Query 007008
Match_columns 621
No_of_seqs 241 out of 1086
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 17:37:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007008hhsearch_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 3E-123 6E-128 1016.5 48.4 414 74-620 1-415 (489)
2 TIGR00757 RNaseEG ribonuclease 100.0 3E-120 7E-125 977.5 45.4 401 88-620 1-403 (414)
3 PRK10811 rne ribonuclease E; R 100.0 2E-113 3E-118 970.8 46.4 410 76-620 2-414 (1068)
4 COG1530 CafA Ribonucleases G a 100.0 9.4E-99 2E-103 825.9 35.9 406 75-621 1-409 (487)
5 PF10150 RNase_E_G: Ribonuclea 100.0 4.5E-82 9.8E-87 649.3 26.2 270 318-599 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.6 4E-16 8.6E-21 135.9 8.5 40 108-147 3-42 (88)
7 PF00575 S1: S1 RNA binding do 97.7 0.00019 4.1E-09 59.3 7.7 36 110-147 2-37 (74)
8 cd04472 S1_PNPase S1_PNPase: P 97.4 0.00058 1.3E-08 55.0 6.9 33 113-147 1-33 (68)
9 cd05704 S1_Rrp5_repeat_hs13 S1 97.1 0.0016 3.5E-08 54.5 6.8 35 112-147 3-37 (72)
10 COG1098 VacB Predicted RNA bin 97.1 0.00052 1.1E-08 63.8 4.1 36 111-148 4-39 (129)
11 cd05692 S1_RPS1_repeat_hs4 S1_ 97.0 0.003 6.4E-08 50.6 7.2 33 113-147 1-33 (69)
12 smart00316 S1 Ribosomal protei 97.0 0.0028 6E-08 50.4 6.8 34 112-147 2-35 (72)
13 PTZ00248 eukaryotic translatio 96.9 0.046 1E-06 58.7 16.9 35 111-147 16-52 (319)
14 cd05698 S1_Rrp5_repeat_hs6_sc5 96.7 0.0054 1.2E-07 50.2 6.7 33 113-147 1-33 (70)
15 cd05685 S1_Tex S1_Tex: The C-t 96.6 0.0058 1.2E-07 48.8 5.9 33 113-147 1-33 (68)
16 cd04461 S1_Rrp5_repeat_hs8_sc7 96.6 0.007 1.5E-07 51.6 6.7 36 110-147 12-47 (83)
17 PRK07252 hypothetical protein; 96.5 0.008 1.7E-07 55.8 7.4 34 112-147 3-36 (120)
18 PRK08059 general stress protei 96.4 0.01 2.2E-07 55.0 7.0 36 110-147 5-40 (123)
19 cd05707 S1_Rrp5_repeat_sc11 S1 96.4 0.0098 2.1E-07 48.6 6.1 33 113-147 1-33 (68)
20 cd05684 S1_DHX8_helicase S1_DH 96.3 0.015 3.3E-07 49.0 7.0 33 113-147 1-36 (79)
21 cd05687 S1_RPS1_repeat_ec1_hs1 96.3 0.016 3.5E-07 47.5 6.9 33 113-147 1-33 (70)
22 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.0 0.02 4.3E-07 46.9 6.4 32 113-146 1-32 (69)
23 cd05686 S1_pNO40 S1_pNO40: pNO 96.0 0.032 6.8E-07 46.6 7.4 34 112-147 3-37 (73)
24 cd05706 S1_Rrp5_repeat_sc10 S1 96.0 0.036 7.8E-07 45.8 7.6 34 112-147 3-36 (73)
25 cd04452 S1_IF2_alpha S1_IF2_al 95.7 0.038 8.3E-07 45.7 6.9 34 112-147 3-38 (76)
26 PRK08582 hypothetical protein; 95.7 0.032 6.9E-07 53.0 7.1 35 111-147 4-38 (139)
27 COG0539 RpsA Ribosomal protein 95.7 0.021 4.5E-07 65.1 6.7 36 109-147 189-224 (541)
28 cd05691 S1_RPS1_repeat_ec6 S1_ 95.6 0.041 8.9E-07 45.0 6.7 33 113-147 1-33 (73)
29 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.5 0.049 1.1E-06 45.4 6.8 34 113-147 1-35 (71)
30 cd05688 S1_RPS1_repeat_ec3 S1_ 95.4 0.043 9.3E-07 43.9 5.8 33 112-147 1-33 (68)
31 cd05694 S1_Rrp5_repeat_hs2_sc2 95.1 0.074 1.6E-06 45.1 6.7 34 111-146 3-37 (74)
32 TIGR02696 pppGpp_PNP guanosine 95.1 0.042 9E-07 64.5 6.7 59 87-147 608-680 (719)
33 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.1 0.11 2.3E-06 44.5 7.6 35 111-147 5-39 (86)
34 PRK05807 hypothetical protein; 94.9 0.11 2.3E-06 49.3 7.8 34 111-147 4-37 (136)
35 cd04455 S1_NusA S1_NusA: N-uti 94.9 0.1 2.3E-06 42.9 6.8 33 111-146 2-34 (67)
36 TIGR03591 polynuc_phos polyrib 94.8 0.055 1.2E-06 63.5 7.1 36 110-147 616-651 (684)
37 cd05708 S1_Rrp5_repeat_sc12 S1 94.7 0.12 2.7E-06 42.5 6.8 34 112-147 2-36 (77)
38 PRK11824 polynucleotide phosph 94.5 0.1 2.2E-06 61.5 8.0 36 110-147 619-654 (693)
39 cd05705 S1_Rrp5_repeat_hs14 S1 94.4 0.12 2.5E-06 43.8 6.3 35 111-147 2-36 (74)
40 cd04454 S1_Rrp4_like S1_Rrp4_l 94.4 0.17 3.8E-06 42.9 7.4 34 111-146 5-38 (82)
41 PRK03987 translation initiatio 94.4 0.18 3.8E-06 52.9 8.8 35 111-147 7-43 (262)
42 cd00164 S1_like S1_like: Ribos 94.0 0.13 2.7E-06 40.0 5.3 29 116-146 1-29 (65)
43 PRK09521 exosome complex RNA-b 93.9 0.4 8.7E-06 47.5 9.8 36 109-146 61-106 (189)
44 PLN00207 polyribonucleotide nu 93.1 0.18 4E-06 60.6 6.9 35 111-147 752-787 (891)
45 PRK04163 exosome complex RNA-b 92.9 0.77 1.7E-05 47.2 10.3 45 101-147 50-96 (235)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 91.8 0.17 3.7E-06 41.0 3.2 33 113-147 1-33 (69)
47 cd05689 S1_RPS1_repeat_ec4 S1_ 91.6 0.23 5E-06 40.8 3.9 34 112-147 3-36 (72)
48 PRK14865 rnpA ribonuclease P; 91.5 0.91 2E-05 41.8 8.0 54 332-385 48-110 (116)
49 PRK07899 rpsA 30S ribosomal pr 91.2 0.45 9.7E-06 54.0 6.7 35 110-147 206-240 (486)
50 PRK00588 rnpA ribonuclease P; 90.9 1.2 2.6E-05 41.3 8.1 53 332-384 46-108 (118)
51 PRK13806 rpsA 30S ribosomal pr 90.4 0.64 1.4E-05 52.7 7.1 36 110-147 200-235 (491)
52 PRK07400 30S ribosomal protein 90.3 0.64 1.4E-05 49.9 6.7 36 110-147 29-64 (318)
53 PRK03459 rnpA ribonuclease P; 90.2 1.6 3.5E-05 40.7 8.5 54 332-385 51-114 (122)
54 PRK07400 30S ribosomal protein 90.0 0.76 1.6E-05 49.4 7.0 38 107-147 191-228 (318)
55 PRK00396 rnpA ribonuclease P; 89.5 1.8 3.9E-05 40.9 8.2 58 333-393 50-117 (130)
56 PRK13806 rpsA 30S ribosomal pr 89.4 0.84 1.8E-05 51.7 7.0 38 108-147 288-325 (491)
57 cd04465 S1_RPS1_repeat_ec2_hs2 89.1 0.42 9.1E-06 38.9 3.3 32 113-147 1-32 (67)
58 PRK06299 rpsA 30S ribosomal pr 89.1 0.88 1.9E-05 52.1 7.0 35 110-147 199-233 (565)
59 cd05702 S1_Rrp5_repeat_hs11_sc 88.9 0.49 1.1E-05 39.0 3.6 33 113-147 1-33 (70)
60 cd04471 S1_RNase_R S1_RNase_R: 88.5 0.52 1.1E-05 39.4 3.5 34 112-147 1-35 (83)
61 PRK12269 bifunctional cytidyla 88.2 1.7 3.7E-05 52.7 8.8 38 108-147 574-611 (863)
62 TIGR00717 rpsA ribosomal prote 87.7 1.3 2.7E-05 50.1 7.0 36 110-147 357-392 (516)
63 PRK00499 rnpA ribonuclease P; 87.6 3.1 6.8E-05 38.0 8.3 55 332-386 41-105 (114)
64 PRK04390 rnpA ribonuclease P; 87.5 3.2 7E-05 38.5 8.4 53 333-385 48-110 (120)
65 COG0539 RpsA Ribosomal protein 87.4 0.96 2.1E-05 51.9 5.8 68 76-147 243-310 (541)
66 cd04473 S1_RecJ_like S1_RecJ_l 86.8 0.93 2E-05 38.3 4.1 35 110-146 14-48 (77)
67 PRK09202 nusA transcription el 86.5 1.5 3.2E-05 49.8 6.6 122 290-461 171-296 (470)
68 PRK07899 rpsA 30S ribosomal pr 86.4 1.7 3.6E-05 49.5 7.0 36 110-147 291-326 (486)
69 PRK12269 bifunctional cytidyla 85.9 1.7 3.6E-05 52.7 7.1 35 110-147 491-525 (863)
70 PRK01313 rnpA ribonuclease P; 85.8 3.9 8.6E-05 38.6 8.1 52 333-384 51-113 (129)
71 PRK06299 rpsA 30S ribosomal pr 84.6 2.3 4.9E-05 48.8 7.1 36 110-147 371-406 (565)
72 PRK06676 rpsA 30S ribosomal pr 84.4 2.3 5E-05 46.3 6.8 35 110-147 190-224 (390)
73 PRK00038 rnpA ribonuclease P; 82.2 7.6 0.00016 36.4 8.3 52 332-383 53-118 (123)
74 cd05693 S1_Rrp5_repeat_hs1_sc1 82.2 1.4 3.1E-05 39.5 3.4 35 111-147 2-36 (100)
75 PRK01903 rnpA ribonuclease P; 81.9 8 0.00017 36.7 8.5 53 333-385 54-129 (133)
76 COG1185 Pnp Polyribonucleotide 81.4 1.3 2.8E-05 51.9 3.5 38 108-147 615-652 (692)
77 PRK01492 rnpA ribonuclease P; 81.3 6.6 0.00014 36.4 7.5 53 332-384 49-115 (118)
78 PRK04820 rnpA ribonuclease P; 81.0 8 0.00017 37.3 8.2 55 332-386 51-115 (145)
79 TIGR00188 rnpA ribonuclease P 81.0 4.9 0.00011 36.2 6.4 51 333-383 45-104 (105)
80 PRK06676 rpsA 30S ribosomal pr 80.9 4.5 9.8E-05 44.1 7.4 36 110-147 15-51 (390)
81 COG2183 Tex Transcriptional ac 80.9 2.4 5.2E-05 50.4 5.5 37 109-147 655-691 (780)
82 TIGR01953 NusA transcription t 79.9 4.3 9.4E-05 44.2 6.7 101 291-435 170-272 (341)
83 PRK01732 rnpA ribonuclease P; 79.5 6.3 0.00014 36.3 6.7 53 333-385 49-111 (114)
84 PRK12327 nusA transcription el 79.0 4.1 9E-05 44.8 6.3 32 111-145 133-164 (362)
85 PRK00087 4-hydroxy-3-methylbut 78.4 4.1 9E-05 47.8 6.5 35 110-147 475-509 (647)
86 cd05703 S1_Rrp5_repeat_hs12_sc 76.8 3 6.6E-05 35.0 3.5 33 113-147 1-33 (73)
87 TIGR00717 rpsA ribosomal prote 75.1 2.5 5.5E-05 47.7 3.5 36 110-147 270-305 (516)
88 COG0594 RnpA RNase P protein c 74.8 17 0.00037 33.7 8.2 54 333-386 45-108 (117)
89 PRK00730 rnpA ribonuclease P; 73.1 9.6 0.00021 36.6 6.3 53 332-385 49-110 (138)
90 PF00825 Ribonuclease_P: Ribon 71.9 10 0.00022 34.3 5.9 54 333-386 46-110 (111)
91 PRK00087 4-hydroxy-3-methylbut 70.1 11 0.00024 44.2 7.3 36 110-147 560-595 (647)
92 PRK03031 rnpA ribonuclease P; 70.1 25 0.00054 32.6 8.2 54 333-386 51-115 (122)
93 cd05695 S1_Rrp5_repeat_hs3 S1_ 66.0 25 0.00054 28.8 6.6 32 113-146 1-32 (66)
94 cd05791 S1_CSL4 S1_CSL4: CSL4, 65.9 7.5 0.00016 34.4 3.6 36 111-148 5-48 (92)
95 COG2996 Predicted RNA-bindinin 64.4 14 0.00029 39.4 5.7 37 110-147 71-107 (287)
96 TIGR02063 RNase_R ribonuclease 63.0 15 0.00032 43.7 6.5 35 111-147 626-661 (709)
97 PRK12328 nusA transcription el 60.9 18 0.0004 40.0 6.2 188 290-536 176-368 (374)
98 PRK11642 exoribonuclease R; Pr 59.6 22 0.00047 43.2 7.1 35 111-147 642-677 (813)
99 COG1093 SUI2 Translation initi 56.4 21 0.00045 37.8 5.4 35 111-147 10-46 (269)
100 cd04460 S1_RpoE S1_RpoE: RpoE, 54.2 14 0.00031 32.5 3.4 31 115-148 2-32 (99)
101 PF08756 YfkB: YfkB-like domai 51.6 8.8 0.00019 37.1 1.7 50 545-617 82-131 (153)
102 TIGR00358 3_prime_RNase VacB a 50.2 33 0.00072 40.5 6.5 35 111-147 571-606 (654)
103 KOG2813 Predicted molecular ch 47.5 17 0.00036 39.6 3.1 119 494-621 61-201 (406)
104 PTZ00162 DNA-directed RNA poly 43.9 82 0.0018 31.2 7.2 36 109-147 78-113 (176)
105 PF00684 DnaJ_CXXCXGXG: DnaJ c 43.3 18 0.00038 30.0 2.1 30 588-619 24-53 (66)
106 TIGR03598 GTPase_YsxC ribosome 42.0 1.1E+02 0.0025 29.0 7.8 49 539-587 124-172 (179)
107 TIGR00448 rpoE DNA-directed RN 40.6 31 0.00067 33.9 3.7 35 110-147 79-113 (179)
108 PF08800 VirE_N: VirE N-termin 36.8 84 0.0018 29.7 5.8 55 541-600 26-81 (136)
109 PRK08563 DNA-directed RNA poly 35.2 42 0.00091 33.0 3.7 35 110-147 79-113 (187)
110 PRK12329 nusA transcription el 35.2 94 0.002 35.4 6.7 32 110-143 150-186 (449)
111 PF11314 DUF3117: Protein of u 33.4 30 0.00066 27.7 1.8 15 486-500 22-36 (51)
112 PHA02945 interferon resistance 32.0 1.3E+02 0.0029 27.0 5.8 33 111-146 10-44 (88)
113 cd05790 S1_Rrp40 S1_Rrp40: Rrp 31.6 69 0.0015 28.4 4.0 34 110-145 4-37 (86)
114 KOG2925 Predicted translation 30.6 27 0.00059 34.1 1.4 23 482-504 54-76 (167)
115 PF13442 Cytochrome_CBB3: Cyto 27.5 11 0.00023 30.6 -1.7 14 605-618 9-22 (67)
116 PF10442 FIST_C: FIST C domain 26.5 1.2E+02 0.0027 27.6 5.0 56 530-589 73-131 (136)
117 cd05792 S1_eIF1AD_like S1_eIF1 26.0 42 0.00092 29.3 1.7 22 480-501 30-51 (78)
118 PF04472 DUF552: Protein of un 25.5 1.3E+02 0.0028 25.3 4.5 41 531-575 10-50 (73)
119 COG2010 CccA Cytochrome c, mon 25.5 28 0.00061 32.1 0.6 14 604-617 56-69 (150)
120 COG3585 MopI Molybdopterin-bin 24.1 51 0.0011 28.1 1.7 24 112-135 5-28 (69)
121 CHL00183 petJ cytochrome c553; 22.1 22 0.00049 31.7 -0.8 13 606-618 33-45 (108)
122 cd06836 PLPDE_III_ODC_DapDC_li 21.9 8.1E+02 0.018 26.8 11.0 149 410-574 73-242 (379)
123 PF08508 DUF1746: Fungal domai 21.8 62 0.0013 30.3 2.0 20 546-566 84-103 (116)
124 COG1107 Archaea-specific RecJ- 21.6 71 0.0015 37.5 2.8 38 108-147 118-155 (715)
125 KOG1070 rRNA processing protei 21.4 1.4E+02 0.003 38.6 5.3 76 68-149 557-634 (1710)
126 cd01884 EF_Tu EF-Tu subfamily. 21.1 4.6E+02 0.01 25.9 8.2 78 534-611 107-193 (195)
127 cd06828 PLPDE_III_DapDC Type I 20.8 6.3E+02 0.014 27.0 9.8 130 410-554 74-221 (373)
128 cd04508 TUDOR Tudor domains ar 20.6 1.2E+02 0.0026 22.7 3.1 26 113-138 12-39 (48)
129 COG5231 VMA13 Vacuolar H+-ATPa 20.6 38 0.00082 37.2 0.4 106 369-484 292-409 (432)
130 TIGR02642 phage_xxxx uncharact 20.4 44 0.00095 33.7 0.8 13 607-619 99-111 (186)
131 PF07013 DUF1314: Protein of u 20.2 80 0.0017 31.5 2.5 34 479-516 5-38 (177)
132 PLN03126 Elongation factor Tu; 20.1 3.6E+02 0.0078 30.9 8.1 56 534-589 186-246 (478)
No 1
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=2.7e-123 Score=1016.51 Aligned_cols=414 Identities=33% Similarity=0.534 Sum_probs=384.0
Q ss_pred cceEEEEEecCCceEEEEEEECCEEeEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcC
Q 007008 74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF 153 (621)
Q Consensus 74 ~~~~ilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~~~~~~ 153 (621)
|+++|+||+.+ .++|+|++|||+|+||++|+.+...++||||+|||+||+|||||||||||.+||||||++|..
T Consensus 1 M~~~i~i~~~~-~e~r~Alledg~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~----- 74 (489)
T PRK11712 1 MTAELLVNVTP-SETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIV----- 74 (489)
T ss_pred CceEEEEecCC-CeEEEEEEECCEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhcc-----
Confidence 78999999987 799999999999999999999999999999999999999999999999999999999999962
Q ss_pred CcccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 007008 154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD 233 (621)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (621)
|++..... ++
T Consensus 75 ~~~~~~~~------------------------------------------------~~---------------------- 84 (489)
T PRK11712 75 PHTECVAG------------------------------------------------EE---------------------- 84 (489)
T ss_pred chhhhccc------------------------------------------------cc----------------------
Confidence 21100000 00
Q ss_pred CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCcee
Q 007008 234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL 313 (621)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~igtKGprL 313 (621)
..+ . + ..++...|++||+|||||+|||+++|||+|
T Consensus 85 -------------~~~--~--~----------------------------~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~l 119 (489)
T PRK11712 85 -------------QKQ--F--V----------------------------VRDISELVRQGQDIMVQVVKDPLGTKGARL 119 (489)
T ss_pred -------------ccc--c--c----------------------------cccHHHhccCCCEEEEEEEeCCcCCCCCeE
Confidence 000 0 0 002235699999999999999999999999
Q ss_pred eecceeeceeEEEeeCCCceeeecccChH-HHHHHHHHHHhcCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 007008 314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH 392 (621)
Q Consensus 314 T~~ISLpGRYlVL~P~~~~IgVSrKI~de-eR~rLk~i~~~l~~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~~ 392 (621)
|++|||||||+||||++++|||||||+++ +|+||+.++..+.++++|+||||+|+++++++|.+|+++|.++|+.|.++
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 99999999999999999999999999876 69999999999988889999999999999999999999999999999999
Q ss_pred HHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCcCCceeeccCCCCcccc
Q 007008 393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472 (621)
Q Consensus 393 ~~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~~y~~~~pLF~~ 472 (621)
++.+ ++|+|||++.+++.+++||++++++++|+||+++.|+++++|++.+.|+...++++|++..|||+.
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 9876 489999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 007008 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (621)
Q Consensus 473 y~Ie~~I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVID 552 (621)
|+|+++|+++++++||||||||||||+||||||||||||++ ++++++++|+++||+|||+||||||||||||||||||
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 99999999999999999999999999999999999999994 5677999999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCchhhccccCCCcccCCccc
Q 007008 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVWFSNSQFSLCYLAFVHLLGLMK 620 (621)
Q Consensus 553 FIdM~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~~~~ 620 (621)
||||+++++|++|+++|+++|++|+++++|+|||+||||||||||+|+||.++++.+||+|||+|.++
T Consensus 348 FidM~~~~~r~~v~~~l~~~l~~D~~k~~v~~~T~lGLvEmTRkR~r~sl~~~l~~~Cp~C~G~G~v~ 415 (489)
T PRK11712 348 FIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVLCGECPTCHGRGTVK 415 (489)
T ss_pred CCCCCCHHHHHHHHHHHHHHhhcCCCCceEcccCCCceEEEEecccCCChHHHhcCCCCCCCCCCCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999875
No 2
>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=3.5e-120 Score=977.45 Aligned_cols=401 Identities=39% Similarity=0.634 Sum_probs=370.8
Q ss_pred EEEEEEECCEEeEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCCcccccchhhhccc
Q 007008 88 QRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNG 167 (621)
Q Consensus 88 ~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~~~~~~~~~~~~~~~~~~~~ 167 (621)
+|+|++|||+|+||++|+.+...++||||+|+|++|+|||||||||||.+++||||++|.. |.+.....
T Consensus 1 ~r~Alledg~l~e~~ie~~~~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-----~~~~~~~~------ 69 (414)
T TIGR00757 1 TRVALVEGGRLFDLIIERPKSRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-----PNYECLAP------ 69 (414)
T ss_pred CEEEEEECCEEEEEEEecCcCcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-----chhhcccc------
Confidence 5999999999999999999999999999999999999999999999999999999999862 11100000
Q ss_pred chhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCCCCccccccccCC
Q 007008 168 SASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGD 247 (621)
Q Consensus 168 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (621)
. +
T Consensus 70 ------------------------------------------~------------------------------~------ 71 (414)
T TIGR00757 70 ------------------------------------------A------------------------------E------ 71 (414)
T ss_pred ------------------------------------------c------------------------------c------
Confidence 0 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceeeecceeeceeEEEe
Q 007008 248 HHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILI 327 (621)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~igtKGprLT~~ISLpGRYlVL~ 327 (621)
.+ .. . ..++...|++||+|+|||+|||+++|||+||++|||||||+|||
T Consensus 72 ~~----~~------------~---------------~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~lT~~Isl~GrylVl~ 120 (414)
T TIGR00757 72 AK----RE------------A---------------GPSISELLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLM 120 (414)
T ss_pred cc----cc------------c---------------cCCHHHhCcCCCEEEEEEeeCCcCCCCCeEEEEEEeccceEEEe
Confidence 00 00 0 00223569999999999999999999999999999999999999
Q ss_pred eCCCceeeecccChH-HHHHHHHHHHh-cCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcc
Q 007008 328 TSCDRIGVSRKITGV-ERTRLKVIAKT-LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVE 405 (621)
Q Consensus 328 P~~~~IgVSrKI~de-eR~rLk~i~~~-l~~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~~~~ 405 (621)
|+.+++||||||.++ +|.||+.++.+ +.++++|+||||+|+++++++|.+|+++|.++|+.|.++++.+
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 999999999999875 79999999995 8888999999999999999999999999999999999999876
Q ss_pred CCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCcCCceeeccCCCCcccccCHHHHHHhHhCC
Q 007008 406 GAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSK 485 (621)
Q Consensus 406 ~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~~y~~~~pLF~~y~Ie~~I~~al~~ 485 (621)
++|+|||++++++.+++||++++++++|+||+++.|+++++|++...|....+|++|.+..|||+.|+|+++|++|+++
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 4899999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred ceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHH
Q 007008 486 RVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLV 565 (621)
Q Consensus 486 rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVIDFIdM~~~~~r~~V 565 (621)
+||||||||||||+||||||||||||++ +++.++++|+++||+|||+||||||||||||||||||||||+++++|++|
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 9999999999999999999999999995 56789999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCchhhccccCCCcccCCccc
Q 007008 566 YEEVKKAVERDRSMVKVSELSRHGLMEITRKRVWFSNSQFSLCYLAFVHLLGLMK 620 (621)
Q Consensus 566 l~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~~~~ 620 (621)
+++|+++|++|+++++|+|||+||||||||||.|+||.++++++||+|||+|.++
T Consensus 349 ~~~l~~~~~~D~~k~~v~~~T~lGLvE~TRkr~~~sL~e~~~~~Cp~C~G~G~v~ 403 (414)
T TIGR00757 349 LERLKEALRRDRARIQISGISEFGLVEMTRKRLRESLMEVLGTVCPHCSGTGIVK 403 (414)
T ss_pred HHHHHHHHhcCCCCcEEcccCCCcceEEeccccCcChHHHhcCCCCCCcCeeEEc
Confidence 9999999999999999999999999999999999999999999999999999875
No 3
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=1.6e-113 Score=970.83 Aligned_cols=410 Identities=33% Similarity=0.585 Sum_probs=379.6
Q ss_pred eEEEEEecCCceEEEEEEECCEEeEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCCc
Q 007008 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP 155 (621)
Q Consensus 76 ~~ilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~~~~~~~~ 155 (621)
++||||.....+.|+||+|||+|.||+||+.++...+||||+|||+||+|||+|||||||.+++|||+++|+..+++...
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 78999998436899999999999999999988888999999999999999999999999999999999999754431100
Q ss_pred ccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCC
Q 007008 156 FRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGE 235 (621)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (621)
|..
T Consensus 82 ~~~----------------------------------------------------------------------------- 84 (1068)
T PRK10811 82 YSA----------------------------------------------------------------------------- 84 (1068)
T ss_pred ccc-----------------------------------------------------------------------------
Confidence 000
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceeee
Q 007008 236 PEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTA 315 (621)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~igtKGprLT~ 315 (621)
+ . .+++...|++||+|||||+||++++|||+||+
T Consensus 85 -------------~-----~----------------------------~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 85 -------------H-----G----------------------------RPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred -------------c-----c----------------------------ccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 0 0 00122469999999999999999999999999
Q ss_pred cceeeceeEEEeeCCCc-eeeecccChHHHHHHHHHHHhc-CCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 007008 316 YPKLRSRFWILITSCDR-IGVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (621)
Q Consensus 316 ~ISLpGRYlVL~P~~~~-IgVSrKI~deeR~rLk~i~~~l-~~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~~~ 393 (621)
+|||+|||+||||++++ +||||||++++|.+|+.++..+ .++++|+||||+|+|+++++|..||++|...|+.|++++
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 99999999999999988 7999999988899999999887 788999999999999999999999999999999999999
Q ss_pred HHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhh-CCCcCCceeeccCCCCcccc
Q 007008 394 KSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLFDK 472 (621)
Q Consensus 394 ~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~-~p~~~~~v~~y~~~~pLF~~ 472 (621)
+++ ++|.|||++.+++.+++|||+..++++|+||+++.|+.++.|+..+ .|++..+|++|.+..|||+.
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 876 4899999999999999999999999999999999999999999987 48877899999999999999
Q ss_pred cCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 007008 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (621)
Q Consensus 473 y~Ie~~I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVID 552 (621)
|+|+.+|++||+++||||||||||||+||||||||||||++ +++++.++|+|+||++||+||||||||||||||||||
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 99999999999999999999999999999999999999995 5667899999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCchhhccccCCCcccCCccc
Q 007008 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVWFSNSQFSLCYLAFVHLLGLMK 620 (621)
Q Consensus 553 FIdM~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~~~~ 620 (621)
||||+.++|+++|++.|+++|++|+.+++|+|||+||||||||||.|+||.++++..||+|.|+|.++
T Consensus 347 FIdM~~ee~r~~l~~~L~~al~~D~~k~~v~g~T~LGLvEmTRKR~r~sL~E~l~e~Cp~C~GtG~v~ 414 (1068)
T PRK10811 347 FIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVR 414 (1068)
T ss_pred CCCCCchHHHHHHHHHHHHHHHhCCCCceEEecccccceEEecccCCCCHHHHhhccCcccCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999774
No 4
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.4e-99 Score=825.90 Aligned_cols=406 Identities=37% Similarity=0.603 Sum_probs=380.3
Q ss_pred ceEEEEEecCCceEEEEEEECCEEeEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCC
Q 007008 75 STVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFP 154 (621)
Q Consensus 75 ~~~ilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~~~~~~~ 154 (621)
.+.||||+++ .|+|||++++|.|.|+++|+....+++||||+|||+||+|||||||||||.+||||||+++..+
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 3689999999 8999999999999999999999999999999999999999999999999999999999998622
Q ss_pred cccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCC
Q 007008 155 PFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDG 234 (621)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (621)
+.....
T Consensus 75 -~~~~~~------------------------------------------------------------------------- 80 (487)
T COG1530 75 -YFRAVL------------------------------------------------------------------------- 80 (487)
T ss_pred -hhhhcc-------------------------------------------------------------------------
Confidence 100000
Q ss_pred CCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceee
Q 007008 235 EPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLT 314 (621)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~igtKGprLT 314 (621)
..++...++.||.++|||.|+++|+|||++|
T Consensus 81 -------------------------------------------------~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 81 -------------------------------------------------EEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred -------------------------------------------------cccceeeecCCceEEEEEEeecCccccccce
Confidence 0011246899999999999999999999999
Q ss_pred ecceeeceeEEEeeCCCcee-eecccChH-HHHHHHHHHHhcCCCC-eeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 007008 315 AYPKLRSRFWILITSCDRIG-VSRKITGV-ERTRLKVIAKTLQPEG-FGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME 391 (621)
Q Consensus 315 ~~ISLpGRYlVL~P~~~~Ig-VSrKI~de-eR~rLk~i~~~l~~~~-~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~ 391 (621)
++||++|||+||||+.+++| +|+||+++ +|++|+.++..+.+.+ +|+|+||+|+|++.++|.+|+++|.+.|+.|+.
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 99999999999999999988 99999984 8999999999988654 799999999999999999999999999999999
Q ss_pred HHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCcCCceeeccCCCCccc
Q 007008 392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFD 471 (621)
Q Consensus 392 ~~~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~~y~~~~pLF~ 471 (621)
++... ++|.+||++.+++.+++|||++.++.+|+||+...|..+++|+..+.|+...++++|.+..|+|+
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 98776 48999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEE
Q 007008 472 KFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVV 551 (621)
Q Consensus 472 ~y~Ie~~I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVI 551 (621)
.|+++.+|.++++|+|||||||||||++|||||+||||||++ ++..+.++|+++||+|||.||||||||||+||||+|
T Consensus 262 ~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~--~~~~~~eeta~~tNleAa~eiarqlrlR~lgGiIiI 339 (487)
T COG1530 262 LFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRF--TGAGDLEETAVNTNLEAAEEIARQLRLRNLGGIIII 339 (487)
T ss_pred hhhHHHHHHHhhhheEecCCCCceeEeccceeEEEEccCccc--cccCchHHhhhhhhHHHHHHHHHHHhhcccCCeEEE
Confidence 999999999999999999999999999999999999999995 444569999999999999999999999999999999
Q ss_pred EcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCchhhccccCCCcccCCcccC
Q 007008 552 DFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVWFSNSQFSLCYLAFVHLLGLMKC 621 (621)
Q Consensus 552 DFIdM~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~~~~~ 621 (621)
|||||..+++++.|+..|+++|+.|++++++.+||+|||+||||||.+.||.++++.+||.|+|+|.++|
T Consensus 340 DfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~~~cp~c~G~g~v~~ 409 (487)
T COG1530 340 DFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLSERCPGCKGTGHVRS 409 (487)
T ss_pred EeeeccchhhhHHHHHHHHHHhccCCcccccccccccCceEEEEEecCCCCceeeeeECCCceeeEEEec
Confidence 9999999999999999999999999999999999999999999999999999999999999999999875
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=4.5e-82 Score=649.31 Aligned_cols=270 Identities=47% Similarity=0.747 Sum_probs=222.0
Q ss_pred eeeceeEEEeeCCCceeeecccChH-HHHHHHHHHHhcCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 007008 318 KLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSA 396 (621)
Q Consensus 318 SLpGRYlVL~P~~~~IgVSrKI~de-eR~rLk~i~~~l~~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~~~~~~ 396 (621)
||||||+||+|++++|+|||||+++ +|++|+++++.+.++++|+||||+|+++++++|.+|+++|.++|+.|+++++..
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 hhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCcCCceeeccCCCCcccccCHH
Q 007008 397 ALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIE 476 (621)
Q Consensus 397 ~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~~y~~~~pLF~~y~Ie 476 (621)
++|+|||++++++.+++||++++++++|+||+++.|+++++|++...|+...+|++|.+..|+|+.|+|+
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 4799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCC
Q 007008 477 EEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDM 556 (621)
Q Consensus 477 ~~I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVIDFIdM 556 (621)
.+|+++++++||||||||||||+||||||||||||++ +++.+.++++++||++||+||||||||||||||||||||||
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 9999999999999999999999999999999999995 56678999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCC
Q 007008 557 ADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVW 599 (621)
Q Consensus 557 ~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r 599 (621)
++++++++|++.|+++|++|+.+++|+|||+||||||||||.|
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 9999999999999999999999999999999999999999986
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=99.65 E-value=4e-16 Score=135.94 Aligned_cols=40 Identities=30% Similarity=0.615 Sum_probs=37.1
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+..+|+||.|+|++|.|.|.|||||+|.+++||||+++.
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=97.66 E-value=0.00019 Score=59.34 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=33.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...|.||.|+|.+|.+ .++||++|.+..||+++++.
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 3589999999999999 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=97.38 E-value=0.00058 Score=55.00 Aligned_cols=33 Identities=33% Similarity=0.479 Sum_probs=30.5
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|++|.|+|.+|.| .++||+|+.+.+|||++.+.
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 99999999999999988663
No 9
>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=97.10 E-value=0.0016 Score=54.52 Aligned_cols=35 Identities=34% Similarity=0.543 Sum_probs=31.3
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+|.||.|+|++|.+. -+|||+++.+..||+|+.+.
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 45799999999999999874
No 10
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.00052 Score=63.84 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=33.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeeccccC
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~ 148 (621)
-+|+++.|+|+.|.|- +|||++-.+..|+.|++++.
T Consensus 4 kvG~~l~GkItgI~~y--GAFV~l~~g~tGLVHISEIa 39 (129)
T COG1098 4 KVGSKLKGKITGITPY--GAFVELEGGKTGLVHISEIA 39 (129)
T ss_pred cccceEEEEEEeeEec--ceEEEecCCCcceEEehHhh
Confidence 4899999999999996 89999999999999998863
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=96.99 E-value=0.003 Score=50.57 Aligned_cols=33 Identities=42% Similarity=0.619 Sum_probs=30.1
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|++|.|+|.++.+ .++||+|+.+..||||..+.
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 7899999999998 69999999999999988763
No 12
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.97 E-value=0.0028 Score=50.43 Aligned_cols=34 Identities=38% Similarity=0.612 Sum_probs=31.2
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.|.+|.|+|.++.+ +++||++|.+..|||+..+.
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
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.86 E-value=0.046 Score=58.68 Aligned_cols=35 Identities=14% Similarity=0.274 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG--~~k~aFL~~~d~ 147 (621)
-+|++..|+|++|.+ .+|||+++ .+..||+|+++.
T Consensus 16 ~~GdvV~g~V~~I~d--~GafV~L~EY~gvEGlIhiSEl 52 (319)
T PTZ00248 16 EEDDLVMVKVVRITE--MGAYVSLLEYDDIEGMILMSEL 52 (319)
T ss_pred CCCCEEEEEEEEEeC--CeEEEEecCCCCcEEEEEHHHh
Confidence 489999999999998 69999996 589999998874
No 14
>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=96.70 E-value=0.0054 Score=50.20 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=30.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.+|.|+|++|.+ .++||+++.+..||+|+++.
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 79999999899999988763
No 15
>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=96.58 E-value=0.0058 Score=48.84 Aligned_cols=33 Identities=39% Similarity=0.552 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|++|.|+|.+|.+ .++||+++....||++..+.
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 16
>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=96.56 E-value=0.007 Score=51.59 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=32.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.||.|+|++|.+ .++||+++.+..||+|+.+.
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 89999999999999988764
No 17
>PRK07252 hypothetical protein; Provisional
Probab=96.54 E-value=0.008 Score=55.76 Aligned_cols=34 Identities=29% Similarity=0.470 Sum_probs=31.3
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+|++|.|+|.+|.+ .+|||+|+.+..||+|+.+.
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 18
>PRK08059 general stress protein 13; Validated
Probab=96.37 E-value=0.01 Score=54.98 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=32.5
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.+|.|+|.+|.+ .++||+|+.+..||+|+.+.
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 89999999999999988763
No 19
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.35 E-value=0.0098 Score=48.63 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.+|.|+|++|.+ .++||+++.+..||+|+.+.
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 7899999999997 67999999999999988764
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=96.28 E-value=0.015 Score=48.99 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=29.3
Q ss_pred CCeEEEEEeeecCCcceEEeccc---CCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIG---NSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG---~~k~aFL~~~d~ 147 (621)
|.+|.|+|.+|.|. ++||+|+ .+.+||+|+.+.
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 468999988763
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=96.26 E-value=0.016 Score=47.46 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|+|+.|+|.++.+. +|||++|.+..|||+..+.
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 78999999999885 9999999999999988763
No 22
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.04 E-value=0.02 Score=46.93 Aligned_cols=32 Identities=31% Similarity=0.518 Sum_probs=29.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
|.+|.|+|++|.+ .++||+++.+..||+++.+
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~v~g~i~~~~ 32 (69)
T cd05697 1 GQVVKGTIRKLRP--SGIFVKLSDHIKGLVPPMH 32 (69)
T ss_pred CCEEEEEEEEEec--cEEEEEecCCcEEEEEHHH
Confidence 7899999999998 5999999999999998765
No 23
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=95.97 E-value=0.032 Score=46.64 Aligned_cols=34 Identities=29% Similarity=0.487 Sum_probs=29.4
Q ss_pred cCCeEEEEEeeecCCcceEEecc-cCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdI-G~~k~aFL~~~d~ 147 (621)
+|.+|.|+|++|.+ .++||++ |....||+|+++.
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 3347899998764
No 24
>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=95.95 E-value=0.036 Score=45.76 Aligned_cols=34 Identities=24% Similarity=0.209 Sum_probs=31.0
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+|.||.|+|++|.+ .++||+++.+..||+|+.+.
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 48999999999999998763
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=95.72 E-value=0.038 Score=45.69 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccC--Ccceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~--~k~aFL~~~d~ 147 (621)
.|.+|.|+|+++.+ .++||++.. +..||||+++.
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 69999999999987 899999963 58999988764
No 26
>PRK08582 hypothetical protein; Provisional
Probab=95.69 E-value=0.032 Score=53.04 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=32.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+|.+|.|+|++|.+. +|||+|+.+..||+|+.+.
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 5899999999999995 8999999999999999874
No 27
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.66 E-value=0.021 Score=65.05 Aligned_cols=36 Identities=33% Similarity=0.536 Sum_probs=33.2
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.-.+|.+..|+|++|-| .+||||||+ -+|+||++++
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 34689999999999999 899999999 9999999885
No 28
>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=95.65 E-value=0.041 Score=44.99 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.+|.|+|++|.+ .++||+++.+-.||+|+.+.
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 89999999999999988763
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=95.49 E-value=0.049 Score=45.44 Aligned_cols=34 Identities=26% Similarity=0.328 Sum_probs=29.0
Q ss_pred CCeEE-EEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~-GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.||. |+|++|... -+|||+++.+.+||+|+++.
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 67999999999999998763
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=95.37 E-value=0.043 Score=43.94 Aligned_cols=33 Identities=30% Similarity=0.475 Sum_probs=28.9
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.|.+|.|+|.++.+. ++||+++ +-.||||..+.
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
>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=95.11 E-value=0.074 Score=45.05 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=29.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-Ccceeeeccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKH 146 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~-~k~aFL~~~d 146 (621)
..|.++.|.|++|.+ .+||||+|. +-.|||+.++
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 469999999999996 599999994 6799997655
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=95.05 E-value=0.042 Score=64.55 Aligned_cols=59 Identities=20% Similarity=0.252 Sum_probs=44.2
Q ss_pred eEEEEEEECCEEeEEEeecC------------CC--CcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 87 MQRIAVLEDEKLVELLLEPV------------KS--NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 87 e~RvAvlEdgkL~El~iE~~------------~~--~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...|-+-+||++.=+-.... .. ...+|.||.|+|++|.+ -+|||+|+.+..||+|+++.
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 35677777777653332211 11 24699999999999998 79999999999999999864
No 33
>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=95.05 E-value=0.11 Score=44.48 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=31.6
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..|+|+.|+|.++.+ .++||+||.+..||||+++.
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 589999999999987 56999999999999998874
No 34
>PRK05807 hypothetical protein; Provisional
Probab=94.87 E-value=0.11 Score=49.31 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=30.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+|.+|.|+|+.|.| .+|||++ .+..||+|+++.
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 578999999874
No 35
>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=94.87 E-value=0.1 Score=42.92 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=28.6
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
+.|.|..|+|.++.+ +.+|||||. -.|||+.++
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 889997654
No 36
>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=94.84 E-value=0.055 Score=63.54 Aligned_cols=36 Identities=28% Similarity=0.457 Sum_probs=33.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.||.|+|++|.+ .+|||+|..+..||||+++.
T Consensus 616 ~~~G~i~~G~V~~I~~--~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 616 PEVGKIYEGKVVRIMD--FGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred cccCcEEEEEEEEEeC--CEEEEEECCCcEEEEEHHHc
Confidence 4689999999999998 89999999999999999874
No 37
>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=94.66 E-value=0.12 Score=42.49 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=29.8
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-Ccceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~-~k~aFL~~~d~ 147 (621)
+|.+|.|+|++|.+ .++||+++. +..||+|+.+.
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 38
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.49 E-value=0.1 Score=61.54 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=33.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.+|.|+|++|.+ .+|||+|+.+..||+|+++.
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 79999999999999999874
No 39
>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=94.44 E-value=0.12 Score=43.76 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=30.8
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+|++..|+|+++.+ .+|||+++.+-.||+|+.+.
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 479999999999974 57999999999999998764
No 40
>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=94.42 E-value=0.17 Score=42.89 Aligned_cols=34 Identities=18% Similarity=0.195 Sum_probs=30.6
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
.+|+|=.|+|++| .-+.+|||||..-.|||++.+
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 5899999999999 567899999999999998866
No 41
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=94.41 E-value=0.18 Score=52.87 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=30.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC--Ccceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~--~k~aFL~~~d~ 147 (621)
.+|+++.|+|++|.+ .+|||++.. +..||+|+++.
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 579999999999976 899999975 78999988764
No 42
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=94.04 E-value=0.13 Score=40.02 Aligned_cols=29 Identities=24% Similarity=0.392 Sum_probs=25.3
Q ss_pred EEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 116 YLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 116 Y~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
|.|+|.++.+ .++||+++.+..||++..+
T Consensus 1 v~g~V~~v~~--~g~~v~l~~~~~g~~~~~~ 29 (65)
T cd00164 1 VTGKVVSITK--FGVFVELEDGVEGLVHISE 29 (65)
T ss_pred CEEEEEEEEe--eeEEEEecCCCEEEEEHHH
Confidence 5799999996 5899999999999998765
No 43
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=93.92 E-value=0.4 Score=47.50 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=28.8
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccC----------Ccceeeeccc
Q 007008 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGN----------SRPSLMDIKH 146 (621)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVdIG~----------~k~aFL~~~d 146 (621)
...+|+|+.|+|++|.+ ..+||||+. +..|||++.+
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 4567776655
No 44
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.08 E-value=0.18 Score=60.58 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=31.7
Q ss_pred ccCCeEE-EEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~-GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+|.||. |+|++|.+ -+|||+|+.+..||+|+++.
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 4999995 69999998 69999999999999999874
No 45
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=92.91 E-value=0.77 Score=47.23 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.2
Q ss_pred EEeecCCCCc--ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 101 LLLEPVKSNV--QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 101 l~iE~~~~~~--~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+.+.+..... .+|+|-.|+|+++.+. .+||||+..-.||||+.+.
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 5999999999999998774
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=91.83 E-value=0.17 Score=41.02 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=30.3
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.+|.|+|++|.| .++||+++.+.+||+|+.+.
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 68999999999999999874
No 47
>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=91.61 E-value=0.23 Score=40.79 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=31.4
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+|.+|.|+|.+|.+ -++||+++.+.+||+|+.+.
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 48
>PRK14865 rnpA ribonuclease P; Provisional
Probab=91.47 E-value=0.91 Score=41.75 Aligned_cols=54 Identities=20% Similarity=0.370 Sum_probs=38.7
Q ss_pred ceeeecccChH-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 007008 332 RIGVSRKITGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~~~l-------~~-~~~GvIIRTaA~~aseeeL~~Dl~~L~~~ 385 (621)
++.||||+... .|+|+|.++.++ .+ .++=+|.|..+.+++.++|++++..|.+.
T Consensus 48 G~sVsKKvg~AV~RNRiKR~lRE~~R~~~~~l~~~divii~r~~~~~~~~~~l~~~l~~ll~~ 110 (116)
T PRK14865 48 GITVSRKVGNAVVRNRIKRLVREFYRLNKSLFIVADYNIIAKKGAEQLDFQQISRELANALER 110 (116)
T ss_pred EEEEecccCcchhHHHHHHHHHHHHHHhhccCCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 36789999765 577766544331 12 24557889999999999999999877554
No 49
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=91.15 E-value=0.45 Score=54.01 Aligned_cols=35 Identities=34% Similarity=0.547 Sum_probs=31.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.|+.|+|++|.|. +|||||| +..||+|+++.
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 59999999874
No 50
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=90.87 E-value=1.2 Score=41.32 Aligned_cols=53 Identities=13% Similarity=0.113 Sum_probs=35.7
Q ss_pred ceeeecccChH-HHHHHHHHHHh----c---CCCCeeEE--EeecCCCCCHHHHHHHHHHHHH
Q 007008 332 RIGVSRKITGV-ERTRLKVIAKT----L---QPEGFGLT--IRTVAAGHSLEELQKDLEGLLS 384 (621)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~~~----l---~~~~~GvI--IRTaA~~aseeeL~~Dl~~L~~ 384 (621)
++.||||+... .|+|+|.++.+ . .+.+.=+| .|..|..++..+|++++..|..
T Consensus 46 G~~VsKKvG~AV~RNRiKR~lRE~~R~~~~~l~~~~~vVviaR~~~~~~~~~~l~~~l~~ll~ 108 (118)
T PRK00588 46 GLIIAKSVGSAVERHRVARRLRHVARPILKELHPSDRVVIRALPSSRHVSSARLEQQLRCGLR 108 (118)
T ss_pred EEEEeeecCchhHHHHHHHHHHHHHHHhhhccCCCCEEEEecCcccccCCHHHHHHHHHHHHH
Confidence 36789999765 67766654432 2 22333333 6888999999999999887644
No 51
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=90.37 E-value=0.64 Score=52.69 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=32.5
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...|.||.|+|++|.+ .+||||||.+..||+|+.+.
T Consensus 200 l~~G~iv~G~V~~v~~--~G~fV~l~~gv~g~v~~sel 235 (491)
T PRK13806 200 VKEGDVVEGTVTRLAP--FGAFVELAPGVEGMVHISEL 235 (491)
T ss_pred CCCCCEEEEEEEEEeC--CeEEEEcCCCcEEEEEHHHC
Confidence 5699999999999988 58999999899999998874
No 52
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.28 E-value=0.64 Score=49.93 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=32.4
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...|.|-.|+|.+|.++ +||||||....|||++.+.
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 56899999999999765 8999999999999998874
No 53
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=90.18 E-value=1.6 Score=40.67 Aligned_cols=54 Identities=24% Similarity=0.249 Sum_probs=37.2
Q ss_pred ceeeecccChH-HHHHHHHHH----HhcC---CCCee--EEEeecCCCCCHHHHHHHHHHHHHH
Q 007008 332 RIGVSRKITGV-ERTRLKVIA----KTLQ---PEGFG--LTIRTVAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~----~~l~---~~~~G--vIIRTaA~~aseeeL~~Dl~~L~~~ 385 (621)
++.||||+... +|+|+|.++ ..+. +.|+- +|.|-.+.+++..+|.+|+..|...
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 46689999765 577665444 3332 34444 5567788899999999999877665
No 54
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.05 E-value=0.76 Score=49.36 Aligned_cols=38 Identities=29% Similarity=0.555 Sum_probs=32.4
Q ss_pred CCCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 107 KSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 107 ~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
-...-+|.||.|+|++|.+ -++||++| +..||+|+.+.
T Consensus 191 ~~~~k~G~vv~G~V~~I~~--~G~fV~i~-gv~Gllhisel 228 (318)
T PRK07400 191 MNRLEVGEVVVGTVRGIKP--YGAFIDIG-GVSGLLHISEI 228 (318)
T ss_pred hccCCCCCEEEEEEEEEEC--CeEEEEEC-CEEEEEEHHHc
Confidence 3445689999999999998 79999997 67899998774
No 55
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=89.50 E-value=1.8 Score=40.91 Aligned_cols=58 Identities=19% Similarity=0.302 Sum_probs=39.7
Q ss_pred eeeecc-cChH-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 007008 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (621)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~l-------~~-~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W~~I~~~~ 393 (621)
+.|||| +... .|+|+|.++.+. .+ -++=+|.|..+.+++..+|.+++..| |+.+...+
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 556899 6655 687777655432 12 24457888899999999999998876 55554443
No 56
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=89.36 E-value=0.84 Score=51.74 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=34.0
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
....+|.+|.|+|++|.| .+|||+++.+-.||+|+++.
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 57
>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=89.11 E-value=0.42 Score=38.92 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=28.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.||.|+|+++.+ .++||++ .+-.|||+.++.
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 7899999999975 8999999 579999988764
No 58
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.07 E-value=0.88 Score=52.08 Aligned_cols=35 Identities=31% Similarity=0.528 Sum_probs=31.8
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
-..|.|+.|+|++|.+. +||||+| +..||+|+++.
T Consensus 199 l~~G~iv~g~V~~v~~~--G~~V~i~-g~~glv~~se~ 233 (565)
T PRK06299 199 LEEGQVVEGVVKNITDY--GAFVDLG-GVDGLLHITDI 233 (565)
T ss_pred CCCCCEEEEEEEEEeCC--eEEEEEC-CEEEEEEHHHh
Confidence 46899999999999994 8999999 89999999875
No 59
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.90 E-value=0.49 Score=38.99 Aligned_cols=33 Identities=9% Similarity=0.159 Sum_probs=30.3
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|.|+.|+|++|.+. .+||+++.+-.||+++.+.
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 7999999999999999885
No 60
>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=88.48 E-value=0.52 Score=39.40 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=30.7
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-Ccceeeecccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG~-~k~aFL~~~d~ 147 (621)
+|.+|.|+|++|.+ .++||+++. +..||+|+.+.
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 89999999874
No 61
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=88.20 E-value=1.7 Score=52.67 Aligned_cols=38 Identities=26% Similarity=0.438 Sum_probs=33.9
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
++..+|+|+.|+|++|.| -+|||+++.+-.||+|+++.
T Consensus 574 ~~~~vG~iV~G~V~~I~~--fG~fVeL~~gveGLvhiSEl 611 (863)
T PRK12269 574 NKFGVNDVVKGRVTKIAD--FGAFIELAEGIEGLAHISEF 611 (863)
T ss_pred ccCCCCCEEEEEEEEEeC--CeEEEEecCCceeeeEHHHh
Confidence 445689999999999998 68999999999999999875
No 62
>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=87.71 E-value=1.3 Score=50.11 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=32.4
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|+++.|+|+++.+. ++||++|.+..||+|+.+.
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 8999999999999998875
No 63
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=87.61 E-value=3.1 Score=38.04 Aligned_cols=55 Identities=29% Similarity=0.387 Sum_probs=39.1
Q ss_pred ceeeecccChH-HHHHHHHHHHh----cC---CC--CeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 007008 332 RIGVSRKITGV-ERTRLKVIAKT----LQ---PE--GFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (621)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~~~----l~---~~--~~GvIIRTaA~~aseeeL~~Dl~~L~~~W 386 (621)
++.||||+... .|+|+|.++.+ .. +. ++=+|+|-.+..++..+|.+|+..|..+.
T Consensus 41 GisVsKKvgkAV~RNriKR~lRE~~R~~~~~~~~~~d~v~i~r~~~~~~~~~~l~~~l~~ll~k~ 105 (114)
T PRK00499 41 GISVSKKVGNAVVRNRIKRLIRESFRELKDEIKKGYDFVVIARKPAAELDYKEIKKSLIHVLKLA 105 (114)
T ss_pred EEEEecccCchhhHhHHHHHHHHHHHHhhhcccCCceEEEEECCCcccCCHHHHHHHHHHHHHHh
Confidence 36789999765 57766554432 21 22 45678888999999999999988877654
No 64
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=87.53 E-value=3.2 Score=38.47 Aligned_cols=53 Identities=17% Similarity=0.282 Sum_probs=36.6
Q ss_pred eeeeccc-ChH-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 007008 333 IGVSRKI-TGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 333 IgVSrKI-~de-eR~rLk~i~~~l-------~~-~~~GvIIRTaA~~aseeeL~~Dl~~L~~~ 385 (621)
+.||||. ... +|+|+|.++.++ .+ -++=+|.|..+.+.+..+|.+|+..|...
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 6678995 444 687776655432 12 23446778888899999999998876544
No 65
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=87.35 E-value=0.96 Score=51.91 Aligned_cols=68 Identities=24% Similarity=0.267 Sum_probs=48.7
Q ss_pred eEEEEEecCCceEEEEEEECCEEeEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 76 ~~ilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+..+|.... ...||.|== -+|.+-=++...+..-+|..+.|+|+|+.|- +|||+|+.+-.||+|+++.
T Consensus 243 kvkVi~~D~-e~~RVsLSl-K~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~--GafVei~~GvEGlvhvSEi 310 (541)
T COG0539 243 KVKVISLDE-ERGRVSLSL-KQLEEDPWEGIEKKYPVGDKVEGKVTNLTDY--GAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred EEEEEEEcc-CCCeEEEEe-hhcccCcHHHHhhhcCCCCEEEEEEEEeecC--cEEEEecCCccceeechhh
Confidence 344555554 345665421 2233333445566778999999999999995 8999999999999999875
No 66
>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=86.82 E-value=0.93 Score=38.30 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=31.8
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
..+|.+|.|+|.++.+ .++||++..+..||+|.++
T Consensus 14 ~~~G~~~~g~V~~i~~--~G~fV~l~~~~~Glv~~se 48 (77)
T cd04473 14 LEVGKLYKGKVNGVAK--YGVFVDLNDHVRGLIHRSN 48 (77)
T ss_pred CCCCCEEEEEEEeEec--ceEEEEECCCcEEEEEchh
Confidence 4589999999999987 8999999999999999876
No 67
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=86.48 E-value=1.5 Score=49.79 Aligned_cols=122 Identities=21% Similarity=0.298 Sum_probs=72.5
Q ss_pred cccCCCEEEEEEeecCCCCCCceeeecceeeceeEEEeeCCCceeeecccChHHHHHHHHHHHhcCCC-Cee-EEEeecC
Q 007008 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (621)
Q Consensus 290 ~lk~Gq~ILVQV~Ke~igtKGprLT~~ISLpGRYlVL~P~~~~IgVSrKI~deeR~rLk~i~~~l~~~-~~G-vIIRTaA 367 (621)
.+++||.|-|-|.+-...+|||.+ -+||+-. .-|+.+++.=.|+ ..| +.|+..|
T Consensus 171 ~~~~GdrIka~I~~Vd~~~kg~qI--------------------ilSRt~p----~~l~~Lf~~EVPEI~~G~ieIk~ia 226 (470)
T PRK09202 171 NFRPGDRVRAYVYEVRKEARGPQI--------------------ILSRTHP----EFLKKLFEQEVPEIADGLIEIKAIA 226 (470)
T ss_pred cCCCCCEEEEEEEEEecCCCCCeE--------------------EEEeCcH----HHHHHHHHHhCcccccCeEEEEEEe
Confidence 377899999999988777777654 4677655 3455566555564 335 5577777
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEE-cChhHHHHHH
Q 007008 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVV-DSPRTYHEVT 446 (621)
Q Consensus 368 ~~aseeeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~Ivv-D~~~~y~~i~ 446 (621)
..+.. ++|-+....+..+- +...|+-.....+..+.+.+-.++++=|.. +|+.
T Consensus 227 R~pG~-------------------RaKvAV~s~d~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~------ 280 (470)
T PRK09202 227 RDPGS-------------------RAKIAVKSNDPRID-PVGACVGMRGSRIQAISNELGGEKIDIILWSDDPA------ 280 (470)
T ss_pred ecCcc-------------------eeEEEEEcCCCCCC-hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH------
Confidence 66641 11111111222222 245677777777777777777888886644 3444
Q ss_pred HHHHh-hCCCcCCcee
Q 007008 447 SYLQD-IAPDLCDRVE 461 (621)
Q Consensus 447 ~~l~~-~~p~~~~~v~ 461 (621)
.|+.. +.|.....|.
T Consensus 281 ~fi~nal~pa~v~~v~ 296 (470)
T PRK09202 281 QFIINALSPAEVSSVV 296 (470)
T ss_pred HHHHHhCCCCEEEEEE
Confidence 34433 4566555553
No 68
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.40 E-value=1.7 Score=49.51 Aligned_cols=36 Identities=36% Similarity=0.480 Sum_probs=32.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.+|.|+|++|.| .++||++..+-.||+|+.+.
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 79999998889999988763
No 69
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=85.94 E-value=1.7 Score=52.72 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=30.8
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|++|.|+|+++.+ .+||||+| +-.||+|+++.
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 3579999999999998 49999996 68999999875
No 70
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=85.77 E-value=3.9 Score=38.62 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=38.0
Q ss_pred eeeecccChH-HHHHHH----HHHHhcCC----C--CeeEEEeecCCCCCHHHHHHHHHHHHH
Q 007008 333 IGVSRKITGV-ERTRLK----VIAKTLQP----E--GFGLTIRTVAAGHSLEELQKDLEGLLS 384 (621)
Q Consensus 333 IgVSrKI~de-eR~rLk----~i~~~l~~----~--~~GvIIRTaA~~aseeeL~~Dl~~L~~ 384 (621)
+.||||+... .|+|+| +++....+ . ++=+|.|..+.+++..+|+++|..+..
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 5679999765 576655 44433321 2 456889999999999999999997776
No 71
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.57 E-value=2.3 Score=48.81 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=32.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|+++.|+|+++.+ .+|||++|.+..||+|+.+.
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 72
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.45 E-value=2.3 Score=46.35 Aligned_cols=35 Identities=34% Similarity=0.502 Sum_probs=31.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.++.|+|+++.+ .++||++| +..||+|+++.
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 73
>PRK00038 rnpA ribonuclease P; Reviewed
Probab=82.21 E-value=7.6 Score=36.43 Aligned_cols=52 Identities=13% Similarity=0.337 Sum_probs=34.5
Q ss_pred ceeeeccc-ChH-HHHHHHHHHHh--------cCCCCeeEEEeecCCCCCHHHH----HHHHHHHH
Q 007008 332 RIGVSRKI-TGV-ERTRLKVIAKT--------LQPEGFGLTIRTVAAGHSLEEL----QKDLEGLL 383 (621)
Q Consensus 332 ~IgVSrKI-~de-eR~rLk~i~~~--------l~~~~~GvIIRTaA~~aseeeL----~~Dl~~L~ 383 (621)
++.||||. ... +|+|+|..+.+ +.+.++=||.|..+.+++.++| ..|+..|.
T Consensus 53 Gi~VsKKv~g~AV~RNRiKR~lRE~~R~~~~~l~~~D~VviaR~~~~~~~~~~l~~~~~~~~~~l~ 118 (123)
T PRK00038 53 GLVIAKRFAARAVTRNTLKRVIREAFRARRLALPAQDYVVRLHSKLTPASLTALKRSARAEVDAHF 118 (123)
T ss_pred EEEEecccCCCchhHHHHHHHHHHHHHHhhccCCCCCEEEEECCCCCcCCHHHHHHHHHHHHHHHH
Confidence 46789995 444 67776654433 2223566788999999999999 55555443
No 74
>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=82.16 E-value=1.4 Score=39.48 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=31.6
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.+|.+-.|+|++|-+. ++||+++.+..||+++.+.
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 3799999999999765 9999999999999999885
No 75
>PRK01903 rnpA ribonuclease P; Reviewed
Probab=81.93 E-value=8 Score=36.70 Aligned_cols=53 Identities=21% Similarity=0.349 Sum_probs=34.1
Q ss_pred eeeecc-cChH-HHHHHHHHHHhc-------CCC-------------CeeEEEee-cCCCCCHHHHHHHHHHHHHH
Q 007008 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QPE-------------GFGLTIRT-VAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~l-------~~~-------------~~GvIIRT-aA~~aseeeL~~Dl~~L~~~ 385 (621)
+.|||| +... .|+|+|.++.+. .+. ..-+|.|. +++..+.+++.+++..|..+
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 455799 6665 688777655331 222 23456776 34447799999999877654
No 76
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=81.41 E-value=1.3 Score=51.91 Aligned_cols=38 Identities=32% Similarity=0.522 Sum_probs=35.1
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...-||-||.|+|+++.+ =+|||++..++.|++|+...
T Consensus 615 ~e~evg~iy~G~V~ri~~--fGaFv~l~~gkdgl~hiS~~ 652 (692)
T COG1185 615 REVEVGEVYEGTVVRIVD--FGAFVELLPGKDGLVHISQL 652 (692)
T ss_pred hhcccccEEEEEEEEEee--cceEEEecCCcceeEEehhh
Confidence 556799999999999999 89999999999999999874
No 77
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=81.30 E-value=6.6 Score=36.45 Aligned_cols=53 Identities=19% Similarity=0.233 Sum_probs=37.5
Q ss_pred ceeeecccC-hH-HHHHHHHHH----HhcCC----C--C--eeEEEeecCCCCCHHHHHHHHHHHHH
Q 007008 332 RIGVSRKIT-GV-ERTRLKVIA----KTLQP----E--G--FGLTIRTVAAGHSLEELQKDLEGLLS 384 (621)
Q Consensus 332 ~IgVSrKI~-de-eR~rLk~i~----~~l~~----~--~--~GvIIRTaA~~aseeeL~~Dl~~L~~ 384 (621)
++.||||+. .. .|+|+|.++ ....+ . | +=+|.|..+.+.+..+|.+|+..|.-
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 44 577666444 33322 1 3 34788999999999999999988764
No 78
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=80.96 E-value=8 Score=37.33 Aligned_cols=55 Identities=29% Similarity=0.405 Sum_probs=38.9
Q ss_pred ceeeecccC-hH-HHHHHHHHHHh--------cCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 007008 332 RIGVSRKIT-GV-ERTRLKVIAKT--------LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (621)
Q Consensus 332 ~IgVSrKI~-de-eR~rLk~i~~~--------l~~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W 386 (621)
++.||||+. .. .|+|+|.++.+ +.+.++=+|.|-.+..++.++|++++..|..+.
T Consensus 51 G~sVSKKvg~~AV~RNRiKR~lRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~l~~LL~k~ 115 (145)
T PRK04820 51 GLAVSRKVDTRAVGRNRIKRVLREAMRQLLPELAPGDYVVVARSAAAKASNPQLRDAFLRLLRRA 115 (145)
T ss_pred EEEEeccccCcchhHHHHHHHHHHHHHHhhhccCCCCEEEEEeCCcccCCHHHHHHHHHHHHHHh
Confidence 367899984 44 57776654433 223355678888999999999999988776653
No 79
>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=80.95 E-value=4.9 Score=36.21 Aligned_cols=51 Identities=25% Similarity=0.317 Sum_probs=37.3
Q ss_pred eeeecccChH-HHHHHHHHHHh----cC----CCCeeEEEeecCCCCCHHHHHHHHHHHH
Q 007008 333 IGVSRKITGV-ERTRLKVIAKT----LQ----PEGFGLTIRTVAAGHSLEELQKDLEGLL 383 (621)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~~~----l~----~~~~GvIIRTaA~~aseeeL~~Dl~~L~ 383 (621)
+.||||+... .|+++|.++.+ .. +-++=+|+|..+..++.++|.+++..|.
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 5679998665 57776655433 22 2245678899999999999999998774
No 80
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=80.91 E-value=4.5 Score=44.10 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=32.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecc-cCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdI-G~~k~aFL~~~d~ 147 (621)
...|.|..|+|.++.++ ++|||| |.+-.|||+..+.
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 8899999988775
No 81
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=80.86 E-value=2.4 Score=50.44 Aligned_cols=37 Identities=30% Similarity=0.484 Sum_probs=32.8
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.-..|.|--|.|+||.- -+||||||....|++|++..
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 34689999999999987 48999999999999999864
No 82
>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=79.92 E-value=4.3 Score=44.25 Aligned_cols=101 Identities=22% Similarity=0.234 Sum_probs=60.6
Q ss_pred ccCCCEEEEEEeecCCCCCCceeeecceeeceeEEEeeCCCceeeecccChHHHHHHHHHHHhcCCC--CeeEEEeecCC
Q 007008 291 VQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE--GFGLTIRTVAA 368 (621)
Q Consensus 291 lk~Gq~ILVQV~Ke~igtKGprLT~~ISLpGRYlVL~P~~~~IgVSrKI~deeR~rLk~i~~~l~~~--~~GvIIRTaA~ 368 (621)
+++||.|-|.|.+-..+.|||. |-+||+-. .-|+.+++.-.|+ +.=+.|+..|.
T Consensus 170 ~~~Gd~ik~~V~~V~~~~kg~q--------------------IivSRt~~----~~v~~Lfe~EVPEI~dG~VeI~~iaR 225 (341)
T TIGR01953 170 FRIGDRIKAYVYEVRKTAKGPQ--------------------IILSRTHP----EFVKELLKLEVPEIADGIIEIKKIAR 225 (341)
T ss_pred CCCCCEEEEEEEEEEcCCCCCe--------------------EEEEeCcH----HHHHHHHHHhCccccCCeEEEEEEee
Confidence 7789999999988877777654 44677765 3355566655664 32366777777
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEE
Q 007008 369 GHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV 435 (621)
Q Consensus 369 ~aseeeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~Iv 435 (621)
.+.. ++|-+....+.++- +..+|+-....-+..+.+.+-.+.++=|-
T Consensus 226 ~pG~-------------------RtKvAV~s~~~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 226 EPGY-------------------RTKIAVESNDENID-PVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCcc-------------------eeEEEEEcCCCCCC-cceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 6641 11111111222222 24567777766676766666677777553
No 83
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=79.54 E-value=6.3 Score=36.30 Aligned_cols=53 Identities=28% Similarity=0.367 Sum_probs=37.2
Q ss_pred eeeecc-cChH-HHHHHHHHHHh----cC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 007008 333 IGVSRK-ITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~----l~---~-~~~GvIIRTaA~~aseeeL~~Dl~~L~~~ 385 (621)
+.|||| +... .|+|+|.++.+ .. + -++=+|.|-.+.+++..+|.+|+..|.+.
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 567899 6654 57766654433 21 2 23446889999999999999999887654
No 84
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=79.02 E-value=4.1 Score=44.75 Aligned_cols=32 Identities=19% Similarity=0.266 Sum_probs=27.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeecc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~ 145 (621)
..|+|-.|+|.++.+ +++|||+|. -.|||+.+
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 68898653
No 85
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=78.41 E-value=4.1 Score=47.79 Aligned_cols=35 Identities=29% Similarity=0.438 Sum_probs=30.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|++|.|+|.++.+. ++||++ .+-.||||+++.
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 34799999999999874 899999 578899998774
No 86
>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=76.75 E-value=3 Score=34.97 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
|++..|+|+++.+ .++||+++.+-.||+++.+.
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 87
>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=75.13 E-value=2.5 Score=47.68 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=32.4
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.||.|+|+++.+ .+|||++|.+..||+|+.+.
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 48999999999999998875
No 88
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=74.77 E-value=17 Score=33.71 Aligned_cols=54 Identities=28% Similarity=0.338 Sum_probs=37.6
Q ss_pred eeeec-ccChH-HHHHHHHHHHh-------cC-CCCeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 007008 333 IGVSR-KITGV-ERTRLKVIAKT-------LQ-PEGFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (621)
Q Consensus 333 IgVSr-KI~de-eR~rLk~i~~~-------l~-~~~~GvIIRTaA~~aseeeL~~Dl~~L~~~W 386 (621)
+.||| |+... +|+|+|.++.. +. +.++=||+|..+.+++..++++++..+...-
T Consensus 45 lsVsKkk~g~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~~ 108 (117)
T COG0594 45 LTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRA 108 (117)
T ss_pred EEEEchhccchhhHHHHHHHHHHHHHhhhhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHHh
Confidence 67799 77754 67666544322 22 2356789999999999999988877665543
No 89
>PRK00730 rnpA ribonuclease P; Reviewed
Probab=73.11 E-value=9.6 Score=36.59 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=37.1
Q ss_pred ceeeecccChH-HHHHHHHHHHh----cC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 007008 332 RIGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (621)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~~~----l~---~-~~~GvIIRTaA~~aseeeL~~Dl~~L~~~ 385 (621)
++.||||+... .|+|+|.++.. .. + -++=||.|..+. ++.++|.+|+..+...
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 46789999765 68777655533 22 2 244578888887 9999999998776653
No 90
>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=71.88 E-value=10 Score=34.29 Aligned_cols=54 Identities=33% Similarity=0.446 Sum_probs=36.2
Q ss_pred eeeecccCh-H-HHHHHHHHHHhc----C---CCC--eeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 007008 333 IGVSRKITG-V-ERTRLKVIAKTL----Q---PEG--FGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (621)
Q Consensus 333 IgVSrKI~d-e-eR~rLk~i~~~l----~---~~~--~GvIIRTaA~~aseeeL~~Dl~~L~~~W 386 (621)
+.||||+.. . .|+++|.++.++ . +.+ +=++.|..+...+.++|.+++..|..+.
T Consensus 46 ~~vsKK~gk~AV~RNriKR~lRe~~R~~~~~l~~~~d~v~~~r~~~~~~~~~~l~~~l~~ll~k~ 110 (111)
T PF00825_consen 46 FSVSKKVGKRAVKRNRIKRRLREAFRLNKPELPPGYDIVFIARPGALELSFEELEKELKKLLKKA 110 (111)
T ss_dssp EEE-STTSS-HHHHHHHHHHHHHHHHHCTTTS-SSSEEEEEE-CGGGGS-HHHHHHHHHHHHHHH
T ss_pred EEecCccccchhHHHHHHHHHHHHHHHHHhhccCCcEEEEEEcCCcCcCCHHHHHHHHHHHHHhh
Confidence 568999976 5 688777655442 2 223 3577888889999999999998887653
No 91
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=70.15 E-value=11 Score=44.25 Aligned_cols=36 Identities=31% Similarity=0.495 Sum_probs=32.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.+|.|+|++|.+ .++||+++.+-.||+|+.+.
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 3589999999999999 49999999999999988763
No 92
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=70.09 E-value=25 Score=32.64 Aligned_cols=54 Identities=28% Similarity=0.427 Sum_probs=36.5
Q ss_pred eeeecccC-hH-HHHHHHH----HHHhcC---CCC--eeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 007008 333 IGVSRKIT-GV-ERTRLKV----IAKTLQ---PEG--FGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (621)
Q Consensus 333 IgVSrKI~-de-eR~rLk~----i~~~l~---~~~--~GvIIRTaA~~aseeeL~~Dl~~L~~~W 386 (621)
+.||||.. .. .|+++|. ++..+. +.+ +=+|+|..+.+++..+|.+|+..|..+.
T Consensus 51 ~~VsKK~~~~AV~RNriKR~lRe~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k~ 115 (122)
T PRK03031 51 ISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQA 115 (122)
T ss_pred EEEecccccchhhhhHHHHHHHHHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHHc
Confidence 56799964 34 5666554 443332 233 3467788999999999999998876653
No 93
>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=65.96 E-value=25 Score=28.79 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=26.7
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeeccc
Q 007008 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (621)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d 146 (621)
|++--|+|++|.+ .+|||++..+-.||++..+
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 5799999667899997655
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=65.92 E-value=7.5 Score=34.36 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecc--------cCCcceeeeccccC
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNI--------GNSRPSLMDIKHYR 148 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdI--------G~~k~aFL~~~d~~ 148 (621)
.+|+|=.|+|++|-+. .|+||| ...-.|+|++.|.+
T Consensus 5 ~~GDiVig~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~~dv~ 48 (92)
T cd05791 5 KVGSIVIARVTRINPR--FAKVDILCVGGRPLKESFRGVIRKEDIR 48 (92)
T ss_pred CCCCEEEEEEEEEcCC--EEEEEEEEecCeecCCCcccEEEHHHcc
Confidence 5899999999999755 499999 88888999998864
No 95
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=64.36 E-value=14 Score=39.39 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.7
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
.++|.-=.|+|+.|-+.++ ||||.|..|.-|+++++.
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 4689999999999999985 799999999999999884
No 96
>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=62.98 E-value=15 Score=43.70 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-Ccceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~-~k~aFL~~~d~ 147 (621)
.+|.+|.|+|++|.+ -++||++.. +..||+|+.+.
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 579999999999988 689999986 79999999874
No 97
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=60.88 E-value=18 Score=40.02 Aligned_cols=188 Identities=13% Similarity=0.156 Sum_probs=93.6
Q ss_pred cccCCCEEEEEEeecCCCCC-CceeeecceeeceeEEEeeCCCceeeecccChHHHHHHHHHHHhcCCC-Cee-EEEeec
Q 007008 290 QVQKGTKVIVQVVKEGLGTK-GPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTV 366 (621)
Q Consensus 290 ~lk~Gq~ILVQV~Ke~igtK-GprLT~~ISLpGRYlVL~P~~~~IgVSrKI~deeR~rLk~i~~~l~~~-~~G-vIIRTa 366 (621)
.+++||.|-|=|.+--..+| ||.+ -+||.-. .-|+.+++.=.|+ ..| +.|+..
T Consensus 176 ~~~~Gdrik~~i~~V~~~~k~gp~I--------------------ilSRt~p----~~v~~Lfe~EVPEI~dG~VeIk~I 231 (374)
T PRK12328 176 KFKVGDVVKAVLKRVKIDKNNGILI--------------------ELSRTSP----KFLEALLELEVPEIKDGEVIIIHS 231 (374)
T ss_pred cCCCCCEEEEEEEEEecCCCCCCEE--------------------EEEcCCH----HHHHHHHHHhCccccCCeEEEEEE
Confidence 47889999998888877777 7654 3555443 3355555555554 224 567777
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEE-cChhHHHHH
Q 007008 367 AAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVV-DSPRTYHEV 445 (621)
Q Consensus 367 A~~aseeeL~~Dl~~L~~~W~~I~~~~~~~~~~~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~Ivv-D~~~~y~~i 445 (621)
|..+.. ++|-+....+..+ -+...|+-....-+..+.+.+-.+.++=|.. ||+.
T Consensus 232 ARepG~-------------------RtKVAV~S~d~~i-DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~----- 286 (374)
T PRK12328 232 ARIPGE-------------------RAKVALFSNNPNI-DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE----- 286 (374)
T ss_pred eccCcc-------------------eeEEEEEcCCCCC-ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH-----
Confidence 666541 1111111112222 1234667666666777777776787876644 3443
Q ss_pred HHHHHh-hCCCcCCceeeccCCCCcccccCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHH
Q 007008 446 TSYLQD-IAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKA 524 (621)
Q Consensus 446 ~~~l~~-~~p~~~~~v~~y~~~~pLF~~y~Ie~~I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t 524 (621)
.|+.. ++|....+|.+-. +...+..+=-+.++..|..+. |-.+-.-.-=+-|-|||-|.... .+...+.
T Consensus 287 -~fI~Nal~Pa~V~~V~i~~-~~~~~~V~V~~~qlslAIGk~-----GqNvrLA~~LtGwkIDI~s~~~~---~~~~~~~ 356 (374)
T PRK12328 287 -IFIARALAPAIISSVKIEE-EEKKAIVTLLSDQKSKAIGKN-----GINIRLASMLTGYEIELNEIGSK---ENASNES 356 (374)
T ss_pred -HHHHHhCCCceeeEEEEcC-CCcEEEEEEChHHhhhhhcCC-----ChhHHHHHHHhCCEEEEEECCCC---ccccccc
Confidence 34433 4576555554322 112222222233343333321 11111111123467888887531 1111122
Q ss_pred HHHHHHHHHHHH
Q 007008 525 ILDVNLAAAKQI 536 (621)
Q Consensus 525 ~l~tNlEAA~EI 536 (621)
--.||.|..+..
T Consensus 357 ~~~~~~~~~~~~ 368 (374)
T PRK12328 357 EKETNKEGVKAL 368 (374)
T ss_pred ccccccccHHHH
Confidence 345777766543
No 98
>PRK11642 exoribonuclease R; Provisional
Probab=59.62 E-value=22 Score=43.25 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=30.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCC-cceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIGNS-RPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG~~-k~aFL~~~d~ 147 (621)
.+|.+|.|+|+.|.+. ++||++... -.||+|+.+.
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 5899999999999885 999999864 9999999874
No 99
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=56.39 E-value=21 Score=37.77 Aligned_cols=35 Identities=17% Similarity=0.438 Sum_probs=27.4
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG--~~k~aFL~~~d~ 147 (621)
-.|.|-.|+|++|... +|||+.- .++.||+|+++.
T Consensus 10 eeGEiVv~tV~~V~~~--GAyv~L~EY~g~Eg~ihiSEv 46 (269)
T COG1093 10 EEGEIVVGTVKQVADY--GAYVELDEYPGKEGFIHISEV 46 (269)
T ss_pred CCCcEEEEEEEEeecc--ccEEEeeccCCeeeeEEHHHH
Confidence 4799999999999874 7888762 357788887663
No 100
>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=54.24 E-value=14 Score=32.50 Aligned_cols=31 Identities=39% Similarity=0.502 Sum_probs=27.1
Q ss_pred eEEEEEeeecCCcceEEecccCCcceeeeccccC
Q 007008 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (621)
Q Consensus 115 IY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~~ 148 (621)
+|.|+|+.|.+ .++||+++ .-.||+++.+..
T Consensus 2 vv~g~V~~i~~--~GifV~l~-~v~G~v~~~~l~ 32 (99)
T cd04460 2 VVEGEVVEVVD--FGAFVRIG-PVDGLLHISQIM 32 (99)
T ss_pred EEEEEEEEEEe--ccEEEEEc-CeEEEEEEEEcc
Confidence 79999999988 49999998 489999998753
No 101
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=51.59 E-value=8.8 Score=37.06 Aligned_cols=50 Identities=24% Similarity=0.270 Sum_probs=35.0
Q ss_pred CCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCchhhccccCCCcccCC
Q 007008 545 IGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVWFSNSQFSLCYLAFVHLLG 617 (621)
Q Consensus 545 IgGIIVIDFIdM~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~ 617 (621)
-|.|||-||-|+..-.+-+ -+.|.+++. ++...+|.+.+.|+||..+|+|
T Consensus 82 tGdviVTDFgD~~~lgNI~--~d~L~~~f~---------------------~W~~~~l~~slnCHCp~v~ClG 131 (153)
T PF08756_consen 82 TGDVIVTDFGDEPPLGNIQ--TDSLTDAFD---------------------RWLDSPLAKSLNCHCPAVKCLG 131 (153)
T ss_pred cCCEEEecCCCCCCccccc--cCcHHHHHH---------------------HHhcCcccccccCcCCcccccC
Confidence 3889999999986654422 134444443 3445577888999999999988
No 102
>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=50.16 E-value=33 Score=40.51 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeecccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG-~~k~aFL~~~d~ 147 (621)
.+|.+|-|+|+.|.+ .++||++. .+-.||+|+.+.
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 479999999999998 46999997 789999999874
No 103
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=47.54 E-value=17 Score=39.56 Aligned_cols=119 Identities=15% Similarity=0.111 Sum_probs=80.3
Q ss_pred EEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHH
Q 007008 494 SLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAV 573 (621)
Q Consensus 494 ~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVIDFIdM~~~~~r~~Vl~~L~~~l 573 (621)
..|.++.+++|.|---+|.+ +.-.+-|+.+...|+.|.-+-.--+ =|.-|-..|=||=+|.--- -+++.+-++
T Consensus 61 ~~v~~rIp~~t~~~~~~~s~--~e~~~~ee~~real~~~~~~~cC~~-S~~ag~l~i~~~e~~~~~~---~~l~tfvee- 133 (406)
T KOG2813|consen 61 KMVFDRIPPSTSIHYILESF--TEARSTEEATREALFAAMSEACCSL-SGGAGALSIWDFEVMPGHL---FVLQTFVEE- 133 (406)
T ss_pred ccccccCCcccccccccccc--chhcccHHHHHHHHHHHhhchhhhc-CCCcccccceehhcCcceE---Eeeeeeecc-
Confidence 35778899999999888874 3345567777888888887765543 2555667788999997632 223333333
Q ss_pred hcCCCCcEEeccCCC-----------eeEEEeecCCCCCch-----------hhccccCCCcccCCcccC
Q 007008 574 ERDRSMVKVSELSRH-----------GLMEITRKRVWFSNS-----------QFSLCYLAFVHLLGLMKC 621 (621)
Q Consensus 574 k~D~~k~~V~g~T~L-----------GLvEiTRkR~r~sL~-----------~~~~~~~~~~~~~~~~~~ 621 (621)
-+.-+++.+||.- ||-++-.+-.++.+. .++-..|..|||.|.|+|
T Consensus 134 --r~~~~q~~PfT~~~~dG~~hg~~prlw~~d~~~~gp~mf~~~~~~~~vphs~~v~~ch~c~gRG~~vc 201 (406)
T KOG2813|consen 134 --RPGSSQINPFTACNSDGTIHGFHPRLWGTDKCSRGPGMFSGVAHPAVVPHSMIVTFCHACLGRGAMVC 201 (406)
T ss_pred --ccccceecccccCCcCCcccccCccccccccccCCCCcccccccceeccchHhhhhhhcccCCCceec
Confidence 3566788888753 455655444445443 455678999999999988
No 104
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=43.94 E-value=82 Score=31.24 Aligned_cols=36 Identities=19% Similarity=0.201 Sum_probs=30.6
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
+...|-|--|+|+++.+ .++||.+|-=. +|+|....
T Consensus 78 rPf~gEVv~g~V~~v~~--~G~~v~~Gp~~-ifI~~~~l 113 (176)
T PTZ00162 78 KPFKDEVLDAIVTDVNK--LGFFAQAGPLK-AFVSRSAI 113 (176)
T ss_pred ecCCCCEEEEEEEEEec--ceEEEEeeCeE-EEEcHHHC
Confidence 34689999999999999 59999999877 88877653
No 105
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=43.34 E-value=18 Score=29.98 Aligned_cols=30 Identities=7% Similarity=-0.196 Sum_probs=21.6
Q ss_pred CeeEEEeecCCCCCchhhccccCCCcccCCcc
Q 007008 588 HGLMEITRKRVWFSNSQFSLCYLAFVHLLGLM 619 (621)
Q Consensus 588 LGLvEiTRkR~r~sL~~~~~~~~~~~~~~~~~ 619 (621)
-|.+.++++ ..........+|+.|||.|.+
T Consensus 24 ~G~~~~~~~--~~~~~~~~~~~C~~C~G~G~~ 53 (66)
T PF00684_consen 24 SGQVTRRQQ--TPGGVFQMQQTCPKCGGTGKI 53 (66)
T ss_dssp SSEEEEEEE--SSSTTEEEEEE-TTTSSSSEE
T ss_pred eeEEEEEEe--CCCeEEEEEEECCCCcceeeE
Confidence 455555555 667777788899999999976
No 106
>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=42.04 E-value=1.1e+02 Score=28.97 Aligned_cols=49 Identities=29% Similarity=0.266 Sum_probs=33.5
Q ss_pred HHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCC
Q 007008 539 ELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSR 587 (621)
Q Consensus 539 QLRLRnIgGIIVIDFIdM~~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~ 587 (621)
.+.-++.-=+|++--+|+..+.++...++.+++.++.......++.+|.
T Consensus 124 ~~~~~~~pviiv~nK~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~Sa 172 (179)
T TIGR03598 124 WLRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSS 172 (179)
T ss_pred HHHHcCCCEEEEEECcccCCHHHHHHHHHHHHHHHhhccCCCceEEEEC
Confidence 3334556667888888987777778888889999987543344555543
No 107
>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=40.57 E-value=31 Score=33.91 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=30.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.++-|+|+++.+ .++||++|. -+|+++..+.
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 3579999999999999 599999985 7888887764
No 108
>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=36.75 E-value=84 Score=29.67 Aligned_cols=55 Identities=18% Similarity=0.184 Sum_probs=39.8
Q ss_pred hcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCC-CcEEeccCCCeeEEEeecCCCC
Q 007008 541 RLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRS-MVKVSELSRHGLMEITRKRVWF 600 (621)
Q Consensus 541 RLRnIgGIIVIDFIdM~~~~~r~~Vl~~L~~~lk~D~~-k~~V~g~T~LGLvEiTRkR~r~ 600 (621)
.|...+|+|+|||-++. .+ + ++.+++.+..|+. -.-.++.|.-||==+.|=....
T Consensus 26 ~l~~~sglv~lDiD~l~-~e---e-~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~~~~~ 81 (136)
T PF08800_consen 26 NLKAYSGLVVLDIDHLD-PE---E-AEELRQLLFEDPYTLAAFVSPSGRGVKIIVPFDYPD 81 (136)
T ss_pred hhhhCCCcEEEEeCCCC-HH---H-HHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEecCCC
Confidence 46678999999998887 32 2 4678888888886 3356778888887776654433
No 109
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=35.24 E-value=42 Score=33.04 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=30.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
..+|.++.|+|+++.+ .++||++|. -+||++..+.
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 8899987764
No 110
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=35.20 E-value=94 Score=35.40 Aligned_cols=32 Identities=9% Similarity=0.101 Sum_probs=24.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccC--C---cceeee
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGN--S---RPSLMD 143 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~--~---k~aFL~ 143 (621)
..+|.|-.|+|.++..+ ..+||+|. + -.|+|+
T Consensus 150 ~~~GeIV~G~V~r~e~~--~viv~l~~~~g~~~~EaiLP 186 (449)
T PRK12329 150 DLEDTVLTARVLRFERQ--SVIMAVSSGFGQPEVEAELP 186 (449)
T ss_pred HhcCcEEEEEEEEEcCC--CEEEEecccCCCcceEEEec
Confidence 36899999999999886 69999842 2 356663
No 111
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=33.44 E-value=30 Score=27.70 Aligned_cols=15 Identities=60% Similarity=1.012 Sum_probs=12.9
Q ss_pred ceecCCCcEEEEecc
Q 007008 486 RVPLPNGGSLVIEQT 500 (621)
Q Consensus 486 rV~L~sGG~LVIE~T 500 (621)
||+|.+||.||+|=+
T Consensus 22 RvPleGGGRLVvEl~ 36 (51)
T PF11314_consen 22 RVPLEGGGRLVVELN 36 (51)
T ss_pred EEecCCCcEEEEEeC
Confidence 699999999999843
No 112
>PHA02945 interferon resistance protein; Provisional
Probab=32.00 E-value=1.3e+02 Score=26.97 Aligned_cols=33 Identities=12% Similarity=0.141 Sum_probs=24.9
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeeccc
Q 007008 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (621)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVdIG--~~k~aFL~~~d 146 (621)
-.|.|-+|+|+. .=.+|||+.- .++.||+|++.
T Consensus 10 ~~GelvigtV~~---~d~ga~v~L~EY~g~eg~i~~se 44 (88)
T PHA02945 10 NVGDVLKGKVYE---NGYALYIDLFDYPHSEAILAESV 44 (88)
T ss_pred CCCcEEEEEEEe---cCceEEEEecccCCcEEEEEeeh
Confidence 378999999999 4468898773 26778887764
No 113
>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=31.57 E-value=69 Score=28.38 Aligned_cols=34 Identities=21% Similarity=0.181 Sum_probs=29.7
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeecc
Q 007008 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (621)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~ 145 (621)
..+|++-+|+|+.+. -..-+||||..-+|+|++.
T Consensus 4 P~~gD~VIG~V~~~~--~~~~~VdI~s~~~a~L~~~ 37 (86)
T cd05790 4 PAKGDHVIGIVVAKA--GDFFKVDIGGSEPASLSYL 37 (86)
T ss_pred CCCCCEEEEEEEEEc--CCeEEEEcCCCcceEechH
Confidence 358999999999996 4889999999999999764
No 114
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=30.62 E-value=27 Score=34.15 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=20.2
Q ss_pred HhCCceecCCCcEEEEecccceE
Q 007008 482 MLSKRVPLPNGGSLVIEQTEALV 504 (621)
Q Consensus 482 al~~rV~L~sGG~LVIE~TEALt 504 (621)
-+.+.||++-|+++||+++|-+-
T Consensus 54 KfRksiWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 54 KFRKSIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred hhhhceEEeeCCEEEEccccccc
Confidence 35678999999999999999876
No 115
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=27.45 E-value=11 Score=30.55 Aligned_cols=14 Identities=21% Similarity=-0.161 Sum_probs=10.8
Q ss_pred hccccCCCcccCCc
Q 007008 605 FSLCYLAFVHLLGL 618 (621)
Q Consensus 605 ~~~~~~~~~~~~~~ 618 (621)
++...|..||+.|-
T Consensus 9 ly~~~C~~CH~~~~ 22 (67)
T PF13442_consen 9 LYEQNCASCHGPGG 22 (67)
T ss_dssp HHHHHTHHHHGTGS
T ss_pred HHHhHhHHhcCCCc
Confidence 44568999999764
No 116
>PF10442 FIST_C: FIST C domain; InterPro: IPR019494 This entry represents a novel sensory domain, designated FIST C (short for F-box and intracellular signal transduction, C-terminal), which is present in signal transduction proteins from bacteria, archaea and eukaryotes. The chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [].
Probab=26.53 E-value=1.2e+02 Score=27.63 Aligned_cols=56 Identities=11% Similarity=0.120 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHhcccCCCcEEEEcCCCC---ChhhHHHHHHHHHHHHhcCCCCcEEeccCCCe
Q 007008 530 LAAAKQIARELRLRDIGGIIVVDFIDMA---DDSNKRLVYEEVKKAVERDRSMVKVSELSRHG 589 (621)
Q Consensus 530 lEAA~EIARQLRLRnIgGIIVIDFIdM~---~~~~r~~Vl~~L~~~lk~D~~k~~V~g~T~LG 589 (621)
++++++.++++.-.+..|++++|.+--. .+....+ ++.+++.+..+ +.++||..+|
T Consensus 73 ~~~~~~~~~~~~~~~p~~~l~f~C~~R~~~l~~~~~~e-~~~~~~~~~~~---~p~~Gf~t~G 131 (136)
T PF10442_consen 73 IESAEEALEKAPGPPPEGALIFSCIGRRLFLGERFDEE-LEAFQEILGGD---APFIGFYTYG 131 (136)
T ss_pred HHHHHHHHHhhcCCCceEEEEEECCCCHHHhCcchHHH-HHHHHHHhCCC---CCEEEEcccc
Confidence 5777777778888899999999998631 1223334 67788888532 4678888777
No 117
>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=26.00 E-value=42 Score=29.28 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=18.6
Q ss_pred HhHhCCceecCCCcEEEEeccc
Q 007008 480 NNMLSKRVPLPNGGSLVIEQTE 501 (621)
Q Consensus 480 ~~al~~rV~L~sGG~LVIE~TE 501 (621)
-.=|.++||.+-|+|+++++.+
T Consensus 30 P~KfRk~iWIkrGd~VlV~p~~ 51 (78)
T cd05792 30 PTKFRKNIWIKRGDFVLVEPIE 51 (78)
T ss_pred chhhcccEEEEeCCEEEEEecc
Confidence 3456789999999999998866
No 118
>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=25.53 E-value=1.3e+02 Score=25.28 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhc
Q 007008 531 AAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVER 575 (621)
Q Consensus 531 EAA~EIARQLRLRnIgGIIVIDFIdM~~~~~r~~Vl~~L~~~lk~ 575 (621)
+-|.+|+.+||=+ -++++||-+|..+. .+++++.|..+...
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 4578899999876 46999999998776 66788888877654
No 119
>COG2010 CccA Cytochrome c, mono- and diheme variants [Energy production and conversion]
Probab=25.53 E-value=28 Score=32.10 Aligned_cols=14 Identities=21% Similarity=-0.047 Sum_probs=10.9
Q ss_pred hhccccCCCcccCC
Q 007008 604 QFSLCYLAFVHLLG 617 (621)
Q Consensus 604 ~~~~~~~~~~~~~~ 617 (621)
.+....|..|||.+
T Consensus 56 ~~f~~~C~~CHg~~ 69 (150)
T COG2010 56 ALFLGNCAACHGPN 69 (150)
T ss_pred HHhcccchhccCCC
Confidence 34558999999976
No 120
>COG3585 MopI Molybdopterin-binding protein [Coenzyme metabolism]
Probab=24.10 E-value=51 Score=28.15 Aligned_cols=24 Identities=21% Similarity=0.184 Sum_probs=20.7
Q ss_pred cCCeEEEEEeeecCCcceEEeccc
Q 007008 112 CDSVYLGVVTKLVPNMGGAFVNIG 135 (621)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVdIG 135 (621)
.-|+++|+|+.|++|+=-+=|+|-
T Consensus 5 aRN~lKG~Vk~iv~G~Vnsev~ie 28 (69)
T COG3585 5 ARNQLKGKVKEIVKGSVNSEVTIE 28 (69)
T ss_pred hhheeccEEEEEEEcccceEEEEE
Confidence 458999999999999988887763
No 121
>CHL00183 petJ cytochrome c553; Provisional
Probab=22.08 E-value=22 Score=31.68 Aligned_cols=13 Identities=23% Similarity=-0.079 Sum_probs=9.6
Q ss_pred ccccCCCcccCCc
Q 007008 606 SLCYLAFVHLLGL 618 (621)
Q Consensus 606 ~~~~~~~~~~~~~ 618 (621)
....|..|||.|.
T Consensus 33 y~~~Ca~CHg~g~ 45 (108)
T CHL00183 33 FSANCAACHAGGN 45 (108)
T ss_pred HHHHHHHHCCCCC
Confidence 3358999998753
No 122
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist 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. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=21.91 E-value=8.1e+02 Score=26.75 Aligned_cols=149 Identities=15% Similarity=0.142 Sum_probs=83.5
Q ss_pred eeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHh-hCCC--cCCceee--ccC------CCCcccccCHHHH
Q 007008 410 ILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQD-IAPD--LCDRVEL--YDK------RIPLFDKFNIEEE 478 (621)
Q Consensus 410 ~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~-~~p~--~~~~v~~--y~~------~~pLF~~y~Ie~~ 478 (621)
.++|..+.....-|+..+...+ .|.+|+....+.+.+.... ..+. ..-||.. ..+ ......+||+..+
T Consensus 73 ~Ii~~gp~K~~~~L~~ai~~gv-~i~iDS~~El~~i~~~a~~~~~~~~~v~lRvnp~~~~~~~~~~~~~~~~skFG~~~~ 151 (379)
T cd06836 73 RIVFDSPAKTRAELREALELGV-AINIDNFQELERIDALVAEFKEASSRIGLRVNPQVGAGKIGALSTATATSKFGVALE 151 (379)
T ss_pred hEEEeCCCCCHHHHHHHHHCCC-EEEECCHHHHHHHHHHHHHhcCCCceEEEEECCCCCCCCccccccCCCCCCCCcCcc
Confidence 5888888777778888888888 7999999999998887754 2222 2222221 111 1124577886654
Q ss_pred ---HHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHH--HHHHHHHHHHHHHHH-----HHhcccCCCc
Q 007008 479 ---INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEK--AILDVNLAAAKQIAR-----ELRLRDIGGI 548 (621)
Q Consensus 479 ---I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~--t~l~tNlEAA~EIAR-----QLRLRnIgGI 548 (621)
+.+++... ..+..| .-|-...|... .+.+. .+++.-+..|.++.+ +++.-||||=
T Consensus 152 ~~~~~~~~~~~---~~~~~l--------~GlH~H~GS~~----~~~~~~~~~~~~~~~l~~~l~~~~g~~~~~~IDiGGG 216 (379)
T cd06836 152 DGARDEIIDAF---ARRPWL--------NGLHVHVGSQG----CELSLLAEGIRRVVDLAEEINRRVGRRQITRIDIGGG 216 (379)
T ss_pred hhHHHHHHHHH---hcCCCe--------EEEEEecccCC----CCHHHHHHHHHHHHHHHHHHHHHhCCCCCcEEEeCCc
Confidence 55555421 111112 24556666421 12221 112223334455543 4677899988
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHHh
Q 007008 549 IVVDFIDMADDSNKRLVYEEVKKAVE 574 (621)
Q Consensus 549 IVIDFIdM~~~~~r~~Vl~~L~~~lk 574 (621)
.-|++-+...+.+-++..+.+.+++.
T Consensus 217 f~v~y~~~~~~~~~~~~~~~i~~~l~ 242 (379)
T cd06836 217 LPVNFESEDITPTFADYAAALKAAVP 242 (379)
T ss_pred cccCCCCCCCCCCHHHHHHHHHHHHH
Confidence 88888665433344445555555544
No 123
>PF08508 DUF1746: Fungal domain of unknown function (DUF1746); InterPro: IPR013715 This is a fungal domain of unknown function.
Probab=21.77 E-value=62 Score=30.29 Aligned_cols=20 Identities=25% Similarity=0.600 Sum_probs=15.9
Q ss_pred CCcEEEEcCCCCChhhHHHHH
Q 007008 546 GGIIVVDFIDMADDSNKRLVY 566 (621)
Q Consensus 546 gGIIVIDFIdM~~~~~r~~Vl 566 (621)
|| ++||||..+-+-.|=+++
T Consensus 84 GG-l~IdFIGq~~p~srl~ll 103 (116)
T PF08508_consen 84 GG-LIIDFIGQKPPPSRLELL 103 (116)
T ss_pred Cc-eEEEeccCCCCcchHHHH
Confidence 45 899999999887776654
No 124
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=21.63 E-value=71 Score=37.54 Aligned_cols=38 Identities=21% Similarity=0.483 Sum_probs=29.0
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecccc
Q 007008 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (621)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~d~ 147 (621)
...-.|.+|+|.|.+|..- +||||...---|.||-.+.
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~--GvFv~Ln~~v~GL~~~~d~ 155 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKY--GVFVELNSHVRGLIHRRDL 155 (715)
T ss_pred hhcccceeeeccccchhhh--cceeecChhhhcccccccc
Confidence 3456899999999999874 7899987766677765553
No 125
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=21.38 E-value=1.4e+02 Score=38.60 Aligned_cols=76 Identities=16% Similarity=0.239 Sum_probs=58.3
Q ss_pred ccccCCcceEEEEEecCCceEEEEEEECCEEeEEEeecCC--CCcccCCeEEEEEeeecCCcceEEecccCCcceeeecc
Q 007008 68 ISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVK--SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (621)
Q Consensus 68 ~~~~~~~~~~ilIn~~~~~e~RvAvlEdgkL~El~iE~~~--~~~~vGnIY~GrV~kV~Pgm~AAFVdIG~~k~aFL~~~ 145 (621)
+...... +.+.+|.. ..|+|+.-++.|++...+-+. +..+-|.||+|-|.++-+ ++|||.+=++-.||++..
T Consensus 557 v~~~~k~-RVl~~~~~---~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~--~g~~V~F~g~lsGf~p~s 630 (1710)
T KOG1070|consen 557 VGSGVKL-RVLSVNRD---RNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKE--NGAFVTFTGGLSGFAPVS 630 (1710)
T ss_pred eccccEE-EEEEEEcc---CCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeecc--CCeEEEecCccccccchh
Confidence 3333334 77778874 469999999999999555433 233459999999999998 599999999999999776
Q ss_pred ccCC
Q 007008 146 HYRE 149 (621)
Q Consensus 146 d~~~ 149 (621)
..-.
T Consensus 631 ~~sd 634 (1710)
T KOG1070|consen 631 EMSD 634 (1710)
T ss_pred hhhh
Confidence 6533
No 126
>cd01884 EF_Tu EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=21.07 E-value=4.6e+02 Score=25.92 Aligned_cols=78 Identities=19% Similarity=0.142 Sum_probs=40.7
Q ss_pred HHHHHHHhcccCCCc-EEEEcCCCCChhh-HHHHHHHHHHHHhc---CCCCcEEeccCCCeeEEEee--cC--CCCCchh
Q 007008 534 KQIARELRLRDIGGI-IVVDFIDMADDSN-KRLVYEEVKKAVER---DRSMVKVSELSRHGLMEITR--KR--VWFSNSQ 604 (621)
Q Consensus 534 ~EIARQLRLRnIgGI-IVIDFIdM~~~~~-r~~Vl~~L~~~lk~---D~~k~~V~g~T~LGLvEiTR--kR--~r~sL~~ 604 (621)
+++++++.-.++..+ |+|-=+|...++. .+.+.+.+++.|++ +...+.++++|.+-=..+.+ .+ ..++|.+
T Consensus 107 ~~~~~~~~~~~~~~iIvviNK~D~~~~~~~~~~~~~~i~~~l~~~g~~~~~v~iipiSa~~g~n~~~~~~w~~~~~~l~~ 186 (195)
T cd01884 107 REHLLLARQVGVPYIVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLD 186 (195)
T ss_pred HHHHHHHHHcCCCcEEEEEeCCCCCCcHHHHHHHHHHHHHHHHHhcccccCCeEEEeeCccccCCCCCCcchhcHhHHHH
Confidence 456666666777644 4555555433333 33455567666653 33456677776653222211 11 2456666
Q ss_pred hccccCC
Q 007008 605 FSLCYLA 611 (621)
Q Consensus 605 ~~~~~~~ 611 (621)
.|-..+|
T Consensus 187 ~l~~~~~ 193 (195)
T cd01884 187 ALDSYIP 193 (195)
T ss_pred HHHhCCC
Confidence 6655554
No 127
>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=20.77 E-value=6.3e+02 Score=27.03 Aligned_cols=130 Identities=15% Similarity=0.147 Sum_probs=69.6
Q ss_pred eeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCcCCceeeccC----------CCCcccccCHH-HH
Q 007008 410 ILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDK----------RIPLFDKFNIE-EE 478 (621)
Q Consensus 410 ~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~~y~~----------~~pLF~~y~Ie-~~ 478 (621)
.+++..+.....-++..+...+..+++|+.+..+.+.++.........--+++.-. ......+||+. ++
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 57776665555667777777788899999998888888775432111111122100 01123677864 23
Q ss_pred HHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-------hcccCCCcEEE
Q 007008 479 INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIAREL-------RLRDIGGIIVV 551 (621)
Q Consensus 479 I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQL-------RLRnIgGIIVI 551 (621)
+.++++.--.+++ | -+.-|=...|.. ..+ ...+..+++.+.+++..| +.-|+||=.-+
T Consensus 154 ~~~~~~~~~~~~~---l------~l~Gi~~H~gs~----~~~--~~~~~~~~~~~~~~~~~l~~~g~~~~~idiGGG~~~ 218 (373)
T cd06828 154 ALEAYRRAKELPG---L------KLVGLHCHIGSQ----ILD--LEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGI 218 (373)
T ss_pred HHHHHHHHHhCCC---C------cEEEEEEecCCC----CCC--HHHHHHHHHHHHHHHHHHHhcCCCCCEEEeCCCCCc
Confidence 4444443222221 1 022333333421 112 245677777777777766 45677765555
Q ss_pred EcC
Q 007008 552 DFI 554 (621)
Q Consensus 552 DFI 554 (621)
.+.
T Consensus 219 ~~~ 221 (373)
T cd06828 219 PYR 221 (373)
T ss_pred ccC
Confidence 553
No 128
>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=20.60 E-value=1.2e+02 Score=22.68 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=20.8
Q ss_pred CCeEEEEEeeecCC--cceEEecccCCc
Q 007008 113 DSVYLGVVTKLVPN--MGGAFVNIGNSR 138 (621)
Q Consensus 113 GnIY~GrV~kV~Pg--m~AAFVdIG~~k 138 (621)
|.-|.|+|.++.++ ..=-|+|.|...
T Consensus 12 ~~wyra~V~~~~~~~~~~V~f~DyG~~~ 39 (48)
T cd04508 12 GKWYRAKITSILSDGKVEVFFVDYGNTE 39 (48)
T ss_pred CeEEEEEEEEECCCCcEEEEEEcCCCcE
Confidence 78999999999953 455688988764
No 129
>COG5231 VMA13 Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]
Probab=20.58 E-value=38 Score=37.20 Aligned_cols=106 Identities=21% Similarity=0.267 Sum_probs=68.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHh-hhh--hccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHH
Q 007008 369 GHSLEELQKDLEGLLSTWKNIMEHAKSA-ALA--ADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEV 445 (621)
Q Consensus 369 ~aseeeL~~Dl~~L~~~W~~I~~~~~~~-~~~--~~~~~~~~~P~lL~~~~~~~~~~lRD~~~~~v~~IvvD~~~~y~~i 445 (621)
+-+.|+|..|++.++.+..+=-++.... .+. -+.|...-.| -|+. .||.+.+++++.-|+-+.++.+
T Consensus 292 kysDEel~~di~~i~s~l~~~~k~l~~fD~Y~~ELdsg~l~wSp--~H~~--------~dFWs~N~d~l~kdny~i~k~L 361 (432)
T COG5231 292 KYSDEELVIDIERIRSRLVQNTKKLCIFDNYLNELDSGRLEWSP--YHHK--------KDFWSTNLDMLIKDNYEIVKVL 361 (432)
T ss_pred CCChHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHhhCcccCCC--cccc--------cCchhhhHHHHhhhhHHHHHHH
Confidence 4568999999999998876544443222 010 1112111111 1222 3566677788888899999999
Q ss_pred HHHHHhhCCCcC---------CceeeccCCCCcccccCHHHHHHhHhC
Q 007008 446 TSYLQDIAPDLC---------DRVELYDKRIPLFDKFNIEEEINNMLS 484 (621)
Q Consensus 446 ~~~l~~~~p~~~---------~~v~~y~~~~pLF~~y~Ie~~I~~al~ 484 (621)
..|++...|... .-|+.|-...++...||..+.|-++++
T Consensus 362 ~~~lq~n~~nt~i~vAc~Di~~~Vr~~PE~~~vl~Kyg~k~~im~L~n 409 (432)
T COG5231 362 KKYLQSNNPNTWICVACSDIFQLVRASPEINAVLSKYGVKEIIMNLIN 409 (432)
T ss_pred HHHHhcCCCCceEeeeHhhHHHHHHhCchHHHHHHHhhhHHHHHHHhc
Confidence 999998877721 124445555577889999988888775
No 130
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=20.35 E-value=44 Score=33.70 Aligned_cols=13 Identities=23% Similarity=0.281 Sum_probs=8.0
Q ss_pred cccCCCcccCCcc
Q 007008 607 LCYLAFVHLLGLM 619 (621)
Q Consensus 607 ~~~~~~~~~~~~~ 619 (621)
...||.|||.|.+
T Consensus 99 ~~~C~~C~G~G~~ 111 (186)
T TIGR02642 99 SCKCPRCRGTGLI 111 (186)
T ss_pred CCcCCCCCCeeEE
Confidence 4566666666654
No 131
>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=20.17 E-value=80 Score=31.52 Aligned_cols=34 Identities=21% Similarity=0.356 Sum_probs=26.4
Q ss_pred HHhHhCCceecCCCcEEEEecccceEEEEecCCCCCCC
Q 007008 479 INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFG 516 (621)
Q Consensus 479 I~~al~~rV~L~sGG~LVIE~TEALtvIDVNSGk~~~~ 516 (621)
++.+-.|.|.||+||++.|-.+-.-+ |+|++.+.
T Consensus 5 l~~LaGR~iDLPgG~el~I~~~~g~~----~~~~f~~~ 38 (177)
T PF07013_consen 5 LRSLAGRTIDLPGGDELRISANTGRP----NTGKFVRS 38 (177)
T ss_pred hhhhcCcceecCCCCeEEEecCCCCc----eEEEEecC
Confidence 56778899999999999998765555 77776543
No 132
>PLN03126 Elongation factor Tu; Provisional
Probab=20.10 E-value=3.6e+02 Score=30.88 Aligned_cols=56 Identities=16% Similarity=0.090 Sum_probs=35.4
Q ss_pred HHHHHHHhcccCC-CcEEEEcCCCCChhhH-HHHHHHHHHHHhc---CCCCcEEeccCCCe
Q 007008 534 KQIARELRLRDIG-GIIVVDFIDMADDSNK-RLVYEEVKKAVER---DRSMVKVSELSRHG 589 (621)
Q Consensus 534 ~EIARQLRLRnIg-GIIVIDFIdM~~~~~r-~~Vl~~L~~~lk~---D~~k~~V~g~T~LG 589 (621)
+|++++++..++. .|++|-=+|+-+.+++ +.+.+.+++.|++ +...+.+++.|.+-
T Consensus 186 ~e~~~~~~~~gi~~iIvvvNK~Dl~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~vp~Sa~~ 246 (478)
T PLN03126 186 KEHILLAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALL 246 (478)
T ss_pred HHHHHHHHHcCCCeEEEEEecccccCHHHHHHHHHHHHHHHHHhcCCCcCcceEEEEEccc
Confidence 6777888888887 4556777776554443 3444577777765 33345666666543
Done!