 Sum_probs=23.2
Q ss_pred EEEEEEEEEee----eeEEEEeC-------CCceEEEecC
Q 034902 50 IFQGIVHKMLK----HGVLFNCV-------SIDMSYLHEN 78 (79)
Q Consensus 50 VvdG~V~~V~~----~G~Fv~~G-------Pld~vFvS~~ 78 (79)
.++|+|+.+.. .|||+.-. +.+++||...
T Consensus 1 ~v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~ 40 (78)
T cd04486 1 TVEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTG 40 (78)
T ss_pred CeEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecC
Confidence 37899999988 79999874 3678999643
No 96
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=66.01 E-value=7.6 Score=32.71 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=20.1
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS 69 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP 69 (79)
+|..+|.|+.|+++|+|+++=.
T Consensus 623 g~~f~g~V~~v~~~g~~V~l~~ 644 (706)
T COG0557 623 GEEFDGVVTGVTSFGFFVELPE 644 (706)
T ss_pred CCEEEEEEEEEEeccEEEEecc
Confidence 8999999999999999998744
No 97
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=64.59 E-value=8.1 Score=30.14 Aligned_cols=31 Identities=10% Similarity=-0.084 Sum_probs=25.7
Q ss_pred CeEEEEEEEEEe-eeeEEEEeCCCceEEEecC
Q 034902 48 GKIFQGIVHKML-KHGVLFNCVSIDMSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~-~~G~Fv~~GPld~vFvS~~ 78 (79)
+|-==++|++|+ +.|+|+..|==.-++||.+
T Consensus 74 g~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~ 105 (287)
T COG2996 74 GEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLD 105 (287)
T ss_pred cceeEEEEEEEcCCcceEEecCCCcceeeehh
Confidence 777778999999 9999999994445888864
No 98
>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=62.38 E-value=9.1 Score=32.09 Aligned_cols=19 Identities=11% Similarity=0.186 Sum_probs=17.7
Q ss_pred eEEEEEEEEEeeeeEEEEe
Q 034902 49 KIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 49 EVvdG~V~~V~~~G~Fv~~ 67 (79)
+..+|+|+.++++|+||++
T Consensus 559 ~~f~g~I~~v~~~g~~v~l 577 (639)
T TIGR02062 559 TRFAAEIVDISRGGMRVRL 577 (639)
T ss_pred cEEEEEEEeeeCCcEEEEE
Confidence 4899999999999999997
No 99
>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=53.19 E-value=34 Score=18.99 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=16.4
Q ss_pred CeEEEEEEEEEeeeeEEE
Q 034902 48 GKIFQGIVHKMLKHGVLF 65 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv 65 (79)
++.++|.+..+.+.|+.+
T Consensus 12 ~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 12 DGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp SCEEEEEEEEEETTSEEE
T ss_pred CeEEEEEEEEECCCCEEE
Confidence 888899999999999875
No 100
>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=52.74 E-value=25 Score=22.05 Aligned_cols=23 Identities=22% Similarity=0.242 Sum_probs=21.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSI 70 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPl 70 (79)
|.+|+|.|.+-++-+++++++|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~ 23 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPE 23 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCC
Confidence 46899999999999999999994
No 101
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=46.49 E-value=61 Score=24.93 Aligned_cols=48 Identities=21% Similarity=0.299 Sum_probs=38.2
Q ss_pred ccceeEEEEEeEeeeeC-CceEEcCCCceEEEEEec--------CeEEEEEEEEEee
Q 034902 13 TKDLGCYLAVTTLESTG-EGKVRENAGEMLFPVVFI--------GKIFQGIVHKMLK 60 (79)
Q Consensus 13 ~~~~G~iv~V~~i~~i~-~G~I~~gdG~~~~~V~f~--------~EVvdG~V~~V~~ 60 (79)
.+=.|++++.-+|+..+ .++|.+.|+...-.+.=+ |.+++|.|-.|..
T Consensus 64 ~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~ 120 (253)
T KOG4134|consen 64 SGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDILEGVVNHVSR 120 (253)
T ss_pred cCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCeeeeeeeecch
Confidence 35579999999998755 489999999877665544 9999999987754
No 102
>PF08729 HUN: HPC2 and ubinuclein domain; InterPro: IPR014840 HPC2 is required for cell-cycle regulation of histone transcription []. It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex, which allows RNA Pol II to elongate through nucleosomes [].
Probab=45.79 E-value=11 Score=22.12 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=13.4
Q ss_pred EEEeeeeEEEEeCCCc
Q 034902 56 HKMLKHGVLFNCVSID 71 (79)
Q Consensus 56 ~~V~~~G~Fv~~GPld 71 (79)
.....-|||+..|||+
T Consensus 39 ~~~~~~GFfv~~G~le 54 (55)
T PF08729_consen 39 VTTKHGGFFVNSGELE 54 (55)
T ss_pred hhhhcCCceEeccccc
Confidence 4567889999999985
No 103
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=44.72 E-value=39 Score=22.13 Aligned_cols=19 Identities=0% Similarity=-0.111 Sum_probs=17.2
Q ss_pred CeEEEEEEEEEeeeeEEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~ 67 (79)
++++. .|+.+.++||++++
T Consensus 17 ~dvv~-~Vv~i~d~~~YV~L 35 (86)
T PHA02858 17 NEVTK-GIVFVKDNIFYVKL 35 (86)
T ss_pred CeEEE-EEEEEeccEEEEEE
Confidence 89999 88899999999876
No 104
>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=41.86 E-value=51 Score=21.01 Aligned_cols=30 Identities=17% Similarity=0.017 Sum_probs=24.6
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
+.+|=|.|+++.--..++++|+-...+++.
T Consensus 7 gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~ 36 (86)
T cd05790 7 GDHVIGIVVAKAGDFFKVDIGGSEPASLSY 36 (86)
T ss_pred CCEEEEEEEEEcCCeEEEEcCCCcceEech
Confidence 788999999999999999997654455543
No 105
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=35.68 E-value=80 Score=19.94 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=14.3
Q ss_pred EEEEEEEEee--eeEEEEe------CCCceEEEecCC
Q 034902 51 FQGIVHKMLK--HGVLFNC------VSIDMSYLHENA 79 (79)
Q Consensus 51 vdG~V~~V~~--~G~Fv~~------GPld~vFvS~~~ 79 (79)
++|+.. +.. +||.-.. ||-| +|||.+.
T Consensus 3 ~~GvLe-i~~dGyGFLR~~~~~y~~~~~D-vYVs~~q 37 (78)
T PF07497_consen 3 VEGVLE-ILPDGYGFLRSPDNNYLPSPDD-VYVSPSQ 37 (78)
T ss_dssp EEEEEE-E-TTS-EEEE-GGGTTS-STTS-EEE-CCC
T ss_pred EEEEEE-ECCCCcEEeECCCcCCCCCCCC-EEECHHH
Confidence 455554 443 5554443 7998 9999763
No 106
>PF08634 Pet127: Mitochondrial protein Pet127; InterPro: IPR013943 Pet127 has been implicated in mitochondrial RNA stability and/or processing and is localised to the mitochondrial membrane [].
Probab=32.68 E-value=15 Score=28.50 Aligned_cols=14 Identities=7% Similarity=0.000 Sum_probs=12.5
Q ss_pred EEeCCCceEEEecC
Q 034902 65 FNCVSIDMSYLHEN 78 (79)
Q Consensus 65 v~~GPld~vFvS~~ 78 (79)
||+|-||||||.=|
T Consensus 216 aRIG~MDGIFVAYH 229 (274)
T PF08634_consen 216 ARIGRMDGIFVAYH 229 (274)
T ss_pred HHHccCceEEEeee
Confidence 89999999999865
No 107
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=28.43 E-value=25 Score=30.47 Aligned_cols=22 Identities=41% Similarity=0.659 Sum_probs=20.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVS 69 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GP 69 (79)
+++-.|.|+.|.++|+|+++-+
T Consensus 123 g~~Y~g~v~~v~~~GvFv~Ln~ 144 (715)
T COG1107 123 GKYYKGIVSRVEKYGVFVELNS 144 (715)
T ss_pred ceeeeccccchhhhcceeecCh
Confidence 9999999999999999998754
No 108
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=27.71 E-value=90 Score=25.10 Aligned_cols=28 Identities=25% Similarity=0.326 Sum_probs=23.3
Q ss_pred CeEEEEEEEEEeee-eEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKH-GVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~-G~Fv~~GPld~vFvS 76 (79)
||++.|+|..+.+. .+|+++|-.+ .++.
T Consensus 139 Geiv~g~V~r~~~~~~i~vdlg~~e-a~LP 167 (374)
T PRK12328 139 GKIVFGTVVRVDNEENTFIEIDEIR-AVLP 167 (374)
T ss_pred CcEEEEEEEEEecCCCEEEEcCCeE-EEeC
Confidence 99999999999975 5999999876 5544
No 109
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=27.44 E-value=1.3e+02 Score=23.56 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=26.0
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCc-eEEEecC
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSID-MSYLHEN 78 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld-~vFvS~~ 78 (79)
|+....+|.+.+++|.|...|--+ .++++++
T Consensus 6 G~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~ 37 (287)
T COG2996 6 GQINSLEVVEFSDFGYFLDAGEDGTTILLPKS 37 (287)
T ss_pred cceEEEEEEEeeceeEEEecCCCceEEecccc
Confidence 677889999999999999998873 4777765
No 110
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=24.64 E-value=61 Score=25.54 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=18.9
Q ss_pred CeEEEEEEEEEeeeeEEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~ 67 (79)
.|+|=+-|.++.++|+|+++
T Consensus 17 ~e~VmvnV~sIaemGayv~L 36 (304)
T KOG2916|consen 17 EEIVMVNVRSIAEMGAYVKL 36 (304)
T ss_pred ccEEEEEeeEehhccceEee
Confidence 89999999999999999986
No 111
>PF07364 DUF1485: Protein of unknown function (DUF1485); InterPro: IPR015995 Proteins in this entry are involved in degradation of the cyanobacterial heptapeptide hepatotoxin microcystin LR, and are encoded in the mlr gene cluster []. MlrC from Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) is believed to mediate the last step of peptidolytic degradation of the tetrapeptide. It is suspected to be a metallopeptidase based on homology to known peptidases and its inhibition by metal chelators. The proteins encoded by the mlr cluster may be involved in cell wall peptidoglycan cycling and subsequently act fortuitously in hydrolysis of microcystin LR. This entry represents the N-terminal region of these proteins.; PDB: 3IUU_A.
Probab=23.14 E-value=45 Score=25.52 Aligned_cols=12 Identities=17% Similarity=0.097 Sum_probs=6.8
Q ss_pred eCCCceEEEecC
Q 034902 67 CVSIDMSYLHEN 78 (79)
Q Consensus 67 ~GPld~vFvS~~ 78 (79)
.||+|+||++-|
T Consensus 94 agp~Dgv~L~LH 105 (292)
T PF07364_consen 94 AGPLDGVLLDLH 105 (292)
T ss_dssp S---SEEEEEE-
T ss_pred cCCcCEEEEecc
Confidence 389999999876
No 112
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=22.52 E-value=1.8e+02 Score=17.24 Aligned_cols=30 Identities=17% Similarity=0.112 Sum_probs=24.8
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEec
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLHE 77 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS~ 77 (79)
--|++|.|+=..+-|.=..++|=|.+|+.+
T Consensus 29 ~~vleG~v~it~~~G~~~~~~aGD~~~~p~ 58 (74)
T PF05899_consen 29 FYVLEGEVTITDEDGETVTFKAGDAFFLPK 58 (74)
T ss_dssp EEEEEEEEEEEETTTEEEEEETTEEEEE-T
T ss_pred EEEEEeEEEEEECCCCEEEEcCCcEEEECC
Confidence 458999999999999999999999777654
No 113
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=22.49 E-value=1.3e+02 Score=17.20 Aligned_cols=18 Identities=11% Similarity=-0.001 Sum_probs=14.6
Q ss_pred EEEEEEEEEeeeeEEEEe
Q 034902 50 IFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 50 VvdG~V~~V~~~G~Fv~~ 67 (79)
-+.+.|..+.-.|..+++
T Consensus 6 ~l~a~V~~v~~~G~~vRl 23 (58)
T PF12857_consen 6 GLPARVRRVRPVGPEVRL 23 (58)
T ss_pred cEeEEEEEEEecCCeEEE
Confidence 367889999999988765
No 114
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=22.14 E-value=1.4e+02 Score=28.73 Aligned_cols=29 Identities=17% Similarity=0.379 Sum_probs=26.3
Q ss_pred CeEEEEEEEEEeeeeEEEEeCCCceEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNCVSIDMSYLH 76 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~GPld~vFvS 76 (79)
+++++|-|.+|...|+|+.+||---.|+.
T Consensus 1163 g~iv~G~V~nv~~~glfi~ls~~v~a~v~ 1191 (1710)
T KOG1070|consen 1163 GDIVRGFVKNVETKGLFIALSRKVEAFVP 1191 (1710)
T ss_pred CceeEEEEEEecCCcEEEEEccceEEEEE
Confidence 99999999999999999999997666664
No 115
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=21.64 E-value=1.5e+02 Score=16.57 Aligned_cols=17 Identities=18% Similarity=0.100 Sum_probs=12.9
Q ss_pred EEEEEEEEEeeeeEEEE
Q 034902 50 IFQGIVHKMLKHGVLFN 66 (79)
Q Consensus 50 VvdG~V~~V~~~G~Fv~ 66 (79)
.+.|.|.++...|.+++
T Consensus 8 ~l~g~I~~i~~~g~~~~ 24 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAE 24 (69)
T ss_pred EEEEEEEEEEECCCeEE
Confidence 47889999988777643
No 116
>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=20.55 E-value=1.8e+02 Score=18.17 Aligned_cols=20 Identities=15% Similarity=0.107 Sum_probs=18.8
Q ss_pred CeEEEEEEEEEeeeeEEEEe
Q 034902 48 GKIFQGIVHKMLKHGVLFNC 67 (79)
Q Consensus 48 ~EVvdG~V~~V~~~G~Fv~~ 67 (79)
|.+|-|.|++++..-+.+++
T Consensus 7 GDiVig~V~~v~~~~~~v~I 26 (92)
T cd05791 7 GSIVIARVTRINPRFAKVDI 26 (92)
T ss_pred CCEEEEEEEEEcCCEEEEEE
Confidence 78999999999999999988
Done!