Query 004498
Match_columns 748
No_of_seqs 258 out of 1108
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 00:25:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004498hhsearch_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 1102.1 57.9 487 74-703 1-488 (489)
2 PRK10811 rne ribonuclease E; R 100.0 4E-122 8E-127 1059.3 55.8 487 76-707 2-492 (1068)
3 TIGR00757 RNaseEG ribonuclease 100.0 2E-120 4E-125 998.2 46.7 412 88-631 1-414 (414)
4 COG1530 CafA Ribonucleases G a 100.0 8E-106 2E-110 898.5 43.2 480 75-705 1-484 (487)
5 PF10150 RNase_E_G: Ribonuclea 100.0 5E-80 1.1E-84 646.6 25.0 270 318-599 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.6 8.8E-16 1.9E-20 136.7 8.6 40 108-147 3-42 (88)
7 PF00575 S1: S1 RNA binding do 97.7 0.00016 3.5E-09 61.2 7.7 36 110-147 2-37 (74)
8 cd04472 S1_PNPase S1_PNPase: P 97.4 0.00068 1.5E-08 55.9 7.1 33 113-147 1-33 (68)
9 cd05704 S1_Rrp5_repeat_hs13 S1 97.2 0.0013 2.8E-08 56.4 7.0 35 112-147 3-37 (72)
10 COG1098 VacB Predicted RNA bin 97.2 0.00061 1.3E-08 64.9 5.3 36 111-148 4-39 (129)
11 cd05692 S1_RPS1_repeat_hs4 S1_ 97.0 0.0027 5.8E-08 52.0 7.4 33 113-147 1-33 (69)
12 smart00316 S1 Ribosomal protei 97.0 0.0024 5.2E-08 52.0 7.0 34 112-147 2-35 (72)
13 cd05698 S1_Rrp5_repeat_hs6_sc5 96.8 0.0041 8.9E-08 52.1 6.9 33 113-147 1-33 (70)
14 cd05685 S1_Tex S1_Tex: The C-t 96.6 0.0051 1.1E-07 50.3 6.2 33 113-147 1-33 (68)
15 cd04461 S1_Rrp5_repeat_hs8_sc7 96.6 0.0067 1.4E-07 53.0 6.9 36 110-147 12-47 (83)
16 PRK07252 hypothetical protein; 96.5 0.0081 1.8E-07 57.0 7.6 34 112-147 3-36 (120)
17 cd05707 S1_Rrp5_repeat_sc11 S1 96.4 0.0087 1.9E-07 50.1 6.4 33 113-147 1-33 (68)
18 PTZ00248 eukaryotic translatio 96.4 0.04 8.8E-07 60.4 12.9 34 112-147 17-52 (319)
19 cd05687 S1_RPS1_repeat_ec1_hs1 96.4 0.012 2.6E-07 49.4 6.9 33 113-147 1-33 (70)
20 cd05684 S1_DHX8_helicase S1_DH 96.4 0.012 2.6E-07 50.8 7.1 33 113-147 1-36 (79)
21 PRK08059 general stress protei 96.3 0.012 2.5E-07 55.9 7.2 36 110-147 5-40 (123)
22 cd05706 S1_Rrp5_repeat_sc10 S1 96.2 0.023 5E-07 48.0 7.8 34 112-147 3-36 (73)
23 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.1 0.019 4.1E-07 48.2 6.7 33 113-147 1-33 (69)
24 cd05686 S1_pNO40 S1_pNO40: pNO 96.0 0.03 6.6E-07 47.9 7.6 34 112-147 3-37 (73)
25 cd05691 S1_RPS1_repeat_ec6 S1_ 95.9 0.031 6.6E-07 46.8 6.9 33 113-147 1-33 (73)
26 cd04452 S1_IF2_alpha S1_IF2_al 95.8 0.033 7.1E-07 47.2 7.1 34 112-147 3-38 (76)
27 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.8 0.03 6.5E-07 47.9 6.9 34 113-147 1-35 (71)
28 COG0539 RpsA Ribosomal protein 95.8 0.018 4E-07 66.9 7.2 36 109-147 189-224 (541)
29 PRK08582 hypothetical protein; 95.7 0.031 6.8E-07 54.3 7.4 35 111-147 4-38 (139)
30 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.5 0.065 1.4E-06 46.9 7.7 35 111-147 5-39 (86)
31 cd05688 S1_RPS1_repeat_ec3 S1_ 95.4 0.04 8.8E-07 45.2 6.0 33 112-147 1-33 (68)
32 cd05694 S1_Rrp5_repeat_hs2_sc2 95.1 0.072 1.6E-06 46.2 6.9 35 111-147 3-38 (74)
33 cd05705 S1_Rrp5_repeat_hs14 S1 95.1 0.066 1.4E-06 46.4 6.4 35 111-147 2-36 (74)
34 PRK03987 translation initiatio 94.9 0.12 2.7E-06 55.2 9.3 35 111-147 7-43 (262)
35 PRK05807 hypothetical protein; 94.9 0.11 2.3E-06 50.5 8.0 34 111-147 4-37 (136)
36 cd04454 S1_Rrp4_like S1_Rrp4_l 94.9 0.12 2.5E-06 45.0 7.6 35 111-147 5-39 (82)
37 TIGR03591 polynuc_phos polyrib 94.9 0.056 1.2E-06 64.9 7.3 37 109-147 615-651 (684)
38 cd04455 S1_NusA S1_NusA: N-uti 94.8 0.11 2.4E-06 43.8 7.1 33 111-146 2-34 (67)
39 TIGR02696 pppGpp_PNP guanosine 94.8 0.059 1.3E-06 64.7 7.2 36 110-147 645-680 (719)
40 cd05690 S1_RPS1_repeat_ec5 S1_ 94.7 0.094 2E-06 43.6 6.2 33 113-147 1-33 (69)
41 cd05708 S1_Rrp5_repeat_sc12 S1 94.6 0.13 2.8E-06 43.4 7.0 34 112-147 2-36 (77)
42 PRK09521 exosome complex RNA-b 94.5 0.25 5.5E-06 50.0 10.0 37 109-147 61-107 (189)
43 PRK11824 polynucleotide phosph 94.5 0.11 2.3E-06 62.7 8.3 36 110-147 619-654 (693)
44 cd00164 S1_like S1_like: Ribos 94.1 0.12 2.6E-06 41.1 5.5 30 116-147 1-30 (65)
45 PRK04163 exosome complex RNA-b 93.7 0.52 1.1E-05 49.6 10.6 45 101-147 50-96 (235)
46 PLN00207 polyribonucleotide nu 93.1 0.19 4.2E-06 61.7 7.2 35 111-147 752-787 (891)
47 PRK13806 rpsA 30S ribosomal pr 91.3 0.47 1E-05 54.9 7.3 36 110-147 200-235 (491)
48 cd05689 S1_RPS1_repeat_ec4 S1_ 91.3 0.3 6.5E-06 41.1 4.3 34 112-147 3-36 (72)
49 PRK07400 30S ribosomal protein 91.2 0.48 1E-05 52.1 6.9 36 110-147 29-64 (318)
50 PRK07899 rpsA 30S ribosomal pr 91.2 0.46 1E-05 55.1 7.1 35 110-147 206-240 (486)
51 cd04473 S1_RecJ_like S1_RecJ_l 91.1 1.1 2.3E-05 38.9 7.6 35 110-146 14-48 (77)
52 cd05693 S1_Rrp5_repeat_hs1_sc1 90.7 0.4 8.7E-06 44.1 4.8 35 111-147 2-36 (100)
53 PRK14865 rnpA ribonuclease P; 90.6 1.3 2.7E-05 41.8 8.1 53 333-385 49-110 (116)
54 PRK07400 30S ribosomal protein 90.3 0.73 1.6E-05 50.6 7.2 39 106-147 190-228 (318)
55 COG1185 Pnp Polyribonucleotide 90.2 0.28 6.1E-06 58.3 4.2 40 106-147 613-652 (692)
56 PRK13806 rpsA 30S ribosomal pr 89.6 0.85 1.9E-05 52.8 7.4 38 108-147 288-325 (491)
57 PRK06299 rpsA 30S ribosomal pr 89.5 0.79 1.7E-05 53.6 7.2 35 110-147 199-233 (565)
58 cd05702 S1_Rrp5_repeat_hs11_sc 89.2 0.51 1.1E-05 39.9 4.0 34 113-148 1-34 (70)
59 COG0539 RpsA Ribosomal protein 89.1 0.62 1.4E-05 54.6 5.9 68 76-147 243-310 (541)
60 TIGR01953 NusA transcription t 89.0 4.7 0.0001 45.0 12.3 107 291-441 170-279 (341)
61 cd04465 S1_RPS1_repeat_ec2_hs2 88.8 0.48 1E-05 39.6 3.5 32 113-147 1-32 (67)
62 PRK00588 rnpA ribonuclease P; 88.8 1.9 4.1E-05 41.0 7.9 53 332-384 46-108 (118)
63 PRK12269 bifunctional cytidyla 88.3 1.4 3.1E-05 54.5 8.5 38 108-147 574-611 (863)
64 cd04471 S1_RNase_R S1_RNase_R: 88.0 0.64 1.4E-05 39.8 3.9 34 112-147 1-35 (83)
65 TIGR00717 rpsA ribosomal prote 87.4 1.5 3.2E-05 50.7 7.5 36 110-147 357-392 (516)
66 PRK07899 rpsA 30S ribosomal pr 86.7 1.6 3.5E-05 50.7 7.3 36 110-147 291-326 (486)
67 PRK03459 rnpA ribonuclease P; 86.2 3.4 7.4E-05 39.5 8.0 54 332-385 51-114 (122)
68 PRK06299 rpsA 30S ribosomal pr 86.1 1.7 3.8E-05 50.8 7.3 36 110-147 371-406 (565)
69 PRK12269 bifunctional cytidyla 86.0 1.8 4E-05 53.6 7.6 36 110-148 491-526 (863)
70 PRK00396 rnpA ribonuclease P; 85.9 3.6 7.8E-05 39.9 8.1 58 333-393 50-117 (130)
71 TIGR00717 rpsA ribosomal prote 85.0 2 4.3E-05 49.6 6.9 36 110-147 270-305 (516)
72 PRK06676 rpsA 30S ribosomal pr 84.7 2.4 5.1E-05 47.4 7.2 36 110-148 190-225 (390)
73 PRK09202 nusA transcription el 84.4 2.2 4.7E-05 49.5 6.8 108 290-441 171-281 (470)
74 PRK00499 rnpA ribonuclease P; 83.4 6.1 0.00013 37.1 8.2 54 333-386 42-105 (114)
75 PRK04390 rnpA ribonuclease P; 82.7 6.5 0.00014 37.4 8.2 53 333-385 48-110 (120)
76 PRK01313 rnpA ribonuclease P; 82.6 6 0.00013 38.4 8.0 52 333-384 51-113 (129)
77 COG2183 Tex Transcriptional ac 82.2 2 4.4E-05 52.2 5.6 37 109-147 655-691 (780)
78 PRK06676 rpsA 30S ribosomal pr 82.0 4.1 8.8E-05 45.5 7.6 36 110-147 15-51 (390)
79 PRK00087 4-hydroxy-3-methylbut 79.0 4.1 8.9E-05 48.9 6.8 34 111-147 476-509 (647)
80 PRK00730 rnpA ribonuclease P; 78.9 8.5 0.00018 37.9 7.7 53 332-385 49-110 (138)
81 PRK01903 rnpA ribonuclease P; 78.4 11 0.00025 36.6 8.4 53 333-385 54-129 (133)
82 cd05703 S1_Rrp5_repeat_hs12_sc 76.2 3.3 7.2E-05 35.6 3.7 33 113-147 1-33 (73)
83 PRK04820 rnpA ribonuclease P; 74.9 14 0.00031 36.5 8.1 53 333-385 52-114 (145)
84 PRK01492 rnpA ribonuclease P; 74.9 13 0.00027 35.5 7.5 53 332-384 49-115 (118)
85 PRK12327 nusA transcription el 74.4 7.5 0.00016 43.8 6.8 33 111-146 133-165 (362)
86 PRK01732 rnpA ribonuclease P; 73.9 10 0.00022 35.8 6.6 53 333-385 49-111 (114)
87 TIGR00188 rnpA ribonuclease P 73.8 9.5 0.00021 35.3 6.3 51 333-383 45-104 (105)
88 PRK00038 rnpA ribonuclease P; 73.1 19 0.00041 34.7 8.2 58 332-389 53-121 (123)
89 PRK00087 4-hydroxy-3-methylbut 71.8 10 0.00022 45.7 7.5 36 110-147 560-595 (647)
90 PRK11642 exoribonuclease R; Pr 69.5 12 0.00025 46.5 7.5 36 111-148 642-678 (813)
91 PRK03031 rnpA ribonuclease P; 69.3 26 0.00057 33.3 8.3 53 333-385 51-114 (122)
92 cd05695 S1_Rrp5_repeat_hs3 S1_ 68.8 21 0.00045 30.1 6.7 32 113-146 1-32 (66)
93 TIGR02063 RNase_R ribonuclease 68.5 11 0.00024 45.7 7.0 35 111-147 626-661 (709)
94 COG0594 RnpA RNase P protein c 67.3 28 0.00061 33.1 8.0 53 333-385 45-107 (117)
95 PF00684 DnaJ_CXXCXGXG: DnaJ c 67.0 4.4 9.5E-05 34.5 2.3 31 588-620 24-54 (66)
96 PF07092 DUF1356: Protein of u 66.4 2.4 5.2E-05 45.1 0.7 64 584-668 24-87 (238)
97 cd05791 S1_CSL4 S1_CSL4: CSL4, 65.1 8.6 0.00019 34.8 4.0 37 111-149 5-49 (92)
98 cd05790 S1_Rrp40 S1_Rrp40: Rrp 62.2 37 0.00081 30.8 7.4 33 111-145 5-37 (86)
99 PF00825 Ribonuclease_P: Ribon 60.7 21 0.00046 33.0 5.8 53 333-385 46-109 (111)
100 TIGR03147 cyt_nit_nrfF cytochr 60.5 13 0.00029 36.1 4.5 56 608-691 41-96 (126)
101 TIGR00358 3_prime_RNase VacB a 58.9 22 0.00047 43.0 7.0 35 111-147 571-606 (654)
102 PRK10144 formate-dependent nit 58.3 15 0.00033 35.7 4.5 56 608-691 41-96 (126)
103 cd04460 S1_RpoE S1_RpoE: RpoE, 57.0 13 0.00029 33.5 3.7 31 115-148 2-32 (99)
104 COG2996 Predicted RNA-bindinin 57.0 22 0.00047 38.8 5.8 37 110-147 71-107 (287)
105 PRK12328 nusA transcription el 53.0 35 0.00075 38.8 6.9 188 290-536 176-368 (374)
106 TIGR00448 rpoE DNA-directed RN 44.0 30 0.00065 34.9 4.2 36 110-148 79-114 (179)
107 PF03918 CcmH: Cytochrome C bi 39.7 27 0.00058 34.7 3.1 33 608-640 41-73 (148)
108 TIGR02642 phage_xxxx uncharact 39.6 15 0.00033 37.8 1.4 18 608-625 116-133 (186)
109 COG1093 SUI2 Translation initi 37.6 29 0.00063 37.6 3.1 35 111-147 10-46 (269)
110 PHA02945 interferon resistance 36.0 1.1E+02 0.0024 28.2 6.1 32 112-146 11-44 (88)
111 PTZ00162 DNA-directed RNA poly 35.6 1.2E+02 0.0027 30.8 7.1 35 110-147 79-113 (176)
112 PF13509 S1_2: S1 domain; PDB: 34.7 1.2E+02 0.0026 25.4 5.8 33 112-146 1-33 (61)
113 PRK08563 DNA-directed RNA poly 33.6 47 0.001 33.5 3.8 35 110-147 79-113 (187)
114 TIGR02642 phage_xxxx uncharact 33.0 22 0.00048 36.7 1.4 16 607-622 99-114 (186)
115 PF02108 FliH: Flagellar assem 33.0 2.8E+02 0.006 25.5 8.6 45 653-703 68-112 (128)
116 PF00013 KH_1: KH domain syndr 31.7 1.1E+02 0.0024 24.8 5.0 37 655-691 2-38 (60)
117 PRK12329 nusA transcription el 29.8 1.3E+02 0.0028 35.1 6.8 33 110-144 150-187 (449)
118 PRK06032 fliH flagellar assemb 29.4 2.1E+02 0.0045 29.4 7.7 47 653-703 128-176 (199)
119 TIGR02499 HrpE_YscL_not type I 27.5 2.9E+02 0.0063 26.8 8.1 45 653-703 114-158 (166)
120 PRK06937 type III secretion sy 26.6 2.1E+02 0.0045 29.5 7.1 49 653-703 131-179 (204)
121 KOG1070 rRNA processing protei 26.1 91 0.002 41.0 5.1 78 68-151 557-636 (1710)
122 COG0484 DnaJ DnaJ-class molecu 26.0 27 0.00059 39.6 0.6 25 333-357 10-35 (371)
123 KOG2925 Predicted translation 25.7 36 0.00078 34.2 1.3 24 481-504 53-76 (167)
124 PRK09098 type III secretion sy 25.6 2.4E+02 0.0052 30.0 7.5 47 653-703 151-199 (233)
125 PF04472 DUF552: Protein of un 25.2 1.3E+02 0.0029 25.9 4.7 41 531-575 10-50 (73)
126 COG3088 CcmH Uncharacterized p 25.2 1E+02 0.0022 31.1 4.3 31 609-639 46-76 (153)
127 PF08800 VirE_N: VirE N-termin 24.8 1.7E+02 0.0036 28.4 5.7 51 541-596 26-77 (136)
128 TIGR00630 uvra excinuclease AB 23.8 1E+02 0.0022 39.1 5.0 35 548-583 199-233 (924)
129 COG0484 DnaJ DnaJ-class molecu 22.9 33 0.00072 38.9 0.6 21 366-386 12-32 (371)
130 COG1568 Predicted methyltransf 22.5 65 0.0014 35.7 2.6 30 606-638 90-119 (354)
131 PF11314 DUF3117: Protein of u 21.6 66 0.0014 26.6 1.8 15 486-500 22-36 (51)
132 PRK14296 chaperone protein Dna 21.2 57 0.0012 36.8 2.0 25 333-357 10-35 (372)
133 PF12401 DUF3662: Protein of u 20.9 5.6E+02 0.012 24.3 8.3 50 653-702 53-115 (116)
134 TIGR03825 FliH_bacil flagellar 20.8 3.9E+02 0.0084 28.5 8.0 47 653-703 176-224 (255)
No 1
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=1.5e-131 Score=1102.07 Aligned_cols=487 Identities=31% Similarity=0.520 Sum_probs=451.1
Q ss_pred CceEEEEEecCCCeEEEEEEECCEEeEEEeecCCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEecccCCCCcC
Q 004498 74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF 153 (748)
Q Consensus 74 m~~~IlIn~s~~~e~RvAvlEdg~LvEl~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~ 153 (748)
|+++|+||+.+ .|+|+|++|||+|+||++|+.+...++||||+|+|+||+|||||||||||.+|+||||++|+.+++.+
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 79999999999999999999999999999999999999999999999999999999999996321100
Q ss_pred CcccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccchhcccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 004498 154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD 233 (748)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (748)
.. . ++ ..
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 004498 234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL 313 (748)
Q Consensus 234 ~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~g~KGp~L 313 (748)
. . ...++...|++||+|||||+|||+|+|||+|
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 0013456799999999999999999999999
Q ss_pred eecceecceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 004498 314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH 392 (748)
Q Consensus 314 T~~IsL~GRylVl~P~~~~vgvSrKI~~e-eR~rLk~i~~~l~p~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~~ 392 (748)
|++|||||||+||||+++++||||||.++ +|.+|+.++..+.++++|+||||+|+++++++|.+|+++|.++|++|.++
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 004498 393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472 (748)
Q Consensus 393 a~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVD~~~~y~~i~~~l~~~~P~~~~~i~ly~~~~pLF~~ 472 (748)
++.+ ++|.|||++.+++.+++||++++++++|+||+++.|+++++|+..++|+...++++|++..|||+.
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 9765 689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHhHhCCceeCCCCceEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 004498 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (748)
Q Consensus 473 y~Ie~qIe~al~r~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~l~tNlEAA~EIARQLRLRnIGGIIVID 552 (748)
|+|+.+|+++++++||||||||||||+||||||||||||++ .+++++++|+++||+|||+||||||||||||||||||
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 4667999999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhhHHHHHHH
Q 004498 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (748)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~giT~LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~i~re 632 (748)
||||+++++|++|+++|+++|++|+++++|+|||+||||||||||+|+||.++++++||+|+|+|+|+|.++++++|+|+
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 004498 633 ISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 633 i~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~l~~~~~~~~~~y~i~~ 703 (748)
|.+...... ..++.+.+||.|++||.+.++.++..|+..+|.+|.|..++.+++++|+|..
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 998765422 2469999999999999988888899999999999999999999999999864
No 2
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=3.8e-122 Score=1059.30 Aligned_cols=487 Identities=31% Similarity=0.532 Sum_probs=451.9
Q ss_pred eEEEEEecCCCeEEEEEEECCEEeEEEeecCCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEecccCCCCcCCc
Q 004498 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP 155 (748)
Q Consensus 76 ~~IlIn~s~~~e~RvAvlEdg~LvEl~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~~ 155 (748)
++||||.....+.|+||++||+|.||+||+..+...+||||+|+|+||+|||+|||||||.+++|||+++|+..+++..+
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 68999998447899999999999999999988888999999999999999999999999999999999999854432110
Q ss_pred ccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccchhcccCCCCCCCCCCCcchhhhhhccCCcccCCCC
Q 004498 156 FRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGE 235 (748)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (748)
+..
T Consensus 82 ~~~----------------------------------------------------------------------------- 84 (1068)
T PRK10811 82 YSA----------------------------------------------------------------------------- 84 (1068)
T ss_pred ccc-----------------------------------------------------------------------------
Confidence 000
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeee
Q 004498 236 PEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTA 315 (748)
Q Consensus 236 ~e~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~g~KGp~LT~ 315 (748)
+ ...++...|++||+|||||+||++++|||+||+
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 cceecceeEEEeeCCCc-eeeecCCChHHHHHHHHHHHhh-CCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 004498 316 YPKLRSRFWILITSCDR-IGVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (748)
Q Consensus 316 ~IsL~GRylVl~P~~~~-vgvSrKI~~eeR~rLk~i~~~l-~p~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~~a 393 (748)
+|||+||||||||++++ +||||||.+++|.+|+.++..+ .++++|+||||+|.|++.++|.+||++|...|+.|++++
T Consensus 119 ~ISLpGRYLVLtP~~~~~IgISRKI~deeR~rLkeil~~l~lpe~~GIIVRTaAegAseE~L~~ELe~L~~~w~~I~k~a 198 (1068)
T PRK10811 119 FISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAA 198 (1068)
T ss_pred eEEecceeEEEeCCCCCcceecCCCchHHHHHHHHHHHhhccCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998 7999999988899999999987 788999999999999999999999999999999999998
Q ss_pred HHhhhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEEEcChHHHHHHHHHHHhh-CCCccCceeeccCCCCcccc
Q 004498 394 KSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLFDK 472 (748)
Q Consensus 394 ~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVD~~~~y~~i~~~l~~~-~P~~~~~i~ly~~~~pLF~~ 472 (748)
..+ ++|.|||++.+++.+++|||+.+++++|+||+++.|+.++.|+..+ .|++..+|++|.+..|||+.
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 004498 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (748)
Q Consensus 473 y~Ie~qIe~al~r~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~l~tNlEAA~EIARQLRLRnIGGIIVID 552 (748)
|+|+.+|++||+++||||||||||||+||||||||||||++ .++.+.++|+|+||++||+||||||||||||||||||
T Consensus 269 YgIE~qIE~aL~rrV~L~sGG~LvIE~TEALtvIDVNSGk~--~~g~d~eet~lktNleAA~EIARQLRLRnLgGIIVID 346 (1068)
T PRK10811 269 YQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARA--TRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVID 346 (1068)
T ss_pred cCHHHHHHHHhCCcEECCCCCEEEEeccceEEEEEccCCCc--CCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEE
Confidence 99999999999999999999999999999999999999985 4567899999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhhHHHHHHH
Q 004498 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (748)
Q Consensus 553 FIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~giT~LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~i~re 632 (748)
||||+.++|+++|++.|+++|++|+.+++|+|||+||||||||||.|+||.+.++++||+|.|+|+|++.+++++.|.|+
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-HhcCCeEEEEeCCCCCCcceEEEEecCC
Q 004498 633 ISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLS-SSLKAWILLKVARGFTRGAFEVIPYTDD 707 (748)
Q Consensus 633 i~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v~~~L~~~~~~~l~~Le-~~~~~~I~l~~~~~~~~~~y~i~~~~~~ 707 (748)
|.+.+...+ ...+.+.+++.+++||+++++..+..|| +.+|+.|.|.+++.++.++|+|.+++..
T Consensus 427 I~re~~~~~----------~~~~~i~~~~~va~~l~~~~~~~~~~ie~e~~g~~i~I~~n~~~~~e~y~v~rvr~g 492 (1068)
T PRK10811 427 IEEEALKEN----------TQEVHAIVPVPIASYLLNEKRSAVNAIETRQGGVRCVIVPNDQMQTPHYSVLRVRKG 492 (1068)
T ss_pred HHHHHhhcc----------cccEEEEECHHHHHHHhhhhhhHHHHHhhhhcCceEEEEecCcCCcccceEEEEecC
Confidence 999876543 2479999999999999999999999999 9999999999999999999999998764
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=1.9e-120 Score=998.20 Aligned_cols=412 Identities=39% Similarity=0.650 Sum_probs=381.7
Q ss_pred EEEEEEECCEEeEEEeecCCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEecccCCCCcCCcccccchhhhccc
Q 004498 88 QRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNG 167 (748)
Q Consensus 88 ~RvAvlEdg~LvEl~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~~~~~~~~~~~~~~ 167 (748)
+|+||+|||+|+||++|+.....++||||+|+|++|+|||||||||||.+++||||++|+..++...+
T Consensus 1 ~r~Alledg~l~e~~ie~~~~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~------------ 68 (414)
T TIGR00757 1 TRVALVEGGRLFDLIIERPKSRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLA------------ 68 (414)
T ss_pred CEEEEEECCEEEEEEEecCcCcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccc------------
Confidence 59999999999999999999999999999999999999999999999999999999998632110000
Q ss_pred cchhhhhhhhcccCCCCCCCCcchhhhcccccchhcccCCCCCCCCCCCcchhhhhhccCCcccCCCCCCccccccccCC
Q 004498 168 SASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGD 247 (748)
Q Consensus 168 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 247 (748)
. ++ ..
T Consensus 69 ----------------------------------------~-~~-------------~~--------------------- 73 (414)
T TIGR00757 69 ----------------------------------------P-AE-------------AK--------------------- 73 (414)
T ss_pred ----------------------------------------c-cc-------------cc---------------------
Confidence 0 00 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCceeeecceecceeEEEe
Q 004498 248 HHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILI 327 (748)
Q Consensus 248 ~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~g~KGp~LT~~IsL~GRylVl~ 327 (748)
. . ...++...|++||+|+|||+|||+++|||+||++|||||||+|||
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 001244679999999999999999999999999999999999999
Q ss_pred eCCCceeeecCCChH-HHHHHHHHHHh-hCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcC
Q 004498 328 TSCDRIGVSRKITGV-ERTRLKVIAKT-LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVE 405 (748)
Q Consensus 328 P~~~~vgvSrKI~~e-eR~rLk~i~~~-l~p~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~ 405 (748)
|+++++||||||.++ +|.+|++++.. +.|+++|+||||+|+++++++|.+|+++|.++|+.|.++++.+
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 8888999999999999999999999999999999999998765
Q ss_pred CCCceeEeecCCchhhhhhhhccCCccEEEEcChHHHHHHHHHHHhhCCCccCceeeccCCCCcccccCHHHHHHhHhCC
Q 004498 406 GAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSK 485 (748)
Q Consensus 406 ~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVD~~~~y~~i~~~l~~~~P~~~~~i~ly~~~~pLF~~y~Ie~qIe~al~r 485 (748)
++|.|||++.+++.+++||++++++++|+||+++.|+++++|++.+.|....+|++|.+..|+|+.|+|+.+|++++++
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 004498 486 RVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLV 565 (748)
Q Consensus 486 ~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~l~tNlEAA~EIARQLRLRnIGGIIVIDFIDM~~~~~r~~V 565 (748)
+||||||||||||+||||||||||||++ +++.++|+|+++||+|||+||||||||||||||||||||||++++||++|
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 45679999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhhHHHHHH
Q 004498 566 YEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (748)
Q Consensus 566 ~~~Lk~alk~Dr~k~~V~giT~LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~i~r 631 (748)
++.|+++|++|+++++|+|||+||||||||||.|+||.++++++||+|+|+|+|+|.++++++|+|
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=8.2e-106 Score=898.48 Aligned_cols=480 Identities=36% Similarity=0.613 Sum_probs=445.2
Q ss_pred ceEEEEEecCCCeEEEEEEECCEEeEEEeecCCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEecccCCCCcCC
Q 004498 75 STVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFP 154 (748)
Q Consensus 75 ~~~IlIn~s~~~e~RvAvlEdg~LvEl~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~~~~~~~ 154 (748)
++.||||+++ .|+|||++++|.|.||++|+....+++||||+|||+||+|||||||||||.+||||||++++.+ +
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 8999999999999999999999999999999999999999999999999999999999999732 1
Q ss_pred cccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccchhcccCCCCCCCCCCCcchhhhhhccCCcccCCC
Q 004498 155 PFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDG 234 (748)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (748)
|.. . .
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 004498 235 EPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLT 314 (748)
Q Consensus 235 ~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~g~KGp~LT 314 (748)
..++...++.||.++|||.|+|+|+|||+||
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 ecceecceeEEEeeCCCcee-eecCCCh-HHHHHHHHHHHhhCCC-CceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 004498 315 AYPKLRSRFWILITSCDRIG-VSRKITG-VERTRLKVIAKTLQPE-GFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME 391 (748)
Q Consensus 315 ~~IsL~GRylVl~P~~~~vg-vSrKI~~-eeR~rLk~i~~~l~p~-~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~ 391 (748)
++||++|||+||||+++++| +|+||++ .+|++|+.++..+.+. ++|+|+||+|+|++.++|.+|+++|...|+.|..
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 99999999999999999997 9999998 5799999999998754 5899999999999999999999999999999999
Q ss_pred HHHHhhhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEEEcChHHHHHHHHHHHhhCCCccCceeeccCCCCccc
Q 004498 392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFD 471 (748)
Q Consensus 392 ~a~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVD~~~~y~~i~~~l~~~~P~~~~~i~ly~~~~pLF~ 471 (748)
.+.+. ++|.+||++.+++.+++|||+..++.+|+||+...|..+++|+..++|+...++++|.+..|+|+
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 004498 472 KFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVV 551 (748)
Q Consensus 472 ~y~Ie~qIe~al~r~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~l~tNlEAA~EIARQLRLRnIGGIIVI 551 (748)
.|+++.+|+++++|+||||||||||||+|||||+||||||+++ +..+.++|+++||+|||.||||||||||+||||+|
T Consensus 262 ~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~~--~~~~~eeta~~tNleAa~eiarqlrlR~lgGiIiI 339 (487)
T COG1530 262 LFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFT--GAGDLEETAVNTNLEAAEEIARQLRLRNLGGIIII 339 (487)
T ss_pred hhhHHHHHHHhhhheEecCCCCceeEeccceeEEEEccCcccc--ccCchHHhhhhhhHHHHHHHHHHHhhcccCCeEEE
Confidence 9999999999999999999999999999999999999999854 34569999999999999999999999999999999
Q ss_pred EcCCCCChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhhHHHHHH
Q 004498 552 DFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (748)
Q Consensus 552 DFIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~giT~LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~i~r 631 (748)
|||||...++++.|+..|+++|+.|++++++.+||+|||+||||||.++||.+.++++||+|.|+|++++.+++++.+.|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred HHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcC-CeEEEEeCCCCCCcceEEEEec
Q 004498 632 EISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLK-AWILLKVARGFTRGAFEVIPYT 705 (748)
Q Consensus 632 ei~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~-~~I~l~~~~~~~~~~y~i~~~~ 705 (748)
.|....... .+..+.+.+++.++.|+.++++..+..+|...+ ..+.+.+++.++.++|++....
T Consensus 420 ~i~~~~~~~----------~~~~~~~~~~~~v~~~~~~~~~~~i~~~e~~~~~~~i~~~~~~~~~~~~~~~~~~~ 484 (487)
T COG1530 420 YIEEEADIN----------KTPEVGVEVPPAVAKYLLNEERGAIAELELFKGYLRVRLRVDDRVEQEQYEVVRLR 484 (487)
T ss_pred cchhhhccc----------cCccceEEechhhhhhhcccccchhhHHHhhccceeEEEeechhhcccceeEeeec
Confidence 887654322 134688999999999999999888999999999 9999999999999999997654
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=5e-80 Score=646.59 Aligned_cols=270 Identities=48% Similarity=0.754 Sum_probs=221.9
Q ss_pred eecceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 004498 318 KLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSA 396 (748)
Q Consensus 318 sL~GRylVl~P~~~~vgvSrKI~~e-eR~rLk~i~~~l~p~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~ 396 (748)
||||||+||+|+++++||||||+++ +|++|+++++.+.++++|+||||+|+++++++|.+|+++|.++|++|++++...
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 799999999999999999999999999999999999999999999999998664
Q ss_pred hhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEEEcChHHHHHHHHHHHhhCCCccCceeeccCCCCcccccCHH
Q 004498 397 ALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIE 476 (748)
Q Consensus 397 ~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVD~~~~y~~i~~~l~~~~P~~~~~i~ly~~~~pLF~~y~Ie 476 (748)
++|+|||++.+++.+++||++.+++++|+||+++.|+++++|++.+.|++..+|++|.+..|+|+.|+|+
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 5899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhCCceeCCCCceEEEecccceEEEEecCCCCCCCCCCCHhhhHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCC
Q 004498 477 EEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDM 556 (748)
Q Consensus 477 ~qIe~al~r~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~l~tNlEAA~EIARQLRLRnIGGIIVIDFIDM 556 (748)
.+|+++++++||||||||||||+||||||||||||++ .++.+.++|+++||+|||+||||||||||||||||||||||
T Consensus 151 ~~i~~~~~~~v~l~~Gg~l~Ie~TeAlt~IDVNsg~~--~~~~~~~~~~~~~N~~Aa~ei~rqirLR~i~GiIviDfi~m 228 (271)
T PF10150_consen 151 EAIEKALSRRVWLPSGGYLVIEQTEALTVIDVNSGKY--TGKKNSEETALKTNLEAAKEIARQIRLRNIGGIIVIDFIDM 228 (271)
T ss_dssp HHHHHTTSSEEE-TTS-EEEEEE-SS-EEEEEE-----------HHHHHHHHHHHHHHHHHHHHHHHT--EEEEEE----
T ss_pred HHHHHHhCCeEEeCCCeEEEEecCceEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCC
Confidence 9999999999999999999999999999999999985 45668999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHhcCCCCceEeccCCceeEEEeecCCC
Q 004498 557 ADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVR 599 (748)
Q Consensus 557 ~~~~~r~~V~~~Lk~alk~Dr~k~~V~giT~LGLvEmTRkR~r 599 (748)
++++++++|++.|+++|++|+++++|+|||+||||||||||.|
T Consensus 229 ~~~~~~~~l~~~~~~~~~~d~~~~~v~~~t~lGl~e~tRkR~r 271 (271)
T PF10150_consen 229 KDKKDREKLLEALKEALKKDPAKTRVLGFTKLGLLEITRKRRR 271 (271)
T ss_dssp SSHHHHHHHHHHHHHHTTT-SS-EEEEEE-TTSEEEEEE--S-
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCcEEecCCCCeeEEEEEecCC
Confidence 9999999999999999999999999999999999999999986
No 6
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.62 E-value=8.8e-16 Score=136.67 Aligned_cols=40 Identities=30% Similarity=0.615 Sum_probs=37.2
Q ss_pred CCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+..+|+||.|+|++|.|.|.|||||+|.+++||||++++
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=97.68 E-value=0.00016 Score=61.18 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=33.3
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...|.||.|+|.+|.+ .++||++|.+..||+++++.
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=0.00068 Score=55.87 Aligned_cols=33 Identities=33% Similarity=0.479 Sum_probs=30.7
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|++|.|+|++|.| .++||+|+...+|||++.+.
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=97.17 E-value=0.0013 Score=56.43 Aligned_cols=35 Identities=34% Similarity=0.543 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+|.||.|+|++|.+. -+|||+++.+..||+|++++
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 35799999999999999875
No 10
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=97.15 E-value=0.00061 Score=64.86 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=33.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
-+|+++.|+|+.|.|- +|||++-.+..|+.|++++.
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 89999999999999999874
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=51.99 Aligned_cols=33 Identities=42% Similarity=0.619 Sum_probs=30.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|++|.|+|+++.+ .++||+++....||||.++.
T Consensus 1 G~~~~g~V~~i~~--~g~~v~i~~~~~g~l~~~~l 33 (69)
T cd05692 1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQI 33 (69)
T ss_pred CCEEEEEEEEEEe--eeEEEEECCCCEEEEEhHHc
Confidence 7899999999998 69999999999999998764
No 12
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.02 E-value=0.0024 Score=51.97 Aligned_cols=34 Identities=38% Similarity=0.612 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.|.+|.|+|.++.+ +++||++|.+..|||++++.
T Consensus 2 ~G~~v~g~V~~v~~--~g~~v~i~~~~~g~l~~~~~ 35 (72)
T smart00316 2 VGDVVEGTVTEITP--FGAFVDLGNGVEGLIPISEL 35 (72)
T ss_pred CCCEEEEEEEEEEc--cEEEEEeCCCCEEEEEHHHC
Confidence 69999999999999 79999999999999988774
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=96.81 E-value=0.0041 Score=52.11 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=30.4
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.+ .++||+++.+..||+|+++.
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 79999999899999998774
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=96.64 E-value=0.0051 Score=50.29 Aligned_cols=33 Identities=39% Similarity=0.552 Sum_probs=30.1
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|++|.|+|.+|.+ .++||+++....||+|..+.
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 69999999999999988764
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=96.60 E-value=0.0067 Score=52.95 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=32.8
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
-.+|.||.|+|++|.+ .++||+++.+..||+|+.+.
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=96.54 E-value=0.0081 Score=57.03 Aligned_cols=34 Identities=29% Similarity=0.470 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+|++|.|+|++|.+ .+|||+|+.+..||+|+++.
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
>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=96.43 E-value=0.0087 Score=50.10 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.+ .++||+++.+..||+|++++
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 18
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.40 E-value=0.04 Score=60.43 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=31.1
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d~ 147 (748)
+|++..|+|++|.+ .+|||+++ .+..||+|++++
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 19
>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=96.38 E-value=0.012 Score=49.40 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=30.3
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|+||.|+|.+|.+. +|||++|....|||+.++.
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 9999999999999998764
No 20
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=96.38 E-value=0.012 Score=50.81 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=29.6
Q ss_pred CCeEEEEEeeecCCcceEEeccc---CCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIG---NSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG---~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.|. ++||+|+ .+.+||+|+++.
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 21
>PRK08059 general stress protein 13; Validated
Probab=96.32 E-value=0.012 Score=55.86 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=32.7
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.+|.|+|.+|.+ .++||+|+.+..||+|+++.
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=96.21 E-value=0.023 Score=48.04 Aligned_cols=34 Identities=24% Similarity=0.209 Sum_probs=31.2
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+|.||.|+|++|.+ .++||+++.+..||+|+.+.
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 48999999999999999774
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=96.10 E-value=0.019 Score=48.21 Aligned_cols=33 Identities=30% Similarity=0.503 Sum_probs=29.8
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.+ .++||+++.+..||+|+.+.
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 49999999999999988764
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=47.89 Aligned_cols=34 Identities=29% Similarity=0.487 Sum_probs=29.7
Q ss_pred cCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdI-G~~r~aFL~~~d~ 147 (748)
+|.+|.|+|++|.+ .++||++ |....||+|+++.
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 3347999999764
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=95.86 E-value=0.031 Score=46.84 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=30.1
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.+ .++||+++.+..||+|+++.
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 89999999999999998764
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=95.84 E-value=0.033 Score=47.22 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.8
Q ss_pred cCCeEEEEEeeecCCcceEEecccC--CcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~--~r~aFL~~~d~ 147 (748)
.|.+|.|+|++|.+ .++||++.. +..||||+++.
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 58999998774
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=95.84 E-value=0.03 Score=47.86 Aligned_cols=34 Identities=26% Similarity=0.328 Sum_probs=29.3
Q ss_pred CCeEE-EEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~-GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.||. |+|++|... -+|||+++.+.+||+|+++.
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 67999999999999999864
No 28
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.82 E-value=0.018 Score=66.86 Aligned_cols=36 Identities=33% Similarity=0.536 Sum_probs=33.4
Q ss_pred CCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.-.+|.+..|+|++|-| .+||||||. -+|+||++++
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 29
>PRK08582 hypothetical protein; Provisional
Probab=95.75 E-value=0.031 Score=54.34 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=32.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|.+|.|+|+.|.+. +|||+|+.+..||+|++++
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 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=95.45 E-value=0.065 Score=46.90 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=31.7
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..|+|+.|+|+++.+ .++||+||.+..||||+++.
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=95.44 E-value=0.04 Score=45.16 Aligned_cols=33 Identities=30% Similarity=0.475 Sum_probs=29.1
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.|.+|.|+|+++.+. ++||+++ +-.||||..+.
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=95.15 E-value=0.072 Score=46.23 Aligned_cols=35 Identities=20% Similarity=0.269 Sum_probs=29.7
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG-~~r~aFL~~~d~ 147 (748)
..|.++.|.|++|.+ .+||||+| .+-.|||+.+++
T Consensus 3 ~~G~~v~g~V~si~d--~G~~v~~g~~gv~Gfl~~~~~ 38 (74)
T cd05694 3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKDA 38 (74)
T ss_pred CCCCEEEEEEEEEeC--CEEEEEeCCCCcEEEEEHHHC
Confidence 369999999999996 59999999 467999987653
No 33
>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=95.08 E-value=0.066 Score=46.38 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=31.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|++..|+|+++.+ .+|||+++.+-.||+|+.+.
T Consensus 2 k~G~~V~g~V~~i~~--~G~fV~l~~~v~G~v~~~~l 36 (74)
T cd05705 2 KEGQLLRGYVSSVTK--QGVFFRLSSSIVGRVLFQNV 36 (74)
T ss_pred CCCCEEEEEEEEEeC--CcEEEEeCCCCEEEEEHHHc
Confidence 379999999999974 57999999999999998775
No 34
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=94.91 E-value=0.12 Score=55.23 Aligned_cols=35 Identities=20% Similarity=0.401 Sum_probs=31.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC--CcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~--~r~aFL~~~d~ 147 (748)
-+|+++.|+|++|.+ .+|||++.. +..||+|+++.
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 78999999875
No 35
>PRK05807 hypothetical protein; Provisional
Probab=94.89 E-value=0.11 Score=50.46 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=30.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|.+|.|+|+.|.| .+|||++ .+..||+|+++.
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 36
>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=94.88 E-value=0.12 Score=45.03 Aligned_cols=35 Identities=17% Similarity=0.169 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|+|=.|+|++| .-+.+|||||..-.|||++.+.
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 37
>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=0.056 Score=64.91 Aligned_cols=37 Identities=27% Similarity=0.453 Sum_probs=33.7
Q ss_pred CCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...+|.||.|+|++|.+ .+|||+|..+..||||++++
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 38
>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=94.84 E-value=0.11 Score=43.78 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=28.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (748)
+.|.|..|+|.++.+ +.+|||||. -.|||+.++
T Consensus 2 ~~g~iV~G~V~~~~~--~~~~vdig~-~eg~lp~~e 34 (67)
T cd04455 2 REGEIVTGIVKRVDR--GNVIVDLGK-VEAILPKKE 34 (67)
T ss_pred CCCCEEEEEEEEEcC--CCEEEEcCC-eEEEeeHHH
Confidence 579999999999999 579999987 899997655
No 39
>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=94.81 E-value=0.059 Score=64.66 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=33.2
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.||.|+|++|.+ -+|||+|+.+..||||++++
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 4699999999999998 69999999999999999875
No 40
>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=94.70 E-value=0.094 Score=43.58 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.+|.|+|++|.| -++||+++.+.+||+|+++.
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 41
>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=94.63 E-value=0.13 Score=43.44 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=30.1
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (748)
+|.+|.|+|++|.+ .++||+++. ...||+|+++.
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 42
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=94.51 E-value=0.25 Score=50.04 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=29.6
Q ss_pred CCccCCeEEEEEeeecCCcceEEecccC----------CcceeeEeccc
Q 004498 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGN----------SRPSLMDIKHY 147 (748)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~----------~r~aFL~~~d~ 147 (748)
...+|+|+.|+|++|.+ ..|||||+. +..||||+.+.
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 45677777654
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.45 E-value=0.11 Score=62.67 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=33.2
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.+|.|+|++|.+ .+|||+|+.+..||+|+++.
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 79999999999999999875
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=94.14 E-value=0.12 Score=41.12 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=26.0
Q ss_pred EEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 116 YLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 116 Y~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.|+|+++.+ .++||+++.+..||++..+.
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=93.65 E-value=0.52 Score=49.60 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.0
Q ss_pred EEeecCCCCC--ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 101 LLLEPVKSNV--QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 101 l~iE~~~~~~--~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+.+.+...+. .+|+|-.|+|+++.+. .+||||+..-.||||+.+.
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 4455444433 5899999999999885 5999999999999999875
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.07 E-value=0.19 Score=61.70 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=31.8
Q ss_pred ccCCeEE-EEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~-GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|.||. |+|++|.+ -+|||+|+.+..||+|+++.
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
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=91.31 E-value=0.47 Score=54.92 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=32.6
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...|.||.|+|++|.+ .+||||||.+..||+|+++.
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 5689999999999988 58999999899999999875
No 48
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=91.27 E-value=0.3 Score=41.13 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=31.6
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+|.+|.|+|++|.+ -++||+++.+.+||+|+.+.
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 69999999999999999875
No 49
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=91.24 E-value=0.48 Score=52.05 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=32.4
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...|.|-.|+|.+|.+. +||||||....|||+++++
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 46899999999999865 8999999999999998875
No 50
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=91.21 E-value=0.46 Score=55.12 Aligned_cols=35 Identities=34% Similarity=0.547 Sum_probs=31.1
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.|+.|+|++|.|. +|||+|| +-.||+|+++.
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
>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=91.14 E-value=1.1 Score=38.91 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=30.9
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (748)
..+|.+|.|+|.++.+ .++||++..+..||+|.++
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 4579999999999987 8999999998999997754
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=90.66 E-value=0.4 Score=44.08 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=31.8
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|.+-.|+|++|.+. ++||+++.+..||+++.++
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=90.58 E-value=1.3 Score=41.85 Aligned_cols=53 Identities=21% Similarity=0.377 Sum_probs=37.2
Q ss_pred eeeecCCChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrKI~~e-eR~rLk~i~~~----l~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||||+... .|+|+|.++.+ .. + .++=+|.|..+.+++.++|+.++..|.+.
T Consensus 49 ~sVsKKvg~AV~RNRiKR~lRE~~R~~~~~l~~~divii~r~~~~~~~~~~l~~~l~~ll~~ 110 (116)
T PRK14865 49 ITVSRKVGNAVVRNRIKRLVREFYRLNKSLFIVADYNIIAKKGAEQLDFQQISRELANALER 110 (116)
T ss_pred EEEecccCcchhHHHHHHHHHHHHHHhhccCCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 5679998765 57776554433 22 2 23456889999999999999998776544
No 54
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.25 E-value=0.73 Score=50.62 Aligned_cols=39 Identities=28% Similarity=0.526 Sum_probs=33.0
Q ss_pred CCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 106 VKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 106 ~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.-...-+|.||.|+|++|.+ -+|||++| +..||+|++++
T Consensus 190 ~~~~~k~G~vv~G~V~~I~~--~G~fV~i~-gv~Gllhisel 228 (318)
T PRK07400 190 KMNRLEVGEVVVGTVRGIKP--YGAFIDIG-GVSGLLHISEI 228 (318)
T ss_pred hhccCCCCCEEEEEEEEEEC--CeEEEEEC-CEEEEEEHHHc
Confidence 33445689999999999998 79999997 68899999875
No 55
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=90.22 E-value=0.28 Score=58.33 Aligned_cols=40 Identities=30% Similarity=0.522 Sum_probs=35.9
Q ss_pred CCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 106 VKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 106 ~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.....-+|-||.|+|+++.+ =+|||++..++.|++|++..
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 34566899999999999999 89999999999999999874
No 56
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=89.58 E-value=0.85 Score=52.85 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=34.2
Q ss_pred CCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
....+|.+|.|+|++|.| .+|||+++.+-.||+|+++.
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 79999999999999999885
No 57
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.55 E-value=0.79 Score=53.62 Aligned_cols=35 Identities=31% Similarity=0.528 Sum_probs=31.8
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...|.|+.|+|++|.+. +||||+| +..||+|+++.
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
>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=89.23 E-value=0.51 Score=39.87 Aligned_cols=34 Identities=9% Similarity=0.123 Sum_probs=31.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
|.|+.|+|++|.+. .+||+++.+-.||+++++..
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 79999999999999999863
No 59
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=89.13 E-value=0.62 Score=54.58 Aligned_cols=68 Identities=24% Similarity=0.261 Sum_probs=50.1
Q ss_pred eEEEEEecCCCeEEEEEEECCEEeEEEeecCCCCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 76 ~~IlIn~s~~~e~RvAvlEdg~LvEl~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
+-.+|.... ...||.|= =-+|.+-=.+....+..+|..+.|+|+|+.|- +|||+|+.+-.||+|++++
T Consensus 243 kvkVi~~D~-e~~RVsLS-lK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~--GafVei~~GvEGlvhvSEi 310 (541)
T COG0539 243 KVKVISLDE-ERGRVSLS-LKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDY--GAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred EEEEEEEcc-CCCeEEEE-ehhcccCcHHHHhhhcCCCCEEEEEEEEeecC--cEEEEecCCccceeechhh
Confidence 445666654 45576652 22333333455566778999999999999995 8999999999999999986
No 60
>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=89.01 E-value=4.7 Score=45.02 Aligned_cols=107 Identities=23% Similarity=0.292 Sum_probs=62.0
Q ss_pred ccCCCEEEEEEEecCCCCCCceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cce-EEEeecCC
Q 004498 291 VQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVAA 368 (748)
Q Consensus 291 lk~Gq~ILVQV~KE~~g~KGp~LT~~IsL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~p~-~~G-vIvRTaA~ 368 (748)
+++||.|-|.|.+-..+.|||. +-+||+-.+ -|+.+++.-.|+ ..| +.|+..|.
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 7779999999988877777654 346777653 356666666665 224 55677666
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEE-EcChHH
Q 004498 369 GHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRT 441 (748)
Q Consensus 369 ~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~Ii-VD~~~~ 441 (748)
.+.. +++-+....+.++. +...++-.....+..+.+.+-.+.++=|- -||+..
T Consensus 226 ~pG~-------------------RtKvAV~s~~~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~ 279 (341)
T TIGR01953 226 EPGY-------------------RTKIAVESNDENID-PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE 279 (341)
T ss_pred CCcc-------------------eeEEEEEcCCCCCC-cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH
Confidence 6541 11111111122222 34567766666666666666577777553 344543
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=88.80 E-value=0.48 Score=39.56 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=28.7
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|.||.|+|+++.+ .++||++ .+-.|||+.++.
T Consensus 1 G~iv~g~V~~v~~--~G~~v~l-~g~~gfip~s~~ 32 (67)
T cd04465 1 GEIVEGKVTEKVK--GGLIVDI-EGVRAFLPASQV 32 (67)
T ss_pred CCEEEEEEEEEEC--CeEEEEE-CCEEEEEEHHHC
Confidence 7899999999975 8999999 579999998875
No 62
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=88.80 E-value=1.9 Score=40.99 Aligned_cols=53 Identities=13% Similarity=0.115 Sum_probs=35.1
Q ss_pred ceeeecCCChH-HHHHHHHHH----HhhC---CCCceEE--EeecCCCCCHHHHHHHHHHHHH
Q 004498 332 RIGVSRKITGV-ERTRLKVIA----KTLQ---PEGFGLT--IRTVAAGHSLEELQKDLEGLLS 384 (748)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~----~~l~---p~~~GvI--vRTaA~~~~~eeL~~Dl~~L~~ 384 (748)
++.||||+... +|+++|.++ .... +.+.-+| .|..+..++..+|+++|..|..
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 35679999765 577665443 3322 2333343 5788899999999999876543
No 63
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=88.34 E-value=1.4 Score=54.49 Aligned_cols=38 Identities=26% Similarity=0.438 Sum_probs=33.9
Q ss_pred CCCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 108 ~~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
++..+|+|+.|+|++|.| -+|||+++.+-.||+|+++.
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 64
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=88.04 E-value=0.64 Score=39.79 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=30.9
Q ss_pred cCCeEEEEEeeecCCcceEEecccC-CcceeeEeccc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (748)
+|.+|.|.|++|.+ .++||+++. +..||+|+.+.
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 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=87.44 E-value=1.5 Score=50.69 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=32.4
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|+++.|+|+++.+. +|||++|.+..||+|+.+.
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 45799999999999776 8999999999999999875
No 66
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.70 E-value=1.6 Score=50.75 Aligned_cols=36 Identities=36% Similarity=0.480 Sum_probs=32.2
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.+|.|+|++|.| -++||++..+-.||+|++++
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 67
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=86.15 E-value=3.4 Score=39.51 Aligned_cols=54 Identities=26% Similarity=0.292 Sum_probs=36.7
Q ss_pred ceeeecCCChH-HHHHHHH----HHHhhC---CCCceE--EEeecCCCCCHHHHHHHHHHHHHH
Q 004498 332 RIGVSRKITGV-ERTRLKV----IAKTLQ---PEGFGL--TIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~----i~~~l~---p~~~Gv--IvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
++.||||+... +|+|+|. ++..+. +.|+-+ |.|-.+.+++..+|.+||..|...
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 35679999765 5776654 443332 344444 556678899999999998877655
No 68
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.15 E-value=1.7 Score=50.85 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=32.3
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|+++.|+|++|.+ .+|||++|.+..||+|+++.
T Consensus 371 ~~~G~~v~g~V~~v~~--~G~fV~l~~~v~g~i~~s~l 406 (565)
T PRK06299 371 YPVGDVVEGKVKNITD--FGAFVGLEGGIDGLVHLSDI 406 (565)
T ss_pred CCCCCEEEEEEEEEec--ceEEEECCCCCEEEEEHHHc
Confidence 3579999999999976 59999999999999999885
No 69
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=86.03 E-value=1.8 Score=53.57 Aligned_cols=36 Identities=25% Similarity=0.482 Sum_probs=31.3
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
..+|++|.|+|.++.+ .+||||+| +-.||+|++++.
T Consensus 491 l~~G~~V~G~Vk~i~~--~G~fVdl~-Gv~Gfvp~SeiS 526 (863)
T PRK12269 491 VHIEDSVSGVVKSFTS--FGAFIDLG-GFDGLLHVNDMS 526 (863)
T ss_pred CCCCCEEEEEEEEEeC--CcEEEEEC-CEEEEEEchhcc
Confidence 4579999999999998 49999996 689999998763
No 70
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=85.88 E-value=3.6 Score=39.87 Aligned_cols=58 Identities=21% Similarity=0.321 Sum_probs=38.5
Q ss_pred eeeecC-CChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 004498 333 IGVSRK-ITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (748)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~----l~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W~~I~~~a 393 (748)
+.|||| +... .|+|+|.++.+ .. + -++=||.|..+.+.+..+|.+++..| |..+...+
T Consensus 50 ~~VsKK~~g~AV~RNRiKR~lRE~fR~~~~~l~g~DiVviaR~~~~~~~~~~l~~~l~~l---l~kl~~~~ 117 (130)
T PRK00396 50 LVIGKKSVKLAVDRNRLKRLIRESFRLNQHSLAGWDIVVVARKGLGELENPELHQQFGKL---WKRLARNR 117 (130)
T ss_pred EEEecccCccHhHHHHHHHHHHHHHHHhhccCCCeeEEEEeCCCcccCCHHHHHHHHHHH---HHHHHHhc
Confidence 456799 6654 68777665533 22 2 13446778899999999999998666 55554444
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=84.97 E-value=2 Score=49.64 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=32.4
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.||.|+|+++.+ .+|||++|.+-.||+|+++.
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
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=84.71 E-value=2.4 Score=47.36 Aligned_cols=36 Identities=33% Similarity=0.486 Sum_probs=31.7
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
...|.++.|+|+++.+ .++||++| +..||+|+++..
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 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=84.36 E-value=2.2 Score=49.54 Aligned_cols=108 Identities=22% Similarity=0.277 Sum_probs=63.2
Q ss_pred cccCCCEEEEEEEecCCCCCCceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cce-EEEeecC
Q 004498 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (748)
Q Consensus 290 ~lk~Gq~ILVQV~KE~~g~KGp~LT~~IsL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~p~-~~G-vIvRTaA 367 (748)
.+++||.|-|-|.+-...+|||.+ -+||+-.+ -|+.+++.-.|+ ..| +.|+..|
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 467799999999988777777654 46776553 466666666665 335 4566666
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEEE-cChHH
Q 004498 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVV-DSPRT 441 (748)
Q Consensus 368 ~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiV-D~~~~ 441 (748)
..+.. +++-+....+.++. +...++-.....+..+.+.+-.+.|+=|.. ||+..
T Consensus 227 R~pG~-------------------RaKvAV~s~d~~iD-pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~ 281 (470)
T PRK09202 227 RDPGS-------------------RAKIAVKSNDPRID-PVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQ 281 (470)
T ss_pred ecCcc-------------------eeEEEEEcCCCCCC-hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHH
Confidence 65541 11111111222222 334567666666777777766777776533 34443
No 74
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=83.43 E-value=6.1 Score=37.08 Aligned_cols=54 Identities=30% Similarity=0.400 Sum_probs=37.7
Q ss_pred eeeecCCChH-HHHHHHHHH----HhhC---CC--CceEEEeecCCCCCHHHHHHHHHHHHHHH
Q 004498 333 IGVSRKITGV-ERTRLKVIA----KTLQ---PE--GFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (748)
Q Consensus 333 vgvSrKI~~e-eR~rLk~i~----~~l~---p~--~~GvIvRTaA~~~~~eeL~~Dl~~L~~~W 386 (748)
+.||||+... .|+++|.++ .... +. ++=+|+|-.+..++..+|.+|+..|...-
T Consensus 42 isVsKKvgkAV~RNriKR~lRE~~R~~~~~~~~~~d~v~i~r~~~~~~~~~~l~~~l~~ll~k~ 105 (114)
T PRK00499 42 ISVSKKVGNAVVRNRIKRLIRESFRELKDEIKKGYDFVVIARKPAAELDYKEIKKSLIHVLKLA 105 (114)
T ss_pred EEEecccCchhhHhHHHHHHHHHHHHhhhcccCCceEEEEECCCcccCCHHHHHHHHHHHHHHh
Confidence 5679999765 577665443 3322 22 34567788899999999999987776653
No 75
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=82.67 E-value=6.5 Score=37.38 Aligned_cols=53 Identities=19% Similarity=0.309 Sum_probs=35.2
Q ss_pred eeeecCC-ChH-HHHHHHHHHHhh----C---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRKI-TGV-ERTRLKVIAKTL----Q---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrKI-~~e-eR~rLk~i~~~l----~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||||. ... +|+++|.++.+. . | -++=+|+|..+.+.+..+|.+|+..|...
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 433 687776655432 1 2 13346778888899999999998766444
No 76
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=82.63 E-value=6 Score=38.36 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=37.8
Q ss_pred eeeecCCChH-HHHHHH----HHHHhhCC----C--CceEEEeecCCCCCHHHHHHHHHHHHH
Q 004498 333 IGVSRKITGV-ERTRLK----VIAKTLQP----E--GFGLTIRTVAAGHSLEELQKDLEGLLS 384 (748)
Q Consensus 333 vgvSrKI~~e-eR~rLk----~i~~~l~p----~--~~GvIvRTaA~~~~~eeL~~Dl~~L~~ 384 (748)
+.||||+... .|+++| +++....+ . ++=||.|..+.+++..+|++||..++.
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 4679999764 576654 44443322 2 346788999999999999999988776
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=82.23 E-value=2 Score=52.15 Aligned_cols=37 Identities=30% Similarity=0.484 Sum_probs=33.0
Q ss_pred CCccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 109 ~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.-..|.|--|.|+||.- -+||||||....|++|++..
T Consensus 655 dLk~Gm~leg~Vrnv~~--fgafVdIgv~qDglvHis~l 691 (780)
T COG2183 655 DLKPGMILEGTVRNVVD--FGAFVDIGVHQDGLVHISQL 691 (780)
T ss_pred hccCCCEEEEEEEEeee--ccceEEeccccceeeeHHHh
Confidence 35689999999999987 58999999999999999875
No 78
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=81.97 E-value=4.1 Score=45.52 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=31.7
Q ss_pred CccCCeEEEEEeeecCCcceEEecc-cCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdI-G~~r~aFL~~~d~ 147 (748)
...|.|..|+|+++.+. ++|||| |.+-.|||+..+.
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=78.95 E-value=4.1 Score=48.90 Aligned_cols=34 Identities=29% Similarity=0.433 Sum_probs=30.1
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.+|++|.|+|+++.+. ++||++ .+-.||||+++.
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 4799999999999874 899999 578999999875
No 80
>PRK00730 rnpA ribonuclease P; Reviewed
Probab=78.92 E-value=8.5 Score=37.88 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=35.9
Q ss_pred ceeeecCCChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 332 RIGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 332 ~vgvSrKI~~e-eR~rLk~i~~~----l~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
++.||||+... .|+|+|.++.. .. | -++=||.|..+. .+.++|..|+..+...
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 35689999765 57776655433 22 2 134567788886 9999999998776553
No 81
>PRK01903 rnpA ribonuclease P; Reviewed
Probab=78.36 E-value=11 Score=36.56 Aligned_cols=53 Identities=21% Similarity=0.339 Sum_probs=32.9
Q ss_pred eeeecC-CChH-HHHHHHHHHHhh-------CCCC-------------ceEEEee-cCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QPEG-------------FGLTIRT-VAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~l-------~p~~-------------~GvIvRT-aA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||+| +... .|+|+|.++.+. .+.+ .-+|.|. ++...+.+++.+++..|+..
T Consensus 54 ~sVsKK~~g~AV~RNRiKR~lREa~R~~~~~l~~~~~~~~~~~~~~~~iv~i~~~~~~~~~~~~~l~~~l~~ll~r 129 (133)
T PRK01903 54 FSVSKKRVPRAVKRNRIKRLMREAYRLEKHVLLDRLETDAGAKNRQLAIAFLYTGRSDEIPSLAEFRREMRKLLQR 129 (133)
T ss_pred EEEecccCCchhhhhHHHHHHHHHHHHhHhhhcccccccccccCcceEEEEEEeccccccCCHHHHHHHHHHHHHH
Confidence 345799 6665 688776654331 2222 3446666 34457799999998777654
No 82
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=76.23 E-value=3.3 Score=35.62 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=30.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
|++..|+|+++.+ .++||+++.+-.||+++.+.
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 59999999999999999885
No 83
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=74.92 E-value=14 Score=36.52 Aligned_cols=53 Identities=30% Similarity=0.449 Sum_probs=37.0
Q ss_pred eeeecCCC-hH-HHHHHHHHHHh----h----CCCCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRKIT-GV-ERTRLKVIAKT----L----QPEGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrKI~-~e-eR~rLk~i~~~----l----~p~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||||+. .. .|+|+|.++.+ + .+.++=+|.|-.+.+++.++|++++..|...
T Consensus 52 ~sVSKKvg~~AV~RNRiKR~lRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~l~~LL~k 114 (145)
T PRK04820 52 LAVSRKVDTRAVGRNRIKRVLREAMRQLLPELAPGDYVVVARSAAAKASNPQLRDAFLRLLRR 114 (145)
T ss_pred EEEeccccCcchhHHHHHHHHHHHHHHhhhccCCCCEEEEEeCCcccCCHHHHHHHHHHHHHH
Confidence 56899984 33 57776654433 2 2234557788888899999999998777665
No 84
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=74.90 E-value=13 Score=35.51 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=37.2
Q ss_pred ceeeecCCC-hH-HHHHHHH----HHHhhCC----C--C--ceEEEeecCCCCCHHHHHHHHHHHHH
Q 004498 332 RIGVSRKIT-GV-ERTRLKV----IAKTLQP----E--G--FGLTIRTVAAGHSLEELQKDLEGLLS 384 (748)
Q Consensus 332 ~vgvSrKI~-~e-eR~rLk~----i~~~l~p----~--~--~GvIvRTaA~~~~~eeL~~Dl~~L~~ 384 (748)
++.||||+. .. .|+|+|. ++....+ . | +=+|+|..+.+.+..+|++||..|+-
T Consensus 49 G~sVSKKv~~kAV~RNRiKR~lRE~fR~~~~~~~l~~~g~DiVviaR~~~~~~~~~~l~~~l~~l~~ 115 (118)
T PRK01492 49 GIKVSRKLNKKAVVRNKIKRRIRHLIRIIVSDSSFKAIKFAMIIIPRKGFEEINFSHLNYELSKIIL 115 (118)
T ss_pred EEEEecccCCchhhHHHHHHHHHHHHHHhCcccccCCCCceEEEEECCCcccCCHHHHHHHHHHHHH
Confidence 467899954 33 5776654 4444333 1 3 34788999999999999999988763
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=74.41 E-value=7.5 Score=43.81 Aligned_cols=33 Identities=18% Similarity=0.262 Sum_probs=28.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (748)
..|+|-.|+|.++.+ +.+|||+|. -.|||+.++
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 86
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=73.94 E-value=10 Score=35.84 Aligned_cols=53 Identities=28% Similarity=0.367 Sum_probs=36.2
Q ss_pred eeeecC-CChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRK-ITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrK-I~~e-eR~rLk~i~~~----l~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||+| +... .|+++|.++.+ .. | -++=+|.|-.+.+++..+|.+|+..|.+.
T Consensus 49 ~~VsKK~~g~AV~RNriKR~lRe~~R~~~~~l~~~diVviar~~~~~~~~~~l~~~l~~ll~k 111 (114)
T PRK01732 49 LTVAKKNVKRAHERNRIKRLTRESFRLHQHELPAMDFVVIAKKGVADLDNRELFELLEKLWRR 111 (114)
T ss_pred EEEEcccCcchhHHHHHHHHHHHHHHHhhhcCCCCeEEEEeCCCcccCCHHHHHHHHHHHHHH
Confidence 457899 6644 57766554433 22 2 23345788899999999999999887654
No 87
>TIGR00188 rnpA ribonuclease P protein component, eubacterial. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead.
Probab=73.82 E-value=9.5 Score=35.27 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=36.2
Q ss_pred eeeecCCChH-HHHHHHHHHHh----hC---C-CCceEEEeecCCCCCHHHHHHHHHHHH
Q 004498 333 IGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLL 383 (748)
Q Consensus 333 vgvSrKI~~e-eR~rLk~i~~~----l~---p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~ 383 (748)
+.||||+... .|+++|.++.+ .. + -++=+|+|..+..++.++|.+++..|.
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 4579998664 57776554433 22 2 234578899999999999999998764
No 88
>PRK00038 rnpA ribonuclease P; Reviewed
Probab=73.06 E-value=19 Score=34.71 Aligned_cols=58 Identities=14% Similarity=0.319 Sum_probs=35.4
Q ss_pred ceeeecCC-ChH-HHHHHHHHHH----hhC---C-CCceEEEeecCCCCCHHHHHHH-HHHHHHHHHHH
Q 004498 332 RIGVSRKI-TGV-ERTRLKVIAK----TLQ---P-EGFGLTIRTVAAGHSLEELQKD-LEGLLSTWKNI 389 (748)
Q Consensus 332 ~vgvSrKI-~~e-eR~rLk~i~~----~l~---p-~~~GvIvRTaA~~~~~eeL~~D-l~~L~~~W~~I 389 (748)
++.||||. ... +|+++|..+. ... | -++=||+|..+.+++.++|..+ ...|..+|..+
T Consensus 53 Gi~VsKKv~g~AV~RNRiKR~lRE~~R~~~~~l~~~D~VviaR~~~~~~~~~~l~~~~~~~~~~l~~~~ 121 (123)
T PRK00038 53 GLVIAKRFAARAVTRNTLKRVIREAFRARRLALPAQDYVVRLHSKLTPASLTALKRSARAEVDAHFTRI 121 (123)
T ss_pred EEEEecccCCCchhHHHHHHHHHHHHHHhhccCCCCCEEEEECCCCCcCCHHHHHHHHHHHHHHHHHHh
Confidence 35679995 443 6777655433 222 2 2455788899999999999333 23345556543
No 89
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=71.83 E-value=10 Score=45.71 Aligned_cols=36 Identities=31% Similarity=0.495 Sum_probs=32.3
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.+|.|+|++|.+ .++||+++.+-.||+|+++.
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 90
>PRK11642 exoribonuclease R; Provisional
Probab=69.53 E-value=12 Score=46.49 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=31.5
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCC-cceeeEecccC
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNS-RPSLMDIKHYR 148 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~-r~aFL~~~d~~ 148 (748)
.+|.+|.|+|+.|.+. ++||++... -.||+|+++..
T Consensus 642 ~iGe~f~G~Is~V~~f--GifVeL~~~~vEGlV~vs~L~ 678 (813)
T PRK11642 642 QVGNVFKGVISSVTGF--GFFVRLDDLFIDGLVHVSSLD 678 (813)
T ss_pred cCCcEEEEEEEEeecC--ceEEEECCCCeeeeEEEeecC
Confidence 4899999999999885 999999864 99999998753
No 91
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=69.33 E-value=26 Score=33.34 Aligned_cols=53 Identities=28% Similarity=0.471 Sum_probs=35.5
Q ss_pred eeeecCCC-hH-HHHHHH----HHHHhhC---CCC--ceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRKIT-GV-ERTRLK----VIAKTLQ---PEG--FGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrKI~-~e-eR~rLk----~i~~~l~---p~~--~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||||.. .. .|+++| +++..+. +.+ +=+|+|..+.+.+..+|.+|+..|...
T Consensus 51 ~~VsKK~~~~AV~RNriKR~lRe~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k 114 (122)
T PRK03031 51 ISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQ 114 (122)
T ss_pred EEEecccccchhhhhHHHHHHHHHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHH
Confidence 45799964 33 566654 4444332 223 345778888999999999998777655
No 92
>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=68.80 E-value=21 Score=30.09 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=27.0
Q ss_pred CCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004498 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (748)
Q Consensus 113 GnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (748)
|++--|+|++|.+ .+|||++..+-.||++..+
T Consensus 1 G~~V~g~V~~i~~--~G~~v~l~~~v~g~v~~~~ 32 (66)
T cd05695 1 GMLVNARVKKVLS--NGLILDFLSSFTGTVDFLH 32 (66)
T ss_pred CCEEEEEEEEEeC--CcEEEEEcCCceEEEEHHH
Confidence 7788999999984 5799999667899997765
No 93
>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=68.48 E-value=11 Score=45.73 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=31.4
Q ss_pred ccCCeEEEEEeeecCCcceEEecccC-CcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~-~r~aFL~~~d~ 147 (748)
.+|.+|.|+|++|.+ -++||++.. +..||+|+++.
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 94
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=67.28 E-value=28 Score=33.13 Aligned_cols=53 Identities=30% Similarity=0.408 Sum_probs=36.4
Q ss_pred eeeec-CCChH-HHHHHHHH----HHh---hCC-CCceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSR-KITGV-ERTRLKVI----AKT---LQP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSr-KI~~e-eR~rLk~i----~~~---l~p-~~~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||+ ++... +|+|+|.+ +.. +.| .++=||+|..+.+.+..+++++|..+...
T Consensus 45 lsVsKkk~g~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~ 107 (117)
T COG0594 45 LTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKR 107 (117)
T ss_pred EEEEchhccchhhHHHHHHHHHHHHHhhhhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHH
Confidence 56799 77754 67666543 332 223 35568899999999999998887665544
No 95
>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=67.04 E-value=4.4 Score=34.47 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=22.4
Q ss_pred ceeEEEeecCCCCCchhhccccCCCCCCceeEe
Q 004498 588 HGLMEITRKRVRPSVTFMISEPCTCCQGTGRVE 620 (748)
Q Consensus 588 LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~ 620 (748)
-|.+.++++ .+........+|+.|+|+|++.
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 355555555 7777778889999999999985
No 96
>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=66.37 E-value=2.4 Score=45.08 Aligned_cols=64 Identities=30% Similarity=0.443 Sum_probs=36.2
Q ss_pred ccCCceeEEEeecCCCCCchhhccccCCCCCCceeEechhhhHHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECHHH
Q 004498 584 ELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQEISRLLAMMEQKADPENPKSWPRFILRVDHHM 663 (748)
Q Consensus 584 giT~LGLvEmTRkR~r~sL~~~l~e~Cp~C~G~G~v~s~et~~~~i~rei~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v 663 (748)
.++.|.-+|.+-+ .+.+||.|+|+|+|.... |.+|-.++.-..++.+| ++-.+.|--.|
T Consensus 24 ~~~~~py~e~~g~---------~~vtCPTCqGtGrIP~eq------e~qLVALIPy~DqRLKP------rRTklyV~~sV 82 (238)
T PF07092_consen 24 DISSFPYVEFTGR---------DSVTCPTCQGTGRIPREQ------ENQLVALIPYSDQRLKP------RRTKLYVFLSV 82 (238)
T ss_pred ccccCccccccCC---------CCCcCCCCcCCccCCccc------hhcEEEEEeccccccCC------ceeEEEeeHHH
Confidence 4566666666642 245899999999997754 33443333323333323 23455555556
Q ss_pred HHHHH
Q 004498 664 CNYLT 668 (748)
Q Consensus 664 ~~~L~ 668 (748)
.-.|+
T Consensus 83 ~~CLl 87 (238)
T PF07092_consen 83 LLCLL 87 (238)
T ss_pred HHHHH
Confidence 65554
No 97
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=65.12 E-value=8.6 Score=34.85 Aligned_cols=37 Identities=24% Similarity=0.303 Sum_probs=31.9
Q ss_pred ccCCeEEEEEeeecCCcceEEecc--------cCCcceeeEecccCC
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNI--------GNSRPSLMDIKHYRE 149 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdI--------G~~r~aFL~~~d~~~ 149 (748)
.+|+|=.|+|++|-+. .|+||| ...-.|+|+..|++.
T Consensus 5 ~~GDiVig~V~~v~~~--~~~v~I~~v~~~~l~~~~~g~l~~~dv~~ 49 (92)
T cd05791 5 KVGSIVIARVTRINPR--FAKVDILCVGGRPLKESFRGVIRKEDIRA 49 (92)
T ss_pred CCCCEEEEEEEEEcCC--EEEEEEEEecCeecCCCcccEEEHHHccc
Confidence 5799999999999755 499999 888899999998743
No 98
>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=62.22 E-value=37 Score=30.83 Aligned_cols=33 Identities=21% Similarity=0.205 Sum_probs=29.0
Q ss_pred ccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~ 145 (748)
.+|++-+|+|+.+. -..-+||||..-+|+|++.
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 99
>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=60.73 E-value=21 Score=33.03 Aligned_cols=53 Identities=34% Similarity=0.465 Sum_probs=34.9
Q ss_pred eeeecCCCh-H-HHHHHHHHHHh----hC---CCC--ceEEEeecCCCCCHHHHHHHHHHHHHH
Q 004498 333 IGVSRKITG-V-ERTRLKVIAKT----LQ---PEG--FGLTIRTVAAGHSLEELQKDLEGLLST 385 (748)
Q Consensus 333 vgvSrKI~~-e-eR~rLk~i~~~----l~---p~~--~GvIvRTaA~~~~~eeL~~Dl~~L~~~ 385 (748)
+.||+|+.. . .|+++|.++.+ .. +.+ +=+++|..+...+.++|.+++..|.+.
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 567999976 5 58777665543 22 223 346777788899999999999887765
No 100
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=60.50 E-value=13 Score=36.10 Aligned_cols=56 Identities=13% Similarity=0.331 Sum_probs=40.0
Q ss_pred ccCCCCCCceeEechhhhHHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEE
Q 004498 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWIL 687 (748)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~i~rei~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~ 687 (748)
--||.|+|.-.-.|-..++..+.+++++.+.... -+.++.+|| -.+||-.|.
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 3699999988888888888888888877665432 133455554 467888888
Q ss_pred EEeC
Q 004498 688 LKVA 691 (748)
Q Consensus 688 l~~~ 691 (748)
..|.
T Consensus 93 y~Pp 96 (126)
T TIGR03147 93 YNPP 96 (126)
T ss_pred ecCC
Confidence 7654
No 101
>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=58.94 E-value=22 Score=43.01 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=31.2
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc-CCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG-~~r~aFL~~~d~ 147 (748)
.+|.+|-|+|+.|.+ .++||++. .+-.||+|+++.
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 102
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=58.29 E-value=15 Score=35.67 Aligned_cols=56 Identities=9% Similarity=0.239 Sum_probs=40.1
Q ss_pred ccCCCCCCceeEechhhhHHHHHHHHHHHHHhhhccCCCCCCCCCCeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEE
Q 004498 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWIL 687 (748)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~i~rei~r~~~~~~~~~~~~~~~~~~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~ 687 (748)
--||.|++.-.-.|-..++..+.+++++.+.... -+.++.+|| ..+||-.|.
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 3699999998888888888888888887665432 133455554 367888888
Q ss_pred EEeC
Q 004498 688 LKVA 691 (748)
Q Consensus 688 l~~~ 691 (748)
..|.
T Consensus 93 ~~Pp 96 (126)
T PRK10144 93 YNPP 96 (126)
T ss_pred ecCC
Confidence 7654
No 103
>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=57.03 E-value=13 Score=33.51 Aligned_cols=31 Identities=39% Similarity=0.488 Sum_probs=27.3
Q ss_pred eEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 115 IY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
+|.|+|+.|.+ .++||+++. -.||+++.+..
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 89999998864
No 104
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=56.96 E-value=22 Score=38.81 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.6
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
.++|.-=.|+|+.|.+.|+ ||||.|..|.-|+++++.
T Consensus 71 ~tvg~~g~~~Vv~v~~~lG-aFlD~Gl~KDl~vp~~el 107 (287)
T COG2996 71 ATVGEYGWLKVVEVNKDLG-AFLDWGLPKDLLVPLDEL 107 (287)
T ss_pred EeecceeEEEEEEEcCCcc-eEEecCCCcceeeehhhc
Confidence 3689999999999999995 799999999999999885
No 105
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=52.98 E-value=35 Score=38.82 Aligned_cols=188 Identities=14% Similarity=0.158 Sum_probs=95.0
Q ss_pred cccCCCEEEEEEEecCCCCC-CceeeecceecceeEEEeeCCCceeeecCCChHHHHHHHHHHHhhCCC-Cce-EEEeec
Q 004498 290 QVQKGTKVIVQVVKEGLGTK-GPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTV 366 (748)
Q Consensus 290 ~lk~Gq~ILVQV~KE~~g~K-Gp~LT~~IsL~GRylVl~P~~~~vgvSrKI~~eeR~rLk~i~~~l~p~-~~G-vIvRTa 366 (748)
.+++||.|-|=|.+-...+| ||.+ -+||.-. .-|+.+++.-.|+ ..| +.|+..
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 47789999998888888887 7654 3565544 2355666665665 224 556666
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcCCCCceeEeecCCchhhhhhhhccCCccEEE-EcChHHHHHH
Q 004498 367 AAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMV-VDSPRTYHEV 445 (748)
Q Consensus 367 A~~~~~eeL~~Dl~~L~~~W~~I~~~a~~~~~~~~eg~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~Ii-VD~~~~y~~i 445 (748)
|..+.. +++-+....+.++ -+...++-.....+..+.+.+-.+.++=|. -||+..
T Consensus 232 ARepG~-------------------RtKVAV~S~d~~i-DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---- 287 (374)
T PRK12328 232 ARIPGE-------------------RAKVALFSNNPNI-DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---- 287 (374)
T ss_pred eccCcc-------------------eeEEEEEcCCCCC-ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH----
Confidence 655441 1110100111222 123456666666676777776677777663 344543
Q ss_pred HHHHH-hhCCCccCceeeccCCCCcccccCHHHHHHhHhCCceeCCCCceEEEecccceEEEEecCCCCCCCCCCCHhhh
Q 004498 446 TSYLQ-DIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKA 524 (748)
Q Consensus 446 ~~~l~-~~~P~~~~~i~ly~~~~pLF~~y~Ie~qIe~al~r~V~LpsGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet 524 (748)
|+. .+.|....+|.+-. +...+..+=-+.|+..|..+ .|-.+-.-.-=+-|-|||-|....-. ...+.
T Consensus 288 --fI~Nal~Pa~V~~V~i~~-~~~~~~V~V~~~qlslAIGk-----~GqNvrLA~~LtGwkIDI~s~~~~~~---~~~~~ 356 (374)
T PRK12328 288 --FIARALAPAIISSVKIEE-EEKKAIVTLLSDQKSKAIGK-----NGINIRLASMLTGYEIELNEIGSKEN---ASNES 356 (374)
T ss_pred --HHHHhCCCceeeEEEEcC-CCcEEEEEEChHHhhhhhcC-----CChhHHHHHHHhCCEEEEEECCCCcc---ccccc
Confidence 343 35676665654432 22222222223333333332 22222222222346788888753211 11223
Q ss_pred HHHHHHHHHHHH
Q 004498 525 ILDVNLAAAKQI 536 (748)
Q Consensus 525 ~l~tNlEAA~EI 536 (748)
--.||.|..+..
T Consensus 357 ~~~~~~~~~~~~ 368 (374)
T PRK12328 357 EKETNKEGVKAL 368 (374)
T ss_pred ccccccccHHHH
Confidence 345777766543
No 106
>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=44.04 E-value=30 Score=34.89 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=31.2
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEecccC
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~~ 148 (748)
..+|.++-|+|+++.+ .++||++|. -+|+++.++..
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 89999888763
No 107
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=39.74 E-value=27 Score=34.71 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=21.4
Q ss_pred ccCCCCCCceeEechhhhHHHHHHHHHHHHHhh
Q 004498 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLAMM 640 (748)
Q Consensus 608 e~Cp~C~G~G~v~s~et~~~~i~rei~r~~~~~ 640 (748)
-.||+|.|.-.-.|...++..+.++|++.+...
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 369999997665666667888888888776553
No 108
>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=39.56 E-value=15 Score=37.82 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=14.9
Q ss_pred ccCCCCCCceeEechhhh
Q 004498 608 EPCTCCQGTGRVEALETS 625 (748)
Q Consensus 608 e~Cp~C~G~G~v~s~et~ 625 (748)
.+|+.|+|+|+++.....
T Consensus 116 ~~C~~C~G~G~v~~~~~~ 133 (186)
T TIGR02642 116 RECDTCAGTGRFRPTVED 133 (186)
T ss_pred CCCCCCCCccEEeeeEEE
Confidence 689999999998887665
No 109
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=37.57 E-value=29 Score=37.62 Aligned_cols=35 Identities=17% Similarity=0.438 Sum_probs=27.9
Q ss_pred ccCCeEEEEEeeecCCcceEEeccc--CCcceeeEeccc
Q 004498 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (748)
Q Consensus 111 ~vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d~ 147 (748)
-.|.|-.|+|++|... +|||++- .++.||+|+++.
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 4799999999999875 7888773 457888888764
No 110
>PHA02945 interferon resistance protein; Provisional
Probab=35.99 E-value=1.1e+02 Score=28.19 Aligned_cols=32 Identities=13% Similarity=0.138 Sum_probs=25.1
Q ss_pred cCCeEEEEEeeecCCcceEEeccc--CCcceeeEecc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG--~~r~aFL~~~d 146 (748)
.|.|-+|+|+. .=.+|||+.- .++.||+|++.
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 4468898873 36788888764
No 111
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=35.59 E-value=1.2e+02 Score=30.79 Aligned_cols=35 Identities=20% Similarity=0.199 Sum_probs=30.5
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
...|-|--|+|+++.+ .++||.+|.=. +|+|...+
T Consensus 79 Pf~gEVv~g~V~~v~~--~G~~v~~Gp~~-ifI~~~~l 113 (176)
T PTZ00162 79 PFKDEVLDAIVTDVNK--LGFFAQAGPLK-AFVSRSAI 113 (176)
T ss_pred cCCCCEEEEEEEEEec--ceEEEEeeCeE-EEEcHHHC
Confidence 4579999999999999 59999999887 99987664
No 112
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=34.74 E-value=1.2e+02 Score=25.39 Aligned_cols=33 Identities=15% Similarity=0.129 Sum_probs=18.1
Q ss_pred cCCeEEEEEeeecCCcceEEecccCCcceeeEecc
Q 004498 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (748)
Q Consensus 112 vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d 146 (748)
+|.|=..+|.++-+ .+||++.|.++.-||+.++
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 7899998888888886654
No 113
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=33.59 E-value=47 Score=33.51 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=30.3
Q ss_pred CccCCeEEEEEeeecCCcceEEecccCCcceeeEeccc
Q 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~d~ 147 (748)
..+|.++.|+|+++.+ .++||++|. -+||++..+.
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 4479999999999987 699999994 8899988765
No 114
>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=33.02 E-value=22 Score=36.65 Aligned_cols=16 Identities=38% Similarity=0.760 Sum_probs=14.0
Q ss_pred cccCCCCCCceeEech
Q 004498 607 SEPCTCCQGTGRVEAL 622 (748)
Q Consensus 607 ~e~Cp~C~G~G~v~s~ 622 (748)
...||.|+|+|.+...
T Consensus 99 ~~~C~~C~G~G~~i~~ 114 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRR 114 (186)
T ss_pred CCcCCCCCCeeEEecC
Confidence 7899999999998763
No 115
>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=32.99 E-value=2.8e+02 Score=25.46 Aligned_cols=45 Identities=13% Similarity=0.033 Sum_probs=33.6
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~l~~~~~~~~~~y~i~~ 703 (748)
..+.|+|||+-+.++.... ......++. .|.+|+++.++.+.|..
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 222233333 89999999999998876
No 116
>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=31.71 E-value=1.1e+02 Score=24.77 Aligned_cols=37 Identities=8% Similarity=0.053 Sum_probs=32.3
Q ss_pred EEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeC
Q 004498 655 FILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVA 691 (748)
Q Consensus 655 ~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~l~~~ 691 (748)
..+.+++..+.++...+...+.+|++.+++.|.+..+
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 4678899999999987778999999999999999555
No 117
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=29.79 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 004498 110 VQCDSVYLGVVTKLVPNMGGAFVNIGN--S---RPSLMDI 144 (748)
Q Consensus 110 ~~vGnIY~GrV~kV~PgmqAAFVdIG~--~---r~aFL~~ 144 (748)
..+|.|-.|+|.++..+ ..+||+|. + -.|+|+-
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 2 3566643
No 118
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=29.39 E-value=2.1e+02 Score=29.42 Aligned_cols=47 Identities=13% Similarity=0.273 Sum_probs=35.7
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHH--hcCCeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSS--SLKAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~--~~~~~I~l~~~~~~~~~~y~i~~ 703 (748)
+++.|+|||+.+..+... +..+.. .+...+.|.+|+++.++...|..
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 233322 35568899999999999988876
No 119
>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=27.51 E-value=2.9e+02 Score=26.76 Aligned_cols=45 Identities=20% Similarity=0.127 Sum_probs=33.5
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~l~~~~~~~~~~y~i~~ 703 (748)
..++|+|||+-+..+... +..+-...+ +.|.+|+.+.++.+-|..
T Consensus 114 ~~v~I~v~P~d~~~l~~~----l~~~~~~~~--~~i~~D~~l~~G~c~vet 158 (166)
T TIGR02499 114 GRLTLRVHPEQLDEVREA----LAERLALEP--WELEPDASLAPGACVLET 158 (166)
T ss_pred CceEEEECHHHHHHHHHH----HHHHhccCC--eEEeeCCCCCCCCEEEEe
Confidence 469999999999988643 233323333 899999999999877765
No 120
>PRK06937 type III secretion system protein; Reviewed
Probab=26.61 E-value=2.1e+02 Score=29.47 Aligned_cols=49 Identities=8% Similarity=0.114 Sum_probs=34.3
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcCCeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~~~I~l~~~~~~~~~~y~i~~ 703 (748)
..++|+|||+-++++.......+..+. ...++.|.+|+++.++.-.|..
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 469999999999998643322222111 1257899999999999866654
No 121
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=26.06 E-value=91 Score=40.99 Aligned_cols=78 Identities=17% Similarity=0.261 Sum_probs=59.4
Q ss_pred ccccCCCceEEEEEecCCCeEEEEEEECCEEeEEEeecCCC--CCccCCeEEEEEeeecCCcceEEecccCCcceeeEec
Q 004498 68 ISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKS--NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (748)
Q Consensus 68 ~~~~~~m~~~IlIn~s~~~e~RvAvlEdg~LvEl~iE~~~~--~~~vGnIY~GrV~kV~PgmqAAFVdIG~~r~aFL~~~ 145 (748)
+...... +.+.+|.. ..|+|+.-.+.|++...+-+.. +.+-|.||+|.|.++-+ ++|||.+-.+-.||++..
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 66677774 4699999999999996553332 23459999999999988 699999999999999887
Q ss_pred ccCCCC
Q 004498 146 HYREPF 151 (748)
Q Consensus 146 d~~~~~ 151 (748)
.+...|
T Consensus 631 ~~sd~~ 636 (1710)
T KOG1070|consen 631 EMSDDF 636 (1710)
T ss_pred hhhhhh
Confidence 765544
No 122
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.03 E-value=27 Score=39.62 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=20.2
Q ss_pred eeeecCCChHH-HHHHHHHHHhhCCC
Q 004498 333 IGVSRKITGVE-RTRLKVIAKTLQPE 357 (748)
Q Consensus 333 vgvSrKI~~ee-R~rLk~i~~~l~p~ 357 (748)
+||||--+.+| ++..|+++..+.|+
T Consensus 10 LGV~k~As~~EIKkAYRkLA~kyHPD 35 (371)
T COG0484 10 LGVSKDASEEEIKKAYRKLAKKYHPD 35 (371)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHhCCC
Confidence 58888888776 77888888888875
No 123
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=25.69 E-value=36 Score=34.15 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=21.0
Q ss_pred hHhCCceeCCCCceEEEecccceE
Q 004498 481 NMLSKRVPLPNGGSLVIEQTEALV 504 (748)
Q Consensus 481 ~al~r~V~LpsGG~LVIE~TEALt 504 (748)
.-|.+.||++-|+++||+++|-+-
T Consensus 53 ~KfRksiWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 53 AKFRKSIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred HhhhhceEEeeCCEEEEccccccc
Confidence 346788999999999999999876
No 124
>PRK09098 type III secretion system protein HrpB; Validated
Probab=25.63 E-value=2.4e+02 Score=30.01 Aligned_cols=47 Identities=9% Similarity=-0.080 Sum_probs=35.6
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhcC--CeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLK--AWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~~--~~I~l~~~~~~~~~~y~i~~ 703 (748)
..++|+|||+-+..+.... ..+....+ ..|.|.+|+++.++..-|..
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 4699999999999986432 33333344 57899999999999987776
No 125
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=25.25 E-value=1.3e+02 Score=25.92 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhc
Q 004498 531 AAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVER 575 (748)
Q Consensus 531 EAA~EIARQLRLRnIGGIIVIDFIDM~~~~~r~~V~~~Lk~alk~ 575 (748)
+-|.+|+.+||=. -++++||-+|..+. .+.+++.|..+...
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 4568899999865 57999999998776 66788898887765
No 126
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=25.18 E-value=1e+02 Score=31.10 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=24.9
Q ss_pred cCCCCCCceeEechhhhHHHHHHHHHHHHHh
Q 004498 609 PCTCCQGTGRVEALETSFSKIEQEISRLLAM 639 (748)
Q Consensus 609 ~Cp~C~G~G~v~s~et~~~~i~rei~r~~~~ 639 (748)
-||.|++.-...|-..++..+..+++.++.+
T Consensus 46 RCp~CQNqsIadSnA~IA~DlR~~V~e~l~e 76 (153)
T COG3088 46 RCPQCQNQSIADSNAPIARDLRHQVYELLQE 76 (153)
T ss_pred CCCcCCCCChhhhccHHHHHHHHHHHHHHHc
Confidence 5999999988888888888777777766554
No 127
>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=24.76 E-value=1.7e+02 Score=28.43 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=35.8
Q ss_pred hcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCC-CceEeccCCceeEEEeec
Q 004498 541 RLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRS-MVKVSELSRHGLMEITRK 596 (748)
Q Consensus 541 RLRnIGGIIVIDFIDM~~~~~r~~V~~~Lk~alk~Dr~-k~~V~giT~LGLvEmTRk 596 (748)
.|...+|+|+|||=++. .+ + ++.+++.+..|+- -..+.+.|.-||==+.|=
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 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=23.77 E-value=1e+02 Score=39.12 Aligned_cols=35 Identities=20% Similarity=0.367 Sum_probs=28.0
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCceEe
Q 004498 548 IIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVS 583 (748)
Q Consensus 548 IIVIDFIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~ 583 (748)
-||||-+-... .++..+.+.+..||+.-...+.+.
T Consensus 199 ~vvvdr~~~~~-~~~~r~~~s~~~a~~~g~g~~~~~ 233 (924)
T TIGR00630 199 DVVIDRLKVKN-ENRSRLAESVETALRLGDGLLEVE 233 (924)
T ss_pred EEEEEEEEeCc-chHHHHHHHHHHHHHhCCCeEEEE
Confidence 48999887764 578889999999999877766654
No 129
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=22.91 E-value=33 Score=38.91 Aligned_cols=21 Identities=29% Similarity=0.376 Sum_probs=18.7
Q ss_pred cCCCCCHHHHHHHHHHHHHHH
Q 004498 366 VAAGHSLEELQKDLEGLLSTW 386 (748)
Q Consensus 366 aA~~~~~eeL~~Dl~~L~~~W 386 (748)
+..+|+.+||++-+..|..+|
T Consensus 12 V~k~As~~EIKkAYRkLA~ky 32 (371)
T COG0484 12 VSKDASEEEIKKAYRKLAKKY 32 (371)
T ss_pred CCCCCCHHHHHHHHHHHHHHh
Confidence 456899999999999999998
No 130
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=22.52 E-value=65 Score=35.69 Aligned_cols=30 Identities=20% Similarity=0.574 Sum_probs=19.5
Q ss_pred ccccCCCCCCceeEechhhhHHHHHHHHHHHHH
Q 004498 606 ISEPCTCCQGTGRVEALETSFSKIEQEISRLLA 638 (748)
Q Consensus 606 l~e~Cp~C~G~G~v~s~et~~~~i~rei~r~~~ 638 (748)
....|++|+|+|..... ...|.+..+..++
T Consensus 90 ~~~~C~~CeGrgi~l~~---f~dll~kf~eiaK 119 (354)
T COG1568 90 YDYTCECCEGRGISLQA---FKDLLEKFREIAK 119 (354)
T ss_pred ccccccCcCCccccchh---HHHHHHHHHHHHh
Confidence 35679999999986555 3445555554443
No 131
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.61 E-value=66 Score=26.62 Aligned_cols=15 Identities=60% Similarity=1.012 Sum_probs=12.9
Q ss_pred ceeCCCCceEEEecc
Q 004498 486 RVPLPNGGSLVIEQT 500 (748)
Q Consensus 486 ~V~LpsGG~LVIE~T 500 (748)
||+|.+||.||+|-+
T Consensus 22 RvPleGGGRLVvEl~ 36 (51)
T PF11314_consen 22 RVPLEGGGRLVVELN 36 (51)
T ss_pred EEecCCCcEEEEEeC
Confidence 789999999998743
No 132
>PRK14296 chaperone protein DnaJ; Provisional
Probab=21.22 E-value=57 Score=36.78 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=19.1
Q ss_pred eeeecCCChHH-HHHHHHHHHhhCCC
Q 004498 333 IGVSRKITGVE-RTRLKVIAKTLQPE 357 (748)
Q Consensus 333 vgvSrKI~~ee-R~rLk~i~~~l~p~ 357 (748)
+|||+..+.++ |+..+.++..+.|.
T Consensus 10 Lgv~~~a~~~eik~ayrkla~~~HPD 35 (372)
T PRK14296 10 LGVSKTASEQEIRQAYRKLAKQYHPD 35 (372)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCcC
Confidence 57888777665 77888888888876
No 133
>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=20.85 E-value=5.6e+02 Score=24.34 Aligned_cols=50 Identities=10% Similarity=0.058 Sum_probs=31.2
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHH-------------hcCCeEEEEeCCCCCCcceEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSS-------------SLKAWILLKVARGFTRGAFEVI 702 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~-------------~~~~~I~l~~~~~~~~~~y~i~ 702 (748)
..+.|.++|.-.+-|.........+|.. .-.+.|.|..++++++.+|+|.
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 3789999999888877653322222221 1246899999999999999986
No 134
>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=20.80 E-value=3.9e+02 Score=28.50 Aligned_cols=47 Identities=17% Similarity=0.133 Sum_probs=35.8
Q ss_pred CeEEEEECHHHHHHHHccchhHHHHHHHhc--CCeEEEEeCCCCCCcceEEEE
Q 004498 653 PRFILRVDHHMCNYLTSGKRTRLAVLSSSL--KAWILLKVARGFTRGAFEVIP 703 (748)
Q Consensus 653 ~~~~l~v~p~v~~~L~~~~~~~l~~Le~~~--~~~I~l~~~~~~~~~~y~i~~ 703 (748)
..++|+|||+-+.++.... ..|...+ ...+.|.+|+.+..+..-|..
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 4699999999999986433 3333443 357889999999999987775
Done!