Query 005219
Match_columns 708
No_of_seqs 279 out of 1124
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 19:59:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005219.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005219hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11712 ribonuclease G; Provi 100.0 8E-122 2E-126 1017.3 54.7 457 74-663 1-488 (489)
2 PRK10811 rne ribonuclease E; R 100.0 8E-113 2E-117 977.0 53.3 458 76-668 2-493 (1068)
3 TIGR00757 RNaseEG ribonuclease 100.0 5E-112 1E-116 925.2 46.6 398 88-617 1-402 (414)
4 COG1530 CafA Ribonucleases G a 100.0 2.1E-98 5E-103 833.3 41.8 451 75-666 1-485 (487)
5 PF10150 RNase_E_G: Ribonuclea 100.0 2.6E-80 5.6E-85 644.3 25.4 270 318-599 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.6 9.5E-16 2.1E-20 135.5 8.7 40 108-147 3-42 (88)
7 PF00575 S1: S1 RNA binding do 97.6 0.00023 5E-09 59.8 7.9 36 110-147 2-37 (74)
8 cd04472 S1_PNPase S1_PNPase: P 97.3 0.00086 1.9E-08 54.8 7.1 33 113-147 1-33 (68)
9 COG1098 VacB Predicted RNA bin 97.1 0.00076 1.6E-08 63.9 5.3 35 111-147 4-38 (129)
10 cd05704 S1_Rrp5_repeat_hs13 S1 97.0 0.0021 4.6E-08 54.7 7.1 35 112-147 3-37 (72)
11 cd05692 S1_RPS1_repeat_hs4 S1_ 96.9 0.0037 7.9E-08 50.8 7.5 33 113-147 1-33 (69)
12 smart00316 S1 Ribosomal protei 96.9 0.0032 7E-08 50.8 7.0 34 112-147 2-35 (72)
13 cd05698 S1_Rrp5_repeat_hs6_sc5 96.6 0.0072 1.6E-07 50.3 6.9 33 113-147 1-33 (70)
14 cd05685 S1_Tex S1_Tex: The C-t 96.5 0.0067 1.5E-07 49.2 6.2 33 113-147 1-33 (68)
15 cd04461 S1_Rrp5_repeat_hs8_sc7 96.4 0.0098 2.1E-07 51.5 6.9 36 110-147 12-47 (83)
16 PRK07252 hypothetical protein; 96.4 0.011 2.3E-07 55.9 7.6 34 112-147 3-36 (120)
17 PTZ00248 eukaryotic translatio 96.4 0.075 1.6E-06 58.0 14.7 34 112-147 17-52 (319)
18 cd05707 S1_Rrp5_repeat_sc11 S1 96.3 0.012 2.7E-07 48.8 6.4 33 113-147 1-33 (68)
19 PRK08059 general stress protei 96.2 0.014 3.1E-07 54.8 7.2 36 110-147 5-40 (123)
20 cd05684 S1_DHX8_helicase S1_DH 96.2 0.018 3.8E-07 49.4 7.1 33 113-147 1-36 (79)
21 cd05687 S1_RPS1_repeat_ec1_hs1 96.2 0.019 4E-07 47.9 6.9 33 113-147 1-33 (70)
22 cd05706 S1_Rrp5_repeat_sc10 S1 96.0 0.032 6.9E-07 46.8 7.8 34 112-147 3-36 (73)
23 cd05697 S1_Rrp5_repeat_hs5 S1_ 95.8 0.031 6.7E-07 46.6 6.7 33 113-147 1-33 (69)
24 cd05686 S1_pNO40 S1_pNO40: pNO 95.8 0.045 9.7E-07 46.5 7.6 34 112-147 3-37 (73)
25 cd04452 S1_IF2_alpha S1_IF2_al 95.6 0.049 1.1E-06 45.8 7.1 34 112-147 3-38 (76)
26 cd05691 S1_RPS1_repeat_ec6 S1_ 95.5 0.05 1.1E-06 45.2 7.0 33 113-147 1-33 (73)
27 PRK08582 hypothetical protein; 95.5 0.046 1E-06 52.8 7.4 35 111-147 4-38 (139)
28 COG0539 RpsA Ribosomal protein 95.5 0.029 6.2E-07 64.9 7.0 36 109-147 189-224 (541)
29 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.4 0.058 1.3E-06 45.8 6.9 34 113-147 1-35 (71)
30 cd05688 S1_RPS1_repeat_ec3 S1_ 95.1 0.06 1.3E-06 43.8 6.1 33 112-147 1-33 (68)
31 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.1 0.1 2.2E-06 45.4 7.7 35 111-147 5-39 (86)
32 TIGR02696 pppGpp_PNP guanosine 94.7 0.054 1.2E-06 64.6 6.5 59 87-147 608-680 (719)
33 TIGR03591 polynuc_phos polyrib 94.7 0.067 1.4E-06 63.8 7.2 37 109-147 615-651 (684)
34 PRK05807 hypothetical protein; 94.6 0.14 2.9E-06 49.4 7.9 34 111-147 4-37 (136)
35 cd05705 S1_Rrp5_repeat_hs14 S1 94.5 0.12 2.5E-06 44.5 6.4 35 111-147 2-36 (74)
36 PRK03987 translation initiatio 94.4 0.2 4.3E-06 53.4 9.3 35 111-147 7-43 (262)
37 cd05694 S1_Rrp5_repeat_hs2_sc2 94.4 0.16 3.4E-06 43.9 7.0 34 111-146 3-37 (74)
38 cd05708 S1_Rrp5_repeat_sc12 S1 94.3 0.17 3.7E-06 42.3 7.0 34 112-147 2-36 (77)
39 cd04454 S1_Rrp4_like S1_Rrp4_l 94.2 0.22 4.8E-06 43.0 7.5 34 111-146 5-38 (82)
40 PRK11824 polynucleotide phosph 94.1 0.14 3E-06 61.2 8.3 36 110-147 619-654 (693)
41 cd04455 S1_NusA S1_NusA: N-uti 94.1 0.22 4.8E-06 41.7 7.2 33 111-146 2-34 (67)
42 PRK09521 exosome complex RNA-b 93.6 0.49 1.1E-05 47.6 10.0 36 109-146 61-106 (189)
43 cd00164 S1_like S1_like: Ribos 93.6 0.18 4E-06 39.7 5.5 30 116-147 1-30 (65)
44 PRK04163 exosome complex RNA-b 93.1 0.75 1.6E-05 48.1 10.6 45 101-147 50-96 (235)
45 PLN00207 polyribonucleotide nu 92.4 0.28 6E-06 60.0 7.2 35 111-147 752-787 (891)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 90.8 0.27 5.9E-06 40.5 3.5 33 113-147 1-33 (69)
47 PRK14865 rnpA ribonuclease P; 90.6 1.3 2.9E-05 41.4 8.3 53 333-385 49-110 (116)
48 cd05689 S1_RPS1_repeat_ec4 S1_ 90.4 0.41 8.8E-06 40.0 4.2 34 112-147 3-36 (72)
49 PRK07400 30S ribosomal protein 90.4 0.65 1.4E-05 50.6 6.9 36 110-147 29-64 (318)
50 PRK13806 rpsA 30S ribosomal pr 90.2 0.71 1.5E-05 53.1 7.3 37 109-147 199-235 (491)
51 PRK07899 rpsA 30S ribosomal pr 89.7 0.76 1.7E-05 53.0 7.0 35 110-147 206-240 (486)
52 PRK07400 30S ribosomal protein 89.0 1.1 2.3E-05 49.0 7.2 39 106-147 190-228 (318)
53 PRK00588 rnpA ribonuclease P; 88.8 2 4.3E-05 40.5 8.0 53 333-385 47-109 (118)
54 TIGR01953 NusA transcription t 88.2 6 0.00013 43.9 12.4 108 290-441 169-279 (341)
55 cd05702 S1_Rrp5_repeat_hs11_sc 87.8 0.73 1.6E-05 38.6 4.0 33 113-147 1-33 (70)
56 PRK06299 rpsA 30S ribosomal pr 87.8 1.2 2.7E-05 51.6 7.2 36 109-147 198-233 (565)
57 PRK13806 rpsA 30S ribosomal pr 87.6 1.4 3E-05 50.8 7.4 38 108-147 288-325 (491)
58 cd04471 S1_RNase_R S1_RNase_R: 87.2 0.78 1.7E-05 39.0 3.9 34 112-147 1-35 (83)
59 cd04465 S1_RPS1_repeat_ec2_hs2 87.0 0.73 1.6E-05 38.2 3.5 32 113-147 1-32 (67)
60 TIGR00717 rpsA ribosomal prote 86.3 1.9 4.1E-05 49.4 7.5 36 110-147 357-392 (516)
61 COG0539 RpsA Ribosomal protein 86.2 2 4.4E-05 50.2 7.7 68 76-147 243-310 (541)
62 PRK12269 bifunctional cytidyla 86.1 2.5 5.5E-05 52.0 8.8 39 107-147 573-611 (863)
63 PRK00396 rnpA ribonuclease P; 86.1 3.6 7.9E-05 39.6 8.2 58 333-393 50-117 (130)
64 PRK03459 rnpA ribonuclease P; 85.8 4.4 9.6E-05 38.5 8.5 54 332-385 51-114 (122)
65 cd04473 S1_RecJ_like S1_RecJ_l 84.7 1.3 2.9E-05 38.0 4.1 36 110-147 14-49 (77)
66 PRK06299 rpsA 30S ribosomal pr 84.6 2.3 5E-05 49.4 7.3 36 110-147 371-406 (565)
67 PRK07899 rpsA 30S ribosomal pr 84.2 2.6 5.5E-05 48.8 7.3 36 110-147 291-326 (486)
68 PRK12269 bifunctional cytidyla 83.8 2.5 5.5E-05 52.0 7.4 35 110-147 491-525 (863)
69 PRK00499 rnpA ribonuclease P; 83.2 6.6 0.00014 36.6 8.3 54 333-386 42-105 (114)
70 PRK06676 rpsA 30S ribosomal pr 83.1 3.1 6.7E-05 46.1 7.2 35 110-147 190-224 (390)
71 TIGR00717 rpsA ribosomal prote 83.1 2.6 5.6E-05 48.3 6.8 36 110-147 270-305 (516)
72 PRK04390 rnpA ribonuclease P; 82.9 6.6 0.00014 37.1 8.3 53 333-385 48-110 (120)
73 PRK09202 nusA transcription el 82.4 2.9 6.4E-05 48.2 6.8 109 290-442 171-282 (470)
74 PRK01313 rnpA ribonuclease P; 82.2 6.7 0.00015 37.8 8.1 52 333-384 51-113 (129)
75 PRK06676 rpsA 30S ribosomal pr 79.4 5.6 0.00012 44.1 7.6 36 110-147 15-51 (390)
76 cd05693 S1_Rrp5_repeat_hs1_sc1 79.3 2.1 4.6E-05 39.1 3.5 35 111-147 2-36 (100)
77 PRK01903 rnpA ribonuclease P; 78.5 13 0.00027 36.0 8.7 53 333-385 54-129 (133)
78 PRK00730 rnpA ribonuclease P; 77.9 10 0.00022 37.2 7.8 53 332-385 49-110 (138)
79 COG1185 Pnp Polyribonucleotide 77.8 2.1 4.4E-05 51.1 3.7 39 107-147 614-652 (692)
80 PRK04820 rnpA ribonuclease P; 75.7 15 0.00032 36.2 8.4 53 333-385 52-114 (145)
81 COG2183 Tex Transcriptional ac 75.5 4.3 9.4E-05 49.1 5.6 37 109-147 655-691 (780)
82 PRK00087 4-hydroxy-3-methylbut 75.3 6.1 0.00013 47.1 6.8 35 110-147 475-509 (647)
83 PRK01492 rnpA ribonuclease P; 74.9 13 0.00028 35.1 7.6 53 332-384 49-115 (118)
84 PRK01732 rnpA ribonuclease P; 74.2 10 0.00023 35.5 6.7 53 333-385 49-111 (114)
85 TIGR00188 rnpA ribonuclease P 73.4 10 0.00022 34.8 6.4 51 333-383 45-104 (105)
86 PRK00038 rnpA ribonuclease P; 72.8 20 0.00044 34.3 8.3 58 332-389 53-121 (123)
87 PRK12327 nusA transcription el 71.7 8.7 0.00019 43.0 6.5 32 111-145 133-164 (362)
88 cd05703 S1_Rrp5_repeat_hs12_sc 71.0 5.3 0.00012 34.1 3.7 33 113-147 1-33 (73)
89 PRK03031 rnpA ribonuclease P; 69.6 27 0.00058 33.0 8.4 53 333-385 51-114 (122)
90 PRK00087 4-hydroxy-3-methylbut 66.9 15 0.00032 43.9 7.5 36 110-147 560-595 (647)
91 COG0594 RnpA RNase P protein c 66.1 32 0.00069 32.5 8.1 53 333-385 45-107 (117)
92 TIGR02063 RNase_R ribonuclease 62.6 17 0.00036 44.0 6.9 35 111-147 626-661 (709)
93 PRK11642 exoribonuclease R; Pr 62.1 20 0.00042 44.3 7.4 35 111-147 642-677 (813)
94 cd05791 S1_CSL4 S1_CSL4: CSL4, 61.8 11 0.00024 33.9 4.0 37 111-149 5-49 (92)
95 PF00825 Ribonuclease_P: Ribon 61.6 21 0.00046 32.8 6.0 53 333-385 46-109 (111)
96 cd05695 S1_Rrp5_repeat_hs3 S1_ 60.2 38 0.00083 28.3 6.7 32 113-146 1-32 (66)
97 TIGR00358 3_prime_RNase VacB a 53.4 31 0.00067 41.4 7.0 35 111-147 571-606 (654)
98 cd04460 S1_RpoE S1_RpoE: RpoE, 53.2 17 0.00037 32.6 3.8 31 115-148 2-32 (99)
99 COG2996 Predicted RNA-bindinin 53.2 28 0.0006 37.8 5.8 37 110-147 71-107 (287)
100 PRK12328 nusA transcription el 48.7 41 0.00088 38.0 6.5 188 290-536 176-368 (374)
101 PF00013 KH_1: KH domain syndr 47.5 43 0.00093 27.0 4.9 37 615-651 2-38 (60)
102 TIGR00448 rpoE DNA-directed RN 41.0 35 0.00077 34.1 4.2 35 110-147 79-113 (179)
103 cd00105 KH-I K homology RNA-bi 39.0 85 0.0019 25.1 5.5 39 615-653 2-40 (64)
104 PHA02945 interferon resistance 30.8 1.6E+02 0.0035 27.0 6.2 32 112-146 11-44 (88)
105 PRK08563 DNA-directed RNA poly 30.0 1.3E+02 0.0028 30.2 6.1 35 110-147 79-113 (187)
106 TIGR02499 HrpE_YscL_not type I 29.7 1.3E+02 0.0029 28.9 6.0 45 613-663 114-158 (166)
107 PF08800 VirE_N: VirE N-termin 29.0 1.2E+02 0.0026 29.2 5.5 52 541-597 26-78 (136)
108 COG1093 SUI2 Translation initi 28.7 49 0.0011 35.7 3.0 34 111-146 10-45 (269)
109 PF02108 FliH: Flagellar assem 27.9 2.1E+02 0.0046 26.0 6.8 45 613-663 68-112 (128)
110 KOG2925 Predicted translation 27.9 32 0.00069 34.3 1.4 25 480-504 52-76 (167)
111 PRK06937 type III secretion sy 27.2 1.1E+02 0.0023 31.3 5.1 47 613-663 131-179 (204)
112 PRK06032 fliH flagellar assemb 25.9 1.5E+02 0.0032 30.3 5.9 46 614-663 129-176 (199)
113 TIGR03598 GTPase_YsxC ribosome 25.5 2.1E+02 0.0047 27.6 6.7 48 540-587 125-172 (179)
114 PRK09098 type III secretion sy 24.4 1.4E+02 0.0031 31.4 5.6 47 613-663 151-199 (233)
115 PRK12329 nusA transcription el 24.0 1.9E+02 0.0042 33.5 6.9 24 110-135 150-173 (449)
116 cd05790 S1_Rrp40 S1_Rrp40: Rrp 22.5 1.2E+02 0.0026 27.4 3.9 33 111-145 5-37 (86)
117 PF04472 DUF552: Protein of un 22.5 1.7E+02 0.0036 25.2 4.7 41 531-575 10-50 (73)
118 cd06828 PLPDE_III_DapDC Type I 21.9 5.6E+02 0.012 27.9 9.8 150 410-574 74-241 (373)
119 cd02394 vigilin_like_KH K homo 21.8 1.2E+02 0.0025 24.6 3.4 38 615-652 2-39 (62)
120 COG3585 MopI Molybdopterin-bin 21.4 62 0.0013 28.2 1.7 23 112-134 5-27 (69)
121 PRK04163 exosome complex RNA-b 21.2 4.6E+02 0.01 27.6 8.6 108 567-692 106-214 (235)
122 cd04508 TUDOR Tudor domains ar 21.1 1.1E+02 0.0025 23.3 3.1 27 113-139 12-40 (48)
123 cd05792 S1_eIF1AD_like S1_eIF1 21.1 59 0.0013 29.0 1.7 23 479-501 29-51 (78)
124 PF07013 DUF1314: Protein of u 21.0 73 0.0016 32.4 2.4 36 478-517 4-39 (177)
125 PF11314 DUF3117: Protein of u 20.8 70 0.0015 26.3 1.8 15 486-500 22-36 (51)
No 1
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=8.4e-122 Score=1017.32 Aligned_cols=457 Identities=30% Similarity=0.500 Sum_probs=416.4
Q ss_pred CceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcC
Q 005219 74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF 153 (708)
Q Consensus 74 m~keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~ 153 (708)
|+++||||+.+ .++|+|++|||+|+||++|+.+...++||||+|+|+||+|||||||||||.+|+||||++|..+++.+
T Consensus 1 M~~~i~i~~~~-~e~r~Alledg~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~ 79 (489)
T PRK11712 1 MTAELLVNVTP-SETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTEC 79 (489)
T ss_pred CceEEEEecCC-CeEEEEEEECCEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhh
Confidence 88999999987 69999999999999999999999999999999999999999999999999999999999986321100
Q ss_pred CcccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 005219 154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD 233 (708)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (708)
.. . ++. .
T Consensus 80 ~~------~-----------------------------------------------~~~-------------~------- 86 (489)
T PRK11712 80 VA------G-----------------------------------------------EEQ-------------K------- 86 (489)
T ss_pred cc------c-----------------------------------------------ccc-------------c-------
Confidence 00 0 000 0
Q ss_pred CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCcee
Q 005219 234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL 313 (708)
Q Consensus 234 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprL 313 (708)
. .. ..++...|++||+|||||+|||+|+|||+|
T Consensus 87 --------------------------------~-~~--------------~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~l 119 (489)
T PRK11712 87 --------------------------------Q-FV--------------VRDISELVRQGQDIMVQVVKDPLGTKGARL 119 (489)
T ss_pred --------------------------------c-cc--------------cccHHHhccCCCEEEEEEEeCCcCCCCCeE
Confidence 0 00 012346799999999999999999999999
Q ss_pred eecceecceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 005219 314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH 392 (708)
Q Consensus 314 Tt~IsL~GRylVl~P~~~~igiSrKI~~~-eR~rLk~i~~~l~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~ 392 (708)
|++|||||||+||||+++++||||||+++ +|+||+.++..+.++++|+||||+|+++++++|.+|+++|.++|++|.++
T Consensus 120 T~~Isl~GrylVl~P~~~~vgiSrKI~de~~R~rLk~i~~~~~~~~~GvIiRT~A~~a~~eel~~dl~~L~~~w~~i~~~ 199 (489)
T PRK11712 120 TTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQGGFIIRTAAEGVGEEELAQDAAFLKRLWTKVMER 199 (489)
T ss_pred EEEEEeccceEEEECCCCCeeEecCCCChHHHHHHHHHHHhhCCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999886 69999999999988889999999999999999999999999999999999
Q ss_pred HHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccCCCCcccc
Q 005219 393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472 (708)
Q Consensus 393 ~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~~~plF~~ 472 (708)
++.+ ++|+|||++.+++.+++||++++++++|+||+++.|+++++|+..++|+...++++|++..|||+.
T Consensus 200 ~~~~----------~~p~ll~~e~~~~~~~lrD~~~~~~~~IivD~~~~~~~i~~~~~~~~p~~~~~v~~y~~~~plF~~ 269 (489)
T PRK11712 200 KKRY----------QTRYQLYGELALAQRVLRDFVGAELDRIRVDSRLTYEELKEFTSEYIPEMTDKLEHYSGRQPIFDL 269 (489)
T ss_pred HhcC----------CCCeEEEcCCcHHHHHHHHhccCCCCEEEECCHHHHHHHHHHHHHhCccccceeEEecCCCChhHh
Confidence 9875 589999999999999999999999999999999999999999999999998999999999999999
Q ss_pred cCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 005219 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (708)
Q Consensus 473 y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVID 552 (708)
|||+.+|+++++++||||||||||||+||||||||||||++ .|+.++++|+++||+|||+||||||||||||||||||
T Consensus 270 y~ie~~i~~~l~~~V~L~sGg~lvIe~TeAlt~IDVnsGk~--~~~~~~eet~~~tN~eAa~eiarqlrLR~igGiIviD 347 (489)
T PRK11712 270 YDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGAF--VGHRNLEETIFNTNIEATQAIARQLRLRNLGGIIIID 347 (489)
T ss_pred cCHHHHHHHHhcCcEEcCCCcEEEEeccccEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEE
Confidence 99999999999999999999999999999999999999984 5677899999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccccCC--CCCC--------------------
Q 005219 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADP--ENPK-------------------- 610 (708)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~--~~~~-------------------- 610 (708)
||||+++++|++|+++|+++|++|+++++|+|||+||||||||||.+.++.... .||+
T Consensus 348 FidM~~~~~r~~v~~~l~~~l~~D~~k~~v~~~T~lGLvEmTRkR~r~sl~~~l~~~Cp~C~G~G~v~s~e~~~~~i~r~ 427 (489)
T PRK11712 348 FIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVLCGECPTCHGRGTVKTVETVCYEIMRE 427 (489)
T ss_pred CCCCCCHHHHHHHHHHHHHHhhcCCCCceEcccCCCceEEEEecccCCChHHHhcCCCCCCCCCCCcCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999876543222 2332
Q ss_pred --------CCCeEEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCCCCCCcCeEEEE
Q 005219 611 --------SWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 611 --------~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~~l~~~~~~i~~ 663 (708)
..+.+++++||.|++||.+.++.++..|+.++|.++.|.+++.+++++|+|..
T Consensus 428 i~~~~~~~~~~~~~~~~~p~v~~~l~~~~~~~~~~le~~~g~~i~i~~~~~~~~~~~~i~~ 488 (489)
T PRK11712 428 IVRVHHAYDSDRFLVYASPAVAEALKGEESHALAELEIFVGKQVKVQIEPLYNQEQFDVVM 488 (489)
T ss_pred HHHHHhhCCCceEEEEECHHHHHHHHccchHHHHHHHHHhCCeEEEEECCCCCccceEEEe
Confidence 13458999999999999998888999999999999999999999999999864
No 2
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=7.9e-113 Score=976.96 Aligned_cols=458 Identities=31% Similarity=0.545 Sum_probs=416.8
Q ss_pred eEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCCc
Q 005219 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP 155 (708)
Q Consensus 76 keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~~~ 155 (708)
++||||.....+.|+||++||+|.||+||+......+||||+|||+||+|||+|||||||.+++|||+++|+..+++...
T Consensus 2 kkIiIn~~~~~e~RvALvEdgrL~EL~IEr~~~e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~ 81 (1068)
T PRK10811 2 KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPAN 81 (1068)
T ss_pred cEEEEeccCCceEEEEEEcCCEEEEEEeccCccccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccc
Confidence 78999998446899999999999999999988888999999999999999999999999999999999999743321000
Q ss_pred ccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCC
Q 005219 156 FRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGE 235 (708)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (708)
+.
T Consensus 82 ~~------------------------------------------------------------------------------ 83 (1068)
T PRK10811 82 YS------------------------------------------------------------------------------ 83 (1068)
T ss_pred cc------------------------------------------------------------------------------
Confidence 00
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeee
Q 005219 236 PEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTA 315 (708)
Q Consensus 236 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprLTt 315 (708)
.+ ...++...|++||+|||||+||++++|||+||+
T Consensus 84 --------------------------------~~-------------~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 84 --------------------------------AH-------------GRPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred --------------------------------cc-------------cccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 00 001233569999999999999999999999999
Q ss_pred cceecceeEEEeeCCCc-eeeecCCChHHHHHHHHHHHhh-CCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 005219 316 YPKLRSRFWILITSCDR-IGVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (708)
Q Consensus 316 ~IsL~GRylVl~P~~~~-igiSrKI~~~eR~rLk~i~~~l-~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~~ 393 (708)
+|||+||||||||++++ +||||||++++|.+|+.++..+ .++++|+||||+|+|++.++|.+||++|...|+.|++++
T Consensus 119 ~ISLpGRYLVLtP~~~~~IgISRKI~deeR~rLkeil~~l~lpe~~GIIVRTaAegAseE~L~~ELe~L~~~w~~I~k~a 198 (1068)
T PRK10811 119 FISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAA 198 (1068)
T ss_pred eEEecceeEEEeCCCCCcceecCCCchHHHHHHHHHHHhhccCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998 7999999988899999999987 788999999999999999999999999999999999998
Q ss_pred HHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhh-CCCcCCceeeccCCCCcccc
Q 005219 394 KSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLFDK 472 (708)
Q Consensus 394 ~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~-~p~~~~~v~~y~~~~plF~~ 472 (708)
..+ ++|.|||++.+++.+++|||+..++++|+||+++.|+.++.|+..+ .|++..+|++|.+..|||+.
T Consensus 199 ~~~----------~aP~LLy~e~~~~~ralRD~l~~dv~eIvVDd~e~~e~ik~yl~~~~~pd~~~kI~lY~~~~pLFe~ 268 (1068)
T PRK10811 199 ESR----------PAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSH 268 (1068)
T ss_pred hcC----------CCceEeecCCchHHHHHHHhcccCccEEEECCHHHHHHHHHHHHHhcccccccceeeecCCCChHHh
Confidence 775 5899999999999999999999999999999999999999999988 58877889999999999999
Q ss_pred cCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 005219 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (708)
Q Consensus 473 y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVID 552 (708)
|+|+.+|++||+++||||||||||||+|||||+||||||++ +++.+.++|+|+||++||+||||||||||||||||||
T Consensus 269 YgIE~qIE~aL~rrV~L~sGG~LvIE~TEALtvIDVNSGk~--~~g~d~eet~lktNleAA~EIARQLRLRnLgGIIVID 346 (1068)
T PRK10811 269 YQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARA--TRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVID 346 (1068)
T ss_pred cCHHHHHHHHhCCcEECCCCCEEEEeccceEEEEEccCCCc--CCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEE
Confidence 99999999999999999999999999999999999999985 4567899999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccccCC--CCCC--------------------
Q 005219 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADP--ENPK-------------------- 610 (708)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~--~~~~-------------------- 610 (708)
||||+.++|+++|++.|+++|++|+.+++|++||+||||||||||.+.++.... .||+
T Consensus 347 FIdM~~ee~r~~l~~~L~~al~~D~~k~~v~g~T~LGLvEmTRKR~r~sL~E~l~e~Cp~C~GtG~v~s~etla~~i~R~ 426 (1068)
T PRK10811 347 FIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRL 426 (1068)
T ss_pred CCCCCchHHHHHHHHHHHHHHHhCCCCceEEecccccceEEecccCCCCHHHHhhccCcccCCCcccccHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999876543211 2331
Q ss_pred --------CCCeEEEEECHHHHHHHHcCchhhHHHHH-hhcCCeEEEEeCCCCCCcCeEEEEeecCc
Q 005219 611 --------SWPRFILRVDHHMCNYLTSGKRTRLAVLS-SSLKAWILLKVARGFTRGAFEVIPYTDDK 668 (708)
Q Consensus 611 --------~~~~~~l~v~p~v~~~l~~~~~~~l~~Le-~~~~~~I~i~~d~~l~~~~~~i~~~~~~~ 668 (708)
..+.+.+.++|.+++||+++++..+..|| +.+|+.+.|.+++.+++++|+|.+++..+
T Consensus 427 I~re~~~~~~~~~~i~~~~~va~~l~~~~~~~~~~ie~e~~g~~i~I~~n~~~~~e~y~v~rvr~ge 493 (1068)
T PRK10811 427 IEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQGGVRCVIVPNDQMQTPHYSVLRVRKGE 493 (1068)
T ss_pred HHHHHhhcccccEEEEECHHHHHHHhhhhhhHHHHHhhhhcCceEEEEecCcCCcccceEEEEecCC
Confidence 23679999999999999999999999999 99999999999999999999999999544
No 3
>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=100.00 E-value=5.4e-112 Score=925.20 Aligned_cols=398 Identities=38% Similarity=0.612 Sum_probs=359.6
Q ss_pred EEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCCcccccchhhhccc
Q 005219 88 QRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNG 167 (708)
Q Consensus 88 ~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~~~~~~~~~~~~~~~ 167 (708)
+|+|++|||+|+||++|+.....++||||+|+|++|+|||||||||||.+++||||++|..+++....
T Consensus 1 ~r~Alledg~l~e~~ie~~~~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~------------ 68 (414)
T TIGR00757 1 TRVALVEGGRLFDLIIERPKSRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLA------------ 68 (414)
T ss_pred CEEEEEECCEEEEEEEecCcCcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccc------------
Confidence 59999999999999999999999999999999999999999999999999999999998632110000
Q ss_pred cchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCCCCccccccccCC
Q 005219 168 SASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGD 247 (708)
Q Consensus 168 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 247 (708)
.++.
T Consensus 69 -----------------------------------------~~~~----------------------------------- 72 (414)
T TIGR00757 69 -----------------------------------------PAEA----------------------------------- 72 (414)
T ss_pred -----------------------------------------cccc-----------------------------------
Confidence 0000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeeecceecceeEEEe
Q 005219 248 HHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILI 327 (708)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprLTt~IsL~GRylVl~ 327 (708)
.. + ...++.+.|++||+|+|||+|||+++|||+||++|||||||+|||
T Consensus 73 -----~~--------------~-------------~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~lT~~Isl~GrylVl~ 120 (414)
T TIGR00757 73 -----KR--------------E-------------AGPSISELLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLM 120 (414)
T ss_pred -----cc--------------c-------------ccCCHHHhCcCCCEEEEEEeeCCcCCCCCeEEEEEEeccceEEEe
Confidence 00 0 001234679999999999999999999999999999999999999
Q ss_pred eCCCceeeecCCChH-HHHHHHHHHHh-hCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCC
Q 005219 328 TSCDRIGVSRKITGV-ERTRLKVIAKT-LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVE 405 (708)
Q Consensus 328 P~~~~igiSrKI~~~-eR~rLk~i~~~-l~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~g~~ 405 (708)
|+.+++||||||.++ +|.+|+.++.. +.|+++|+||||+|+++++++|.+|+++|.++|+.|.++++.+
T Consensus 121 P~~~~v~ISrkI~d~~eR~rL~~i~~~~~~~~~~GvIiRT~A~~a~~eel~~el~~L~~~w~~I~~~~~~~--------- 191 (414)
T TIGR00757 121 PNNSHVGVSRRIESGEERERLKKLLRSEELPEGMGLIIRTAAEGASEEALIKDLEFLLRKWEKIKEKAQKR--------- 191 (414)
T ss_pred cCCCCceeecccCCHHHHHHHHHHHHhhccCCCceEEEEeccCCCCHHHHHHHHHHHHHHHHHHHHHHhcC---------
Confidence 999999999999975 69999999995 8889999999999999999999999999999999999999765
Q ss_pred CCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccCCCCcccccCHHHHHHHHhCC
Q 005219 406 GAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSK 485 (708)
Q Consensus 406 ~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~~~plF~~y~Ie~qIe~al~r 485 (708)
++|.|||++++++.+++||++++++++|+||+++.|+++++|++.+.|+...+|++|.+..|||+.|+|+.+|++++++
T Consensus 192 -~~p~ll~~~~~~~~~~lrd~~~~~~~~iivd~~~~~~~~~~~~~~~~p~~~~~v~~y~~~~~lf~~y~ie~~i~~~l~~ 270 (414)
T TIGR00757 192 -PAPCLIYGEPDIIKRVIRDYLDTDIKEILIDSKEIYEEAKEFIQLYAPELVSKLKLYRGSDPLFEGFQIEKQIDKATQR 270 (414)
T ss_pred -CCCeEEEcCCcHHHHHHHHhccCCCCEEEECCHHHHHHHHHHHHHhCcccccceEEecCCCChhHhhCHHHHHHHhcCC
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHH
Q 005219 486 RVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLV 565 (708)
Q Consensus 486 ~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVIDFIDM~~~~~r~~V 565 (708)
+||||||||||||+||||||||||||++ +++.++|+|+++||+|||+||||||||||||||||||||||++++|+++|
T Consensus 271 ~V~L~~Gg~lvIe~TEALtvIDVNsG~~--~~~~~~eet~~~~NleAa~EIaRQlRLRnigGiIvIDFIdM~~~~~~~~v 348 (414)
T TIGR00757 271 KVWLPSGGYIVIDQTEALTTIDVNSGRF--TGGGNLEETALNTNLEAAKEIARQLRLRNLGGIIIIDFIDMKSEKNQRRV 348 (414)
T ss_pred cEECCCCeEEEEecCccEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEEECCCCCCHHHHHHH
Confidence 9999999999999999999999999985 56678999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccccCC--CCCCCCCeEEE
Q 005219 566 YEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADP--ENPKSWPRFIL 617 (708)
Q Consensus 566 ~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~--~~~~~~~~~~l 617 (708)
++.|+++|++|+++++|+|||+||||||||||.+.++.... .||+..++=.+
T Consensus 349 ~~~l~~~~~~D~~k~~v~~~T~lGLvE~TRkr~~~sL~e~~~~~Cp~C~G~G~v 402 (414)
T TIGR00757 349 LERLKEALRRDRARIQISGISEFGLVEMTRKRLRESLMEVLGTVCPHCSGTGIV 402 (414)
T ss_pred HHHHHHHHhcCCCCcEEcccCCCcceEEeccccCcChHHHhcCCCCCCcCeeEE
Confidence 99999999999999999999999999999999987654433 36643343333
No 4
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-98 Score=833.26 Aligned_cols=451 Identities=36% Similarity=0.594 Sum_probs=411.5
Q ss_pred ceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCC
Q 005219 75 STVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFP 154 (708)
Q Consensus 75 ~keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~~ 154 (708)
+++||||+++ +|+|||++++|.|.||++|+....+++||||+|||+||+|||||||||||.+||||||++++.+
T Consensus 1 ~k~~~i~~~~-~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~----- 74 (487)
T COG1530 1 MKKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP----- 74 (487)
T ss_pred CceEEEeccc-ceeEEEEEeCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccch-----
Confidence 4789999999 8999999999999999999999999999999999999999999999999999999999998632
Q ss_pred cccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCC
Q 005219 155 PFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDG 234 (708)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (708)
.|....
T Consensus 75 ~~~~~~-------------------------------------------------------------------------- 80 (487)
T COG1530 75 YFRAVL-------------------------------------------------------------------------- 80 (487)
T ss_pred hhhhcc--------------------------------------------------------------------------
Confidence 110000
Q ss_pred CCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceee
Q 005219 235 EPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLT 314 (708)
Q Consensus 235 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprLT 314 (708)
..++...++.||.++|||+|+|+|+|||+||
T Consensus 81 -------------------------------------------------~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 81 -------------------------------------------------EEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred -------------------------------------------------cccceeeecCCceEEEEEEeecCccccccce
Confidence 0012357999999999999999999999999
Q ss_pred ecceecceeEEEeeCCCcee-eecCCCh-HHHHHHHHHHHhhCCC-CeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 005219 315 AYPKLRSRFWILITSCDRIG-VSRKITG-VERTRLKVIAKTLQPE-GFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME 391 (708)
Q Consensus 315 t~IsL~GRylVl~P~~~~ig-iSrKI~~-~eR~rLk~i~~~l~p~-~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~ 391 (708)
++||++|||+||||+.+++| +|+||++ .+|++||.++..+.+. ++|+|+||+|+|++.++|.+|+++|.+.|+.|+.
T Consensus 112 ~~Is~~grylVl~p~~~~~g~is~ri~~~~er~~Lk~~~~~l~~~~~~g~iiRTa~~g~~~eel~~d~~~l~~~w~~i~~ 191 (487)
T COG1530 112 TDISLAGRYLVLMPNAPDVGGISRRIEGEIERERLKEIVRELVDPGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILE 191 (487)
T ss_pred eEEeeceeEEEEcCCCCcccceeeEeCCHHHHHhHHHHHhhccCcCCceEEEeecccCccHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999998 9999999 5799999999998754 5799999999999999999999999999999999
Q ss_pred HHHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccCCCCccc
Q 005219 392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFD 471 (708)
Q Consensus 392 ~~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~~~plF~ 471 (708)
++.+. ++|.+||++.+++.+++|||+..++.+|+||+...|..+++|+..++|+...++++|.+..|+|+
T Consensus 192 ~~~~~----------~ap~ll~~e~~~v~r~~rd~~~~~~~~I~Vd~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~f~ 261 (487)
T COG1530 192 RAKKR----------PAPGLLYEETSLVVRVIRDYVGKDITEIVVDGKEAYLEAKEFILEIMPELRSKLKLYRGTTPLFA 261 (487)
T ss_pred HhhcC----------CCCeEEEecCcceEEEeeccccCccceEEEcCchHHHHHHHHHHhcChhhhhheEeccCCCcccc
Confidence 98775 58999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEE
Q 005219 472 KFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVV 551 (708)
Q Consensus 472 ~y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVI 551 (708)
.|+++.+|+++++|+|||||||||||++|||||+||||||+++ +..+.++|+++||+|||.||||||||||+||+|+|
T Consensus 262 ~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~~--~~~~~eeta~~tNleAa~eiarqlrlR~lgGiIiI 339 (487)
T COG1530 262 LFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFT--GAGDLEETAVNTNLEAAEEIARQLRLRNLGGIIII 339 (487)
T ss_pred hhhHHHHHHHhhhheEecCCCCceeEeccceeEEEEccCcccc--ccCchHHhhhhhhHHHHHHHHHHHhhcccCCeEEE
Confidence 9999999999999999999999999999999999999999854 44569999999999999999999999999999999
Q ss_pred EcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccccCC--CCCC-------------------
Q 005219 552 DFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADP--ENPK------------------- 610 (708)
Q Consensus 552 DFIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~--~~~~------------------- 610 (708)
|||||...++++.|+..|+++|+.|++++++.++|+|||+||||||.+.++.... .||.
T Consensus 340 DfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~~~cp~c~G~g~v~~~~~~~~~i~R 419 (487)
T COG1530 340 DFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLSERCPGCKGTGHVRSTESELLHILR 419 (487)
T ss_pred EeeeccchhhhHHHHHHHHHHhccCCcccccccccccCceEEEEEecCCCCceeeeeECCCceeeEEEecCchhhhhhhc
Confidence 9999999999999999999999999999999999999999999999754322111 1221
Q ss_pred ---------CCCeEEEEECHHHHHHHHcCchhhHHHHHhhcC-CeEEEEeCCCCCCcCeEEEEeec
Q 005219 611 ---------SWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLK-AWILLKVARGFTRGAFEVIPYTD 666 (708)
Q Consensus 611 ---------~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~-~~I~i~~d~~l~~~~~~i~~~~~ 666 (708)
....+.+.+++.++.|+.++++..+..+|...+ ..+.+.+++.++.+||++.....
T Consensus 420 ~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~~~e~~~~~~~i~~~~~~~~~~~~~~~~~~~~ 485 (487)
T COG1530 420 YIEEEADINKTPEVGVEVPPAVAKYLLNEERGAIAELELFKGYLRVRLRVDDRVEQEQYEVVRLRE 485 (487)
T ss_pred cchhhhccccCccceEEechhhhhhhcccccchhhHHHhhccceeEEEeechhhcccceeEeeecc
Confidence 235678899999999999999888999999999 99999999999999999976553
No 5
>PF10150 RNase_E_G: Ribonuclease E/G family; InterPro: IPR019307 Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs []. RNA-binding protein AU-1 binds to RNA loop regions that are with AU-rich sequences [].; PDB: 2BX2_L 2VRT_D 2VMK_D 2C4R_L 1SMX_B 1SLJ_A 2C0B_L 1SN8_B.
Probab=100.00 E-value=2.6e-80 Score=644.33 Aligned_cols=270 Identities=47% Similarity=0.748 Sum_probs=221.8
Q ss_pred eecceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 005219 318 KLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSA 396 (708)
Q Consensus 318 sL~GRylVl~P~~~~igiSrKI~~~-eR~rLk~i~~~l~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~~~~~ 396 (708)
||||||+||+|+++++||||||+++ +|++|+++++.+.++++|+||||+|+++++++|.+|+++|.++|++|++++...
T Consensus 1 sl~GRYlVl~P~~~~i~vSrKI~d~~~R~~Lk~i~~~~~~~~~GvIiRT~A~~a~~e~L~~El~~L~~~w~~I~~~~~~~ 80 (271)
T PF10150_consen 1 SLPGRYLVLTPGGNGIGVSRKISDEEERERLKKILESLLPEGEGVIIRTAAAGASEEELEKELEELREKWEEIQKKAKSR 80 (271)
T ss_dssp SEETSSEEEETT-TT-EE-TTS-TH-HHHHHHHHHHTS--TT-EEEE-GGGGGS-HHHHHHHHHHHHHHHHHHHHHHCTS
T ss_pred CCCCceEEEecCCCCceecCCCCCchhHHHHHHHHHHhCCCCCeEEEecCcCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7999999999999999999999987 799999999999999999999999999999999999999999999999998765
Q ss_pred hhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccCCCCcccccCHH
Q 005219 397 ALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIE 476 (708)
Q Consensus 397 ~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~~~plF~~y~Ie 476 (708)
++|+|||++.+++.+++|||+.+++++|+||+++.|+++++|++.+.|++..+|++|.+..|+|+.|+|+
T Consensus 81 ----------~~P~LLy~~~~~~~~~lrd~~~~~~~~Iivd~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~lf~~~~i~ 150 (271)
T PF10150_consen 81 ----------KAPSLLYREPDLYERVLRDYLDEDVDEIIVDDKEIYEEIKEYLKEFSPDLKDKIELYKDEEPLFELYGIE 150 (271)
T ss_dssp -----------STEEEE-STSHHHHHHHHH--TTEEEEEES-HHHHHHHHHHHHTT-GGGTTTEEE--SSS-HHHHTT-H
T ss_pred ----------CCCeEEEeCCChhhHHHhhcCcCCCCEEEECCcHHHHHHHHHHHHhCccccceEEEecCCCChHHhCCHH
Confidence 5799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCC
Q 005219 477 EEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDM 556 (708)
Q Consensus 477 ~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVIDFIDM 556 (708)
.+|+++++++||||||||||||+||||||||||||++ .++.+.++|+++||+|||+||||||||||||||||||||||
T Consensus 151 ~~i~~~~~~~v~l~~Gg~l~Ie~TeAlt~IDVNsg~~--~~~~~~~~~~~~~N~~Aa~ei~rqirLR~i~GiIviDfi~m 228 (271)
T PF10150_consen 151 EAIEKALSRRVWLPSGGYLVIEQTEALTVIDVNSGKY--TGKKNSEETALKTNLEAAKEIARQIRLRNIGGIIVIDFIDM 228 (271)
T ss_dssp HHHHHTTSSEEE-TTS-EEEEEE-SS-EEEEEE-----------HHHHHHHHHHHHHHHHHHHHHHHT--EEEEEE----
T ss_pred HHHHHHhCCeEEeCCCeEEEEecCceEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 9999999999999999999999999999999999985 55678999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCC
Q 005219 557 ADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAM 599 (708)
Q Consensus 557 ~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~ 599 (708)
++++++++|++.|+++|++|+++++|+|||+||||||||||.+
T Consensus 229 ~~~~~~~~l~~~~~~~~~~d~~~~~v~~~t~lGl~e~tRkR~r 271 (271)
T PF10150_consen 229 KDKKDREKLLEALKEALKKDPAKTRVLGFTKLGLLEITRKRRR 271 (271)
T ss_dssp SSHHHHHHHHHHHHHHTTT-SS-EEEEEE-TTSEEEEEE--S-
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCcEEecCCCCeeEEEEEecCC
Confidence 9999999999999999999999999999999999999999964
No 6
>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=99.62 E-value=9.5e-16 Score=135.55 Aligned_cols=40 Identities=30% Similarity=0.615 Sum_probs=37.0
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
++..+|+||.|+|++|+|.|.+||||+|.+++||||++++
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~sei 42 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDI 42 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHc
Confidence 4567999999999999999999999999999999999874
No 7
>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=97.63 E-value=0.00023 Score=59.77 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=33.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...|.||.|+|.+|.+ .++||++|.+..||+++++.
T Consensus 2 ~~~G~iv~g~V~~v~~--~g~~V~l~~~~~g~ip~~~l 37 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVED--FGVFVDLGNGIEGFIPISEL 37 (74)
T ss_dssp SSTTSEEEEEEEEEET--TEEEEEESTSSEEEEEGGGS
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCcEEEEEEeehh
Confidence 3579999999999999 99999999999999998774
No 8
>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=97.31 E-value=0.00086 Score=54.83 Aligned_cols=33 Identities=33% Similarity=0.479 Sum_probs=30.5
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|++|.|+|++|.| .++||+++...+|||++.+.
T Consensus 1 g~~~~g~V~~v~~--~G~~v~l~~~~~g~l~~~~l 33 (68)
T cd04472 1 GKIYEGKVVKIKD--FGAFVEILPGKDGLVHISEL 33 (68)
T ss_pred CCEEEEEEEEEEE--eEEEEEeCCCCEEEEEhHHc
Confidence 7899999999999 99999999999999998653
No 9
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.00076 Score=63.88 Aligned_cols=35 Identities=29% Similarity=0.520 Sum_probs=32.5
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
-+|+++.|+|+.|.|- +|||++-.+..|+.|++++
T Consensus 4 kvG~~l~GkItgI~~y--GAFV~l~~g~tGLVHISEI 38 (129)
T COG1098 4 KVGSKLKGKITGITPY--GAFVELEGGKTGLVHISEI 38 (129)
T ss_pred cccceEEEEEEeeEec--ceEEEecCCCcceEEehHh
Confidence 4899999999999995 8999999999999999886
No 10
>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=97.04 E-value=0.0021 Score=54.70 Aligned_cols=35 Identities=34% Similarity=0.543 Sum_probs=31.2
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+|.||.|+|++|.+. -+|||+++.+..||+|+++.
T Consensus 3 ~G~iv~G~V~~i~~~-~g~~v~l~~~~~Glvhis~~ 37 (72)
T cd05704 3 EGAVTLGMVTKVIPH-SGLTVQLPFGKTGLVSIFHL 37 (72)
T ss_pred CCCEEEEEEEEeeCC-cEEEEECCCCCEEEEEHHHh
Confidence 799999999999876 35799999999999999874
No 11
>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=96.94 E-value=0.0037 Score=50.78 Aligned_cols=33 Identities=42% Similarity=0.619 Sum_probs=30.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|++|.|+|+++.+ .+|||+++.+..|||+..+.
T Consensus 1 G~~~~g~V~~i~~--~g~~v~i~~~~~g~l~~~~l 33 (69)
T cd05692 1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQI 33 (69)
T ss_pred CCEEEEEEEEEEe--eeEEEEECCCCEEEEEhHHc
Confidence 7899999999999 69999999999999988663
No 12
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.93 E-value=0.0032 Score=50.77 Aligned_cols=34 Identities=38% Similarity=0.612 Sum_probs=31.3
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.|.+|.|+|.++.+ +++||++|.+..|||++.+.
T Consensus 2 ~G~~v~g~V~~v~~--~g~~v~i~~~~~g~l~~~~~ 35 (72)
T smart00316 2 VGDVVEGTVTEITP--FGAFVDLGNGVEGLIPISEL 35 (72)
T ss_pred CCCEEEEEEEEEEc--cEEEEEeCCCCEEEEEHHHC
Confidence 69999999999999 79999999999999988764
No 13
>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=96.61 E-value=0.0072 Score=50.25 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=30.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.+ .++||+++.+..||++.++.
T Consensus 1 g~~~~g~V~~v~~--~G~~V~l~~~~~gli~~s~l 33 (70)
T cd05698 1 GLKTHGTIVKVKP--NGCIVSFYNNVKGFLPKSEL 33 (70)
T ss_pred CCEEEEEEEEEec--CcEEEEECCCCEEEEEHHHc
Confidence 7899999999988 79999999889999998764
No 14
>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=96.54 E-value=0.0067 Score=49.21 Aligned_cols=33 Identities=39% Similarity=0.552 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|++|.|+|++|.+ .++||+++....||++..+.
T Consensus 1 g~~~~g~V~~i~~--~G~fv~l~~~~~g~~~~~~l 33 (68)
T cd05685 1 GMVLEGVVTNVTD--FGAFVDIGVKQDGLIHISKM 33 (68)
T ss_pred CCEEEEEEEEEec--ccEEEEcCCCCEEEEEHHHC
Confidence 7899999999998 69999999999999987653
No 15
>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=96.44 E-value=0.0098 Score=51.51 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=32.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.||.|+|++|.+ .++||+++.+..||+|..+.
T Consensus 12 ~~~G~i~~g~V~~v~~--~G~fv~l~~~~~g~v~~~el 47 (83)
T cd04461 12 LKPGMVVHGYVRNITP--YGVFVEFLGGLTGLAPKSYI 47 (83)
T ss_pred CCCCCEEEEEEEEEee--ceEEEEcCCCCEEEEEHHHC
Confidence 4589999999999998 89999999999999998764
No 16
>PRK07252 hypothetical protein; Provisional
Probab=96.43 E-value=0.011 Score=55.86 Aligned_cols=34 Identities=29% Similarity=0.470 Sum_probs=31.3
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+|++|.|+|++|.+ .+|||+|+.+..||+|+.+.
T Consensus 3 vG~iv~G~V~~V~~--~G~fVei~~~~~GllhiseL 36 (120)
T PRK07252 3 IGDKLKGTITGIKP--YGAFVALENGTTGLIHISEI 36 (120)
T ss_pred CCCEEEEEEEEEeC--cEEEEEECCCCEEEEEHHHc
Confidence 69999999999998 89999999999999998764
No 17
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.38 E-value=0.075 Score=58.02 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=30.8
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG--~~k~aFL~~~d~ 147 (708)
+|++..|+|++|.+ .+|||+++ .+..||+|+++.
T Consensus 17 ~GdvV~g~V~~I~d--~GafV~L~EY~gvEGlIhiSEl 52 (319)
T PTZ00248 17 EDDLVMVKVVRITE--MGAYVSLLEYDDIEGMILMSEL 52 (319)
T ss_pred CCCEEEEEEEEEeC--CeEEEEecCCCCcEEEEEHHHh
Confidence 79999999999998 69999996 589999999774
No 18
>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=96.27 E-value=0.012 Score=48.81 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.+ .++||+++.+..||+++.+.
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~~~G~v~~s~l 33 (68)
T cd05707 1 GDVVRGFVKNIAN--NGVFVTLGRGVDARVRVSEL 33 (68)
T ss_pred CCEEEEEEEEEEC--ccEEEEeCCCCEEEEEHHHC
Confidence 7899999999998 67999999999999998764
No 19
>PRK08059 general stress protein 13; Validated
Probab=96.21 E-value=0.014 Score=54.84 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=32.5
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|.+|.+ .++||+|+.+..||+++.+.
T Consensus 5 ~k~G~iv~G~V~~i~~--~G~fV~i~~~~~Gli~~sel 40 (123)
T PRK08059 5 YEVGSVVTGKVTGIQP--YGAFVALDEETQGLVHISEI 40 (123)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEECCCCEEEEEHHHC
Confidence 3479999999999999 89999999999999998764
No 20
>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=96.19 E-value=0.018 Score=49.39 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=29.3
Q ss_pred CCeEEEEEeeecCCcceEEeccc---CCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIG---NSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG---~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.|. ++||+++ .+.+||+|+.+.
T Consensus 1 G~~~~g~V~~v~~~--G~fv~l~~~~~~~~gll~~s~l 36 (79)
T cd05684 1 GKIYKGKVTSIMDF--GCFVQLEGLKGRKEGLVHISQL 36 (79)
T ss_pred CCEEEEEEEEEEee--eEEEEEeCCCCCcEEEEEhHhc
Confidence 78999999999996 9999998 468999998763
No 21
>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=96.17 E-value=0.019 Score=47.86 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|+|+.|+|.+|.+. .|||++|....|||+..+.
T Consensus 1 G~iv~g~V~~i~~~--~~~v~l~~~~~g~l~~~e~ 33 (70)
T cd05687 1 GDIVKGTVVSVDDD--EVLVDIGYKSEGIIPISEF 33 (70)
T ss_pred CCEEEEEEEEEeCC--EEEEEeCCCceEEEEHHHh
Confidence 78999999999985 9999999999999988763
No 22
>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=96.04 E-value=0.032 Score=46.83 Aligned_cols=34 Identities=24% Similarity=0.209 Sum_probs=31.0
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+|.||.|+|++|.+ .++||+++.+..||+++.+.
T Consensus 3 ~G~iv~g~V~~v~~--~gi~v~l~~~~~g~v~~s~l 36 (73)
T cd05706 3 VGDILPGRVTKVND--RYVLVQLGNKVTGPSFITDA 36 (73)
T ss_pred CCCEEEEEEEEEeC--CeEEEEeCCCcEEEEEhhhc
Confidence 79999999999988 48999999999999998764
No 23
>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=95.81 E-value=0.031 Score=46.59 Aligned_cols=33 Identities=30% Similarity=0.503 Sum_probs=29.5
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.+ .++||+++.+..||+++.+.
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~v~g~i~~~~l 33 (69)
T cd05697 1 GQVVKGTIRKLRP--SGIFVKLSDHIKGLVPPMHL 33 (69)
T ss_pred CCEEEEEEEEEec--cEEEEEecCCcEEEEEHHHC
Confidence 7899999999998 49999999889999987653
No 24
>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=95.77 E-value=0.045 Score=46.51 Aligned_cols=34 Identities=29% Similarity=0.487 Sum_probs=29.4
Q ss_pred cCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDI-G~~k~aFL~~~d~ 147 (708)
+|.+|.|+|++|.+ .++||++ |....||+|+++.
T Consensus 3 ~g~~~~g~V~~i~~--fG~fv~l~~~~~eGlvh~sel 37 (73)
T cd05686 3 LYQIFKGEVASVTE--YGAFVKIPGCRKQGLVHKSHM 37 (73)
T ss_pred CCCEEEEEEEEEEe--eeEEEEECCCCeEEEEEchhh
Confidence 79999999999998 7999999 3347999998764
No 25
>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=95.57 E-value=0.049 Score=45.80 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.4
Q ss_pred cCCeEEEEEeeecCCcceEEecccC--CcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~--~k~aFL~~~d~ 147 (708)
.|.+|.|+|++|.+ .++||++.. +..||||+++.
T Consensus 3 ~G~~~~g~V~~v~~--~g~~v~l~~~~~~~gll~~s~l 38 (76)
T cd04452 3 EGELVVVTVKSIAD--MGAYVSLLEYGNIEGMILLSEL 38 (76)
T ss_pred CCCEEEEEEEEEEc--cEEEEEEcCCCCeEEEEEhHHc
Confidence 59999999999997 899999963 48999988764
No 26
>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=95.54 E-value=0.05 Score=45.20 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.+ .++||+++.+-.||++..+.
T Consensus 1 G~~v~g~V~~v~~--~g~~v~l~~~~~g~i~~~~~ 33 (73)
T cd05691 1 GSIVTGKVTEVDA--KGATVKLGDGVEGFLRAAEL 33 (73)
T ss_pred CCEEEEEEEEEEC--CeEEEEeCCCCEEEEEHHHC
Confidence 7899999999986 79999999999999988764
No 27
>PRK08582 hypothetical protein; Provisional
Probab=95.47 E-value=0.046 Score=52.80 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=32.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.+|.+|.|+|+.|.+. +|||+|+.+..||+|+.+.
T Consensus 4 kvG~iv~G~V~~I~~f--G~fV~L~~~~~GlVhiSel 38 (139)
T PRK08582 4 EVGSKLQGKVTGITNF--GAFVELPEGKTGLVHISEV 38 (139)
T ss_pred cCCCEEEEEEEEEECC--eEEEEECCCCEEEEEeecc
Confidence 4799999999999994 8999999999999999774
No 28
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.46 E-value=0.029 Score=64.90 Aligned_cols=36 Identities=33% Similarity=0.536 Sum_probs=33.2
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.-.+|.+..|+|++|-| .+||||||+ =+|+||++++
T Consensus 189 ~l~~G~vV~G~V~~It~--~GafVdigG-vdGLlHisei 224 (541)
T COG0539 189 KLEVGEVVEGVVKNITD--YGAFVDIGG-VDGLLHISEI 224 (541)
T ss_pred cCCCCceEEEEEEEeec--CcEEEEecC-eeeEEehhhc
Confidence 45689999999999999 899999999 9999999875
No 29
>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=95.37 E-value=0.058 Score=45.78 Aligned_cols=34 Identities=26% Similarity=0.328 Sum_probs=29.0
Q ss_pred CCeEE-EEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~-GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|-||. |+|++|+.. -+|||+++.+..||+|.++.
T Consensus 1 G~v~~~g~V~~v~~~-~G~~V~l~~gv~G~i~~s~l 35 (71)
T cd05696 1 GAVVDSVKVTKVEPD-LGAVFELKDGLLGFVHISHL 35 (71)
T ss_pred CcEeeeeEEEEEccC-ceEEEEeCCCCEEEEEHHHC
Confidence 78999 999999622 67999999899999998763
No 30
>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=95.13 E-value=0.06 Score=43.81 Aligned_cols=33 Identities=30% Similarity=0.475 Sum_probs=28.9
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.|.+|.|+|+++.+. ++||++| +-.|||+..+.
T Consensus 1 ~g~~~~g~V~~v~~~--g~~v~l~-~~~g~l~~~e~ 33 (68)
T cd05688 1 EGDVVEGTVKSITDF--GAFVDLG-GVDGLLHISDM 33 (68)
T ss_pred CCCEEEEEEEEEEee--eEEEEEC-CeEEEEEhHHC
Confidence 489999999999985 8999998 68999988763
No 31
>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=95.09 E-value=0.1 Score=45.35 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=31.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..|+|+.|+|++|.+ .++||+||.+..|||++++.
T Consensus 5 ~~GdiV~g~V~~i~~--~g~~v~i~~~~~G~l~~se~ 39 (86)
T cd05789 5 EVGDVVIGRVTEVGF--KRWKVDINSPYDAVLPLSEV 39 (86)
T ss_pred CCCCEEEEEEEEECC--CEEEEECCCCeEEEEEHHHc
Confidence 479999999999988 56999999999999998764
No 32
>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=94.70 E-value=0.054 Score=64.60 Aligned_cols=59 Identities=20% Similarity=0.252 Sum_probs=43.5
Q ss_pred eEEEEEEECCEEEEEEeecC------------CC--CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 87 MQRIAVLEDEKLVELLLEPV------------KS--NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 87 e~RvAvlEdgkL~El~iE~~------------~~--~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...|-+-+||++.=+-.... .. ...+|.||.|+|++|.+ -+|||+|+.+..||+|+++.
T Consensus 608 g~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~d--fGaFVel~~G~eGLvHISei 680 (719)
T TIGR02696 608 GAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTA--FGAFVSLLPGKDGLLHISQI 680 (719)
T ss_pred CCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEEC--ceEEEEecCCceEEEEhhhc
Confidence 34566667776653332211 11 24699999999999998 79999999999999999864
No 33
>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=94.67 E-value=0.067 Score=63.80 Aligned_cols=37 Identities=27% Similarity=0.453 Sum_probs=33.5
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...+|.||.|+|++|.+ .+|||++..+..||||+++.
T Consensus 615 ~~~~G~i~~G~V~~I~~--~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMD--FGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred ccccCcEEEEEEEEEeC--CEEEEEECCCcEEEEEHHHc
Confidence 34689999999999998 89999999999999999764
No 34
>PRK05807 hypothetical protein; Provisional
Probab=94.62 E-value=0.14 Score=49.39 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=30.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.+|.+|.|+|+.|.| .+|||++ .+..||+|+++.
T Consensus 4 ~vG~vv~G~Vt~i~~--~GafV~L-~~~~Glvhisei 37 (136)
T PRK05807 4 KAGSILEGTVVNITN--FGAFVEV-EGKTGLVHISEV 37 (136)
T ss_pred cCCCEEEEEEEEEEC--CeEEEEE-CCEEEEEEhhhc
Confidence 479999999999998 5999999 578999998774
No 35
>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=94.49 E-value=0.12 Score=44.54 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=30.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.+|++..|+|++|.+ .+|||+++.+-.||+|+.+.
T Consensus 2 k~G~~V~g~V~~i~~--~G~fV~l~~~v~G~v~~~~l 36 (74)
T cd05705 2 KEGQLLRGYVSSVTK--QGVFFRLSSSIVGRVLFQNV 36 (74)
T ss_pred CCCCEEEEEEEEEeC--CcEEEEeCCCCEEEEEHHHc
Confidence 379999999999974 56999999999999998764
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=94.40 E-value=0.2 Score=53.37 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=30.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC--CcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~--~k~aFL~~~d~ 147 (708)
-+|+++.|+|++|.+ .+|||++.. +..||+|+++.
T Consensus 7 ~~GdiV~G~V~~I~~--~G~fV~L~e~~gieGlI~iSEl 43 (262)
T PRK03987 7 EEGELVVGTVKEVKD--FGAFVTLDEYPGKEGFIHISEV 43 (262)
T ss_pred CCCCEEEEEEEEEEC--CEEEEEECCCCCcEEEEEHHHc
Confidence 479999999999976 899999975 68999998764
No 37
>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=94.36 E-value=0.16 Score=43.86 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=29.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-CcceeeEecc
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKH 146 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~-~k~aFL~~~d 146 (708)
..|.|+.|.|++|.+ .+||||+|. +-.|||+.++
T Consensus 3 ~~G~~v~g~V~si~d--~G~~v~~g~~gv~Gfl~~~~ 37 (74)
T cd05694 3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKD 37 (74)
T ss_pred CCCCEEEEEEEEEeC--CEEEEEeCCCCcEEEEEHHH
Confidence 369999999999996 599999994 6799998655
No 38
>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=94.29 E-value=0.17 Score=42.30 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=29.9
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~-~k~aFL~~~d~ 147 (708)
+|.+|.|+|++|.+ .++||+++. +..||+++.+.
T Consensus 2 ~g~~v~g~V~~i~~--~g~~v~l~~~~~~g~i~~~~l 36 (77)
T cd05708 2 VGQKIDGTVRRVED--YGVFIDIDGTNVSGLCHKSEI 36 (77)
T ss_pred CCCEEEEEEEEEEc--ceEEEEECCCCeEEEEEHHHC
Confidence 59999999999987 899999984 78999988763
No 39
>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=94.16 E-value=0.22 Score=43.00 Aligned_cols=34 Identities=18% Similarity=0.195 Sum_probs=30.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d 146 (708)
.+|+|=.|+|++| .-+.+|||||..-.|||++.+
T Consensus 5 ~~GdiV~G~V~~v--~~~~~~V~i~~~~~g~l~~~~ 38 (82)
T cd04454 5 DVGDIVIGIVTEV--NSRFWKVDILSRGTARLEDSS 38 (82)
T ss_pred CCCCEEEEEEEEE--cCCEEEEEeCCCceEEeechh
Confidence 5799999999999 557899999999999998866
No 40
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.12 E-value=0.14 Score=61.23 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=33.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|++|.+ .+|||+|+.+..||+|+++.
T Consensus 619 ~~vG~v~~G~V~~I~~--fGafVei~~~~~GllhiSel 654 (693)
T PRK11824 619 PEVGEIYEGKVVRIVD--FGAFVEILPGKDGLVHISEI 654 (693)
T ss_pred CcCCeEEEEEEEEEEC--CeEEEEECCCCEEEEEeeec
Confidence 4689999999999998 89999999999999999764
No 41
>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=94.09 E-value=0.22 Score=41.69 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=28.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d 146 (708)
+.|.|..|+|.++-+ +.+|||||. -.|||+.++
T Consensus 2 ~~g~iV~G~V~~~~~--~~~~vdig~-~eg~lp~~e 34 (67)
T cd04455 2 REGEIVTGIVKRVDR--GNVIVDLGK-VEAILPKKE 34 (67)
T ss_pred CCCCEEEEEEEEEcC--CCEEEEcCC-eEEEeeHHH
Confidence 579999999999999 579999987 899997654
No 42
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=93.63 E-value=0.49 Score=47.63 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=28.6
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccC----------CcceeeEecc
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGN----------SRPSLMDIKH 146 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~----------~k~aFL~~~d 146 (708)
...+|+|+.|+|++|.+ ..|||||+. +..|||++.+
T Consensus 61 ~~~~GdiV~GkV~~i~~--~g~~V~I~~~~~~~~~l~~~~~G~l~~s~ 106 (189)
T PRK09521 61 LLKKGDIVYGRVVDVKE--QRALVRIVSIEGSERELATSKLAYIHISQ 106 (189)
T ss_pred CCCCCCEEEEEEEEEcC--CeEEEEEEEecccccccCCCceeeEEhhH
Confidence 44689999999999977 899999974 4556666655
No 43
>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=93.55 E-value=0.18 Score=39.73 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=25.7
Q ss_pred EEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 116 YLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 116 Y~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.|+|+++.+ .++||+++.+..||++..+.
T Consensus 1 v~g~V~~v~~--~g~~v~l~~~~~g~~~~~~~ 30 (65)
T cd00164 1 VTGKVVSITK--FGVFVELEDGVEGLVHISEL 30 (65)
T ss_pred CEEEEEEEEe--eeEEEEecCCCEEEEEHHHC
Confidence 5799999996 58999999999999987653
No 44
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.06 E-value=0.75 Score=48.09 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.1
Q ss_pred EEeecCCCCc--ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 101 LLLEPVKSNV--QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 101 l~iE~~~~~~--~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+.+.+...+. .+|+|-.|+|++|.+. .+||||+..-.||||+.+.
T Consensus 50 i~V~p~~~~y~P~vGDiViG~V~~i~~~--~~~vdI~~~~~g~L~~s~i 96 (235)
T PRK04163 50 VRVIPLEGKYIPKVGDLVIGKVTDVTFS--GWEVDINSPYKAYLPVSEV 96 (235)
T ss_pred EEEEECCCcccCCCCCEEEEEEEEEeCc--eEEEEeCCCceeEEEHHHc
Confidence 4555544443 5899999999999885 4999999999999998774
No 45
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=92.37 E-value=0.28 Score=59.98 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=31.6
Q ss_pred ccCCeEE-EEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~-GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
-+|.||. |+|++|.+ -+|||+|+.+..||+|+++.
T Consensus 752 ~vG~iy~~g~V~~I~~--FGaFVeL~~g~EGLVHISeL 787 (891)
T PLN00207 752 TVGDIYRNCEIKSIAP--YGAFVEIAPGREGLCHISEL 787 (891)
T ss_pred CCCcEEECcEEEEEec--cEEEEEeCCCCEEEEEhhhc
Confidence 4899995 69999998 69999999999999999874
No 46
>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=90.80 E-value=0.27 Score=40.48 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=30.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.+|.|+|++|.| -++||+++.+..||+|+.+.
T Consensus 1 G~~~~g~V~~i~~--~G~fv~l~~~~~Glv~~~~l 33 (69)
T cd05690 1 GTVVSGKIKSITD--FGIFVGLDGGIDGLVHISDI 33 (69)
T ss_pred CCEEEEEEEEEEe--eeEEEEeCCCCEEEEEHHHC
Confidence 7899999999998 58999999999999999874
No 47
>PRK14865 rnpA ribonuclease P; Provisional
Probab=90.63 E-value=1.3 Score=41.43 Aligned_cols=53 Identities=21% Similarity=0.377 Sum_probs=37.2
Q ss_pred eeeecCCChH-HHHHHHHHHHh----hC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI~~~-eR~rLk~i~~~----l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||+... .|+|+|.++.+ .. + .++=+|.|..+.+++.++|+.++..|.+.
T Consensus 49 ~sVsKKvg~AV~RNRiKR~lRE~~R~~~~~l~~~divii~r~~~~~~~~~~l~~~l~~ll~~ 110 (116)
T PRK14865 49 ITVSRKVGNAVVRNRIKRLVREFYRLNKSLFIVADYNIIAKKGAEQLDFQQISRELANALER 110 (116)
T ss_pred EEEecccCcchhHHHHHHHHHHHHHHhhccCCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 5679998764 57766554432 22 2 23456889999999999999998776544
No 48
>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=90.39 E-value=0.41 Score=40.01 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=31.4
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+|.+|.|+|++|.+ -++||+++.+-.||+|+.+.
T Consensus 3 ~g~~~~g~V~~i~~--~G~fv~l~~~~~Gl~~~~~l 36 (72)
T cd05689 3 EGTRLFGKVTNLTD--YGCFVELEEGVEGLVHVSEM 36 (72)
T ss_pred CCCEEEEEEEEEEe--eEEEEEcCCCCEEEEEEEec
Confidence 68999999999999 69999999999999999874
No 49
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.35 E-value=0.65 Score=50.65 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=32.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...|.|-.|+|.+|.++ +||||||....|||++.+.
T Consensus 29 ~~~G~iv~G~V~~i~~~--g~~Vdig~k~~g~lp~sEi 64 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPR--GALIDIGAKTAAFMPIQEM 64 (318)
T ss_pred cCCCCEEEEEEEEEECC--EEEEEECCCeEEEEEHHHh
Confidence 56899999999999866 8999999999999998774
No 50
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=90.15 E-value=0.71 Score=53.12 Aligned_cols=37 Identities=32% Similarity=0.492 Sum_probs=32.8
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
....|.||.|+|++|.+ .+||||||.+..||+|+++.
T Consensus 199 ~l~~G~iv~G~V~~v~~--~G~fV~l~~gv~g~v~~sel 235 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAP--FGAFVELAPGVEGMVHISEL 235 (491)
T ss_pred hCCCCCEEEEEEEEEeC--CeEEEEcCCCcEEEEEHHHC
Confidence 35689999999999988 58999999899999998874
No 51
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.67 E-value=0.76 Score=52.99 Aligned_cols=35 Identities=34% Similarity=0.547 Sum_probs=30.9
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.|+.|+|++|.|. +|||||| +-.||+|+++.
T Consensus 206 lk~G~iv~G~V~~i~~~--G~FVdlg-gv~Glv~~Sel 240 (486)
T PRK07899 206 LQKGQVRKGVVSSIVNF--GAFVDLG-GVDGLVHVSEL 240 (486)
T ss_pred ccCCCEEEEEEEEEECC--eEEEEEC-CEEEEEEHHHC
Confidence 45899999999999985 8999998 59999998774
No 52
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=89.00 E-value=1.1 Score=49.04 Aligned_cols=39 Identities=28% Similarity=0.526 Sum_probs=32.8
Q ss_pred CCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 106 VKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 106 ~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.-...-+|.||.|+|++|.+ -+|||++| +-.||+|+++.
T Consensus 190 ~~~~~k~G~vv~G~V~~I~~--~G~fV~i~-gv~Gllhisel 228 (318)
T PRK07400 190 KMNRLEVGEVVVGTVRGIKP--YGAFIDIG-GVSGLLHISEI 228 (318)
T ss_pred hhccCCCCCEEEEEEEEEEC--CeEEEEEC-CEEEEEEHHHc
Confidence 33446689999999999998 79999997 57899998764
No 53
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=88.78 E-value=2 Score=40.53 Aligned_cols=53 Identities=15% Similarity=0.143 Sum_probs=35.1
Q ss_pred eeeecCCChH-HHHHHHHH----HHhhC---CCCeeEE--EeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKITGV-ERTRLKVI----AKTLQ---PEGFGLT--IRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI~~~-eR~rLk~i----~~~l~---p~~~GvI--iRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||+... +|+|+|.+ +.... +.+.-+| .|..+..++..+|+++|..|...
T Consensus 47 ~~VsKKvG~AV~RNRiKR~lRE~~R~~~~~l~~~~~vVviaR~~~~~~~~~~l~~~l~~ll~~ 109 (118)
T PRK00588 47 LIIAKSVGSAVERHRVARRLRHVARPILKELHPSDRVVIRALPSSRHVSSARLEQQLRCGLRR 109 (118)
T ss_pred EEEeeecCchhHHHHHHHHHHHHHHHhhhccCCCCEEEEecCcccccCCHHHHHHHHHHHHHH
Confidence 5679999764 57766544 33322 3333343 58889999999999998766433
No 54
>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=88.24 E-value=6 Score=43.90 Aligned_cols=108 Identities=23% Similarity=0.294 Sum_probs=62.2
Q ss_pred cccCCCEEEEEEEecCCCCCCceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cee-EEEeecC
Q 005219 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (708)
Q Consensus 290 ~lk~Gq~ILVQV~KE~~gtKGprLTt~IsL~GRylVl~P~~~~igiSrKI~~~eR~rLk~i~~~l~p~-~~G-vIiRTaA 367 (708)
.+++||.|-|.|.+-..++|||. +-+||+-.+ -|+.+++.-.|+ ..| +.|+..|
T Consensus 169 ~~~~Gd~ik~~V~~V~~~~kg~q--------------------IivSRt~~~----~v~~Lfe~EVPEI~dG~VeI~~ia 224 (341)
T TIGR01953 169 KFRIGDRIKAYVYEVRKTAKGPQ--------------------IILSRTHPE----FVKELLKLEVPEIADGIIEIKKIA 224 (341)
T ss_pred CCCCCCEEEEEEEEEEcCCCCCe--------------------EEEEeCcHH----HHHHHHHHhCccccCCeEEEEEEe
Confidence 37779999999988877766653 457777653 356666666665 224 5566666
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEE-EcCHHH
Q 005219 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRT 441 (708)
Q Consensus 368 ~g~~~eeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~Ii-VDd~~~ 441 (708)
..+.. +++-+-...+.++. +..+|+-.....+..+.+.+-.+.++=|. -||+..
T Consensus 225 R~pG~-------------------RtKvAV~s~~~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~ 279 (341)
T TIGR01953 225 REPGY-------------------RTKIAVESNDENID-PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE 279 (341)
T ss_pred eCCcc-------------------eeEEEEEcCCCCCC-cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH
Confidence 65541 11111011223332 35667777666666666666677776553 344443
No 55
>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=87.84 E-value=0.73 Score=38.65 Aligned_cols=33 Identities=9% Similarity=0.159 Sum_probs=30.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.|+.|+|++|.+. .+||+++.+-.||+++.+.
T Consensus 1 G~iV~g~V~~i~~~--gi~v~l~~~i~g~i~~~~i 33 (70)
T cd05702 1 GDLVKAKVKSVKPT--QLNVQLADNVHGRIHVSEV 33 (70)
T ss_pred CCEEEEEEEEEECC--cEEEEeCCCcEEEEEHHHh
Confidence 78999999999884 6999999999999999885
No 56
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=87.80 E-value=1.2 Score=51.63 Aligned_cols=36 Identities=33% Similarity=0.549 Sum_probs=31.9
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
....|.|+.|+|++|.+. +||||+| +-.||+|+++.
T Consensus 198 ~l~~G~iv~g~V~~v~~~--G~~V~i~-g~~glv~~se~ 233 (565)
T PRK06299 198 NLEEGQVVEGVVKNITDY--GAFVDLG-GVDGLLHITDI 233 (565)
T ss_pred cCCCCCEEEEEEEEEeCC--eEEEEEC-CEEEEEEHHHh
Confidence 345899999999999994 8999999 89999998774
No 57
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=87.62 E-value=1.4 Score=50.78 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=34.1
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...-+|.+|.|+|++|.| .+|||+++.+-.||+|+++.
T Consensus 288 ~~~~~G~~v~G~V~~v~~--~G~fV~l~~gv~Glvh~sel 325 (491)
T PRK13806 288 DRLKAGDKVTGKVVRLAP--FGAFVEILPGIEGLVHVSEM 325 (491)
T ss_pred ccCCCCCEEEEEEEEEeC--ceEEEEeCCCcEEEEEHHHc
Confidence 345689999999999988 79999999999999999875
No 58
>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=87.20 E-value=0.78 Score=38.97 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=30.7
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG~-~k~aFL~~~d~ 147 (708)
+|.+|.|+|++|.+ .++||+++. +..||+++.+.
T Consensus 1 ~g~~~~g~V~~v~~--~G~fv~l~~~~~~G~v~~~~l 35 (83)
T cd04471 1 VGEEFDGVISGVTS--FGLFVELDNLTVEGLVHVSTL 35 (83)
T ss_pred CCCEEEEEEEeEEe--eeEEEEecCCCEEEEEEEEec
Confidence 48899999999998 599999998 79999999874
No 59
>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=86.98 E-value=0.73 Score=38.16 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=28.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|.||.|+|+++.+ .++||++ .+-.|||+.++.
T Consensus 1 G~iv~g~V~~v~~--~G~~v~l-~g~~gfip~s~~ 32 (67)
T cd04465 1 GEIVEGKVTEKVK--GGLIVDI-EGVRAFLPASQV 32 (67)
T ss_pred CCEEEEEEEEEEC--CeEEEEE-CCEEEEEEHHHC
Confidence 7899999999976 8999999 579999998764
No 60
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=86.30 E-value=1.9 Score=49.42 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=32.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.++.|+|+++.+. +|||++|.+..||+++.+.
T Consensus 357 ~~~G~~v~g~V~~v~~~--G~fV~l~~~v~glv~~s~l 392 (516)
T TIGR00717 357 HPVGDRVTGKIKKITDF--GAFVELEGGIDGLIHLSDI 392 (516)
T ss_pred CCCCCEEEEEEEEEecc--eEEEECCCCCEEEEEHHHC
Confidence 45899999999999776 7999999999999998774
No 61
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=86.19 E-value=2 Score=50.15 Aligned_cols=68 Identities=24% Similarity=0.260 Sum_probs=51.4
Q ss_pred eEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 76 keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
+..+|.... .-.||.| -=.+|.+-=.+...++.-+|..+.|+|+|+.| .+|||+|+.+=.||+|++++
T Consensus 243 kvkVi~~D~-e~~RVsL-SlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~--~GafVei~~GvEGlvhvSEi 310 (541)
T COG0539 243 KVKVISLDE-ERGRVSL-SLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTD--YGAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred EEEEEEEcc-CCCeEEE-EehhcccCcHHHHhhhcCCCCEEEEEEEEeec--CcEEEEecCCccceeechhh
Confidence 455666654 3567754 22344444555667778899999999999999 48999999999999999875
No 62
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=86.13 E-value=2.5 Score=52.03 Aligned_cols=39 Identities=26% Similarity=0.437 Sum_probs=34.1
Q ss_pred CCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 107 KSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 107 ~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.++.-+|+|+.|+|++|.| -+|||+++.+-.||+|+++.
T Consensus 573 ~~~~~vG~iV~G~V~~I~~--fG~fVeL~~gveGLvhiSEl 611 (863)
T PRK12269 573 ENKFGVNDVVKGRVTKIAD--FGAFIELAEGIEGLAHISEF 611 (863)
T ss_pred hccCCCCCEEEEEEEEEeC--CeEEEEecCCceeeeEHHHh
Confidence 3445689999999999998 67999999999999999875
No 63
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=86.12 E-value=3.6 Score=39.58 Aligned_cols=58 Identities=21% Similarity=0.321 Sum_probs=38.3
Q ss_pred eeeecC-CChH-HHHHHHHHHHh----hC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 005219 333 IGVSRK-ITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (708)
Q Consensus 333 igiSrK-I~~~-eR~rLk~i~~~----l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~~ 393 (708)
+.|||| +... .|+|+|.++.+ .. + -++=+|.|..+.+.+..+|.+++..| |+.+...+
T Consensus 50 ~~VsKK~~g~AV~RNRiKR~lRE~fR~~~~~l~g~DiVviaR~~~~~~~~~~l~~~l~~l---l~kl~~~~ 117 (130)
T PRK00396 50 LVIGKKSVKLAVDRNRLKRLIRESFRLNQHSLAGWDIVVVARKGLGELENPELHQQFGKL---WKRLARNR 117 (130)
T ss_pred EEEecccCccHhHHHHHHHHHHHHHHHhhccCCCeeEEEEeCCCcccCCHHHHHHHHHHH---HHHHHHhc
Confidence 456799 6654 68777655433 22 2 13446778899999999999998666 55554444
No 64
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=85.84 E-value=4.4 Score=38.50 Aligned_cols=54 Identities=26% Similarity=0.292 Sum_probs=36.9
Q ss_pred ceeeecCCChH-HHHHHH----HHHHhhC---CCCeeE--EEeecCCCCCHHHHHHHHHHHHHH
Q 005219 332 RIGVSRKITGV-ERTRLK----VIAKTLQ---PEGFGL--TIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 332 ~igiSrKI~~~-eR~rLk----~i~~~l~---p~~~Gv--IiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
++.||||+... +|+|+| +++..+. |.|+-+ |.|-.+.+++..+|.+||..|+..
T Consensus 51 G~~VsKKvG~AV~RNRiKR~lRe~~R~~~~~l~~g~D~Viiar~~~~~~~~~~l~~~l~~ll~k 114 (122)
T PRK03459 51 GLVVSKAVGNAVIRHRVSRRLRHICADIVDQVPETHHVVIRALPGAATASSAELERDVRAGLGK 114 (122)
T ss_pred EEEEeeeccchhHHHHHHHHHHHHHHHhhhccCCCcEEEEEECcccccCCHHHHHHHHHHHHHH
Confidence 35679999774 576655 4444332 345544 556678899999999998877665
No 65
>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=84.72 E-value=1.3 Score=37.99 Aligned_cols=36 Identities=19% Similarity=0.409 Sum_probs=32.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|.++.+ .++||++..+..||+|.++.
T Consensus 14 ~~~G~~~~g~V~~i~~--~G~fV~l~~~~~Glv~~se~ 49 (77)
T cd04473 14 LEVGKLYKGKVNGVAK--YGVFVDLNDHVRGLIHRSNL 49 (77)
T ss_pred CCCCCEEEEEEEeEec--ceEEEEECCCcEEEEEchhc
Confidence 4579999999999987 89999999999999998763
No 66
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.56 E-value=2.3 Score=49.43 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=32.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|+++.|+|++|.+ .+|||++|.+..||+|+.+.
T Consensus 371 ~~~G~~v~g~V~~v~~--~G~fV~l~~~v~g~i~~s~l 406 (565)
T PRK06299 371 YPVGDVVEGKVKNITD--FGAFVGLEGGIDGLVHLSDI 406 (565)
T ss_pred CCCCCEEEEEEEEEec--ceEEEECCCCCEEEEEHHHc
Confidence 3579999999999976 59999999999999999875
No 67
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.17 E-value=2.6 Score=48.81 Aligned_cols=36 Identities=36% Similarity=0.480 Sum_probs=32.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|++|.| -++||++..+-.||+|+.+.
T Consensus 291 ~~vG~vv~G~V~~I~~--fGvFVeL~~gieGLvh~SeL 326 (486)
T PRK07899 291 HAIGQIVPGKVTKLVP--FGAFVRVEEGIEGLVHISEL 326 (486)
T ss_pred cCCCCEEEEEEEEEec--cEEEEEeCCCcEEEEEHHHc
Confidence 3479999999999999 79999998889999988764
No 68
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=83.80 E-value=2.5 Score=52.03 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=30.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|++|.|+|.++.+ .+||||+| +-.||+|+++.
T Consensus 491 l~~G~~V~G~Vk~i~~--~G~fVdl~-Gv~Gfvp~Sei 525 (863)
T PRK12269 491 VHIEDSVSGVVKSFTS--FGAFIDLG-GFDGLLHVNDM 525 (863)
T ss_pred CCCCCEEEEEEEEEeC--CcEEEEEC-CEEEEEEchhc
Confidence 3479999999999998 49999996 68999998875
No 69
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=83.21 E-value=6.6 Score=36.57 Aligned_cols=54 Identities=30% Similarity=0.391 Sum_probs=37.7
Q ss_pred eeeecCCChH-HHHHHHHH----HHhhC---CC--CeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 005219 333 IGVSRKITGV-ERTRLKVI----AKTLQ---PE--GFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (708)
Q Consensus 333 igiSrKI~~~-eR~rLk~i----~~~l~---p~--~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W 386 (708)
+.||||+... .|+++|.+ +.... +. .+-+|+|-.+..++..+|.+|+..|..+-
T Consensus 42 isVsKKvgkAV~RNriKR~lRE~~R~~~~~~~~~~d~v~i~r~~~~~~~~~~l~~~l~~ll~k~ 105 (114)
T PRK00499 42 ISVSKKVGNAVVRNRIKRLIRESFRELKDEIKKGYDFVVIARKPAAELDYKEIKKSLIHVLKLA 105 (114)
T ss_pred EEEecccCchhhHhHHHHHHHHHHHHhhhcccCCceEEEEECCCcccCCHHHHHHHHHHHHHHh
Confidence 5679999764 57666544 33322 22 44567788899999999999987777653
No 70
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.10 E-value=3.1 Score=46.10 Aligned_cols=35 Identities=34% Similarity=0.502 Sum_probs=31.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
...|.++.|+|+++.+ .++||++| +-.||+|+++.
T Consensus 190 ~~~G~~v~g~V~~v~~--~G~fV~l~-~v~g~v~~sel 224 (390)
T PRK06676 190 LKEGDVVEGTVARLTD--FGAFVDIG-GVDGLVHISEL 224 (390)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEeC-CeEEEEEHHHc
Confidence 4689999999999998 67999997 59999999875
No 71
>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=83.06 E-value=2.6 Score=48.31 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=32.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.||.|+|+++.+ .+|||++|.+-.||+|+++.
T Consensus 270 ~~~G~i~~g~V~~v~~--~G~fV~l~~~v~g~v~~sel 305 (516)
T TIGR00717 270 FPVGDKITGRVTNLTD--YGVFVEIEEGIEGLVHVSEM 305 (516)
T ss_pred ccCCCEEEEEEEEeeC--CcEEEEeCCCCEEEEEHHHc
Confidence 4589999999999987 48999999999999998774
No 72
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=82.89 E-value=6.6 Score=37.06 Aligned_cols=53 Identities=21% Similarity=0.315 Sum_probs=35.2
Q ss_pred eeeecCC-Ch-HHHHHHHHHHHh----hC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKI-TG-VERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI-~~-~eR~rLk~i~~~----l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||. .. -+|+|+|.++.+ .. | -++=+|.|..+.+.+..+|.+|+..|...
T Consensus 48 ~~VsKK~~~~AV~RNRiKR~lRE~~R~~~~~l~~~DiVvi~r~~~~~~~~~~l~~~l~~ll~k 110 (120)
T PRK04390 48 LVVGKKTAKRAVERNYMKRVIREWFRLNQHRLPPVDFVVRVQRKFDRATAKQAVAELAQLMAK 110 (120)
T ss_pred EEEecccCcchhhhhHHHHHHHHHHHhccccCCCceEEEEeCCCcccCCHHHHHHHHHHHHHH
Confidence 5678995 43 368777655433 22 2 13346778888899999999998766444
No 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=82.41 E-value=2.9 Score=48.15 Aligned_cols=109 Identities=23% Similarity=0.293 Sum_probs=63.7
Q ss_pred cccCCCEEEEEEEecCCCCCCceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cee-EEEeecC
Q 005219 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (708)
Q Consensus 290 ~lk~Gq~ILVQV~KE~~gtKGprLTt~IsL~GRylVl~P~~~~igiSrKI~~~eR~rLk~i~~~l~p~-~~G-vIiRTaA 367 (708)
.+++||.|-|-|.+-...+|||. |-+||+-.. -|+.+++.=.|+ ..| +.|+..|
T Consensus 171 ~~~~GdrIka~I~~Vd~~~kg~q--------------------IilSRt~p~----~l~~Lf~~EVPEI~~G~ieIk~ia 226 (470)
T PRK09202 171 NFRPGDRVRAYVYEVRKEARGPQ--------------------IILSRTHPE----FLKKLFEQEVPEIADGLIEIKAIA 226 (470)
T ss_pred cCCCCCEEEEEEEEEecCCCCCe--------------------EEEEeCcHH----HHHHHHHHhCcccccCeEEEEEEe
Confidence 46779999999988877777754 457777553 366666665665 335 4566666
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEE-cCHHHH
Q 005219 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVV-DSPRTY 442 (708)
Q Consensus 368 ~g~~~eeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiV-Dd~~~y 442 (708)
..+.. +++-+....+.++. +...|+-.....+..+.+.+-.+.|+=|.. +|+..|
T Consensus 227 R~pG~-------------------RaKvAV~s~d~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f 282 (470)
T PRK09202 227 RDPGS-------------------RAKIAVKSNDPRID-PVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQF 282 (470)
T ss_pred ecCcc-------------------eeEEEEEcCCCCCC-hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHHH
Confidence 65541 11111111223332 345677777667777777776777775533 344433
No 74
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=82.15 E-value=6.7 Score=37.75 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=37.8
Q ss_pred eeeecCCChH-HHHHHH----HHHHhhCC----C--CeeEEEeecCCCCCHHHHHHHHHHHHH
Q 005219 333 IGVSRKITGV-ERTRLK----VIAKTLQP----E--GFGLTIRTVAAGHSLEELQKDLEGLLS 384 (708)
Q Consensus 333 igiSrKI~~~-eR~rLk----~i~~~l~p----~--~~GvIiRTaA~g~~~eeL~~Dl~~L~~ 384 (708)
+.||||+... .|+|+| +++....+ . ++=+|.|..+.+++..+|++||..++.
T Consensus 51 ~~VSKKvG~AV~RNRiKR~lRE~fR~~~~~~~~~g~DiVivar~~~~~~~~~~l~~~L~~~l~ 113 (129)
T PRK01313 51 FTVTKKNGNAVERNRIRRRLKEAVRLHAGFDMAPGTDYVIVARRDALNAPFSQLTEELSRRIE 113 (129)
T ss_pred EEEecccCcchHHHHHHHHHHHHHHHhchhccCCCceEEEEECcccccCCHHHHHHHHHHHHH
Confidence 5679999764 566654 44443322 2 446788999999999999999988776
No 75
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=79.38 E-value=5.6 Score=44.05 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=31.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDI-G~~k~aFL~~~d~ 147 (708)
...|.|..|+|+++.+. ++|||| |.+-.|||+..+.
T Consensus 15 ~~~G~iv~G~V~~i~~~--g~~V~i~~~~~~g~lp~~e~ 51 (390)
T PRK06676 15 VEVGDVVTGEVLKVEDK--QVFVNIEGYKVEGVIPISEL 51 (390)
T ss_pred ccCCCEEEEEEEEEECC--eEEEEEecCCcEEEEEHHHh
Confidence 46899999999999984 799999 8889999987764
No 76
>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=79.27 E-value=2.1 Score=39.05 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=31.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.+|.+-.|+|++|.+. ++||+++.+..||+++.++
T Consensus 2 ~~G~vV~G~V~~v~~~--gl~v~L~~g~~G~v~~sei 36 (100)
T cd05693 2 SEGMLVLGQVKEITKL--DLVISLPNGLTGYVPITNI 36 (100)
T ss_pred CCCCEEEEEEEEEcCC--CEEEECCCCcEEEEEHHHh
Confidence 3799999999999766 9999999999999999885
No 77
>PRK01903 rnpA ribonuclease P; Reviewed
Probab=78.49 E-value=13 Score=36.04 Aligned_cols=53 Identities=21% Similarity=0.358 Sum_probs=33.0
Q ss_pred eeeecC-CChH-HHHHHHHHHHh-------hCCCC-------------eeEEEee-cCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRK-ITGV-ERTRLKVIAKT-------LQPEG-------------FGLTIRT-VAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrK-I~~~-eR~rLk~i~~~-------l~p~~-------------~GvIiRT-aA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.|||| +... .|+|+|.++.+ ..+.+ .-+|.|. +++..+.+++.+++..|+..
T Consensus 54 ~sVsKK~~g~AV~RNRiKR~lREa~R~~~~~l~~~~~~~~~~~~~~~~iv~i~~~~~~~~~~~~~l~~~l~~ll~r 129 (133)
T PRK01903 54 FSVSKKRVPRAVKRNRIKRLMREAYRLEKHVLLDRLETDAGAKNRQLAIAFLYTGRSDEIPSLAEFRREMRKLLQR 129 (133)
T ss_pred EEEecccCCchhhhhHHHHHHHHHHHHhHhhhcccccccccccCcceEEEEEEeccccccCCHHHHHHHHHHHHHH
Confidence 345799 6664 68777655433 12322 3456666 34457899999998777655
No 78
>PRK00730 rnpA ribonuclease P; Reviewed
Probab=77.92 E-value=10 Score=37.16 Aligned_cols=53 Identities=21% Similarity=0.299 Sum_probs=36.0
Q ss_pred ceeeecCCChH-HHHHHHHHH----HhhC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 332 RIGVSRKITGV-ERTRLKVIA----KTLQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 332 ~igiSrKI~~~-eR~rLk~i~----~~l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
++.||||+... .|+|+|.++ .... | -++=||.|..+. .+.++|..|+..++..
T Consensus 49 G~sVSKKvg~AV~RNRiKR~lREafR~~~~~l~g~DiVviaR~~~~-~~f~~L~~~l~~~~~~ 110 (138)
T PRK00730 49 GITVSKKFGKAHQRNRFKRIVREAFRHVRHNLPGCQIVVSPKGNSQ-PDFLKLLQDFLQQIPE 110 (138)
T ss_pred EEEEecccccchhHHHHHHHHHHHHHHhhcccCCceEEEEeccccC-CCHHHHHHHHHHHHHH
Confidence 35689999764 577766544 3322 2 134567788887 9999999998776654
No 79
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=77.80 E-value=2.1 Score=51.07 Aligned_cols=39 Identities=31% Similarity=0.509 Sum_probs=35.5
Q ss_pred CCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 107 KSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 107 ~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.+..-||-||.|+|+++.+ =+|||++..++.|++|++..
T Consensus 614 ~~e~evg~iy~G~V~ri~~--fGaFv~l~~gkdgl~hiS~~ 652 (692)
T COG1185 614 TREVEVGEVYEGTVVRIVD--FGAFVELLPGKDGLVHISQL 652 (692)
T ss_pred HhhcccccEEEEEEEEEee--cceEEEecCCcceeEEehhh
Confidence 3567899999999999999 89999999999999999874
No 80
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=75.74 E-value=15 Score=36.21 Aligned_cols=53 Identities=30% Similarity=0.449 Sum_probs=37.1
Q ss_pred eeeecCCC-hH-HHHHHHHHH----Hhh----CCCCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKIT-GV-ERTRLKVIA----KTL----QPEGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI~-~~-eR~rLk~i~----~~l----~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||+. .. .|+|+|.++ ..+ .+.++=+|.|-.+..++.++|++++..|+.+
T Consensus 52 ~sVSKKvg~~AV~RNRiKR~lRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~l~~LL~k 114 (145)
T PRK04820 52 LAVSRKVDTRAVGRNRIKRVLREAMRQLLPELAPGDYVVVARSAAAKASNPQLRDAFLRLLRR 114 (145)
T ss_pred EEEeccccCcchhHHHHHHHHHHHHHHhhhccCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 56899984 33 577665543 322 2335557788888999999999998777665
No 81
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=75.48 E-value=4.3 Score=49.12 Aligned_cols=37 Identities=30% Similarity=0.484 Sum_probs=32.7
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.-..|.|--|.|+||.- -+||||||....|++|++..
T Consensus 655 dLk~Gm~leg~Vrnv~~--fgafVdIgv~qDglvHis~l 691 (780)
T COG2183 655 DLKPGMILEGTVRNVVD--FGAFVDIGVHQDGLVHISQL 691 (780)
T ss_pred hccCCCEEEEEEEEeee--ccceEEeccccceeeeHHHh
Confidence 35689999999999987 58999999999999999764
No 82
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=75.28 E-value=6.1 Score=47.14 Aligned_cols=35 Identities=29% Similarity=0.438 Sum_probs=30.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|+++.+. ++||++ .+-.||||+++.
T Consensus 475 l~~G~iV~g~V~~v~~~--G~fV~l-~gv~Gll~~sel 509 (647)
T PRK00087 475 LEEGDVVEGEVKRLTDF--GAFVDI-GGVDGLLHVSEI 509 (647)
T ss_pred CCCCCEEEEEEEEEeCC--cEEEEE-CCEEEEEEHHHc
Confidence 34799999999999884 899999 578899998774
No 83
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=74.94 E-value=13 Score=35.13 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=37.3
Q ss_pred ceeeecCCC-hH-HHHHHHH----HHHhhCC----C--C--eeEEEeecCCCCCHHHHHHHHHHHHH
Q 005219 332 RIGVSRKIT-GV-ERTRLKV----IAKTLQP----E--G--FGLTIRTVAAGHSLEELQKDLEGLLS 384 (708)
Q Consensus 332 ~igiSrKI~-~~-eR~rLk~----i~~~l~p----~--~--~GvIiRTaA~g~~~eeL~~Dl~~L~~ 384 (708)
++.||||+. .. .|+|+|. ++....+ . | +=+|.|..+.+.+..+|.+|+..|+-
T Consensus 49 G~sVSKKv~~kAV~RNRiKR~lRE~fR~~~~~~~l~~~g~DiVviaR~~~~~~~~~~l~~~l~~l~~ 115 (118)
T PRK01492 49 GIKVSRKLNKKAVVRNKIKRRIRHLIRIIVSDSSFKAIKFAMIIIPRKGFEEINFSHLNYELSKIIL 115 (118)
T ss_pred EEEEecccCCchhhHHHHHHHHHHHHHHhCcccccCCCCceEEEEECCCcccCCHHHHHHHHHHHHH
Confidence 467899954 33 5776654 4444333 1 3 34788999999999999999988764
No 84
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=74.21 E-value=10 Score=35.52 Aligned_cols=53 Identities=28% Similarity=0.360 Sum_probs=36.3
Q ss_pred eeeecC-CChH-HHHHHHHHH----HhhC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRK-ITGV-ERTRLKVIA----KTLQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrK-I~~~-eR~rLk~i~----~~l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.|||| +... .|+++|.++ .... | -++=+|.|-.+.+++..+|.+|+..|.+.
T Consensus 49 ~~VsKK~~g~AV~RNriKR~lRe~~R~~~~~l~~~diVviar~~~~~~~~~~l~~~l~~ll~k 111 (114)
T PRK01732 49 LTVAKKNVKRAHERNRIKRLTRESFRLHQHELPAMDFVVIAKKGVADLDNRELFELLEKLWRR 111 (114)
T ss_pred EEEEcccCcchhHHHHHHHHHHHHHHHhhhcCCCCeEEEEeCCCcccCCHHHHHHHHHHHHHH
Confidence 457899 6654 577665544 3222 2 23445788999999999999999887654
No 85
>TIGR00188 rnpA ribonuclease P protein component, eubacterial. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead.
Probab=73.36 E-value=10 Score=34.76 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=36.1
Q ss_pred eeeecCCChH-HHHHHHHHH----HhhC---C-CCeeEEEeecCCCCCHHHHHHHHHHHH
Q 005219 333 IGVSRKITGV-ERTRLKVIA----KTLQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLL 383 (708)
Q Consensus 333 igiSrKI~~~-eR~rLk~i~----~~l~---p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~ 383 (708)
+.||||+... +|+++|.++ .... + -++=+|+|..+..++.++|.+++..|.
T Consensus 45 i~vsKK~g~AV~RNriKR~lRe~~R~~~~~l~~~d~v~i~r~~~~~~~~~~l~~~l~~l~ 104 (105)
T TIGR00188 45 LSVSKKVKNAVERNRIKRLIREVFRERQELLKALDVVVIVRKGFSELTYEAFLKLLLQLF 104 (105)
T ss_pred EEEecccCchhHHHHHHHHHHHHHHHhhcccCCccEEEEECCCcCcCCHHHHHHHHHHHh
Confidence 4579998764 577665544 3322 2 234578899999999999999988764
No 86
>PRK00038 rnpA ribonuclease P; Reviewed
Probab=72.77 E-value=20 Score=34.26 Aligned_cols=58 Identities=16% Similarity=0.338 Sum_probs=35.4
Q ss_pred ceeeecCC-Ch-HHHHHHHHHH----HhhC---C-CCeeEEEeecCCCCCHHHHHHH-HHHHHHHHHHH
Q 005219 332 RIGVSRKI-TG-VERTRLKVIA----KTLQ---P-EGFGLTIRTVAAGHSLEELQKD-LEGLLSTWKNI 389 (708)
Q Consensus 332 ~igiSrKI-~~-~eR~rLk~i~----~~l~---p-~~~GvIiRTaA~g~~~eeL~~D-l~~L~~~W~~I 389 (708)
++.||||. .. -+|+|+|..+ .... | .++=+|.|..+.+++.++|..+ ...|.++|..+
T Consensus 53 Gi~VsKKv~g~AV~RNRiKR~lRE~~R~~~~~l~~~D~VviaR~~~~~~~~~~l~~~~~~~~~~l~~~~ 121 (123)
T PRK00038 53 GLVIAKRFAARAVTRNTLKRVIREAFRARRLALPAQDYVVRLHSKLTPASLTALKRSARAEVDAHFTRI 121 (123)
T ss_pred EEEEecccCCCchhHHHHHHHHHHHHHHhhccCCCCCEEEEECCCCCcCCHHHHHHHHHHHHHHHHHHh
Confidence 35679995 44 3677765443 3222 2 3556788899999999999333 23345555543
No 87
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=71.69 E-value=8.7 Score=43.02 Aligned_cols=32 Identities=19% Similarity=0.266 Sum_probs=27.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~ 145 (708)
..|+|-.|+|.++.+ +.+|||+|. -.|||+.+
T Consensus 133 k~GeiV~G~V~~~~~--~~~~Vdlg~-vEa~LP~~ 164 (362)
T PRK12327 133 REGDIVTGVVQRRDN--RFVYVNLGK-IEAVLPPA 164 (362)
T ss_pred hcCCEEEEEEEEEeC--CcEEEEeCC-eEEEecHH
Confidence 789999999999988 589999987 68888653
No 88
>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=70.99 E-value=5.3 Score=34.11 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
|++..|+|+++.+ .++||+++.+-.||+++.+.
T Consensus 1 G~~V~g~V~~i~~--~g~~V~l~~~i~G~i~~~~l 33 (73)
T cd05703 1 GQEVTGFVNNVSK--EFVWLTISPDVKGRIPLLDL 33 (73)
T ss_pred CCEEEEEEEEEeC--CEEEEEeCCCcEEEEEHHHc
Confidence 7899999999965 59999999999999999874
No 89
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=69.61 E-value=27 Score=33.01 Aligned_cols=53 Identities=28% Similarity=0.471 Sum_probs=35.6
Q ss_pred eeeecCCC-hH-HHHHHH----HHHHhhC---CCC--eeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKIT-GV-ERTRLK----VIAKTLQ---PEG--FGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI~-~~-eR~rLk----~i~~~l~---p~~--~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||.. .. .|+++| +++..+. +.+ +=+|+|..+.+++..+|..|+..|..+
T Consensus 51 ~~VsKK~~~~AV~RNriKR~lRe~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k 114 (122)
T PRK03031 51 ISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQ 114 (122)
T ss_pred EEEecccccchhhhhHHHHHHHHHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHH
Confidence 45799964 33 566554 4444332 233 346778889999999999998777665
No 90
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=66.88 E-value=15 Score=43.93 Aligned_cols=36 Identities=31% Similarity=0.495 Sum_probs=32.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.+|.|+|++|.+ .++||+++.+-.||+++.+.
T Consensus 560 ~~~G~~v~g~V~~i~~--~G~fV~l~~~i~Gli~~sel 595 (647)
T PRK00087 560 YPVGSIVLGKVVRIAP--FGAFVELEPGVDGLVHISQI 595 (647)
T ss_pred ccCCeEEEEEEEEEEC--CeEEEEECCCCEEEEEhhhc
Confidence 4589999999999999 59999999999999998764
No 91
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=66.10 E-value=32 Score=32.50 Aligned_cols=53 Identities=30% Similarity=0.408 Sum_probs=36.5
Q ss_pred eeeec-CCChH-HHHHHHHH----HHh---hCC-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSR-KITGV-ERTRLKVI----AKT---LQP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSr-KI~~~-eR~rLk~i----~~~---l~p-~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||| ++... +|.|+|.+ +.. +.| .++=+|+|..+.+.+..+++++|.+++..
T Consensus 45 lsVsKkk~g~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~ 107 (117)
T COG0594 45 LTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKR 107 (117)
T ss_pred EEEEchhccchhhHHHHHHHHHHHHHhhhhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHH
Confidence 56799 77754 67666543 332 222 35668899999999999998887666554
No 92
>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=62.64 E-value=17 Score=43.97 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~-~k~aFL~~~d~ 147 (708)
.+|.+|.|+|++|.+ -++||++.. +-.||+|+.+.
T Consensus 626 ~iG~~~~g~V~~v~~--fGifV~L~~~~~eGlvhis~l 661 (709)
T TIGR02063 626 KIGEEFEGVISGVTS--FGLFVELENNTIEGLVHISTL 661 (709)
T ss_pred cCCcEEEEEEEEEEe--CCEEEEecCCceEEEEEeeec
Confidence 479999999999988 689999986 79999999875
No 93
>PRK11642 exoribonuclease R; Provisional
Probab=62.12 E-value=20 Score=44.27 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=30.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCC-cceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNS-RPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~-k~aFL~~~d~ 147 (708)
.+|.+|.|+|+.|.+. ++||++... -.||+++.+.
T Consensus 642 ~iGe~f~G~Is~V~~f--GifVeL~~~~vEGlV~vs~L 677 (813)
T PRK11642 642 QVGNVFKGVISSVTGF--GFFVRLDDLFIDGLVHVSSL 677 (813)
T ss_pred cCCcEEEEEEEEeecC--ceEEEECCCCeeeeEEEeec
Confidence 4799999999999884 999999864 9999999875
No 94
>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=61.76 E-value=11 Score=33.94 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=31.5
Q ss_pred ccCCeEEEEEeeecCCcceEEecc--------cCCcceeeEeccCCC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNI--------GNSRPSLMDIKHYRE 149 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDI--------G~~k~aFL~~~d~~~ 149 (708)
.+|+|=.|+|++|-+.+ |+||| ...-.|+|+..+.+.
T Consensus 5 ~~GDiVig~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~~dv~~ 49 (92)
T cd05791 5 KVGSIVIARVTRINPRF--AKVDILCVGGRPLKESFRGVIRKEDIRA 49 (92)
T ss_pred CCCCEEEEEEEEEcCCE--EEEEEEEecCeecCCCcccEEEHHHccc
Confidence 47999999999997554 99999 888899999888643
No 95
>PF00825 Ribonuclease_P: Ribonuclease P; InterPro: IPR000100 Ribonuclease P (3.1.26.5 from EC) (RNase P) [, , ] is a site specific endonuclease that generates mature tRNAs by catalysing the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. In bacteria RNase P is known to be composed of two components: a large RNA (about 400 base pairs) encoded by rnpB, and a small protein (119 to 133 amino acids) encoded by rnpA. The RNA moiety of RNase P carries the catalytic activity; the protein component plays an auxiliary, but essential, role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. The sequence of rnpA is not highly conserved, however there is, in the central part of the protein, a conserved basic region.; GO: 0000049 tRNA binding, 0004526 ribonuclease P activity, 0008033 tRNA processing; PDB: 1D6T_A 1A6F_A 2LJP_A 1NZ0_C 3Q1Q_A 3Q1R_A.
Probab=61.62 E-value=21 Score=32.79 Aligned_cols=53 Identities=34% Similarity=0.491 Sum_probs=34.9
Q ss_pred eeeecCCCh-H-HHHHHHHHHHh----hC---CCCe--eEEEeecCCCCCHHHHHHHHHHHHHH
Q 005219 333 IGVSRKITG-V-ERTRLKVIAKT----LQ---PEGF--GLTIRTVAAGHSLEELQKDLEGLLST 385 (708)
Q Consensus 333 igiSrKI~~-~-eR~rLk~i~~~----l~---p~~~--GvIiRTaA~g~~~eeL~~Dl~~L~~~ 385 (708)
+.||||+.. . .|+++|.++.+ .. +.++ =++.|..+...+.++|.+++..|..+
T Consensus 46 ~~vsKK~gk~AV~RNriKR~lRe~~R~~~~~l~~~~d~v~~~r~~~~~~~~~~l~~~l~~ll~k 109 (111)
T PF00825_consen 46 FSVSKKVGKRAVKRNRIKRRLREAFRLNKPELPPGYDIVFIARPGALELSFEELEKELKKLLKK 109 (111)
T ss_dssp EEE-STTSS-HHHHHHHHHHHHHHHHHCTTTS-SSSEEEEEE-CGGGGS-HHHHHHHHHHHHHH
T ss_pred EEecCccccchhHHHHHHHHHHHHHHHHHhhccCCcEEEEEEcCCcCcCCHHHHHHHHHHHHHh
Confidence 567999977 4 58777655433 22 2233 46777788899999999999888765
No 96
>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=60.20 E-value=38 Score=28.25 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=26.6
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 005219 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (708)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d 146 (708)
|++--|+|++|.+ .+|||++..+-.||++..+
T Consensus 1 G~~V~g~V~~i~~--~G~~v~l~~~v~g~v~~~~ 32 (66)
T cd05695 1 GMLVNARVKKVLS--NGLILDFLSSFTGTVDFLH 32 (66)
T ss_pred CCEEEEEEEEEeC--CcEEEEEcCCceEEEEHHH
Confidence 7788999999984 5699999667899997755
No 97
>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=53.42 E-value=31 Score=41.44 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=31.0
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeEeccC
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG-~~k~aFL~~~d~ 147 (708)
.+|.+|.|+|+.|.+ .++||++. .+-.||+++.+.
T Consensus 571 ~iG~~~~g~I~~v~~--~GifV~L~~~~veGlV~~s~l 606 (654)
T TIGR00358 571 KVGTEFSGEISSVTR--FGMFVRLDDNGIDGLIHISTL 606 (654)
T ss_pred CCCcEEEEEEEeEEc--CcEEEEecCCceEEEEEeEeC
Confidence 469999999999998 46999998 789999999875
No 98
>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=53.23 E-value=17 Score=32.58 Aligned_cols=31 Identities=39% Similarity=0.488 Sum_probs=27.1
Q ss_pred eEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 005219 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (708)
Q Consensus 115 IY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~ 148 (708)
+|.|+|+.|.+ .++||+++. -.||+++.+..
T Consensus 2 vv~g~V~~i~~--~GifV~l~~-v~G~v~~~~l~ 32 (99)
T cd04460 2 VVEGEVVEVVD--FGAFVRIGP-VDGLLHISQIM 32 (99)
T ss_pred EEEEEEEEEEe--ccEEEEEcC-eEEEEEEEEcc
Confidence 79999999988 599999984 89999998753
No 99
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=53.16 E-value=28 Score=37.81 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
.++|.-=.|+|+.|-+.|+ ||||.|..|.-|+++++.
T Consensus 71 ~tvg~~g~~~Vv~v~~~lG-aFlD~Gl~KDl~vp~~el 107 (287)
T COG2996 71 ATVGEYGWLKVVEVNKDLG-AFLDWGLPKDLLVPLDEL 107 (287)
T ss_pred EeecceeEEEEEEEcCCcc-eEEecCCCcceeeehhhc
Confidence 3689999999999999995 799999999999999874
No 100
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=48.68 E-value=41 Score=38.03 Aligned_cols=188 Identities=14% Similarity=0.160 Sum_probs=95.3
Q ss_pred cccCCCEEEEEEEecCCCCC-CceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cee-EEEeec
Q 005219 290 QVQKGTKVIVQVVKEGLGTK-GPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTV 366 (708)
Q Consensus 290 ~lk~Gq~ILVQV~KE~~gtK-GprLTt~IsL~GRylVl~P~~~~igiSrKI~~~eR~rLk~i~~~l~p~-~~G-vIiRTa 366 (708)
.+++||.|-|=|.+-...+| ||. +-+||.-.+ -|+.+++.-.|+ ..| +-|+..
T Consensus 176 ~~~~Gdrik~~i~~V~~~~k~gp~--------------------IilSRt~p~----~v~~Lfe~EVPEI~dG~VeIk~I 231 (374)
T PRK12328 176 KFKVGDVVKAVLKRVKIDKNNGIL--------------------IELSRTSPK----FLEALLELEVPEIKDGEVIIIHS 231 (374)
T ss_pred cCCCCCEEEEEEEEEecCCCCCCE--------------------EEEEcCCHH----HHHHHHHHhCccccCCeEEEEEE
Confidence 47789999888888777777 664 345665442 355666655564 224 456666
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEE-EcCHHHHHHH
Q 005219 367 AAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRTYHEV 445 (708)
Q Consensus 367 A~g~~~eeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~Ii-VDd~~~y~~i 445 (708)
|..+.. +++-+....+.++. +...|+-.....+..+.+.+-.+.++=|. -||+..|
T Consensus 232 ARepG~-------------------RtKVAV~S~d~~iD-PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~f--- 288 (374)
T PRK12328 232 ARIPGE-------------------RAKVALFSNNPNID-PIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIF--- 288 (374)
T ss_pred eccCcc-------------------eeEEEEEcCCCCCC-hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH---
Confidence 655441 01101001122222 34567776666677777776677777553 3445443
Q ss_pred HHHHH-hhCCCcCCceeeccCCCCcccccCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHH
Q 005219 446 TSYLQ-DIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKA 524 (708)
Q Consensus 446 ~~~l~-~~~p~~~~~v~~y~~~~plF~~y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet 524 (708)
+. .++|.....|.+- .+...+..+=-+.|+..|.++ .|-.+-.-.-=+-|-|||-|....-. ...+.
T Consensus 289 ---I~Nal~Pa~V~~V~i~-~~~~~~~V~V~~~qlslAIGk-----~GqNvrLA~~LtGwkIDI~s~~~~~~---~~~~~ 356 (374)
T PRK12328 289 ---IARALAPAIISSVKIE-EEEKKAIVTLLSDQKSKAIGK-----NGINIRLASMLTGYEIELNEIGSKEN---ASNES 356 (374)
T ss_pred ---HHHhCCCceeeEEEEc-CCCcEEEEEEChHHhhhhhcC-----CChhHHHHHHHhCCEEEEEECCCCcc---ccccc
Confidence 33 3567665555443 222222222223444444443 22222222222446788888753211 11223
Q ss_pred HHHHHHHHHHHH
Q 005219 525 ILDVNLAAAKQI 536 (708)
Q Consensus 525 ~lktNLEAA~EI 536 (708)
--.||.|..+.+
T Consensus 357 ~~~~~~~~~~~~ 368 (374)
T PRK12328 357 EKETNKEGVKAL 368 (374)
T ss_pred ccccccccHHHH
Confidence 345677766544
No 101
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=47.51 E-value=43 Score=26.99 Aligned_cols=37 Identities=8% Similarity=0.053 Sum_probs=33.7
Q ss_pred EEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeC
Q 005219 615 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVA 651 (708)
Q Consensus 615 ~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d 651 (708)
..+.+++..+.++.+.+...+.+|++.++..|.+..+
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~ 38 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD 38 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC
Confidence 5688999999999999999999999999999998665
No 102
>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=41.01 E-value=35 Score=34.09 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=30.5
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.++-|+|+++.+ .++||++|. -.|+++..+.
T Consensus 79 p~~gEvv~G~V~~v~~--~GifV~lg~-~~gi~~~~~l 113 (179)
T TIGR00448 79 PELGEIVEGEVIEIVE--FGAFVSLGP-FDGLFHVSQV 113 (179)
T ss_pred ccCCCEEEEEEEEEEe--eEEEEEeCC-ceEEEEcHHh
Confidence 4479999999999999 599999985 8899988775
No 103
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=39.03 E-value=85 Score=25.07 Aligned_cols=39 Identities=8% Similarity=-0.003 Sum_probs=34.5
Q ss_pred EEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCCC
Q 005219 615 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARG 653 (708)
Q Consensus 615 ~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~~ 653 (708)
..+.+++..+.++.+.+...+..|++.++..|.+.+...
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~ 40 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC
Confidence 467889999999999999999999999999999887655
No 104
>PHA02945 interferon resistance protein; Provisional
Probab=30.76 E-value=1.6e+02 Score=27.05 Aligned_cols=32 Identities=13% Similarity=0.138 Sum_probs=24.7
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEecc
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDIG--~~k~aFL~~~d 146 (708)
.|.|=+|+|.. .=.+|||+.- .++.||++++.
T Consensus 11 ~GelvigtV~~---~d~ga~v~L~EY~g~eg~i~~se 44 (88)
T PHA02945 11 VGDVLKGKVYE---NGYALYIDLFDYPHSEAILAESV 44 (88)
T ss_pred CCcEEEEEEEe---cCceEEEEecccCCcEEEEEeeh
Confidence 69999999999 4468888774 36788887764
No 105
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=29.95 E-value=1.3e+02 Score=30.19 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=30.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~ 147 (708)
..+|.++.|+|+++.+ .++||++|. -.||++..+.
T Consensus 79 P~~GEVv~g~V~~v~~--~Gi~V~lg~-~~g~v~~~~l 113 (187)
T PRK08563 79 PELQEVVEGEVVEVVE--FGAFVRIGP-VDGLLHISQI 113 (187)
T ss_pred ccCCCEEEEEEEEEEc--cEEEEEEeC-ceEEEEcHHc
Confidence 4579999999999987 699999994 8899988764
No 106
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=29.69 E-value=1.3e+02 Score=28.94 Aligned_cols=45 Identities=20% Similarity=0.127 Sum_probs=33.9
Q ss_pred CeEEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCCCCCCcCeEEEE
Q 005219 613 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 613 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~~l~~~~~~i~~ 663 (708)
+.++|+|||+-.+.+... +..+-...+ +.|.+||.+..+.+-|..
T Consensus 114 ~~v~I~v~P~d~~~l~~~----l~~~~~~~~--~~i~~D~~l~~G~c~vet 158 (166)
T TIGR02499 114 GRLTLRVHPEQLDEVREA----LAERLALEP--WELEPDASLAPGACVLET 158 (166)
T ss_pred CceEEEECHHHHHHHHHH----HHHHhccCC--eEEeeCCCCCCCCEEEEe
Confidence 468999999999988643 233323333 889999999999988875
No 107
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=28.96 E-value=1.2e+02 Score=29.21 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=37.4
Q ss_pred hcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCC-CcEEeccCCceeEEEeecC
Q 005219 541 RLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRS-MVKVSELSRHGLMEITRKR 597 (708)
Q Consensus 541 RLRnIGGIIVIDFIDM~~~~~r~~V~~~Lk~alk~Dr~-k~~V~~iT~lGLvEmTRkR 597 (708)
.|...+|+|+|||-++. .+ + .+.+++.+..|+. -.-..+.|.-||==+.|=.
T Consensus 26 ~l~~~sglv~lDiD~l~-~e---e-~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~~ 78 (136)
T PF08800_consen 26 NLKAYSGLVVLDIDHLD-PE---E-AEELRQLLFEDPYTLAAFVSPSGRGVKIIVPFD 78 (136)
T ss_pred hhhhCCCcEEEEeCCCC-HH---H-HHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEec
Confidence 35568999999998886 32 3 3677888888874 5566677778876666543
No 108
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=28.66 E-value=49 Score=35.75 Aligned_cols=34 Identities=18% Similarity=0.462 Sum_probs=26.7
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeEecc
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG--~~k~aFL~~~d 146 (708)
-.|.|-.|+|++|... +|||+.- .++.||+|+++
T Consensus 10 eeGEiVv~tV~~V~~~--GAyv~L~EY~g~Eg~ihiSE 45 (269)
T COG1093 10 EEGEIVVGTVKQVADY--GAYVELDEYPGKEGFIHISE 45 (269)
T ss_pred CCCcEEEEEEEEeecc--ccEEEeeccCCeeeeEEHHH
Confidence 4799999999999874 7888764 45778887765
No 109
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=27.88 E-value=2.1e+02 Score=26.01 Aligned_cols=45 Identities=13% Similarity=0.036 Sum_probs=33.8
Q ss_pred CeEEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCCCCCCcCeEEEE
Q 005219 613 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 613 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~~l~~~~~~i~~ 663 (708)
+.++|+|||+-.+++..... .....++. .|.+|+.+..+.+.|..
T Consensus 68 ~~v~I~v~p~d~~~l~~~~~----~~~~~~~~--~l~~D~~l~~G~c~iet 112 (128)
T PF02108_consen 68 EKVTIRVHPDDYEALEELLE----DELPELGW--ELVADPSLAPGDCRIET 112 (128)
T ss_pred CCeEEEECHHHHHHHHHHHH----HHHhhcCC--EEEecCCCCCCCEEEEE
Confidence 46899999999998865322 22233333 89999999999999985
No 110
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=27.88 E-value=32 Score=34.33 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=21.7
Q ss_pred HHHhCCceeCCCCcEEEEecccceE
Q 005219 480 NNMLSKRVPLPNGGSLVIEQTEALV 504 (708)
Q Consensus 480 e~al~r~V~L~sGG~LVIE~TEALt 504 (708)
=.-|.+.||++-|+++||+++|-+-
T Consensus 52 P~KfRksiWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 52 PAKFRKSIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred CHhhhhceEEeeCCEEEEccccccc
Confidence 3457789999999999999999876
No 111
>PRK06937 type III secretion system protein; Reviewed
Probab=27.18 E-value=1.1e+02 Score=31.32 Aligned_cols=47 Identities=9% Similarity=0.164 Sum_probs=35.1
Q ss_pred CeEEEEECHHHHHHHHcCchhhHHHHHhhcC--CeEEEEeCCCCCCcCeEEEE
Q 005219 613 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLK--AWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 613 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~--~~I~i~~d~~l~~~~~~i~~ 663 (708)
..++|+|||+-.+++.... ..+-..++ .++.|.+||++.++..-|..
T Consensus 131 ~~v~I~V~P~D~~~v~~~~----~~~~~~~~~~~~l~i~~D~~L~~Ggc~iET 179 (204)
T PRK06937 131 KQVVVRVNPDQAAAVREQI----AKVLKDFPEVGYLEVVADARLDQGGCILET 179 (204)
T ss_pred CeEEEEECHHHHHHHHHHH----HHHHHhCCCCccEEEEeCCCCCCCCeEEec
Confidence 4689999999999997533 22222322 46899999999999988874
No 112
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=25.88 E-value=1.5e+02 Score=30.27 Aligned_cols=46 Identities=13% Similarity=0.235 Sum_probs=35.6
Q ss_pred eEEEEECHHHHHHHHcCchhhHHHH--HhhcCCeEEEEeCCCCCCcCeEEEE
Q 005219 614 RFILRVDHHMCNYLTSGKRTRLAVL--SSSLKAWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 614 ~~~l~v~p~v~~~l~~~~~~~l~~L--e~~~~~~I~i~~d~~l~~~~~~i~~ 663 (708)
.++|+|||...+.+... +..+ ...+...+.|.+||++..+...|..
T Consensus 129 ~v~I~v~P~d~~~l~~~----l~~~~~~~~~~~~~~l~~D~~L~~G~c~vet 176 (199)
T PRK06032 129 HLVVRVNDALVEAARER----LERLARESGFEGRLVVLADPDMAPGDCRLEW 176 (199)
T ss_pred cEEEEECHHHHHHHHHH----HHHHHHhcCcCccEEEeeCCCCCCCCeEEEe
Confidence 68999999988887542 2222 2245677899999999999999987
No 113
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=25.54 E-value=2.1e+02 Score=27.59 Aligned_cols=48 Identities=29% Similarity=0.302 Sum_probs=33.4
Q ss_pred HhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCC
Q 005219 540 LRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSR 587 (708)
Q Consensus 540 LRLRnIGGIIVIDFIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~ 587 (708)
+.-++.-=+||+=-+|+.+..++....+.+++.++.......++.+|.
T Consensus 125 ~~~~~~pviiv~nK~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~Sa 172 (179)
T TIGR03598 125 LRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSS 172 (179)
T ss_pred HHHcCCCEEEEEECcccCCHHHHHHHHHHHHHHHhhccCCCceEEEEC
Confidence 333456667888888987777777888899999987543445555543
No 114
>PRK09098 type III secretion system protein HrpB; Validated
Probab=24.44 E-value=1.4e+02 Score=31.40 Aligned_cols=47 Identities=9% Similarity=-0.043 Sum_probs=36.3
Q ss_pred CeEEEEECHHHHHHHHcCchhhHHHHHhhcC--CeEEEEeCCCCCCcCeEEEE
Q 005219 613 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLK--AWILLKVARGFTRGAFEVIP 663 (708)
Q Consensus 613 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~--~~I~i~~d~~l~~~~~~i~~ 663 (708)
..++|+|||+-.+.+... +..+....+ ..+.|.+||++.++..-|..
T Consensus 151 ~~v~IrV~P~D~~~v~~~----~~~~~~~~g~~~~l~Iv~Dp~L~~GgCviET 199 (233)
T PRK09098 151 SYLTVRVHPADLDAARAA----FGAAAAAGGRNVPVEVVGDPRLAPGACVCEW 199 (233)
T ss_pred CcEEEEECHHHHHHHHHH----HHHHHHhcCCCcceEEEeCCCCCCCCeEEEe
Confidence 478999999999998643 333333344 57889999999999998886
No 115
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=24.04 E-value=1.9e+02 Score=33.55 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=20.7
Q ss_pred cccCCeEEEEEeeecCCcceEEeccc
Q 005219 110 VQCDSVYLGVVTKLVPNMGGAFVNIG 135 (708)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVDIG 135 (708)
..+|.|-.|+|.++..+ ..+||+|
T Consensus 150 ~~~GeIV~G~V~r~e~~--~viv~l~ 173 (449)
T PRK12329 150 DLEDTVLTARVLRFERQ--SVIMAVS 173 (449)
T ss_pred HhcCcEEEEEEEEEcCC--CEEEEec
Confidence 46899999999999886 6899984
No 116
>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=22.55 E-value=1.2e+02 Score=27.43 Aligned_cols=33 Identities=21% Similarity=0.205 Sum_probs=29.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 005219 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (708)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~ 145 (708)
.+|++=.|+|+.+. -..-+||||..-+|+|++.
T Consensus 5 ~~gD~VIG~V~~~~--~~~~~VdI~s~~~a~L~~~ 37 (86)
T cd05790 5 AKGDHVIGIVVAKA--GDFFKVDIGGSEPASLSYL 37 (86)
T ss_pred CCCCEEEEEEEEEc--CCeEEEEcCCCcceEechH
Confidence 57999999999995 4889999999999999764
No 117
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=22.48 E-value=1.7e+02 Score=25.15 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhc
Q 005219 531 AAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVER 575 (708)
Q Consensus 531 EAA~EIARQLRLRnIGGIIVIDFIDM~~~~~r~~V~~~Lk~alk~ 575 (708)
+-|.+|+.+||=. -++++||-+|..+. .+.+++.|..+...
T Consensus 10 ~D~~~i~~~l~~g---~~Vivnl~~l~~~~-~~Ri~Dfl~G~~~a 50 (73)
T PF04472_consen 10 EDAREIVDALREG---KIVIVNLENLDDEE-AQRILDFLSGAVYA 50 (73)
T ss_dssp GGHHHHHHHHHTT-----EEEE-TTS-HHH-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcC---CEEEEECCCCCHHH-HHHHHHHHhchhee
Confidence 4578899999865 57999999998776 56677888887754
No 118
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=21.93 E-value=5.6e+02 Score=27.93 Aligned_cols=150 Identities=15% Similarity=0.145 Sum_probs=76.9
Q ss_pred eeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccC----------CCCcccccCHH-HH
Q 005219 410 ILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDK----------RIPLFDKFNIE-EE 478 (708)
Q Consensus 410 ~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~----------~~plF~~y~Ie-~q 478 (708)
.+++..+.....-++..+...+..+.+|+.+..+.+.++.........--+++.-+ ......+||+. ++
T Consensus 74 ~I~~~~p~k~~~~l~~a~~~g~~~~~ids~~el~~l~~~a~~~~~~~~v~lRv~~~~~~~~~~~~~~g~~~srfGi~~~e 153 (373)
T cd06828 74 RIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVALRVNPGVDAGTHPYISTGGKDSKFGIPLEQ 153 (373)
T ss_pred cEEEeCCCCCHHHHHHHHHcCCeEEEECCHHHHHHHHHHHHhcCCCCeEEEEECCCCCCCCCCCeecCCCCCCCCCCHHH
Confidence 57777765555667777777778899999998888888775421111111122100 01223677864 23
Q ss_pred HHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-------hcccCCCcEEE
Q 005219 479 INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIAREL-------RLRDIGGIIVV 551 (708)
Q Consensus 479 Ie~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQL-------RLRnIGGIIVI 551 (708)
+.+++..--.+++ -. +.-|=...|. .......+..+++.+.+++..| +.-|+||=.-+
T Consensus 154 ~~~~~~~~~~~~~-l~--------l~Gi~~H~gs------~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~idiGGG~~~ 218 (373)
T cd06828 154 ALEAYRRAKELPG-LK--------LVGLHCHIGS------QILDLEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGI 218 (373)
T ss_pred HHHHHHHHHhCCC-Cc--------EEEEEEecCC------CCCCHHHHHHHHHHHHHHHHHHHhcCCCCCEEEeCCCCCc
Confidence 4444433222221 11 2223333332 1112245677777777777776 45677765555
Q ss_pred EcCCCCChhhHHHHHHHHHHHHh
Q 005219 552 DFIDMADDSNKRLVYEEVKKAVE 574 (708)
Q Consensus 552 DFIDM~~~~~r~~V~~~Lk~alk 574 (708)
.+......-+-.++.+.+.++++
T Consensus 219 ~~~~~~~~~~~~~~~~~i~~~~~ 241 (373)
T cd06828 219 PYRDEDEPLDIEEYAEAIAEALK 241 (373)
T ss_pred ccCCCCCCCCHHHHHHHHHHHHH
Confidence 55332111233344444544444
No 119
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.80 E-value=1.2e+02 Score=24.63 Aligned_cols=38 Identities=5% Similarity=0.070 Sum_probs=33.4
Q ss_pred EEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCC
Q 005219 615 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVAR 652 (708)
Q Consensus 615 ~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~ 652 (708)
..+.|++..+.+|.+.+...+..|++++|..|.+-...
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~ 39 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG 39 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC
Confidence 46889999999999999999999999999998876654
No 120
>COG3585 MopI Molybdopterin-binding protein [Coenzyme metabolism]
Probab=21.35 E-value=62 Score=28.24 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=20.4
Q ss_pred cCCeEEEEEeeecCCcceEEecc
Q 005219 112 CDSVYLGVVTKLVPNMGGAFVNI 134 (708)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVDI 134 (708)
.-|+++|+|+.|++|+=-+=|+|
T Consensus 5 aRN~lKG~Vk~iv~G~Vnsev~i 27 (69)
T COG3585 5 ARNQLKGKVKEIVKGSVNSEVTI 27 (69)
T ss_pred hhheeccEEEEEEEcccceEEEE
Confidence 45999999999999998888777
No 121
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=21.17 E-value=4.6e+02 Score=27.55 Aligned_cols=108 Identities=18% Similarity=0.219 Sum_probs=72.4
Q ss_pred HHHHHHHh-cCCCCcEEeccCCceeEEEeecCCCcccccCCCCCCCCCeEEEEECHHHHHHHHcCchhhHHHHHhhcCCe
Q 005219 567 EEVKKAVE-RDRSMVKVSELSRHGLMEITRKRAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAW 645 (708)
Q Consensus 567 ~~Lk~alk-~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~ 645 (708)
..++..|+ .|-.+++|..+++-+=+++|-+-.... .. ..-+.+.++|..+..|...+...+..|.+.++..
T Consensus 106 ~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG---~L-----~~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~ 177 (235)
T PRK04163 106 TDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLG---KI-----EGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCD 177 (235)
T ss_pred hhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCC---cc-----CCCEEEEECHHHHHhhcCCCChhHhhhhhhhCcE
Confidence 35566676 588999999998766677775433211 10 1247899999999999877777889999999999
Q ss_pred EEEEeCCCCCCcCeEEEEeecCccccchhhhHHHHhhhhhhhhccCC
Q 005219 646 ILLKVARGFTRGAFEVIPYTDDKASENQHQVAISLLRSAEARANKSG 692 (708)
Q Consensus 646 I~i~~d~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 692 (708)
|.+-.+ ....|.. .+...-..+..++..-|..++-+|
T Consensus 178 I~ig~N-----G~VwI~~-----~~~~~~~~a~~~I~~~e~~~~~~~ 214 (235)
T PRK04163 178 IIVGQN-----GRIWIKG-----PDEEDEEIAIEAIKKIEREAHTSG 214 (235)
T ss_pred EEEcCC-----cEEEEee-----CCHHHHHHHHHHHHHHHhhhhccC
Confidence 877654 4455554 223334456666666666555554
No 122
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=21.10 E-value=1.1e+02 Score=23.26 Aligned_cols=27 Identities=22% Similarity=0.402 Sum_probs=21.4
Q ss_pred CCeEEEEEeeecCC--cceEEecccCCcc
Q 005219 113 DSVYLGVVTKLVPN--MGGAFVNIGNSRP 139 (708)
Q Consensus 113 GnIY~GrV~kV~Pg--mqAAFVDIG~~k~ 139 (708)
|.-|.|+|.++.++ ..--|+|+|....
T Consensus 12 ~~wyra~V~~~~~~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 12 GKWYRAKITSILSDGKVEVFFVDYGNTEV 40 (48)
T ss_pred CeEEEEEEEEECCCCcEEEEEEcCCCcEE
Confidence 78999999999953 4567889987644
No 123
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=21.09 E-value=59 Score=28.97 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=19.4
Q ss_pred HHHHhCCceeCCCCcEEEEeccc
Q 005219 479 INNMLSKRVPLPNGGSLVIEQTE 501 (708)
Q Consensus 479 Ie~al~r~V~L~sGG~LVIE~TE 501 (708)
|-.-|.++||.+-|+|+++++.+
T Consensus 29 iP~KfRk~iWIkrGd~VlV~p~~ 51 (78)
T cd05792 29 MPTKFRKNIWIKRGDFVLVEPIE 51 (78)
T ss_pred echhhcccEEEEeCCEEEEEecc
Confidence 34567899999999999998866
No 124
>PF07013 DUF1314: Protein of unknown function (DUF1314); InterPro: IPR010741 This family consists of several alphaherpesvirus proteins of around 200 residues in length. They belong to the varicellovirus ORF2 family and their function is unknown.
Probab=20.95 E-value=73 Score=32.40 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=27.6
Q ss_pred HHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCC
Q 005219 478 EINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGH 517 (708)
Q Consensus 478 qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~ 517 (708)
-++.+-.|.|.||+||++.|-.+-.-+ |+|++++.|
T Consensus 4 Ll~~LaGR~iDLPgG~el~I~~~~g~~----~~~~f~~~g 39 (177)
T PF07013_consen 4 LLRSLAGRTIDLPGGDELRISANTGRP----NTGKFVRSG 39 (177)
T ss_pred hhhhhcCcceecCCCCeEEEecCCCCc----eEEEEecCC
Confidence 467788999999999999987665554 677765544
No 125
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.77 E-value=70 Score=26.30 Aligned_cols=15 Identities=60% Similarity=1.012 Sum_probs=12.9
Q ss_pred ceeCCCCcEEEEecc
Q 005219 486 RVPLPNGGSLVIEQT 500 (708)
Q Consensus 486 ~V~L~sGG~LVIE~T 500 (708)
||+|.+||-||+|-+
T Consensus 22 RvPleGGGRLVvEl~ 36 (51)
T PF11314_consen 22 RVPLEGGGRLVVELN 36 (51)
T ss_pred EEecCCCcEEEEEeC
Confidence 789999999998743
Done!