Query 004669
Match_columns 738
No_of_seqs 235 out of 1106
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:11:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004669.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004669hhsearch_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 2E-131 3E-136 1100.6 57.7 487 74-703 1-488 (489)
2 PRK10811 rne ribonuclease E; R 100.0 2E-121 5E-126 1051.5 55.3 485 76-705 2-490 (1068)
3 TIGR00757 RNaseEG ribonuclease 100.0 1E-120 3E-125 998.3 46.4 412 88-631 1-414 (414)
4 COG1530 CafA Ribonucleases G a 100.0 2E-104 4E-109 886.2 43.0 479 75-704 1-483 (487)
5 PF10150 RNase_E_G: Ribonuclea 100.0 3E-80 6.5E-85 647.4 24.9 270 318-599 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.6 8.8E-16 1.9E-20 136.5 8.4 40 108-147 3-42 (88)
7 PF00575 S1: S1 RNA binding do 97.7 0.00017 3.7E-09 60.9 7.6 36 110-147 2-37 (74)
8 cd04472 S1_PNPase S1_PNPase: P 97.4 0.00066 1.4E-08 55.8 7.1 33 113-147 1-33 (68)
9 cd05704 S1_Rrp5_repeat_hs13 S1 97.2 0.0013 2.8E-08 56.3 7.0 35 112-147 3-37 (72)
10 COG1098 VacB Predicted RNA bin 97.1 0.00082 1.8E-08 63.9 5.2 36 111-148 4-39 (129)
11 cd05692 S1_RPS1_repeat_hs4 S1_ 97.0 0.0027 5.8E-08 51.9 7.4 33 113-147 1-33 (69)
12 smart00316 S1 Ribosomal protei 97.0 0.0025 5.4E-08 51.8 7.0 34 112-147 2-35 (72)
13 cd05698 S1_Rrp5_repeat_hs6_sc5 96.8 0.0043 9.3E-08 51.9 6.9 33 113-147 1-33 (70)
14 cd05685 S1_Tex S1_Tex: The C-t 96.6 0.0052 1.1E-07 50.2 6.1 33 113-147 1-33 (68)
15 cd04461 S1_Rrp5_repeat_hs8_sc7 96.6 0.0067 1.4E-07 52.9 6.9 36 110-147 12-47 (83)
16 PRK07252 hypothetical protein; 96.5 0.0083 1.8E-07 56.9 7.6 34 112-147 3-36 (120)
17 PTZ00248 eukaryotic translatio 96.4 0.066 1.4E-06 58.7 14.5 34 112-147 17-52 (319)
18 cd05707 S1_Rrp5_repeat_sc11 S1 96.4 0.0095 2.1E-07 49.8 6.3 33 113-147 1-33 (68)
19 cd05684 S1_DHX8_helicase S1_DH 96.4 0.012 2.6E-07 50.7 7.1 33 113-147 1-36 (79)
20 cd05687 S1_RPS1_repeat_ec1_hs1 96.4 0.013 2.8E-07 49.1 7.0 33 113-147 1-33 (70)
21 PRK08059 general stress protei 96.3 0.011 2.5E-07 55.8 7.2 36 110-147 5-40 (123)
22 cd05706 S1_Rrp5_repeat_sc10 S1 96.1 0.025 5.5E-07 47.7 7.8 34 112-147 3-36 (73)
23 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.1 0.02 4.3E-07 48.0 6.7 33 113-147 1-33 (69)
24 cd05686 S1_pNO40 S1_pNO40: pNO 96.0 0.03 6.4E-07 47.9 7.6 34 112-147 3-37 (73)
25 cd05691 S1_RPS1_repeat_ec6 S1_ 95.8 0.032 6.9E-07 46.6 6.9 33 113-147 1-33 (73)
26 cd04452 S1_IF2_alpha S1_IF2_al 95.8 0.034 7.3E-07 47.1 7.0 34 112-147 3-38 (76)
27 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.8 0.034 7.3E-07 47.5 6.9 34 113-147 1-35 (71)
28 PRK08582 hypothetical protein; 95.7 0.033 7.1E-07 54.1 7.4 35 111-147 4-38 (139)
29 COG0539 RpsA Ribosomal protein 95.7 0.022 4.7E-07 66.2 7.1 36 109-147 189-224 (541)
30 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.5 0.063 1.4E-06 46.9 7.6 35 111-147 5-39 (86)
31 cd05688 S1_RPS1_repeat_ec3 S1_ 95.4 0.04 8.7E-07 45.1 6.0 33 112-147 1-33 (68)
32 cd05694 S1_Rrp5_repeat_hs2_sc2 95.0 0.08 1.7E-06 45.9 6.9 34 111-146 3-37 (74)
33 TIGR03591 polynuc_phos polyrib 94.9 0.054 1.2E-06 64.9 7.2 37 109-147 615-651 (684)
34 cd05705 S1_Rrp5_repeat_hs14 S1 94.8 0.084 1.8E-06 45.6 6.4 35 111-147 2-36 (74)
35 cd04454 S1_Rrp4_like S1_Rrp4_l 94.8 0.13 2.8E-06 44.7 7.5 35 111-147 5-39 (82)
36 PRK05807 hypothetical protein; 94.8 0.12 2.5E-06 50.1 7.9 34 111-147 4-37 (136)
37 TIGR02696 pppGpp_PNP guanosine 94.7 0.069 1.5E-06 64.0 7.4 36 110-147 645-680 (719)
38 PRK03987 translation initiatio 94.7 0.15 3.3E-06 54.4 9.3 35 111-147 7-43 (262)
39 cd05708 S1_Rrp5_repeat_sc12 S1 94.7 0.12 2.6E-06 43.5 6.9 34 112-147 2-36 (77)
40 cd04455 S1_NusA S1_NusA: N-uti 94.7 0.13 2.8E-06 43.3 7.0 33 111-146 2-34 (67)
41 cd05690 S1_RPS1_repeat_ec5 S1_ 94.6 0.1 2.2E-06 43.3 6.2 33 113-147 1-33 (69)
42 PRK09521 exosome complex RNA-b 94.5 0.26 5.7E-06 49.9 10.0 37 109-147 61-107 (189)
43 PRK11824 polynucleotide phosph 94.5 0.1 2.3E-06 62.6 8.3 36 110-147 619-654 (693)
44 cd00164 S1_like S1_like: Ribos 94.1 0.12 2.7E-06 41.0 5.5 30 116-147 1-30 (65)
45 PRK04163 exosome complex RNA-b 93.6 0.52 1.1E-05 49.5 10.6 45 101-147 50-96 (235)
46 PLN00207 polyribonucleotide nu 93.0 0.2 4.3E-06 61.5 7.2 35 111-147 752-787 (891)
47 cd04473 S1_RecJ_like S1_RecJ_l 91.2 1 2.2E-05 39.0 7.6 35 110-146 14-48 (77)
48 PRK13806 rpsA 30S ribosomal pr 91.1 0.51 1.1E-05 54.6 7.3 36 110-147 200-235 (491)
49 cd05689 S1_RPS1_repeat_ec4 S1_ 91.1 0.32 6.9E-06 40.9 4.2 34 112-147 3-36 (72)
50 PRK07899 rpsA 30S ribosomal pr 91.1 0.48 1E-05 54.9 7.0 35 110-147 206-240 (486)
51 PRK07400 30S ribosomal protein 90.9 0.54 1.2E-05 51.6 6.8 36 110-147 29-64 (318)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 90.7 0.44 9.6E-06 43.7 5.1 35 111-147 2-36 (100)
53 PRK14865 rnpA ribonuclease P; 90.4 1.3 2.9E-05 41.6 8.2 54 332-385 48-110 (116)
54 PRK07400 30S ribosomal protein 90.2 0.72 1.6E-05 50.6 7.1 38 107-147 191-228 (318)
55 COG1185 Pnp Polyribonucleotide 89.9 0.32 6.8E-06 57.9 4.2 40 106-147 613-652 (692)
56 TIGR01953 NusA transcription t 89.6 3.9 8.5E-05 45.5 12.2 108 291-442 170-280 (341)
57 PRK06299 rpsA 30S ribosomal pr 89.4 0.8 1.7E-05 53.5 7.2 35 110-147 199-233 (565)
58 PRK13806 rpsA 30S ribosomal pr 89.3 0.9 1.9E-05 52.6 7.4 38 108-147 288-325 (491)
59 cd05702 S1_Rrp5_repeat_hs11_sc 88.8 0.58 1.2E-05 39.5 4.0 34 113-148 1-34 (70)
60 PRK00588 rnpA ribonuclease P; 88.3 2.1 4.7E-05 40.5 7.9 53 332-384 46-108 (118)
61 cd04465 S1_RPS1_repeat_ec2_hs2 88.3 0.53 1.1E-05 39.2 3.4 32 113-147 1-32 (67)
62 COG0539 RpsA Ribosomal protein 88.0 0.81 1.8E-05 53.6 5.8 68 76-147 243-310 (541)
63 cd04471 S1_RNase_R S1_RNase_R: 87.9 0.64 1.4E-05 39.7 3.8 34 112-147 1-35 (83)
64 PRK12269 bifunctional cytidyla 87.5 2 4.4E-05 53.1 9.1 38 108-147 574-611 (863)
65 TIGR00717 rpsA ribosomal prote 87.3 1.5 3.3E-05 50.5 7.5 36 110-147 357-392 (516)
66 PRK03459 rnpA ribonuclease P; 87.0 2.8 6E-05 40.0 7.9 54 332-385 51-114 (122)
67 PRK07899 rpsA 30S ribosomal pr 86.5 1.7 3.6E-05 50.6 7.2 36 110-147 291-326 (486)
68 PRK00396 rnpA ribonuclease P; 86.2 3.3 7.1E-05 40.1 7.9 58 333-393 50-117 (130)
69 PRK06299 rpsA 30S ribosomal pr 86.0 1.8 3.8E-05 50.7 7.2 35 111-147 372-406 (565)
70 PRK12269 bifunctional cytidyla 85.6 1.9 4.2E-05 53.3 7.5 35 110-147 491-525 (863)
71 TIGR00717 rpsA ribosomal prote 84.9 2 4.3E-05 49.6 6.9 36 110-147 270-305 (516)
72 PRK09202 nusA transcription el 84.6 2.1 4.5E-05 49.6 6.7 109 290-442 171-282 (470)
73 PRK06676 rpsA 30S ribosomal pr 84.2 2.5 5.5E-05 47.1 7.1 36 110-148 190-225 (390)
74 PRK00499 rnpA ribonuclease P; 83.7 5.5 0.00012 37.3 8.0 55 332-386 41-105 (114)
75 PRK01313 rnpA ribonuclease P; 82.8 5.5 0.00012 38.5 7.9 52 333-384 51-113 (129)
76 PRK04390 rnpA ribonuclease P; 82.8 6 0.00013 37.6 8.0 53 333-385 48-110 (120)
77 COG2183 Tex Transcriptional ac 82.6 1.9 4.1E-05 52.3 5.5 37 109-147 655-691 (780)
78 PRK06676 rpsA 30S ribosomal pr 81.5 4.2 9.2E-05 45.3 7.5 36 110-147 15-51 (390)
79 PRK00087 4-hydroxy-3-methylbut 78.6 4.2 9.2E-05 48.7 6.7 34 111-147 476-509 (647)
80 PRK01903 rnpA ribonuclease P; 76.7 12 0.00027 36.3 8.1 53 333-385 54-129 (133)
81 PRK01492 rnpA ribonuclease P; 76.3 11 0.00024 35.8 7.5 53 332-384 49-115 (118)
82 TIGR00188 rnpA ribonuclease P 75.8 7.9 0.00017 35.7 6.3 51 333-383 45-104 (105)
83 PRK04820 rnpA ribonuclease P; 75.8 13 0.00029 36.7 8.2 54 332-385 51-114 (145)
84 PRK12327 nusA transcription el 75.3 6.1 0.00013 44.4 6.4 33 111-146 133-165 (362)
85 PRK01732 rnpA ribonuclease P; 75.1 9.2 0.0002 36.1 6.6 53 333-385 49-111 (114)
86 PRK00038 rnpA ribonuclease P; 74.6 16 0.00036 35.0 8.3 58 332-389 53-121 (123)
87 cd05703 S1_Rrp5_repeat_hs12_sc 74.3 4 8.6E-05 35.1 3.7 33 113-147 1-33 (73)
88 PRK00087 4-hydroxy-3-methylbut 71.0 11 0.00023 45.4 7.5 36 110-147 560-595 (647)
89 PF07092 DUF1356: Protein of u 70.6 1.7 3.8E-05 46.0 0.7 31 584-623 24-54 (238)
90 PF00684 DnaJ_CXXCXGXG: DnaJ c 69.2 3.7 8.1E-05 34.8 2.3 31 588-620 24-54 (66)
91 PRK03031 rnpA ribonuclease P; 68.6 26 0.00057 33.3 8.1 53 333-385 51-114 (122)
92 PRK00730 rnpA ribonuclease P; 67.0 14 0.00031 36.3 6.1 53 332-385 49-110 (138)
93 COG0594 RnpA RNase P protein c 66.6 28 0.00062 33.0 7.9 53 333-385 45-107 (117)
94 cd05695 S1_Rrp5_repeat_hs3 S1_ 66.4 24 0.00053 29.6 6.7 32 113-146 1-32 (66)
95 TIGR02063 RNase_R ribonuclease 65.4 13 0.00029 45.0 6.8 35 111-147 626-661 (709)
96 PF00825 Ribonuclease_P: Ribon 64.3 17 0.00037 33.6 5.9 53 333-385 46-109 (111)
97 PRK11642 exoribonuclease R; Pr 63.8 17 0.00038 45.0 7.4 35 111-147 642-677 (813)
98 cd05791 S1_CSL4 S1_CSL4: CSL4, 62.1 11 0.00023 34.2 3.9 36 111-148 5-48 (92)
99 cd05790 S1_Rrp40 S1_Rrp40: Rrp 61.9 37 0.00081 30.8 7.4 33 111-145 5-37 (86)
100 COG2996 Predicted RNA-bindinin 59.1 19 0.00041 39.2 5.8 37 110-147 71-107 (287)
101 TIGR03147 cyt_nit_nrfF cytochr 57.1 16 0.00035 35.4 4.5 56 608-691 41-96 (126)
102 cd04460 S1_RpoE S1_RpoE: RpoE, 55.5 15 0.00032 33.2 3.7 31 115-148 2-32 (99)
103 PRK12328 nusA transcription el 54.6 27 0.00058 39.6 6.3 189 290-536 176-368 (374)
104 PRK10144 formate-dependent nit 54.6 19 0.00042 35.0 4.5 56 608-691 41-96 (126)
105 TIGR00358 3_prime_RNase VacB a 52.2 32 0.00069 41.6 6.8 35 111-147 571-606 (654)
106 TIGR02642 phage_xxxx uncharact 42.6 13 0.00028 38.3 1.4 18 608-625 116-133 (186)
107 TIGR00448 rpoE DNA-directed RN 42.5 32 0.00069 34.6 4.2 36 110-148 79-114 (179)
108 PF02108 FliH: Flagellar assem 39.8 1E+02 0.0022 28.3 6.8 45 653-703 68-112 (128)
109 PF03918 CcmH: Cytochrome C bi 38.0 29 0.00063 34.4 3.0 33 608-640 41-73 (148)
110 PRK06032 fliH flagellar assemb 36.8 1.4E+02 0.0031 30.5 8.0 47 653-703 128-176 (199)
111 TIGR02642 phage_xxxx uncharact 35.1 21 0.00045 36.8 1.5 16 607-622 99-114 (186)
112 PF13509 S1_2: S1 domain; PDB: 34.3 1.2E+02 0.0026 25.3 5.7 33 112-146 1-33 (61)
113 PHA02945 interferon resistance 33.7 1.3E+02 0.0027 27.8 6.1 32 112-146 11-44 (88)
114 PRK08563 DNA-directed RNA poly 32.4 50 0.0011 33.3 3.8 35 110-147 79-113 (187)
115 COG1093 SUI2 Translation initi 32.0 40 0.00086 36.6 3.1 35 111-147 10-46 (269)
116 PRK06937 type III secretion sy 32.0 1.5E+02 0.0032 30.5 7.1 49 653-703 131-179 (204)
117 PRK09098 type III secretion sy 30.9 1.7E+02 0.0037 31.1 7.5 47 653-703 151-199 (233)
118 TIGR02499 HrpE_YscL_not type I 30.7 2.4E+02 0.0051 27.3 8.1 45 653-703 114-158 (166)
119 PF00013 KH_1: KH domain syndr 30.1 1.2E+02 0.0027 24.4 5.1 37 655-691 2-38 (60)
120 PRK12329 nusA transcription el 29.8 1.3E+02 0.0028 35.1 6.8 33 110-144 150-187 (449)
121 COG0484 DnaJ DnaJ-class molecu 28.6 23 0.00049 40.1 0.6 25 333-357 10-35 (371)
122 COG1568 Predicted methyltransf 27.8 45 0.00098 36.8 2.6 31 606-639 90-120 (354)
123 PF04472 DUF552: Protein of un 26.1 1.3E+02 0.0028 26.0 4.7 41 531-575 10-50 (73)
124 KOG2925 Predicted translation 26.0 36 0.00078 34.1 1.4 24 481-504 53-76 (167)
125 TIGR03825 FliH_bacil flagellar 25.3 2.8E+02 0.006 29.5 8.0 47 653-703 176-224 (255)
126 PF08800 VirE_N: VirE N-termin 25.3 1.6E+02 0.0035 28.5 5.7 51 541-596 26-77 (136)
127 COG0484 DnaJ DnaJ-class molecu 25.2 28 0.00061 39.4 0.6 21 366-386 12-32 (371)
128 TIGR00630 uvra excinuclease AB 24.4 98 0.0021 39.2 5.0 35 548-583 199-233 (924)
129 PF11314 DUF3117: Protein of u 22.9 60 0.0013 26.8 1.8 15 486-500 22-36 (51)
130 PRK14296 chaperone protein Dna 22.7 51 0.0011 37.1 2.0 25 333-357 10-35 (372)
131 PRK06328 type III secretion sy 22.7 2.1E+02 0.0046 30.1 6.4 47 653-703 132-180 (223)
132 PF12401 DUF3662: Protein of u 22.6 5E+02 0.011 24.6 8.3 50 653-702 53-115 (116)
133 PRK14298 chaperone protein Dna 21.4 51 0.0011 37.2 1.7 26 333-358 11-37 (377)
134 cd05792 S1_eIF1AD_like S1_eIF1 21.1 59 0.0013 29.1 1.7 22 480-501 30-51 (78)
135 COG3088 CcmH Uncharacterized p 20.9 98 0.0021 31.1 3.3 31 609-639 46-76 (153)
136 cd00105 KH-I K homology RNA-bi 20.8 2.3E+02 0.0049 22.7 5.0 39 655-693 2-40 (64)
137 PRK00349 uvrA excinuclease ABC 20.4 1.2E+02 0.0025 38.7 4.6 35 548-583 203-237 (943)
138 PRK06921 hypothetical protein; 20.2 52 0.0011 35.3 1.3 13 608-620 33-45 (266)
139 KOG1070 rRNA processing protei 20.1 1.4E+02 0.0029 39.5 4.9 78 68-151 557-636 (1710)
140 PF10442 FIST_C: FIST C domain 20.1 1.7E+02 0.0037 27.4 4.7 56 530-589 73-131 (136)
No 1
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=1.6e-131 Score=1100.57 Aligned_cols=487 Identities=31% Similarity=0.519 Sum_probs=451.0
Q ss_pred CceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcC
Q 004669 74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF 153 (738)
Q Consensus 74 m~~~IlIn~s~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~ 153 (738)
|+++|+||+.+ .++|+|++|||+|+||++|+.+...++||||+|+|+||+|||||||||||.+|+||||++|..+++.+
T Consensus 1 M~~~i~i~~~~-~e~r~Alledg~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~ 79 (489)
T PRK11712 1 MTAELLVNVTP-SETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTEC 79 (489)
T ss_pred CceEEEEecCC-CeEEEEEEECCEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhh
Confidence 88999999987 79999999999999999999999999999999999999999999999999999999999996221100
Q ss_pred CcccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhccccchhhcccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 004669 154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD 233 (738)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (738)
.. . ++ ..
T Consensus 80 ~~-----~------------------------------------------------~~-------------~~------- 86 (489)
T PRK11712 80 VA-----G------------------------------------------------EE-------------QK------- 86 (489)
T ss_pred cc-----c------------------------------------------------cc-------------cc-------
Confidence 00 0 00 00
Q ss_pred CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCcee
Q 004669 234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL 313 (738)
Q Consensus 234 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~~g~KGprl 313 (738)
. . ...++...|++||+|||||+|||+|+|||+|
T Consensus 87 --------------------------------~-~--------------~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~l 119 (489)
T PRK11712 87 --------------------------------Q-F--------------VVRDISELVRQGQDIMVQVVKDPLGTKGARL 119 (489)
T ss_pred --------------------------------c-c--------------ccccHHHhccCCCEEEEEEEeCCcCCCCCeE
Confidence 0 0 0012446799999999999999999999999
Q ss_pred eecccccceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 004669 314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH 392 (738)
Q Consensus 314 T~~ISL~GRylVl~P~~~~vgvSrKI~~e-eR~rLk~i~~~l~~~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~~ 392 (738)
|++|||||||+||||+++++||||||.++ +|+||+.++..+.++++|+||||+|+++++++|.+|+++|.++|++|.++
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 99999999999999999999999999875 69999999999988889999999999999999999999999999999999
Q ss_pred HHHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEEEcCHHHHHHHHHHHHhhCCCccCceeeccCCCCcccc
Q 004669 393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472 (738)
Q Consensus 393 a~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~IvVD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~plF~~ 472 (738)
++.+ ++|.|||++.+++.+++||++++++++|+||+++.|+++++|+..+.|++..++++|++..|||+.
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 9775 689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHhHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 004669 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (738)
Q Consensus 473 y~Ie~qI~~al~rrV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNlEAA~EIARQLRLRnIgGIIVID 552 (738)
|||+.+|+++++++||||||||||||+||||||||||||++ .+++++++|+++||+|||+||||||||||||||||||
T Consensus 270 y~ie~~i~~~l~~~V~L~sGg~lvIe~TeAlt~IDVnsGk~--~~~~~~eet~~~tN~eAa~eiarqlrLR~igGiIviD 347 (489)
T PRK11712 270 YDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGAF--VGHRNLEETIFNTNIEATQAIARQLRLRNLGGIIIID 347 (489)
T ss_pred cCHHHHHHHHhcCcEEcCCCcEEEEeccccEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEE
Confidence 99999999999999999999999999999999999999984 5667999999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhHHHHHHHH
Q 004669 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (738)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~D~~kt~V~giT~LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~iere 632 (738)
||||+++++|++|++.|+++|++|+++++|+|||+||||||||||+|+||.++++++||+|+|+|+|+|.++++++|+|+
T Consensus 348 FidM~~~~~r~~v~~~l~~~l~~D~~k~~v~~~T~lGLvEmTRkR~r~sl~~~l~~~Cp~C~G~G~v~s~e~~~~~i~r~ 427 (489)
T PRK11712 348 FIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVLCGECPTCHGRGTVKTVETVCYEIMRE 427 (489)
T ss_pred CCCCCCHHHHHHHHHHHHHHhhcCCCCceEcccCCCceEEEEecccCCChHHHhcCCCCCCCCCCCcCCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004669 633 ISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 633 i~~~~~~~~~k~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d~~~~~~~y~I~~ 703 (738)
|.+...... ...+.+.+||.|++||.+.++.++..|++.+|++|.|..++++++++|+|..
T Consensus 428 i~~~~~~~~----------~~~~~~~~~p~v~~~l~~~~~~~~~~le~~~g~~i~i~~~~~~~~~~~~i~~ 488 (489)
T PRK11712 428 IVRVHHAYD----------SDRFLVYASPAVAEALKGEESHALAELEIFVGKQVKVQIEPLYNQEQFDVVM 488 (489)
T ss_pred HHHHHhhCC----------CceEEEEECHHHHHHHHccchHHHHHHHHHhCCeEEEEECCCCCccceEEEe
Confidence 998765432 2469999999999999988878899999999999999999999999999864
No 2
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=2.4e-121 Score=1051.49 Aligned_cols=485 Identities=31% Similarity=0.537 Sum_probs=449.8
Q ss_pred eEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCCc
Q 004669 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP 155 (738)
Q Consensus 76 ~~IlIn~s~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~~ 155 (738)
++||||.....+.|+||++||+|.||+||+......+||||+|+|+||+|||+|||||||.+++|||+++|+..+++..+
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 68999998447899999999999999999988888999999999999999999999999999999999999854432100
Q ss_pred ccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhccccchhhcccCCCCCCCCCCCcchhhhhhccCCcccCCCC
Q 004669 156 FRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGE 235 (738)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (738)
+..
T Consensus 82 ~~~----------------------------------------------------------------------------- 84 (1068)
T PRK10811 82 YSA----------------------------------------------------------------------------- 84 (1068)
T ss_pred ccc-----------------------------------------------------------------------------
Confidence 000
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeee
Q 004669 236 PEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTA 315 (738)
Q Consensus 236 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~~g~KGprlT~ 315 (738)
+ ...++...|++||+|||||+||++++|||+||+
T Consensus 85 ---------------------------------~-------------~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 85 ---------------------------------H-------------GRPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred ---------------------------------c-------------cccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 0 001233569999999999999999999999999
Q ss_pred cccccceeEEEeeCCCc-eeeecCCChHHHHHHHHHHHhh-CCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 004669 316 YPKLRSRFWILITSCDR-IGVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (738)
Q Consensus 316 ~ISL~GRylVl~P~~~~-vgvSrKI~~eeR~rLk~i~~~l-~~~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~~a 393 (738)
+|||+||||||||+.++ +||||||.+++|.+|+.++..+ .++++|+||||+|.|++.++|..||++|...|+.|++++
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 7999999988899999999987 788999999999999999999999999999999999998
Q ss_pred HHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEEEcCHHHHHHHHHHHHhh-CCCccCceeeccCCCCcccc
Q 004669 394 KSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLFDK 472 (738)
Q Consensus 394 ~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~IvVD~~~~y~~i~~~l~~~-~p~~~~~v~ly~~~~plF~~ 472 (738)
+.+ ++|.|||++.+++.+++|||+.+++++|+||+++.|+.++.|+..+ .|++..+|++|.+..|||+.
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 765 6899999999999999999999999999999999999999999988 58877899999999999999
Q ss_pred cCHHHHHHhHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 004669 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (738)
Q Consensus 473 y~Ie~qI~~al~rrV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNlEAA~EIARQLRLRnIgGIIVID 552 (738)
|+|+.+|++||+++||||||||||||+||||||||||||++ .++.+.++|+|+||++||+||||||||||||||||||
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 99999999999999999999999999999999999999984 4567899999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhHHHHHHHH
Q 004669 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (738)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~D~~kt~V~giT~LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~iere 632 (738)
||||+.++|+++|++.|+++|++|+.+++|+|||+||||||||||.|+||.+.+++.||+|+|+|+|++.+++++.|+|+
T Consensus 347 FIdM~~ee~r~~l~~~L~~al~~D~~k~~v~g~T~LGLvEmTRKR~r~sL~E~l~e~Cp~C~GtG~v~s~etla~~i~R~ 426 (1068)
T PRK10811 347 FIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRL 426 (1068)
T ss_pred CCCCCchHHHHHHHHHHHHHHHhCCCCceEEecccccceEEecccCCCCHHHHhhccCcccCCCcccccHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHH-HhcCCeEEEEeCCCCCCcceEEEEec
Q 004669 633 ISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLS-SSLKAWILLKVARGFTRGAFEVIPYT 705 (738)
Q Consensus 633 i~~~~~~~~~k~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le-~~~~~~I~l~~d~~~~~~~y~I~~~~ 705 (738)
|.+.+...+ ...+.+.+++.+++||.+.++..+..|| +.+|+.|.|..++.++++.|+|..+.
T Consensus 427 I~re~~~~~----------~~~~~i~~~~~va~~l~~~~~~~~~~ie~e~~g~~i~I~~n~~~~~e~y~v~rvr 490 (1068)
T PRK10811 427 IEEEALKEN----------TQEVHAIVPVPIASYLLNEKRSAVNAIETRQGGVRCVIVPNDQMQTPHYSVLRVR 490 (1068)
T ss_pred HHHHHhhcc----------cccEEEEECHHHHHHHhhhhhhHHHHHhhhhcCceEEEEecCcCCcccceEEEEe
Confidence 999876543 2469999999999999999888999999 99999999999999999999998764
No 3
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=100.00 E-value=1.3e-120 Score=998.30 Aligned_cols=412 Identities=39% Similarity=0.650 Sum_probs=381.9
Q ss_pred EEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCCcccccchhhhccc
Q 004669 88 QRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNG 167 (738)
Q Consensus 88 ~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~~~~~~~~~~~~~~ 167 (738)
+|+||+|||+|+||++|+.....++||||+|+|++|+|||||||||||.+++||||++|...++...+ .
T Consensus 1 ~r~Alledg~l~e~~ie~~~~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~----~------- 69 (414)
T TIGR00757 1 TRVALVEGGRLFDLIIERPKSRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLA----P------- 69 (414)
T ss_pred CEEEEEECCEEEEEEEecCcCcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccc----c-------
Confidence 59999999999999999999999999999999999999999999999999999999998632110000 0
Q ss_pred cchhhhhhhhcccCCCCCCCCcchhhhccccchhhcccCCCCCCCCCCCcchhhhhhccCCcccCCCCCCccccccccCC
Q 004669 168 SASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGD 247 (738)
Q Consensus 168 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 247 (738)
++ ..
T Consensus 70 ------------------------------------------~~-------------~~--------------------- 73 (414)
T TIGR00757 70 ------------------------------------------AE-------------AK--------------------- 73 (414)
T ss_pred ------------------------------------------cc-------------cc---------------------
Confidence 00 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeeecccccceeEEEe
Q 004669 248 HHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILI 327 (738)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~~g~KGprlT~~ISL~GRylVl~ 327 (738)
. . ...++...|++||+|+|||+|||+++|||+||++|||||||+|||
T Consensus 74 ------------------~-~--------------~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~lT~~Isl~GrylVl~ 120 (414)
T TIGR00757 74 ------------------R-E--------------AGPSISELLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLM 120 (414)
T ss_pred ------------------c-c--------------ccCCHHHhCcCCCEEEEEEeeCCcCCCCCeEEEEEEeccceEEEe
Confidence 0 0 001234679999999999999999999999999999999999999
Q ss_pred eCCCceeeecCCChH-HHHHHHHHHHh-hCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcC
Q 004669 328 TSCDRIGVSRKITGV-ERTRLKVIAKT-LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVE 405 (738)
Q Consensus 328 P~~~~vgvSrKI~~e-eR~rLk~i~~~-l~~~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~ 405 (738)
|+.+++||||||.++ +|.+|+.++.. +.|+++|+||||+|+++++++|.+|+++|.+.|++|.++++.+
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 69999999995 8888999999999999999999999999999999999999765
Q ss_pred CCCceeeeecCCchhhhhhhhccCCccEEEEcCHHHHHHHHHHHHhhCCCccCceeeccCCCCcccccCHHHHHHhHhCC
Q 004669 406 GAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSK 485 (738)
Q Consensus 406 ~~~P~LLy~e~~~~~~~lRD~~~~~v~~IvVD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~plF~~y~Ie~qI~~al~r 485 (738)
++|.|||++.+++.+++||++++++++|+||+++.|+++++|++.+.|.+..+|++|.+..|||+.|+|+.+|++++++
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 6899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHH
Q 004669 486 RVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLV 565 (738)
Q Consensus 486 rV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNlEAA~EIARQLRLRnIgGIIVIDFIDM~~~~~r~~V 565 (738)
+||||||||||||+||||||||||||++ +++.++++|+++||+|||+||||||||||||||||||||||+++++|++|
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 9999999999999999999999999984 56679999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhHHHHHHH
Q 004669 566 YEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (738)
Q Consensus 566 ~~~Lk~alk~D~~kt~V~giT~LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~ier 631 (738)
++.|+++|++|+++++|+|||+||||||||||.|+||.++++++||+|+|+|+|+|.++++++|+|
T Consensus 349 ~~~l~~~~~~D~~k~~v~~~T~lGLvE~TRkr~~~sL~e~~~~~Cp~C~G~G~v~s~~~~~~~i~r 414 (414)
T TIGR00757 349 LERLKEALRRDRARIQISGISEFGLVEMTRKRLRESLMEVLGTVCPHCSGTGIVKTSETVLYEIER 414 (414)
T ss_pred HHHHHHHHhcCCCCcEEcccCCCcceEEeccccCcChHHHhcCCCCCCcCeeEEccHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999999999999999999999988764
No 4
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-104 Score=886.17 Aligned_cols=479 Identities=37% Similarity=0.614 Sum_probs=444.6
Q ss_pred ceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcCC
Q 004669 75 STVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFP 154 (738)
Q Consensus 75 ~~~IlIn~s~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~ 154 (738)
++.||||+++ .|+|||++++|.|.|+++|+....+++||||+|||+||+|||||||||||.+||||||++++.+ +
T Consensus 1 ~k~~~i~~~~-~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~--- 75 (487)
T COG1530 1 MKKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-Y--- 75 (487)
T ss_pred CceEEEeccc-ceeEEEEEeCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccch-h---
Confidence 4679999999 8999999999999999999999999999999999999999999999999999999999998632 1
Q ss_pred cccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhccccchhhcccCCCCCCCCCCCcchhhhhhccCCcccCCC
Q 004669 155 PFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDG 234 (738)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (738)
|.. . .
T Consensus 76 -~~~---~---------------~-------------------------------------------------------- 80 (487)
T COG1530 76 -FRA---V---------------L-------------------------------------------------------- 80 (487)
T ss_pred -hhh---c---------------c--------------------------------------------------------
Confidence 100 0 0
Q ss_pred CCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceee
Q 004669 235 EPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLT 314 (738)
Q Consensus 235 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~Ke~~g~KGprlT 314 (738)
..++...++.||.++|||+|+|+|+|||+||
T Consensus 81 -------------------------------------------------~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 81 -------------------------------------------------EEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred -------------------------------------------------cccceeeecCCceEEEEEEeecCccccccce
Confidence 0013357999999999999999999999999
Q ss_pred ecccccceeEEEeeCCCcee-eecCCCh-HHHHHHHHHHHhhCCC-CceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 004669 315 AYPKLRSRFWILITSCDRIG-VSRKITG-VERTRLKVIAKTLQPE-GFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME 391 (738)
Q Consensus 315 ~~ISL~GRylVl~P~~~~vg-vSrKI~~-eeR~rLk~i~~~l~~~-~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~ 391 (738)
++||++|||+||||+.+++| +|+||++ .+|++|+.++..+.+. ++|+|+||+|+|++.++|.+|+++|...|+.|+.
T Consensus 112 ~~Is~~grylVl~p~~~~~g~is~ri~~~~er~~Lk~~~~~l~~~~~~g~iiRTa~~g~~~eel~~d~~~l~~~w~~i~~ 191 (487)
T COG1530 112 TDISLAGRYLVLMPNAPDVGGISRRIEGEIERERLKEIVRELVDPGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILE 191 (487)
T ss_pred eEEeeceeEEEEcCCCCcccceeeEeCCHHHHHhHHHHHhhccCcCCceEEEeecccCccHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999998 9999998 4799999999999865 4799999999999999999999999999999999
Q ss_pred HHHHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEEEcCHHHHHHHHHHHHhhCCCccCceeeccCCCCccc
Q 004669 392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFD 471 (738)
Q Consensus 392 ~a~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~IvVD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~plF~ 471 (738)
++... ++|.+||++.+++.+++|||+..++.+|+||+...|..+++|+..+.|+...++++|.+..|+|+
T Consensus 192 ~~~~~----------~ap~ll~~e~~~v~r~~rd~~~~~~~~I~Vd~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~f~ 261 (487)
T COG1530 192 RAKKR----------PAPGLLYEETSLVVRVIRDYVGKDITEIVVDGKEAYLEAKEFILEIMPELRSKLKLYRGTTPLFA 261 (487)
T ss_pred HhhcC----------CCCeEEEecCcceEEEeeccccCccceEEEcCchHHHHHHHHHHhcChhhhhheEeccCCCcccc
Confidence 98775 68999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCHHHHHHhHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEE
Q 004669 472 KFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVV 551 (738)
Q Consensus 472 ~y~Ie~qI~~al~rrV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNlEAA~EIARQLRLRnIgGIIVI 551 (738)
.|+++.+|+++++|+|||||||||||++|||||+||||||+++ +..+.++|+++||+|||.||||||||||+||||+|
T Consensus 262 ~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~~--~~~~~eeta~~tNleAa~eiarqlrlR~lgGiIiI 339 (487)
T COG1530 262 LFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFT--GAGDLEETAVNTNLEAAEEIARQLRLRNLGGIIII 339 (487)
T ss_pred hhhHHHHHHHhhhheEecCCCCceeEeccceeEEEEccCcccc--ccCchHHhhhhhhHHHHHHHHHHHhhcccCCeEEE
Confidence 9999999999999999999999999999999999999999853 44569999999999999999999999999999999
Q ss_pred EcCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhHHHHHHH
Q 004669 552 DFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (738)
Q Consensus 552 DFIDM~~~~~r~~V~~~Lk~alk~D~~kt~V~giT~LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~ier 631 (738)
|||||...++++.|+..|+++|+.|++++++.+||+|||+||||||.++||.+.++++||+|.|+|++++.+++++.+.|
T Consensus 340 DfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~~~cp~c~G~g~v~~~~~~~~~i~R 419 (487)
T COG1530 340 DFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLSERCPGCKGTGHVRSTESELLHILR 419 (487)
T ss_pred EeeeccchhhhHHHHHHHHHHhccCCcccccccccccCceEEEEEecCCCCceeeeeECCCceeeEEEecCchhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcC-CeEEEEeCCCCCCcceEEEEe
Q 004669 632 EISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLK-AWILLKVARGFTRGAFEVIPY 704 (738)
Q Consensus 632 ei~~~~~~~~~k~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~-~~I~l~~d~~~~~~~y~I~~~ 704 (738)
.|........ +..+.+.+++.++.|+.+.++..+..+|...+ ..+.+..++.++.++|++...
T Consensus 420 ~i~~~~~~~~----------~~~~~~~~~~~v~~~~~~~~~~~i~~~e~~~~~~~i~~~~~~~~~~~~~~~~~~ 483 (487)
T COG1530 420 YIEEEADINK----------TPEVGVEVPPAVAKYLLNEERGAIAELELFKGYLRVRLRVDDRVEQEQYEVVRL 483 (487)
T ss_pred cchhhhcccc----------CccceEEechhhhhhhcccccchhhHHHhhccceeEEEeechhhcccceeEeee
Confidence 9887543321 34689999999999999988778999999999 999999999999999999654
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=3e-80 Score=647.41 Aligned_cols=270 Identities=48% Similarity=0.754 Sum_probs=221.9
Q ss_pred cccceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 004669 318 KLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSA 396 (738)
Q Consensus 318 SL~GRylVl~P~~~~vgvSrKI~~e-eR~rLk~i~~~l~~~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~ 396 (738)
||||||+||+|++++++|||||+++ +|++|+++++.+.++++|+||||+|+++++++|.+|+++|.++|++|+++++..
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 799999999999999999999999999999999999999999999999998764
Q ss_pred hhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEEEcCHHHHHHHHHHHHhhCCCccCceeeccCCCCcccccCHH
Q 004669 397 ALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIE 476 (738)
Q Consensus 397 ~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~IvVD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~plF~~y~Ie 476 (738)
++|+|||++.+++.+++||++++++++|+||+++.|+++++|++.+.|++..+|++|.+..|+|+.|+|+
T Consensus 81 ----------~~P~LLy~~~~~~~~~lrd~~~~~~~~Iivd~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~lf~~~~i~ 150 (271)
T PF10150_consen 81 ----------KAPSLLYREPDLYERVLRDYLDEDVDEIIVDDKEIYEEIKEYLKEFSPDLKDKIELYKDEEPLFELYGIE 150 (271)
T ss_dssp -----------STEEEE-STSHHHHHHHHH--TTEEEEEES-HHHHHHHHHHHHTT-GGGTTTEEE--SSS-HHHHTT-H
T ss_pred ----------CCCeEEEeCCChhhHHHhhcCcCCCCEEEECCcHHHHHHHHHHHHhCccccceEEEecCCCChHHhCCHH
Confidence 5799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCC
Q 004669 477 EEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDM 556 (738)
Q Consensus 477 ~qI~~al~rrV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNlEAA~EIARQLRLRnIgGIIVIDFIDM 556 (738)
.+|+++++++||||||||||||+||||||||||||++ .++.+.++++++||+|||+||||||||||||||||||||||
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 9999999999999999999999999999999999984 45678999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCC
Q 004669 557 ADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVR 599 (738)
Q Consensus 557 ~~~~~r~~V~~~Lk~alk~D~~kt~V~giT~LGLvEmTRKR~r 599 (738)
++++++++|++.|+++|++|+++++|+|||+||||||||||.|
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 9999999999999999999999999999999999999999987
No 6
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.62 E-value=8.8e-16 Score=136.47 Aligned_cols=40 Identities=30% Similarity=0.615 Sum_probs=37.1
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+..+|+||.|+|++|.|.|.|||||+|.+++||||++++
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 4567999999999999999999999999999999999875
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=97.67 E-value=0.00017 Score=60.93 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=33.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
...|.||.|+|.+|.+ .++||++|.+..||+++++.
T Consensus 2 ~~~G~iv~g~V~~v~~--~g~~V~l~~~~~g~ip~~~l 37 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVED--FGVFVDLGNGIEGFIPISEL 37 (74)
T ss_dssp SSTTSEEEEEEEEEET--TEEEEEESTSSEEEEEGGGS
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCcEEEEEEeehh
Confidence 3579999999999999 99999999999999999874
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=97.36 E-value=0.00066 Score=55.85 Aligned_cols=33 Identities=33% Similarity=0.479 Sum_probs=30.7
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|++|.|+|++|.| .++||+|+...+|||++.+.
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 99999999999999998764
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=97.16 E-value=0.0013 Score=56.34 Aligned_cols=35 Identities=34% Similarity=0.543 Sum_probs=31.4
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+|.||.|+|++|.+. -+|||+++.+..||+|+++.
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 45799999999999999875
No 10
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.07 E-value=0.00082 Score=63.89 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=33.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (738)
-+|+++.|+|+.|.|- +|||++-.+..|+.|++++.
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 89999999999999999864
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=97.03 E-value=0.0027 Score=51.90 Aligned_cols=33 Identities=42% Similarity=0.619 Sum_probs=30.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|++|.|+|+++.+ .++||+|+.+..||||..+.
T Consensus 1 G~~~~g~V~~i~~--~g~~v~i~~~~~g~l~~~~l 33 (69)
T cd05692 1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQI 33 (69)
T ss_pred CCEEEEEEEEEEe--eeEEEEECCCCEEEEEhHHc
Confidence 7899999999999 69999999999999988764
No 12
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.00 E-value=0.0025 Score=51.81 Aligned_cols=34 Identities=38% Similarity=0.612 Sum_probs=31.4
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.|.+|.|+|.++.+ +++||++|.+..|||++.+.
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 59999999999999 79999999999999988764
No 13
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.79 E-value=0.0043 Score=51.90 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=30.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.+ .++||+++.+..||+|+++.
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 79999999899999998764
No 14
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=96.63 E-value=0.0052 Score=50.19 Aligned_cols=33 Identities=39% Similarity=0.552 Sum_probs=30.1
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|++|.|+|.+|.+ .++||+++....||+|..+.
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 69999999999999988664
No 15
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.59 E-value=0.0067 Score=52.86 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=32.7
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.||.|+|++|.+ .++||+++.+..||+|..+.
T Consensus 12 ~~~G~i~~g~V~~v~~--~G~fv~l~~~~~g~v~~~el 47 (83)
T cd04461 12 LKPGMVVHGYVRNITP--YGVFVEFLGGLTGLAPKSYI 47 (83)
T ss_pred CCCCCEEEEEEEEEee--ceEEEEcCCCCEEEEEHHHC
Confidence 4589999999999998 89999999999999998764
No 16
>PRK07252 hypothetical protein; Provisional
Probab=96.53 E-value=0.0083 Score=56.87 Aligned_cols=34 Identities=29% Similarity=0.470 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+|++|.|+|++|.+ .+|||+|+.+..||+|+.+.
T Consensus 3 vG~iv~G~V~~V~~--~G~fVei~~~~~GllhiseL 36 (120)
T PRK07252 3 IGDKLKGTITGIKP--YGAFVALENGTTGLIHISEI 36 (120)
T ss_pred CCCEEEEEEEEEeC--cEEEEEECCCCEEEEEHHHc
Confidence 69999999999998 89999999999999998764
No 17
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.40 E-value=0.066 Score=58.73 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=31.0
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d~ 147 (738)
+|++..|+|++|.+ .+|||+++ .+..||+|+++.
T Consensus 17 ~GdvV~g~V~~I~d--~GafV~L~EY~gvEGlIhiSEl 52 (319)
T PTZ00248 17 EDDLVMVKVVRITE--MGAYVSLLEYDDIEGMILMSEL 52 (319)
T ss_pred CCCEEEEEEEEEeC--CeEEEEecCCCCcEEEEEHHHh
Confidence 79999999999998 69999996 589999999875
No 18
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.39 E-value=0.0095 Score=49.80 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.+ .++||+++.+..||+|+.+.
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 67999999999999998764
No 19
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=96.37 E-value=0.012 Score=50.71 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=29.5
Q ss_pred CCeEEEEEeeecCCcceEEeccc---CCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIG---NSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG---~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.|. ++||+|+ .+.+||+|+.+.
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 469999998764
No 20
>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=96.36 E-value=0.013 Score=49.08 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=30.2
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|+|+.|+|.+|.+. +|||++|....|||+.++.
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 9999999999999988764
No 21
>PRK08059 general stress protein 13; Validated
Probab=96.32 E-value=0.011 Score=55.83 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=32.7
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.+|.|+|.+|.+ .++||+|+.+..||+|+++.
T Consensus 5 ~k~G~iv~G~V~~i~~--~G~fV~i~~~~~Gli~~sel 40 (123)
T PRK08059 5 YEVGSVVTGKVTGIQP--YGAFVALDEETQGLVHISEI 40 (123)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEECCCCEEEEEHHHC
Confidence 3479999999999999 89999999999999998764
No 22
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.15 E-value=0.025 Score=47.70 Aligned_cols=34 Identities=24% Similarity=0.209 Sum_probs=31.2
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+|.||.|+|++|.+ .++||+++.+..||+|+.+.
T Consensus 3 ~G~iv~g~V~~v~~--~gi~v~l~~~~~g~v~~s~l 36 (73)
T cd05706 3 VGDILPGRVTKVND--RYVLVQLGNKVTGPSFITDA 36 (73)
T ss_pred CCCEEEEEEEEEeC--CeEEEEeCCCcEEEEEhhhc
Confidence 79999999999988 48999999999999998764
No 23
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.06 E-value=0.02 Score=47.99 Aligned_cols=33 Identities=30% Similarity=0.503 Sum_probs=29.7
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.+ .++||+++.+..||+++.+.
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~v~g~i~~~~l 33 (69)
T cd05697 1 GQVVKGTIRKLRP--SGIFVKLSDHIKGLVPPMHL 33 (69)
T ss_pred CCEEEEEEEEEec--cEEEEEecCCcEEEEEHHHC
Confidence 7899999999998 49999999999999988653
No 24
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=96.01 E-value=0.03 Score=47.85 Aligned_cols=34 Identities=29% Similarity=0.487 Sum_probs=29.7
Q ss_pred cCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdI-G~~r~aFL~~~d~ 147 (738)
+|.+|.|+|++|.+ .++||++ |....||+|+++.
T Consensus 3 ~g~~~~g~V~~i~~--fG~fv~l~~~~~eGlvh~sel 37 (73)
T cd05686 3 LYQIFKGEVASVTE--YGAFVKIPGCRKQGLVHKSHM 37 (73)
T ss_pred CCCEEEEEEEEEEe--eeEEEEECCCCeEEEEEchhh
Confidence 79999999999998 7999999 3347999998764
No 25
>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=95.83 E-value=0.032 Score=46.64 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.+ .++||+++.+-.||+|+++.
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 89999999999999988764
No 26
>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=95.81 E-value=0.034 Score=47.06 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.7
Q ss_pred cCCeEEEEEeeecCCcceEEecccC--CcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~--~r~aFL~~~d~ 147 (738)
.|.+|.|+|+++.+ .++||++.. +..||||+++.
T Consensus 3 ~G~~~~g~V~~v~~--~g~~v~l~~~~~~~gll~~s~l 38 (76)
T cd04452 3 EGELVVVTVKSIAD--MGAYVSLLEYGNIEGMILLSEL 38 (76)
T ss_pred CCCEEEEEEEEEEc--cEEEEEEcCCCCeEEEEEhHHc
Confidence 59999999999997 899999963 58999998764
No 27
>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=95.76 E-value=0.034 Score=47.46 Aligned_cols=34 Identities=26% Similarity=0.328 Sum_probs=29.2
Q ss_pred CCeEE-EEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~-GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.||. |+|++|... -+|||+++.+.+||+|+++.
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 67999999999999998764
No 28
>PRK08582 hypothetical protein; Provisional
Probab=95.71 E-value=0.033 Score=54.10 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=32.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|.+|.|+|+.|.+. +|||+|+.+..||+|+++.
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 4799999999999995 8999999999999999875
No 29
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.70 E-value=0.022 Score=66.19 Aligned_cols=36 Identities=33% Similarity=0.536 Sum_probs=33.3
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.-.+|.+..|+|++|-| .+||||||. -+|+||++++
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 9999999886
No 30
>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=95.46 E-value=0.063 Score=46.89 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=31.6
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..|+|+.|+|.++.+ .++||+||.+..||||+++.
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 479999999999987 56999999999999999874
No 31
>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=95.43 E-value=0.04 Score=45.10 Aligned_cols=33 Identities=30% Similarity=0.475 Sum_probs=29.1
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.|.+|.|+|.++.+. ++||++| +-.||||..+.
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 68999988764
No 32
>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=95.04 E-value=0.08 Score=45.88 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=29.2
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeEecc
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKH 146 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG-~~r~aFL~~~d 146 (738)
..|.+..|.|++|.+ .+||||+| .+-.|||+.++
T Consensus 3 ~~G~~v~g~V~si~d--~G~~v~~g~~gv~Gfl~~~~ 37 (74)
T cd05694 3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKD 37 (74)
T ss_pred CCCCEEEEEEEEEeC--CEEEEEeCCCCcEEEEEHHH
Confidence 369999999999996 59999999 46799997765
No 33
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=94.87 E-value=0.054 Score=64.91 Aligned_cols=37 Identities=27% Similarity=0.453 Sum_probs=33.6
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
...+|.||.|+|++|.+ .+|||+|..+..||||+++.
T Consensus 615 ~~~~G~i~~G~V~~I~~--~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMD--FGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred ccccCcEEEEEEEEEeC--CEEEEEECCCcEEEEEHHHc
Confidence 34689999999999998 89999999999999999875
No 34
>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=94.82 E-value=0.084 Score=45.65 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|++..|+|+++.+ .+|||+++.+-.||+|+.+.
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 369999999999974 57999999999999998775
No 35
>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=94.78 E-value=0.13 Score=44.74 Aligned_cols=35 Identities=17% Similarity=0.169 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|+|=.|+|++| .-+.+|||||..-.|||++.+.
T Consensus 5 ~~GdiV~G~V~~v--~~~~~~V~i~~~~~g~l~~~~~ 39 (82)
T cd04454 5 DVGDIVIGIVTEV--NSRFWKVDILSRGTARLEDSSA 39 (82)
T ss_pred CCCCEEEEEEEEE--cCCEEEEEeCCCceEEeechhc
Confidence 5799999999999 5678999999999999988764
No 36
>PRK05807 hypothetical protein; Provisional
Probab=94.77 E-value=0.12 Score=50.11 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=30.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|.+|.|+|+.|.| .+|||++ .+..||+|+++.
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 578999999875
No 37
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=94.71 E-value=0.069 Score=64.03 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=33.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.||.|+|++|.+ -+|||+|+.+..||+|++++
T Consensus 645 ~~vG~i~~GkV~~I~d--fGaFVel~~G~eGLvHISei 680 (719)
T TIGR02696 645 PEVGERFLGTVVKTTA--FGAFVSLLPGKDGLLHISQI 680 (719)
T ss_pred CCCCCEEEEEEEEEEC--ceEEEEecCCceEEEEhhhc
Confidence 4689999999999998 69999999999999999864
No 38
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=94.67 E-value=0.15 Score=54.45 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=30.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC--CcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~--~r~aFL~~~d~ 147 (738)
-+|+++.|+|++|.+ .+|||++.. +..||+|+++.
T Consensus 7 ~~GdiV~G~V~~I~~--~G~fV~L~e~~gieGlI~iSEl 43 (262)
T PRK03987 7 EEGELVVGTVKEVKD--FGAFVTLDEYPGKEGFIHISEV 43 (262)
T ss_pred CCCCEEEEEEEEEEC--CEEEEEECCCCCcEEEEEHHHc
Confidence 479999999999976 899999975 78999999874
No 39
>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=94.67 E-value=0.12 Score=43.55 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=30.1
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (738)
+|.+|.|+|++|.+ .++||+++. ...||+|+.+.
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 78999988764
No 40
>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=94.66 E-value=0.13 Score=43.32 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=28.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (738)
+.|.|..|+|.++.+ +.+|||||. -.|||+.++
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 479999999999999 579999987 899997654
No 41
>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=94.62 E-value=0.1 Score=43.34 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.+|.|+|++|.| -++||+++.+.+||+|+.+.
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 58999999999999998764
No 42
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=94.46 E-value=0.26 Score=49.88 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=29.6
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccC----------CcceeeEeccC
Q 004669 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGN----------SRPSLMDIKHY 147 (738)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~----------~r~aFL~~~d~ 147 (738)
...+|+|+.|+|++|.+ ..|||||+. +..||||+.+.
T Consensus 61 ~~~~GdiV~GkV~~i~~--~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i 107 (189)
T PRK09521 61 LLKKGDIVYGRVVDVKE--QRALVRIVSIEGSERELATSKLAYIHISQV 107 (189)
T ss_pred CCCCCCEEEEEEEEEcC--CeEEEEEEEecccccccCCCceeeEEhhHc
Confidence 34689999999999977 899999974 45677777653
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.46 E-value=0.1 Score=62.62 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=33.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.+|.|+|++|.+ .+|||+|+.+..||+|+++.
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 44
>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=94.11 E-value=0.12 Score=41.00 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=25.9
Q ss_pred EEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 116 YLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 116 Y~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.|+|+++.+ .++||+++.+..||++..+.
T Consensus 1 v~g~V~~v~~--~g~~v~l~~~~~g~~~~~~~ 30 (65)
T cd00164 1 VTGKVVSITK--FGVFVELEDGVEGLVHISEL 30 (65)
T ss_pred CEEEEEEEEe--eeEEEEecCCCEEEEEHHHC
Confidence 5799999996 58999999999999988664
No 45
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.63 E-value=0.52 Score=49.55 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.1
Q ss_pred EEeecCCCCc--ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 101 LLLEPVKSNV--QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 101 l~iE~~~~~~--~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+.+.+..... .+|+|-.|+|+++.+. .+||||+..-.||||+.+.
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 4455544433 5799999999999885 5999999999999999875
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.00 E-value=0.2 Score=61.48 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=31.7
Q ss_pred ccCCeEE-EEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~-GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
-+|.||. |+|++|.+ -+|||+|+.+..||+|+++.
T Consensus 752 ~vG~iy~~g~V~~I~~--FGaFVeL~~g~EGLVHISeL 787 (891)
T PLN00207 752 TVGDIYRNCEIKSIAP--YGAFVEIAPGREGLCHISEL 787 (891)
T ss_pred CCCcEEECcEEEEEec--cEEEEEeCCCCEEEEEhhhc
Confidence 4899995 69999998 69999999999999999875
No 47
>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=91.24 E-value=1 Score=38.99 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=30.9
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (738)
..+|.+|.|+|.++.+ .++||++..+..||+|.++
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 4479999999999987 8999999998999997754
No 48
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=91.09 E-value=0.51 Score=54.59 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=32.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
...|.||.|+|++|.+ .+||||||.+..||+|+++.
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 4589999999999988 58999999899999999875
No 49
>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=91.08 E-value=0.32 Score=40.90 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+|.+|.|+|++|.+ -++||+++.+.+||+|+.+.
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 50
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=91.08 E-value=0.48 Score=54.93 Aligned_cols=35 Identities=34% Similarity=0.547 Sum_probs=31.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.|+.|+|++|.|. +|||||| +-.||+|+++.
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 59999999875
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.86 E-value=0.54 Score=51.58 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=32.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
...|.|-.|+|.+|.+. +||||||....|||++++.
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 46799999999999865 8999999999999998875
No 52
>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=90.69 E-value=0.44 Score=43.71 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=31.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|.+-.|+|++|.+. ++||+++.+..||+++.++
T Consensus 2 ~~G~vV~G~V~~v~~~--gl~v~L~~g~~G~v~~sei 36 (100)
T cd05693 2 SEGMLVLGQVKEITKL--DLVISLPNGLTGYVPITNI 36 (100)
T ss_pred CCCCEEEEEEEEEcCC--CEEEECCCCcEEEEEHHHh
Confidence 3799999999999766 9999999999999999886
No 53
>PRK14865 rnpA ribonuclease P; Provisional
Probab=90.41 E-value=1.3 Score=41.59 Aligned_cols=54 Identities=20% Similarity=0.364 Sum_probs=37.7
Q ss_pred ceeeecCCChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 332 RIGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~~~----l~---~-~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
++.||||+... .|+|+|.++.+ .. + .++=+|.|..+.+++.++|++++..|...
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 36689998765 57776554433 22 2 23456889999999999999998776544
No 54
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.22 E-value=0.72 Score=50.58 Aligned_cols=38 Identities=29% Similarity=0.555 Sum_probs=32.6
Q ss_pred CCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 107 KSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 107 ~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
-...-+|.||.|+|++|.+ -+|||++| +-.||+|+++.
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 67899999875
No 55
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=89.88 E-value=0.32 Score=57.85 Aligned_cols=40 Identities=30% Similarity=0.522 Sum_probs=35.9
Q ss_pred CCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 106 VKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 106 ~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.....-+|-||.|+|+++.+ =+|||++..++.|++|++..
T Consensus 613 i~~e~evg~iy~G~V~ri~~--fGaFv~l~~gkdgl~hiS~~ 652 (692)
T COG1185 613 ITREVEVGEVYEGTVVRIVD--FGAFVELLPGKDGLVHISQL 652 (692)
T ss_pred HHhhcccccEEEEEEEEEee--cceEEEecCCcceeEEehhh
Confidence 34566799999999999999 89999999999999999864
No 56
>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=89.60 E-value=3.9 Score=45.53 Aligned_cols=108 Identities=22% Similarity=0.267 Sum_probs=62.9
Q ss_pred ccCCCEEEEEEEecCCCCCCceeeecccccceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC--CceEEEeecCC
Q 004669 291 VQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE--GFGLTIRTVAA 368 (738)
Q Consensus 291 lk~Gq~ILVQV~Ke~~g~KGprlT~~ISL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~~~--~~GvIiRT~A~ 368 (738)
+++||.|-|.|.+-..+.|||. +-+||+-.+ -|+.+++.-.|+ +.=+.|+..|.
T Consensus 170 ~~~Gd~ik~~V~~V~~~~kg~q--------------------IivSRt~~~----~v~~Lfe~EVPEI~dG~VeI~~iaR 225 (341)
T TIGR01953 170 FRIGDRIKAYVYEVRKTAKGPQ--------------------IILSRTHPE----FVKELLKLEVPEIADGIIEIKKIAR 225 (341)
T ss_pred CCCCCEEEEEEEEEEcCCCCCe--------------------EEEEeCcHH----HHHHHHHHhCccccCCeEEEEEEee
Confidence 7789999999988877777654 446777653 355666665665 32356777777
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEE-EcCHHHH
Q 004669 369 GHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRTY 442 (738)
Q Consensus 369 ~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~Iv-VD~~~~y 442 (738)
.+.. +++-+....+.++. +...++-.....+..+.+.+-.+.++=|- -||+..|
T Consensus 226 ~pG~-------------------RtKvAV~s~~~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f 280 (341)
T TIGR01953 226 EPGY-------------------RTKIAVESNDENID-PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEF 280 (341)
T ss_pred CCcc-------------------eeEEEEEcCCCCCC-cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHH
Confidence 6641 11111111223322 34567766666666666666677777553 3445433
No 57
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.44 E-value=0.8 Score=53.50 Aligned_cols=35 Identities=31% Similarity=0.528 Sum_probs=31.7
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
...|.|+.|+|++|.+. +||||+| +..||+|+++.
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 45899999999999994 8999999 89999999875
No 58
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=89.34 E-value=0.9 Score=52.59 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=34.1
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
....+|.+|.|+|++|.| .+|||+++.+-.||+|+++.
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 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=88.76 E-value=0.58 Score=39.49 Aligned_cols=34 Identities=9% Similarity=0.123 Sum_probs=30.9
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (738)
|.|+.|+|++|.+. .+||+++.+-.||+++++..
T Consensus 1 G~iV~g~V~~i~~~--gi~v~l~~~i~g~i~~~~i~ 34 (70)
T cd05702 1 GDLVKAKVKSVKPT--QLNVQLADNVHGRIHVSEVF 34 (70)
T ss_pred CCEEEEEEEEEECC--cEEEEeCCCcEEEEEHHHhc
Confidence 78999999999884 79999999999999998863
No 60
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=88.33 E-value=2.1 Score=40.55 Aligned_cols=53 Identities=13% Similarity=0.115 Sum_probs=35.3
Q ss_pred ceeeecCCChH-HHHHHHHHH----HhhC---CCCceEE--EeecCCCCCHHHHHHHHHHHHH
Q 004669 332 RIGVSRKITGV-ERTRLKVIA----KTLQ---PEGFGLT--IRTVAAGHSLEELQKDLEGLLS 384 (738)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~----~~l~---~~~~GvI--iRT~A~~~~~eeL~~Dl~~L~~ 384 (738)
++.||||+... +|+|+|.++ .... +.+.-+| .|..|..++..+|++++..|..
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 46689999765 577665544 3322 2333343 5788999999999999876543
No 61
>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=88.33 E-value=0.53 Score=39.23 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=28.6
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|.||.|+|+++.+ .++||++ .+-.|||+.++.
T Consensus 1 G~iv~g~V~~v~~--~G~~v~l-~g~~gfip~s~~ 32 (67)
T cd04465 1 GEIVEGKVTEKVK--GGLIVDI-EGVRAFLPASQV 32 (67)
T ss_pred CCEEEEEEEEEEC--CeEEEEE-CCEEEEEEHHHC
Confidence 7899999999976 8999999 579999998775
No 62
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=88.04 E-value=0.81 Score=53.59 Aligned_cols=68 Identities=24% Similarity=0.267 Sum_probs=50.2
Q ss_pred eEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 76 ~~IlIn~s~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
+-.+|.... ...||.|== -+|.+-=.+....+.-+|..+.|+|+++.|- +|||+|+.+-.||+|++++
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 445666654 356766532 2233333455667778999999999999995 8999999999999999886
No 63
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=87.94 E-value=0.64 Score=39.72 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=30.9
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (738)
+|.+|.|.|++|.+ .++||+++. +..||+|+.+.
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 89999999875
No 64
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=87.52 E-value=2 Score=53.14 Aligned_cols=38 Identities=26% Similarity=0.438 Sum_probs=33.9
Q ss_pred CCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
++..+|+|+.|+|++|.| -+|||+++.+-.||+|+++.
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 65
>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=87.26 E-value=1.5 Score=50.47 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=32.4
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|+++.|+|+++.+. +|||++|.+..||+|+.+.
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 35799999999999776 8999999999999999875
No 66
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=87.04 E-value=2.8 Score=40.04 Aligned_cols=54 Identities=26% Similarity=0.292 Sum_probs=36.8
Q ss_pred ceeeecCCChH-HHHHHHH----HHHhhC---CCCceE--EEeecCCCCCHHHHHHHHHHHHHH
Q 004669 332 RIGVSRKITGV-ERTRLKV----IAKTLQ---PEGFGL--TIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~----i~~~l~---~~~~Gv--IiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
++.||||+... +|+|+|. ++..+. +.|+-+ |.|-.+.+++..+|.+|+..|...
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 5766554 443332 344444 556678899999999998877655
No 67
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.48 E-value=1.7 Score=50.55 Aligned_cols=36 Identities=36% Similarity=0.480 Sum_probs=32.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.+|.|+|++|.| -++||++..+-.||+|+++.
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 79999998889999998764
No 68
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=86.23 E-value=3.3 Score=40.10 Aligned_cols=58 Identities=21% Similarity=0.326 Sum_probs=38.7
Q ss_pred eeeecC-CChH-HHHHHHHHHHhh----C---C-CCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 004669 333 IGVSRK-ITGV-ERTRLKVIAKTL----Q---P-EGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (738)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~l----~---~-~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W~~I~~~a 393 (738)
+.|||| +... .|+|+|.++.+. . + -++=||.|..+.+++..+|.+++..| |+.+...+
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 456899 6654 587776655432 2 2 13346778899999999999998666 55554444
No 69
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.97 E-value=1.8 Score=50.69 Aligned_cols=35 Identities=23% Similarity=0.330 Sum_probs=31.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|+++.|+|++|.+ .+|||++|.+..||+|+++.
T Consensus 372 ~~G~~v~g~V~~v~~--~G~fV~l~~~v~g~i~~s~l 406 (565)
T PRK06299 372 PVGDVVEGKVKNITD--FGAFVGLEGGIDGLVHLSDI 406 (565)
T ss_pred CCCCEEEEEEEEEec--ceEEEECCCCCEEEEEHHHc
Confidence 479999999999976 59999999999999999875
No 70
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=85.63 E-value=1.9 Score=53.32 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=30.8
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|++|.|+|.++.+ .+||||+| +-.||+|++++
T Consensus 491 l~~G~~V~G~Vk~i~~--~G~fVdl~-Gv~Gfvp~Sei 525 (863)
T PRK12269 491 VHIEDSVSGVVKSFTS--FGAFIDLG-GFDGLLHVNDM 525 (863)
T ss_pred CCCCCEEEEEEEEEeC--CcEEEEEC-CEEEEEEchhc
Confidence 3479999999999998 49999996 68999999875
No 71
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=84.93 E-value=2 Score=49.55 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=32.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.||.|+|+++.+ .+|||++|.+-.||+|+++.
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 48999999999999999875
No 72
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=84.59 E-value=2.1 Score=49.64 Aligned_cols=109 Identities=22% Similarity=0.295 Sum_probs=64.1
Q ss_pred cccCCCEEEEEEEecCCCCCCceeeecccccceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cce-EEEeecC
Q 004669 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (738)
Q Consensus 290 ~lk~Gq~ILVQV~Ke~~g~KGprlT~~ISL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~~~-~~G-vIiRT~A 367 (738)
.+++||.|-|-|.+-...+|||.+ -+||+-.+ -|+.+++.=.|+ ..| +.|+..|
T Consensus 171 ~~~~GdrIka~I~~Vd~~~kg~qI--------------------ilSRt~p~----~l~~Lf~~EVPEI~~G~ieIk~ia 226 (470)
T PRK09202 171 NFRPGDRVRAYVYEVRKEARGPQI--------------------ILSRTHPE----FLKKLFEQEVPEIADGLIEIKAIA 226 (470)
T ss_pred cCCCCCEEEEEEEEEecCCCCCeE--------------------EEEeCcHH----HHHHHHHHhCcccccCeEEEEEEe
Confidence 467899999999988777777654 46776553 355666655565 335 5577777
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEE-EcCHHHH
Q 004669 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRTY 442 (738)
Q Consensus 368 ~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~Iv-VD~~~~y 442 (738)
..+.. ++|-+....+.++. +...++-.....+..+.+.+-.+.|+=|. -+|+..|
T Consensus 227 R~pG~-------------------RaKvAV~s~d~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f 282 (470)
T PRK09202 227 RDPGS-------------------RAKIAVKSNDPRID-PVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQF 282 (470)
T ss_pred ecCcc-------------------eeEEEEEcCCCCCC-hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHHH
Confidence 66651 11111111223222 33456766666777777776677777553 3444433
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.24 E-value=2.5 Score=47.07 Aligned_cols=36 Identities=33% Similarity=0.486 Sum_probs=31.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (738)
...|.++.|+|+++.+ .++||++| +..||+|+++..
T Consensus 190 ~~~G~~v~g~V~~v~~--~G~fV~l~-~v~g~v~~sels 225 (390)
T PRK06676 190 LKEGDVVEGTVARLTD--FGAFVDIG-GVDGLVHISELS 225 (390)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEeC-CeEEEEEHHHcC
Confidence 4689999999999998 67999997 599999998863
No 74
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=83.68 E-value=5.5 Score=37.30 Aligned_cols=55 Identities=29% Similarity=0.387 Sum_probs=38.2
Q ss_pred ceeeecCCChH-HHHHHHHHH----HhhC---CC--CceEEEeecCCCCCHHHHHHHHHHHHHHH
Q 004669 332 RIGVSRKITGV-ERTRLKVIA----KTLQ---PE--GFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (738)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~----~~l~---~~--~~GvIiRT~A~~~~~eeL~~Dl~~L~~~W 386 (738)
++.||||+... .|+++|.++ .... +. ++=+|+|-.+.+++..+|.+|+..|...-
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 476665544 3322 22 34567788899999999999987776653
No 75
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=82.85 E-value=5.5 Score=38.53 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=37.8
Q ss_pred eeeecCCChH-HHHHHH----HHHHhhCC----C--CceEEEeecCCCCCHHHHHHHHHHHHH
Q 004669 333 IGVSRKITGV-ERTRLK----VIAKTLQP----E--GFGLTIRTVAAGHSLEELQKDLEGLLS 384 (738)
Q Consensus 333 vgvSrKI~~e-eR~rLk----~i~~~l~~----~--~~GvIiRT~A~~~~~eeL~~Dl~~L~~ 384 (738)
+.||||+... .|+|+| +++....+ . ++=||.|..+.+++..+|++||..++.
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 466654 44443322 2 345788999999999999999988776
No 76
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=82.81 E-value=6 Score=37.56 Aligned_cols=53 Identities=19% Similarity=0.309 Sum_probs=35.3
Q ss_pred eeeecCC-ChH-HHHHHHHHHHhh----C---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSRKI-TGV-ERTRLKVIAKTL----Q---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSrKI-~~e-eR~rLk~i~~~l----~---~-~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.||||. ... +|+++|.++.+. . | -++=+|.|..+.+.+..+|.+|+..|...
T Consensus 48 ~~VsKK~~~~AV~RNRiKR~lRE~~R~~~~~l~~~DiVvi~r~~~~~~~~~~l~~~l~~ll~k 110 (120)
T PRK04390 48 LVVGKKTAKRAVERNYMKRVIREWFRLNQHRLPPVDFVVRVQRKFDRATAKQAVAELAQLMAK 110 (120)
T ss_pred EEEecccCcchhhhhHHHHHHHHHHHhccccCCCceEEEEeCCCcccCCHHHHHHHHHHHHHH
Confidence 5678995 434 687776655442 1 2 13345778888899999999998766444
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=82.57 E-value=1.9 Score=52.28 Aligned_cols=37 Identities=30% Similarity=0.484 Sum_probs=32.9
Q ss_pred CcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.-..|.|--|.|+||.- -+||||||....|++|++..
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 34679999999999987 58999999999999999875
No 78
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=81.52 E-value=4.2 Score=45.31 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=31.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdI-G~~r~aFL~~~d~ 147 (738)
...|.|..|+|+++.+. ++|||| |.+-.|||+..+.
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 45799999999999984 799999 8899999988764
No 79
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=78.55 E-value=4.2 Score=48.72 Aligned_cols=34 Identities=29% Similarity=0.433 Sum_probs=30.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.+|++|.|+|+++.+. ++||++ .+-.||||+++.
T Consensus 476 ~~G~iV~g~V~~v~~~--G~fV~l-~gv~Gll~~sel 509 (647)
T PRK00087 476 EEGDVVEGEVKRLTDF--GAFVDI-GGVDGLLHVSEI 509 (647)
T ss_pred CCCCEEEEEEEEEeCC--cEEEEE-CCEEEEEEHHHc
Confidence 4799999999999884 899999 578999999875
No 80
>PRK01903 rnpA ribonuclease P; Reviewed
Probab=76.74 E-value=12 Score=36.26 Aligned_cols=53 Identities=21% Similarity=0.339 Sum_probs=33.2
Q ss_pred eeeecC-CChH-HHHHHHHHHHhh-------CCCC-------------ceEEEee-cCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QPEG-------------FGLTIRT-VAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~l-------~~~~-------------~GvIiRT-~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.|||| +... .|+|+|.++.+. .+.+ .-+|.|. +++..+.+++.+++..|+..
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 445799 6665 587776655331 2222 3456666 34447799999998777654
No 81
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=76.31 E-value=11 Score=35.80 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=37.3
Q ss_pred ceeeecCCC-hH-HHHHHHH----HHHhhCC----C--C--ceEEEeecCCCCCHHHHHHHHHHHHH
Q 004669 332 RIGVSRKIT-GV-ERTRLKV----IAKTLQP----E--G--FGLTIRTVAAGHSLEELQKDLEGLLS 384 (738)
Q Consensus 332 ~vgvSrKI~-~e-eR~rLk~----i~~~l~~----~--~--~GvIiRT~A~~~~~eeL~~Dl~~L~~ 384 (738)
++.||||+. .. .|+|+|. ++....+ . | +=+|.|..+.+.+..+|.+|+..|+-
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 567899954 34 5776654 4444333 1 3 34788999999999999999988764
No 82
>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=75.83 E-value=7.9 Score=35.72 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=36.4
Q ss_pred eeeecCCChH-HHHHHHHHHHh----hCC----CCceEEEeecCCCCCHHHHHHHHHHHH
Q 004669 333 IGVSRKITGV-ERTRLKVIAKT----LQP----EGFGLTIRTVAAGHSLEELQKDLEGLL 383 (738)
Q Consensus 333 vgvSrKI~~e-eR~rLk~i~~~----l~~----~~~GvIiRT~A~~~~~eeL~~Dl~~L~ 383 (738)
+.||||+... .|+++|.++.+ ..+ -++=+|+|..+..++.++|.+++..|.
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 57766554433 222 234578899999999999999998764
No 83
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=75.81 E-value=13 Score=36.67 Aligned_cols=54 Identities=30% Similarity=0.434 Sum_probs=37.4
Q ss_pred ceeeecCCC-hH-HHHHHHHHHHh----h----CCCCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 332 RIGVSRKIT-GV-ERTRLKVIAKT----L----QPEGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 332 ~vgvSrKI~-~e-eR~rLk~i~~~----l----~~~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
++.||||+. .. .|+|+|.++.+ + .+.++=+|.|-.+.+++.++|++++..|+..
T Consensus 51 G~sVSKKvg~~AV~RNRiKR~lRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~l~~LL~k 114 (145)
T PRK04820 51 GLAVSRKVDTRAVGRNRIKRVLREAMRQLLPELAPGDYVVVARSAAAKASNPQLRDAFLRLLRR 114 (145)
T ss_pred EEEEeccccCcchhHHHHHHHHHHHHHHhhhccCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 366899984 44 57766654433 2 2234556788888899999999998777665
No 84
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=75.27 E-value=6.1 Score=44.40 Aligned_cols=33 Identities=18% Similarity=0.262 Sum_probs=28.3
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (738)
..|+|-.|+|.++.+ +++|||+|. -.|||+.++
T Consensus 133 k~GeiV~G~V~~~~~--~~~~Vdlg~-vEa~LP~~E 165 (362)
T PRK12327 133 REGDIVTGVVQRRDN--RFVYVNLGK-IEAVLPPAE 165 (362)
T ss_pred hcCCEEEEEEEEEeC--CcEEEEeCC-eEEEecHHH
Confidence 689999999999988 589999987 688986543
No 85
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=75.14 E-value=9.2 Score=36.08 Aligned_cols=53 Identities=28% Similarity=0.367 Sum_probs=36.3
Q ss_pred eeeecC-CChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSRK-ITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~----l~---~-~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.|||| +... .|+++|.++.+ .. + -++=+|.|-.+.+++..+|.+|+..|.+.
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 57766554433 22 2 13345788899999999999999887654
No 86
>PRK00038 rnpA ribonuclease P; Reviewed
Probab=74.62 E-value=16 Score=35.03 Aligned_cols=58 Identities=14% Similarity=0.315 Sum_probs=35.4
Q ss_pred ceeeecCC-ChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHH-HHHHHHHHHHH
Q 004669 332 RIGVSRKI-TGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKD-LEGLLSTWKNI 389 (738)
Q Consensus 332 ~vgvSrKI-~~e-eR~rLk~i~~~----l~---~-~~~GvIiRT~A~~~~~eeL~~D-l~~L~~~W~~I 389 (738)
++.||||. ... +|+|+|..+.+ .. | -++=||.|..+.+++.++|..+ ...|...|..+
T Consensus 53 Gi~VsKKv~g~AV~RNRiKR~lRE~~R~~~~~l~~~D~VviaR~~~~~~~~~~l~~~~~~~~~~l~~~~ 121 (123)
T PRK00038 53 GLVIAKRFAARAVTRNTLKRVIREAFRARRLALPAQDYVVRLHSKLTPASLTALKRSARAEVDAHFTRI 121 (123)
T ss_pred EEEEecccCCCchhHHHHHHHHHHHHHHhhccCCCCCEEEEECCCCCcCCHHHHHHHHHHHHHHHHHHh
Confidence 46689995 444 57776554433 22 2 2455788899999999999333 22345555543
No 87
>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=74.35 E-value=4 Score=35.09 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
|++..|+|+++.+ .++||+++.+-.||+++.+.
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 59999999999999999875
No 88
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=70.97 E-value=11 Score=45.41 Aligned_cols=36 Identities=31% Similarity=0.495 Sum_probs=32.3
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.+|.|+|++|.+ .++||+++.+-.||+|+++.
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 49999999999999998764
No 89
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=70.60 E-value=1.7 Score=46.04 Aligned_cols=31 Identities=35% Similarity=0.639 Sum_probs=21.6
Q ss_pred ccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechh
Q 004669 584 ELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALE 623 (738)
Q Consensus 584 giT~LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~s~e 623 (738)
.++.|.-+|.+-+ -+.+||.|+|+|+|.+..
T Consensus 24 ~~~~~py~e~~g~---------~~vtCPTCqGtGrIP~eq 54 (238)
T PF07092_consen 24 DISSFPYVEFTGR---------DSVTCPTCQGTGRIPREQ 54 (238)
T ss_pred ccccCccccccCC---------CCCcCCCCcCCccCCccc
Confidence 4556666666542 245899999999997754
No 90
>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=69.17 E-value=3.7 Score=34.82 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=22.8
Q ss_pred ceeEEEeecCCCCCchhhccccCCCCCCceeEe
Q 004669 588 HGLMEITRKRVRPSVTFMISEPCTCCQGTGRVE 620 (738)
Q Consensus 588 LGLvEmTRKR~r~sL~~~l~e~Cp~C~G~G~v~ 620 (738)
-|.+.++++ .+........+|+.|+|+|++.
T Consensus 24 ~G~~~~~~~--~~~~~~~~~~~C~~C~G~G~~i 54 (66)
T PF00684_consen 24 SGQVTRRQQ--TPGGVFQMQQTCPKCGGTGKII 54 (66)
T ss_dssp SSEEEEEEE--SSSTTEEEEEE-TTTSSSSEE-
T ss_pred eeEEEEEEe--CCCeEEEEEEECCCCcceeeEE
Confidence 455655555 7777788889999999999985
No 91
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=68.59 E-value=26 Score=33.27 Aligned_cols=53 Identities=28% Similarity=0.481 Sum_probs=35.5
Q ss_pred eeeecCCC-hH-HHHHHH----HHHHhhC---CCCc--eEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSRKIT-GV-ERTRLK----VIAKTLQ---PEGF--GLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSrKI~-~e-eR~rLk----~i~~~l~---~~~~--GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.||||.. .. .|+++| +++..+. +.++ =+|+|..+.+++..+|.+|+..|...
T Consensus 51 ~~VsKK~~~~AV~RNriKR~lRe~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k 114 (122)
T PRK03031 51 ISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQ 114 (122)
T ss_pred EEEecccccchhhhhHHHHHHHHHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHH
Confidence 56799964 33 466554 4444332 2333 45778888999999999998777655
No 92
>PRK00730 rnpA ribonuclease P; Reviewed
Probab=67.02 E-value=14 Score=36.27 Aligned_cols=53 Identities=19% Similarity=0.261 Sum_probs=36.1
Q ss_pred ceeeecCCChH-HHHHHHHHHHh----hCC--C--CceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 332 RIGVSRKITGV-ERTRLKVIAKT----LQP--E--GFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~~~----l~~--~--~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
++.||||+... .|+|+|.++.. ..+ . ++=||.|..+. .+.++|.+|+..+...
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 57776655433 222 1 34467788886 9999999998776654
No 93
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=66.57 E-value=28 Score=33.03 Aligned_cols=53 Identities=30% Similarity=0.417 Sum_probs=36.3
Q ss_pred eeeec-CCChH-HHHHHHHHH----Hh---hCC-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSR-KITGV-ERTRLKVIA----KT---LQP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSr-KI~~e-eR~rLk~i~----~~---l~~-~~~GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.||| |+... +|+|+|.++ .. +.| .++=||+|..+.+++..+++++|..+...
T Consensus 45 lsVsKkk~g~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~ 107 (117)
T COG0594 45 LTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKR 107 (117)
T ss_pred EEEEchhccchhhHHHHHHHHHHHHHhhhhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHH
Confidence 56799 77754 576665443 32 222 25568899999999999998887665544
No 94
>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=66.41 E-value=24 Score=29.59 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=26.9
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004669 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (738)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (738)
|++--|+|++|.+ .+|||++..+-.||++..+
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 6788999999984 5799999667899997765
No 95
>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=65.37 E-value=13 Score=45.00 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=31.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-CcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (738)
.+|.+|.|+|++|.+ -++||++.. +-.||+|+++.
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 79999999875
No 96
>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=64.26 E-value=17 Score=33.62 Aligned_cols=53 Identities=34% Similarity=0.491 Sum_probs=35.1
Q ss_pred eeeecCCCh-H-HHHHHHHHHHh----hC---CCCc--eEEEeecCCCCCHHHHHHHHHHHHHH
Q 004669 333 IGVSRKITG-V-ERTRLKVIAKT----LQ---PEGF--GLTIRTVAAGHSLEELQKDLEGLLST 385 (738)
Q Consensus 333 vgvSrKI~~-e-eR~rLk~i~~~----l~---~~~~--GvIiRT~A~~~~~eeL~~Dl~~L~~~ 385 (738)
+.||||+.. . .|+++|.++.+ .. +.+. =++.|..+...+.++|.+++..|...
T Consensus 46 ~~vsKK~gk~AV~RNriKR~lRe~~R~~~~~l~~~~d~v~~~r~~~~~~~~~~l~~~l~~ll~k 109 (111)
T PF00825_consen 46 FSVSKKVGKRAVKRNRIKRRLREAFRLNKPELPPGYDIVFIARPGALELSFEELEKELKKLLKK 109 (111)
T ss_dssp EEE-STTSS-HHHHHHHHHHHHHHHHHCTTTS-SSSEEEEEE-CGGGGS-HHHHHHHHHHHHHH
T ss_pred EEecCccccchhHHHHHHHHHHHHHHHHHhhccCCcEEEEEEcCCcCcCCHHHHHHHHHHHHHh
Confidence 568999977 5 58777665544 22 2233 46777888899999999999887765
No 97
>PRK11642 exoribonuclease R; Provisional
Probab=63.84 E-value=17 Score=44.96 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCC-cceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNS-RPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~-r~aFL~~~d~ 147 (738)
.+|.+|.|+|+.|.+. ++||++... -.||+|+.+.
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 4899999999999885 999999864 9999999875
No 98
>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=62.07 E-value=11 Score=34.23 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=31.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecc--------cCCcceeeEeccCC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNI--------GNSRPSLMDIKHYR 148 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdI--------G~~r~aFL~~~d~~ 148 (738)
.+|+|=.|+|++|-+. .|+||| ...-.|+|+..|.+
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 4799999999999755 499999 88889999998864
No 99
>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=61.86 E-value=37 Score=30.77 Aligned_cols=33 Identities=21% Similarity=0.205 Sum_probs=29.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~ 145 (738)
.+|++=+|+|+.+. -..-+||||..-+|+|++.
T Consensus 5 ~~gD~VIG~V~~~~--~~~~~VdI~s~~~a~L~~~ 37 (86)
T cd05790 5 AKGDHVIGIVVAKA--GDFFKVDIGGSEPASLSYL 37 (86)
T ss_pred CCCCEEEEEEEEEc--CCeEEEEcCCCcceEechH
Confidence 57999999999996 4889999999999999763
No 100
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=59.08 E-value=19 Score=39.17 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.6
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
.++|.-=.|+|+.|.+.|+ ||||.|..|.-|+++++.
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 4689999999999999995 799999999999999884
No 101
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=57.11 E-value=16 Score=35.43 Aligned_cols=56 Identities=13% Similarity=0.331 Sum_probs=40.0
Q ss_pred ccCCCCCCceeEechhhHHHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEE
Q 004669 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWIL 687 (738)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~ierei~~~~~~~~~k~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~ 687 (738)
--||.|+|.-.-.|-..++..+.+++++...... -+.++.+|| ..+||-.|.
T Consensus 41 LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~-----------------Sd~eI~~~~-----------v~RYG~~Vl 92 (126)
T TIGR03147 41 LRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGK-----------------SNQQIIDFM-----------TARFGDFVL 92 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCC-----------------CHHHHHHHH-----------HHhcCCeEE
Confidence 3699999998888888888888888877664432 123455554 467888888
Q ss_pred EEeC
Q 004669 688 LKVA 691 (738)
Q Consensus 688 l~~d 691 (738)
..|.
T Consensus 93 y~Pp 96 (126)
T TIGR03147 93 YNPP 96 (126)
T ss_pred ecCC
Confidence 7654
No 102
>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=55.47 E-value=15 Score=33.20 Aligned_cols=31 Identities=39% Similarity=0.488 Sum_probs=27.2
Q ss_pred eEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 004669 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (738)
Q Consensus 115 IY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (738)
+|.|+|+.|.+ .++||+++. -.||+++.+..
T Consensus 2 vv~g~V~~i~~--~GifV~l~~-v~G~v~~~~l~ 32 (99)
T cd04460 2 VVEGEVVEVVD--FGAFVRIGP-VDGLLHISQIM 32 (99)
T ss_pred EEEEEEEEEEe--ccEEEEEcC-eEEEEEEEEcc
Confidence 79999999988 499999984 89999998764
No 103
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=54.57 E-value=27 Score=39.62 Aligned_cols=189 Identities=14% Similarity=0.163 Sum_probs=95.8
Q ss_pred cccCCCEEEEEEEecCCCCC-CceeeecccccceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cce-EEEeec
Q 004669 290 QVQKGTKVIVQVVKEGLGTK-GPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTV 366 (738)
Q Consensus 290 ~lk~Gq~ILVQV~Ke~~g~K-GprlT~~ISL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~~~-~~G-vIiRT~ 366 (738)
.+++||.|-|=|.+--..+| ||.+ -+||.-. .-|+.+++.-.|+ ..| +-|+..
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 47789999998888877787 7654 3565544 2355566555554 224 556776
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeeeecCCchhhhhhhhccCCccEEE-EcCHHHHHHH
Q 004669 367 AAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRTYHEV 445 (738)
Q Consensus 367 A~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~~~lRD~~~~~v~~Iv-VD~~~~y~~i 445 (738)
|..+.. +++-+....+.++. +...++-.....+..+.+.+-.+.++=|. -||+..| +
T Consensus 232 ARepG~-------------------RtKVAV~S~d~~iD-PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~f--I 289 (374)
T PRK12328 232 ARIPGE-------------------RAKVALFSNNPNID-PIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIF--I 289 (374)
T ss_pred eccCcc-------------------eeEEEEEcCCCCCC-hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH--H
Confidence 666541 11111001122221 23456666666677777777677787663 3455444 2
Q ss_pred HHHHHhhCCCccCceeeccCCCCcccccCHHHHHHhHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHhhhH
Q 004669 446 TSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAI 525 (738)
Q Consensus 446 ~~~l~~~~p~~~~~v~ly~~~~plF~~y~Ie~qI~~al~rrV~LpsGGyLVIE~TEALtvIDVNSGk~~~~~~~~~eet~ 525 (738)
. ..++|....+|.+-. +...+..+=-+.|+..|..+ .|-++-.-.-=+-|-|||-|....-.. ..+.-
T Consensus 290 ~---Nal~Pa~V~~V~i~~-~~~~~~V~V~~~qlslAIGk-----~GqNvrLA~~LtGwkIDI~s~~~~~~~---~~~~~ 357 (374)
T PRK12328 290 A---RALAPAIISSVKIEE-EEKKAIVTLLSDQKSKAIGK-----NGINIRLASMLTGYEIELNEIGSKENA---SNESE 357 (374)
T ss_pred H---HhCCCceeeEEEEcC-CCcEEEEEEChHHhhhhhcC-----CChhHHHHHHHhCCEEEEEECCCCccc---ccccc
Confidence 2 245676665654432 22222222223333333332 222222222223467888887532111 11223
Q ss_pred HHHHHHHHHHH
Q 004669 526 LDVNLAAAKQI 536 (738)
Q Consensus 526 lktNlEAA~EI 536 (738)
-.||.|..+.+
T Consensus 358 ~~~~~~~~~~~ 368 (374)
T PRK12328 358 KETNKEGVKAL 368 (374)
T ss_pred cccccccHHHH
Confidence 45777766543
No 104
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=54.56 E-value=19 Score=34.95 Aligned_cols=56 Identities=9% Similarity=0.239 Sum_probs=40.2
Q ss_pred ccCCCCCCceeEechhhHHHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEE
Q 004669 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWIL 687 (738)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~ierei~~~~~~~~~k~~~~~~~~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~ 687 (738)
--||.|+|.-.-.|-..++..+.+++++...... -+.++.+|| ..+||-.|.
T Consensus 41 LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~-----------------sd~eI~~~~-----------v~RYG~~Vl 92 (126)
T PRK10144 41 LRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGK-----------------SEVEIIGWM-----------TERYGDFVR 92 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCC-----------------CHHHHHHHH-----------HHhcCCeEE
Confidence 3699999998888888888888888887664432 133455554 367888888
Q ss_pred EEeC
Q 004669 688 LKVA 691 (738)
Q Consensus 688 l~~d 691 (738)
..|.
T Consensus 93 ~~Pp 96 (126)
T PRK10144 93 YNPP 96 (126)
T ss_pred ecCC
Confidence 7654
No 105
>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=52.16 E-value=32 Score=41.58 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG-~~r~aFL~~~d~ 147 (738)
.+|.+|-|+|+.|.+ .++||++. .+-.||+|+.+.
T Consensus 571 ~iG~~~~g~I~~v~~--~GifV~L~~~~veGlV~~s~l 606 (654)
T TIGR00358 571 KVGTEFSGEISSVTR--FGMFVRLDDNGIDGLIHISTL 606 (654)
T ss_pred CCCcEEEEEEEeEEc--CcEEEEecCCceEEEEEeEeC
Confidence 469999999999998 46999997 789999999875
No 106
>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=42.60 E-value=13 Score=38.29 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=14.9
Q ss_pred ccCCCCCCceeEechhhH
Q 004669 608 EPCTCCQGTGRVEALETS 625 (738)
Q Consensus 608 e~Cp~C~G~G~v~s~et~ 625 (738)
.+|+.|+|+|+++.....
T Consensus 116 ~~C~~C~G~G~v~~~~~~ 133 (186)
T TIGR02642 116 RECDTCAGTGRFRPTVED 133 (186)
T ss_pred CCCCCCCCccEEeeeEEE
Confidence 689999999998887665
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=42.52 E-value=32 Score=34.60 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=31.0
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (738)
..+|.++.|+|+++.+ .++||++|. -+|+++..+..
T Consensus 79 p~~gEvv~G~V~~v~~--~GifV~lg~-~~gi~~~~~l~ 114 (179)
T TIGR00448 79 PELGEIVEGEVIEIVE--FGAFVSLGP-FDGLFHVSQVT 114 (179)
T ss_pred ccCCCEEEEEEEEEEe--eEEEEEeCC-ceEEEEcHHhC
Confidence 3479999999999999 599999985 89999888753
No 108
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=39.80 E-value=1e+02 Score=28.30 Aligned_cols=45 Identities=13% Similarity=0.033 Sum_probs=33.5
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d~~~~~~~y~I~~ 703 (738)
..+.|+|||+-..++.... ......++. .|.+|+++..+.+.|..
T Consensus 68 ~~v~I~v~p~d~~~l~~~~----~~~~~~~~~--~l~~D~~l~~G~c~iet 112 (128)
T PF02108_consen 68 EKVTIRVHPDDYEALEELL----EDELPELGW--ELVADPSLAPGDCRIET 112 (128)
T ss_pred CCeEEEECHHHHHHHHHHH----HHHHhhcCC--EEEecCCCCCCCEEEEE
Confidence 4699999999999986433 222223333 88999999999999885
No 109
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=37.95 E-value=29 Score=34.40 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=21.7
Q ss_pred ccCCCCCCceeEechhhHHHHHHHHHHHHHHhh
Q 004669 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMM 640 (738)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~ierei~~~~~~~ 640 (738)
-.||+|.|.-.-.|...++..+.++|++.+...
T Consensus 41 LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G 73 (148)
T PF03918_consen 41 LRCPVCQNQSIADSNAPIARDMRREIREMLAEG 73 (148)
T ss_dssp CE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT
T ss_pred ccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcC
Confidence 369999997666666677888888888776543
No 110
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=36.85 E-value=1.4e+02 Score=30.53 Aligned_cols=47 Identities=13% Similarity=0.273 Sum_probs=35.7
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHH--hcCCeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSS--SLKAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~--~~~~~I~l~~d~~~~~~~y~I~~ 703 (738)
+.+.|+|||+.+..+... +..+.. -+...+.|.+|+++..+...|.+
T Consensus 128 ~~v~I~v~P~d~~~l~~~----l~~~~~~~~~~~~~~l~~D~~L~~G~c~vet 176 (199)
T PRK06032 128 PHLVVRVNDALVEAARER----LERLARESGFEGRLVVLADPDMAPGDCRLEW 176 (199)
T ss_pred CcEEEEECHHHHHHHHHH----HHHHHHhcCcCccEEEeeCCCCCCCCeEEEe
Confidence 469999999988887532 223222 34567889999999999998886
No 111
>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=35.15 E-value=21 Score=36.83 Aligned_cols=16 Identities=38% Similarity=0.760 Sum_probs=14.0
Q ss_pred cccCCCCCCceeEech
Q 004669 607 SEPCTCCQGTGRVEAL 622 (738)
Q Consensus 607 ~e~Cp~C~G~G~v~s~ 622 (738)
..+||.|+|+|++...
T Consensus 99 ~~~C~~C~G~G~~i~~ 114 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRR 114 (186)
T ss_pred CCcCCCCCCeeEEecC
Confidence 7899999999998763
No 112
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=34.30 E-value=1.2e+02 Score=25.34 Aligned_cols=33 Identities=15% Similarity=0.129 Sum_probs=18.3
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (738)
+|.|=..+|.++-+ .+||++.|.++.-||+.++
T Consensus 1 iG~~~~L~V~~~~~--~g~fL~~~~~~~vlLp~~e 33 (61)
T PF13509_consen 1 IGQINTLKVVDKNE--FGYFLDDGEGKEVLLPKSE 33 (61)
T ss_dssp --------EEEE-S--SEEEEEETT-EEEEEEGGG
T ss_pred CCCCcceEEEEEeC--CEEEEECCCCCEEEechHH
Confidence 35666677777775 7899999888888886654
No 113
>PHA02945 interferon resistance protein; Provisional
Probab=33.71 E-value=1.3e+02 Score=27.79 Aligned_cols=32 Identities=13% Similarity=0.138 Sum_probs=25.3
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEecc
Q 004669 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (738)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d 146 (738)
.|.|=+|+|+. .=.+|||+.- .++.||+|++.
T Consensus 11 ~GelvigtV~~---~d~ga~v~L~EY~g~eg~i~~se 44 (88)
T PHA02945 11 VGDVLKGKVYE---NGYALYIDLFDYPHSEAILAESV 44 (88)
T ss_pred CCcEEEEEEEe---cCceEEEEecccCCcEEEEEeeh
Confidence 69999999999 4468898874 36888888864
No 114
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=32.44 E-value=50 Score=33.26 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=30.2
Q ss_pred cccCCeEEEEEeeecCCcceEEecccCCcceeeEeccC
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (738)
..+|.++.|+|+++.+ .++||++|. -+||++..+.
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 3479999999999987 699999994 8899988764
No 115
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=32.01 E-value=40 Score=36.57 Aligned_cols=35 Identities=17% Similarity=0.438 Sum_probs=28.1
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeEeccC
Q 004669 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (738)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d~ 147 (738)
-.|.|-.|+|++|... +|||++- .++.||+|+++.
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 3699999999999875 7888873 457888888764
No 116
>PRK06937 type III secretion system protein; Reviewed
Probab=31.95 E-value=1.5e+02 Score=30.51 Aligned_cols=49 Identities=8% Similarity=0.114 Sum_probs=34.5
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d~~~~~~~y~I~~ 703 (738)
..++|+|||+-++++.......+..+. ...++.|.+|+++.++.--|..
T Consensus 131 ~~v~I~V~P~D~~~v~~~~~~~~~~~~--~~~~l~i~~D~~L~~Ggc~iET 179 (204)
T PRK06937 131 KQVVVRVNPDQAAAVREQIAKVLKDFP--EVGYLEVVADARLDQGGCILET 179 (204)
T ss_pred CeEEEEECHHHHHHHHHHHHHHHHhCC--CCccEEEEeCCCCCCCCeEEec
Confidence 469999999999998653322222111 1257899999999999877664
No 117
>PRK09098 type III secretion system protein HrpB; Validated
Probab=30.88 E-value=1.7e+02 Score=31.07 Aligned_cols=47 Identities=9% Similarity=-0.080 Sum_probs=35.5
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcC--CeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLK--AWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~--~~I~l~~d~~~~~~~y~I~~ 703 (738)
+.++|+|||+-.+.+.... ..+...++ ..|.|.+|+++.++..-|..
T Consensus 151 ~~v~IrV~P~D~~~v~~~~----~~~~~~~g~~~~l~Iv~Dp~L~~GgCviET 199 (233)
T PRK09098 151 SYLTVRVHPADLDAARAAF----GAAAAAGGRNVPVEVVGDPRLAPGACVCEW 199 (233)
T ss_pred CcEEEEECHHHHHHHHHHH----HHHHHhcCCCcceEEEeCCCCCCCCeEEEe
Confidence 4699999999999986433 33333343 57899999999999988875
No 118
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=30.67 E-value=2.4e+02 Score=27.34 Aligned_cols=45 Identities=18% Similarity=0.082 Sum_probs=33.6
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d~~~~~~~y~I~~ 703 (738)
..++|+|||+-.+.+.... ..+-...+ +.|.+|+++..+.+-|..
T Consensus 114 ~~v~I~v~P~d~~~l~~~l----~~~~~~~~--~~i~~D~~l~~G~c~vet 158 (166)
T TIGR02499 114 GRLTLRVHPEQLDEVREAL----AERLALEP--WELEPDASLAPGACVLET 158 (166)
T ss_pred CceEEEECHHHHHHHHHHH----HHHhccCC--eEEeeCCCCCCCCEEEEe
Confidence 4699999999999986432 22223333 889999999999987764
No 119
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=30.10 E-value=1.2e+02 Score=24.42 Aligned_cols=37 Identities=8% Similarity=0.053 Sum_probs=32.2
Q ss_pred EEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeC
Q 004669 655 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVA 691 (738)
Q Consensus 655 ~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d 691 (738)
..+.+++..+.++...+...+.+|++.++..|.+..+
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~ 38 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD 38 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC
Confidence 4678899999999987778999999999999998655
No 120
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=29.84 E-value=1.3e+02 Score=35.11 Aligned_cols=33 Identities=9% Similarity=0.077 Sum_probs=25.1
Q ss_pred cccCCeEEEEEeeecCCcceEEecccC--C---cceeeEe
Q 004669 110 VQCDSVYLGVVTKLVPNMGGAFVNIGN--S---RPSLMDI 144 (738)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~--~---r~aFL~~ 144 (738)
..+|.|-.|+|.++..+ ..+||+|. + -.|+|+.
T Consensus 150 ~~~GeIV~G~V~r~e~~--~viv~l~~~~g~~~~EaiLP~ 187 (449)
T PRK12329 150 DLEDTVLTARVLRFERQ--SVIMAVSSGFGQPEVEAELPK 187 (449)
T ss_pred HhcCcEEEEEEEEEcCC--CEEEEecccCCCcceEEEecH
Confidence 36899999999999886 69999842 3 3566643
No 121
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=28.63 E-value=23 Score=40.13 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=20.1
Q ss_pred eeeecCCChHH-HHHHHHHHHhhCCC
Q 004669 333 IGVSRKITGVE-RTRLKVIAKTLQPE 357 (738)
Q Consensus 333 vgvSrKI~~ee-R~rLk~i~~~l~~~ 357 (738)
+||||--+.+| ++..|.++..+.|.
T Consensus 10 LGV~k~As~~EIKkAYRkLA~kyHPD 35 (371)
T COG0484 10 LGVSKDASEEEIKKAYRKLAKKYHPD 35 (371)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHhCCC
Confidence 68888888766 77888888888875
No 122
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=27.82 E-value=45 Score=36.80 Aligned_cols=31 Identities=19% Similarity=0.523 Sum_probs=20.9
Q ss_pred ccccCCCCCCceeEechhhHHHHHHHHHHHHHHh
Q 004669 606 ISEPCTCCQGTGRVEALETSFSKIEQEISRLLAM 639 (738)
Q Consensus 606 l~e~Cp~C~G~G~v~s~et~~~~ierei~~~~~~ 639 (738)
....|++|+|+|..... ...|.+..+.+++.
T Consensus 90 ~~~~C~~CeGrgi~l~~---f~dll~kf~eiaK~ 120 (354)
T COG1568 90 YDYTCECCEGRGISLQA---FKDLLEKFREIAKD 120 (354)
T ss_pred ccccccCcCCccccchh---HHHHHHHHHHHHhc
Confidence 35689999999996655 44555555555443
No 123
>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=26.06 E-value=1.3e+02 Score=26.01 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhc
Q 004669 531 AAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVER 575 (738)
Q Consensus 531 EAA~EIARQLRLRnIgGIIVIDFIDM~~~~~r~~V~~~Lk~alk~ 575 (738)
+-|.+|+.+||=. -++++||-+|..+. .+++++.|..+...
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 4478899999865 57999999998775 66788999887765
No 124
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=26.04 E-value=36 Score=34.09 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=20.9
Q ss_pred hHhCCceeCCCCcEEEEecccceE
Q 004669 481 NMLSKRVPLPNGGSLVIEQTEALV 504 (738)
Q Consensus 481 ~al~rrV~LpsGGyLVIE~TEALt 504 (738)
.-|.+.||++-|+++||+++|-+-
T Consensus 53 ~KfRksiWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 53 AKFRKSIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred HhhhhceEEeeCCEEEEccccccc
Confidence 346788999999999999999876
No 125
>TIGR03825 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Probab=25.31 E-value=2.8e+02 Score=29.52 Aligned_cols=47 Identities=17% Similarity=0.133 Sum_probs=36.0
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhc--CCeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSL--KAWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~--~~~I~l~~d~~~~~~~y~I~~ 703 (738)
..++|+|||+-+.++.... ..|...+ ...+.|.+|+.+..+..-|..
T Consensus 176 ~~i~I~v~p~d~~~v~~~~----~~l~~~~~~~~~i~i~~D~~l~~GgcvIEt 224 (255)
T TIGR03825 176 DEVSIYVHPHWYERVAAQK----DELQSILPACEHLAVYPDEKLPDGGCYVET 224 (255)
T ss_pred CcEEEEECHHHHHHHHHhH----HHHHhhcCCCCceEEEeCCCCCCCCeEEEc
Confidence 4699999999999987543 3333444 357889999999999988775
No 126
>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=25.30 E-value=1.6e+02 Score=28.48 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=35.6
Q ss_pred hcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCC-CceEeccCCceeEEEeec
Q 004669 541 RLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRS-MVKVSELSRHGLMEITRK 596 (738)
Q Consensus 541 RLRnIgGIIVIDFIDM~~~~~r~~V~~~Lk~alk~D~~-kt~V~giT~LGLvEmTRK 596 (738)
.|..-+|+|+|||=++. .+ + ++.+++.+..|+- -..+++.|.-||==+.|=
T Consensus 26 ~l~~~sglv~lDiD~l~-~e---e-~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~ 77 (136)
T PF08800_consen 26 NLKAYSGLVVLDIDHLD-PE---E-AEELRQLLFEDPYTLAAFVSPSGRGVKIIVPF 77 (136)
T ss_pred hhhhCCCcEEEEeCCCC-HH---H-HHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEe
Confidence 35568999999998886 32 3 3677778888774 445566777777666643
No 127
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.17 E-value=28 Score=39.42 Aligned_cols=21 Identities=29% Similarity=0.376 Sum_probs=18.8
Q ss_pred cCCCCCHHHHHHHHHHHHHHH
Q 004669 366 VAAGHSLEELQKDLEGLLSTW 386 (738)
Q Consensus 366 ~A~~~~~eeL~~Dl~~L~~~W 386 (738)
+..+|+.+||++-+..|..+|
T Consensus 12 V~k~As~~EIKkAYRkLA~ky 32 (371)
T COG0484 12 VSKDASEEEIKKAYRKLAKKY 32 (371)
T ss_pred CCCCCCHHHHHHHHHHHHHHh
Confidence 466899999999999999998
No 128
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.36 E-value=98 Score=39.20 Aligned_cols=35 Identities=20% Similarity=0.367 Sum_probs=28.0
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCceEe
Q 004669 548 IIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVS 583 (738)
Q Consensus 548 IIVIDFIDM~~~~~r~~V~~~Lk~alk~D~~kt~V~ 583 (738)
-||||-+-... .++..+.+.+..||+.-...+.+.
T Consensus 199 ~vvvdr~~~~~-~~~~r~~~s~~~a~~~g~g~~~~~ 233 (924)
T TIGR00630 199 DVVIDRLKVKN-ENRSRLAESVETALRLGDGLLEVE 233 (924)
T ss_pred EEEEEEEEeCc-chHHHHHHHHHHHHHhCCCeEEEE
Confidence 48999877764 578889999999999877766654
No 129
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=22.90 E-value=60 Score=26.80 Aligned_cols=15 Identities=60% Similarity=1.012 Sum_probs=12.9
Q ss_pred ceeCCCCcEEEEecc
Q 004669 486 RVPLPNGGSLVIEQT 500 (738)
Q Consensus 486 rV~LpsGGyLVIE~T 500 (738)
||+|.+||.||+|-+
T Consensus 22 RvPleGGGRLVvEl~ 36 (51)
T PF11314_consen 22 RVPLEGGGRLVVELN 36 (51)
T ss_pred EEecCCCcEEEEEeC
Confidence 789999999998743
No 130
>PRK14296 chaperone protein DnaJ; Provisional
Probab=22.70 E-value=51 Score=37.09 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=19.0
Q ss_pred eeeecCCChHH-HHHHHHHHHhhCCC
Q 004669 333 IGVSRKITGVE-RTRLKVIAKTLQPE 357 (738)
Q Consensus 333 vgvSrKI~~ee-R~rLk~i~~~l~~~ 357 (738)
+|||+..+.++ |+..+.++..+.|.
T Consensus 10 Lgv~~~a~~~eik~ayrkla~~~HPD 35 (372)
T PRK14296 10 LGVSKTASEQEIRQAYRKLAKQYHPD 35 (372)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCcC
Confidence 57787777665 77888888888876
No 131
>PRK06328 type III secretion system protein; Validated
Probab=22.69 E-value=2.1e+02 Score=30.08 Aligned_cols=47 Identities=13% Similarity=0.206 Sum_probs=35.2
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcC--CeEEEEeCCCCCCcceEEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLK--AWILLKVARGFTRGAFEVIP 703 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~--~~I~l~~d~~~~~~~y~I~~ 703 (738)
..++|+|||+=+.++.... ..+...++ ..+.|.+|+++..+..-|..
T Consensus 132 ~~v~I~VnP~D~~~v~~~~----~~l~~~~~~~~~~~I~~D~~L~~GgCiIET 180 (223)
T PRK06328 132 KRIIIHVNPKDLAIVEKSR----PELKKIVEYADSLIISPKADVTPGGCIIET 180 (223)
T ss_pred CceEEEECHHHHHHHHHHH----HHHHHhccCCCceEEEeCCCCCCCCeEEEe
Confidence 4699999999999987543 23333333 46889999999999977764
No 132
>PF12401 DUF3662: Protein of unknown function (DUF2662) ; InterPro: IPR022128 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00498 from PFAM. ; PDB: 2LC0_A.
Probab=22.57 E-value=5e+02 Score=24.62 Aligned_cols=50 Identities=10% Similarity=0.058 Sum_probs=31.8
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHH-------------hcCCeEEEEeCCCCCCcceEEE
Q 004669 653 PRFILRVDHHMCNYLTSGKRTRLAVLSS-------------SLKAWILLKVARGFTRGAFEVI 702 (738)
Q Consensus 653 ~~~~l~v~p~v~~~l~~~~~~~l~~Le~-------------~~~~~I~l~~d~~~~~~~y~I~ 702 (738)
..+.|.++|.-.+.|.........+|.. .-.+.|.|..+++++.++|+|.
T Consensus 53 N~y~V~Ls~~D~~~l~~~~~~l~~el~~~l~~~a~~qgy~~~G~v~V~~~~d~~L~~G~~rv~ 115 (116)
T PF12401_consen 53 NVYTVELSPEDYERLSPWGDRLARELADYLAEHAREQGYTFVGPVTVEFEEDPDLHTGQFRVR 115 (116)
T ss_dssp -EEEEEEEHHHHHHH-S-SHHHHHHHHHHHHHHHHHHT-B-SS--EEEEEEETTS-TT-EEEE
T ss_pred eeEEEEECHHHHHHHhhhHHHHHHHHHHHHHHHHHHCCCeecCCEEEEEEECCCCCCceEEEe
Confidence 3789999999888877654333333322 2246899999999999999986
No 133
>PRK14298 chaperone protein DnaJ; Provisional
Probab=21.45 E-value=51 Score=37.17 Aligned_cols=26 Identities=15% Similarity=0.415 Sum_probs=20.0
Q ss_pred eeeecCCChHH-HHHHHHHHHhhCCCC
Q 004669 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (738)
Q Consensus 333 vgvSrKI~~ee-R~rLk~i~~~l~~~~ 358 (738)
+||++..+.++ ++..+.++..+.|..
T Consensus 11 Lgv~~~a~~~eik~ayr~la~~~HPD~ 37 (377)
T PRK14298 11 LGLSKDASVEDIKKAYRKLAMKYHPDK 37 (377)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHhCccc
Confidence 57888777665 788888888888764
No 134
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=21.08 E-value=59 Score=29.11 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=18.7
Q ss_pred HhHhCCceeCCCCcEEEEeccc
Q 004669 480 NNMLSKRVPLPNGGSLVIEQTE 501 (738)
Q Consensus 480 ~~al~rrV~LpsGGyLVIE~TE 501 (738)
-.=|.++||.+-|+|+++++.+
T Consensus 30 P~KfRk~iWIkrGd~VlV~p~~ 51 (78)
T cd05792 30 PTKFRKNIWIKRGDFVLVEPIE 51 (78)
T ss_pred chhhcccEEEEeCCEEEEEecc
Confidence 4457789999999999998866
No 135
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=20.93 E-value=98 Score=31.12 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=25.4
Q ss_pred cCCCCCCceeEechhhHHHHHHHHHHHHHHh
Q 004669 609 PCTCCQGTGRVEALETSFSKIEQEISRLLAM 639 (738)
Q Consensus 609 ~Cp~C~G~G~v~s~et~~~~ierei~~~~~~ 639 (738)
-||.|++.-...|-..++..+..++...+..
T Consensus 46 RCp~CQNqsIadSnA~IA~DlR~~V~e~l~e 76 (153)
T COG3088 46 RCPQCQNQSIADSNAPIARDLRHQVYELLQE 76 (153)
T ss_pred CCCcCCCCChhhhccHHHHHHHHHHHHHHHc
Confidence 5999999999888888888877777766554
No 136
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=20.82 E-value=2.3e+02 Score=22.68 Aligned_cols=39 Identities=8% Similarity=-0.003 Sum_probs=32.5
Q ss_pred EEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCC
Q 004669 655 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARG 693 (738)
Q Consensus 655 ~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~l~~d~~ 693 (738)
..+.+++..+.++...+...+..|+..++..|.|.....
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~ 40 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC
Confidence 467788889999887777799999999999999876544
No 137
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=20.41 E-value=1.2e+02 Score=38.65 Aligned_cols=35 Identities=17% Similarity=0.297 Sum_probs=26.2
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCceEe
Q 004669 548 IIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVS 583 (738)
Q Consensus 548 IIVIDFIDM~~~~~r~~V~~~Lk~alk~D~~kt~V~ 583 (738)
-||||=+-.. +.++..+.+.+..+|+.=...+.+.
T Consensus 203 ~vvvdr~~~~-~~~~~r~~~s~~~a~~~g~g~~~~~ 237 (943)
T PRK00349 203 EVVVDRLVVK-EDIRQRLADSIETALKLSDGLVVVE 237 (943)
T ss_pred EEEEEEEEeC-cchHHHHHHHHHHHHHhcCceEEEE
Confidence 4888877766 3477889999999999766665553
No 138
>PRK06921 hypothetical protein; Provisional
Probab=20.23 E-value=52 Score=35.26 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=11.4
Q ss_pred ccCCCCCCceeEe
Q 004669 608 EPCTCCQGTGRVE 620 (738)
Q Consensus 608 e~Cp~C~G~G~v~ 620 (738)
..||.|+++|.|.
T Consensus 33 ~~Cp~C~dtG~i~ 45 (266)
T PRK06921 33 YDCPKCKDRGIII 45 (266)
T ss_pred CCCCCCCCCEEEE
Confidence 4599999999994
No 139
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=20.07 E-value=1.4e+02 Score=39.48 Aligned_cols=78 Identities=17% Similarity=0.261 Sum_probs=58.9
Q ss_pred ccccCCCceEEEEEecCCCeEEEEEEECCEEEEEEeecCCC--CcccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 004669 68 ISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKS--NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (738)
Q Consensus 68 ~~~~~~m~~~IlIn~s~~~e~RvAvlEdgkL~El~iE~~~~--~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~ 145 (738)
+...... +.+.+|.. ..|+|+.-.+.|++...+-+.. +.+-|.||+|.|.++-+ ++|||.+-.+-.||++..
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 66667774 4699999999999996554432 23459999999999998 699999999999999887
Q ss_pred cCCCCC
Q 004669 146 HYREPF 151 (738)
Q Consensus 146 d~~~~~ 151 (738)
.+...|
T Consensus 631 ~~sd~~ 636 (1710)
T KOG1070|consen 631 EMSDDF 636 (1710)
T ss_pred hhhhhh
Confidence 665444
No 140
>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=20.07 E-value=1.7e+02 Score=27.37 Aligned_cols=56 Identities=11% Similarity=0.120 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHhcccCCCcEEEEcCCCC---ChhhHHHHHHHHHHHHhcCCCCceEeccCCce
Q 004669 530 LAAAKQIARELRLRDIGGIIVVDFIDMA---DDSNKRLVYEEVKKAVERDRSMVKVSELSRHG 589 (738)
Q Consensus 530 lEAA~EIARQLRLRnIgGIIVIDFIDM~---~~~~r~~V~~~Lk~alk~D~~kt~V~giT~LG 589 (738)
++++++.++++.-....|++++|++--. .+....+ ++.+++.+..+ +.+.||..+|
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 6677777778888899999999998631 1222334 57788888643 5677888777
Done!