Query 006020
Match_columns 664
No_of_seqs 224 out of 1091
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 17:12:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006020hhsearch_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 6E-126 1E-130 1045.5 51.3 446 74-655 1-447 (489)
2 TIGR00757 RNaseEG ribonuclease 100.0 9E-122 2E-126 997.4 46.5 412 88-631 1-414 (414)
3 PRK10811 rne ribonuclease E; R 100.0 1E-116 2E-121 1003.4 49.7 442 76-654 2-446 (1068)
4 COG1530 CafA Ribonucleases G a 100.0 2E-100 5E-105 844.9 38.7 437 75-652 1-440 (487)
5 PF10150 RNase_E_G: Ribonuclea 100.0 5.2E-81 1.1E-85 646.5 25.6 270 318-599 1-271 (271)
6 cd04453 S1_RNase_E S1_RNase_E: 99.6 1.1E-15 2.4E-20 134.2 8.3 40 108-147 3-42 (88)
7 PF00575 S1: S1 RNA binding do 97.6 0.00026 5.6E-09 59.1 7.7 36 110-147 2-37 (74)
8 cd04472 S1_PNPase S1_PNPase: P 97.2 0.0014 3.1E-08 53.2 6.9 32 113-146 1-32 (68)
9 COG1098 VacB Predicted RNA bin 96.9 0.00095 2.1E-08 62.6 4.0 36 111-148 4-39 (129)
10 cd05692 S1_RPS1_repeat_hs4 S1_ 96.8 0.0051 1.1E-07 49.6 7.2 32 113-146 1-32 (69)
11 smart00316 S1 Ribosomal protei 96.8 0.0051 1.1E-07 49.4 7.0 34 112-147 2-35 (72)
12 PTZ00248 eukaryotic translatio 96.7 0.04 8.8E-07 59.6 14.7 35 111-147 16-52 (319)
13 cd05698 S1_Rrp5_repeat_hs6_sc5 96.4 0.01 2.2E-07 49.0 6.7 32 113-146 1-32 (70)
14 cd05704 S1_Rrp5_repeat_hs13 S1 96.4 0.004 8.8E-08 52.6 3.9 36 112-148 3-38 (72)
15 cd04461 S1_Rrp5_repeat_hs8_sc7 96.2 0.013 2.9E-07 50.3 6.7 36 110-147 12-47 (83)
16 PRK07252 hypothetical protein; 96.2 0.015 3.2E-07 54.4 7.3 33 112-146 3-35 (120)
17 cd05685 S1_Tex S1_Tex: The C-t 96.2 0.012 2.7E-07 47.4 5.8 32 113-146 1-32 (68)
18 PRK08059 general stress protei 96.0 0.018 3.9E-07 53.8 6.9 35 110-146 5-39 (123)
19 cd05687 S1_RPS1_repeat_ec1_hs1 96.0 0.024 5.1E-07 46.9 6.9 33 113-147 1-33 (70)
20 cd05707 S1_Rrp5_repeat_sc11 S1 95.9 0.021 4.6E-07 47.1 6.1 32 113-146 1-32 (68)
21 cd05706 S1_Rrp5_repeat_sc10 S1 95.6 0.056 1.2E-06 45.0 7.6 33 112-146 3-35 (73)
22 cd05697 S1_Rrp5_repeat_hs5 S1_ 95.5 0.043 9.3E-07 45.4 6.5 32 113-146 1-32 (69)
23 COG0539 RpsA Ribosomal protein 95.4 0.03 6.5E-07 64.3 6.9 36 109-147 189-224 (541)
24 cd05686 S1_pNO40 S1_pNO40: pNO 95.4 0.069 1.5E-06 45.0 7.3 33 112-146 3-36 (73)
25 PRK08582 hypothetical protein; 95.3 0.052 1.1E-06 52.0 7.0 35 111-147 4-38 (139)
26 cd05691 S1_RPS1_repeat_ec6 S1_ 95.2 0.068 1.5E-06 44.1 6.6 32 113-146 1-32 (73)
27 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.1 0.076 1.6E-06 44.7 6.7 33 113-146 1-34 (71)
28 cd04452 S1_IF2_alpha S1_IF2_al 95.1 0.083 1.8E-06 44.1 6.9 34 112-147 3-38 (76)
29 cd05694 S1_Rrp5_repeat_hs2_sc2 94.7 0.11 2.3E-06 44.5 6.7 34 111-146 3-37 (74)
30 cd04455 S1_NusA S1_NusA: N-uti 94.7 0.12 2.5E-06 43.0 6.7 33 111-146 2-34 (67)
31 cd05688 S1_RPS1_repeat_ec3 S1_ 94.7 0.086 1.9E-06 42.6 5.8 32 112-146 1-32 (68)
32 TIGR02696 pppGpp_PNP guanosine 94.6 0.062 1.3E-06 63.7 6.7 36 110-147 645-680 (719)
33 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 94.6 0.15 3.1E-06 44.0 7.4 35 111-147 5-39 (86)
34 PRK03987 translation initiatio 94.5 0.21 4.6E-06 52.7 9.7 36 110-147 6-43 (262)
35 PRK05807 hypothetical protein; 94.4 0.16 3.4E-06 48.6 7.7 34 111-147 4-37 (136)
36 cd05705 S1_Rrp5_repeat_hs14 S1 94.4 0.12 2.6E-06 44.1 6.2 35 111-147 2-36 (74)
37 cd05684 S1_DHX8_helicase S1_DH 94.2 0.048 1E-06 46.4 3.4 33 113-147 1-36 (79)
38 TIGR03591 polynuc_phos polyrib 94.1 0.098 2.1E-06 62.0 7.0 37 109-147 615-651 (684)
39 PRK11824 polynucleotide phosph 93.8 0.15 3.4E-06 60.5 7.9 36 110-147 619-654 (693)
40 cd04454 S1_Rrp4_like S1_Rrp4_l 93.8 0.3 6.5E-06 41.8 7.6 35 110-146 4-38 (82)
41 cd05708 S1_Rrp5_repeat_sc12 S1 93.7 0.24 5.3E-06 41.1 6.7 33 112-146 2-35 (77)
42 PRK09521 exosome complex RNA-b 93.4 0.48 1E-05 47.4 9.4 36 109-146 61-106 (189)
43 cd00164 S1_like S1_like: Ribos 93.1 0.22 4.8E-06 39.0 5.3 29 116-146 1-29 (65)
44 PRK04163 exosome complex RNA-b 92.6 0.85 1.8E-05 47.3 10.3 45 101-147 50-96 (235)
45 PLN00207 polyribonucleotide nu 91.6 0.35 7.5E-06 58.8 6.8 35 111-147 752-787 (891)
46 cd05690 S1_RPS1_repeat_ec5 S1_ 91.4 0.19 4.2E-06 41.0 3.2 33 113-147 1-33 (69)
47 cd05689 S1_RPS1_repeat_ec4 S1_ 91.0 0.29 6.2E-06 40.6 3.8 34 112-147 3-36 (72)
48 PRK14865 rnpA ribonuclease P; 90.3 1.3 2.9E-05 41.0 8.0 53 333-385 49-110 (116)
49 PRK00588 rnpA ribonuclease P; 90.2 1.5 3.2E-05 41.1 8.1 52 333-384 47-108 (118)
50 PRK07899 rpsA 30S ribosomal pr 89.7 0.7 1.5E-05 52.9 6.8 35 110-147 206-240 (486)
51 PRK07400 30S ribosomal protein 89.3 0.82 1.8E-05 49.5 6.6 36 110-147 29-64 (318)
52 PRK03459 rnpA ribonuclease P; 89.1 2.1 4.6E-05 40.3 8.4 54 333-386 52-115 (122)
53 PRK07400 30S ribosomal protein 89.0 0.99 2.1E-05 48.9 6.9 39 106-147 190-228 (318)
54 PRK13806 rpsA 30S ribosomal pr 89.0 0.93 2E-05 51.8 7.1 36 110-147 200-235 (491)
55 cd04465 S1_RPS1_repeat_ec2_hs2 88.5 0.46 1E-05 39.0 3.2 32 113-147 1-32 (67)
56 cd05702 S1_Rrp5_repeat_hs11_sc 88.4 0.54 1.2E-05 39.1 3.6 33 113-147 1-33 (70)
57 PRK06299 rpsA 30S ribosomal pr 87.7 1.2 2.6E-05 51.5 7.0 35 110-147 199-233 (565)
58 cd04471 S1_RNase_R S1_RNase_R: 87.6 0.61 1.3E-05 39.3 3.5 34 112-147 1-35 (83)
59 PRK00396 rnpA ribonuclease P; 87.4 2.9 6.4E-05 39.8 8.2 58 333-393 50-117 (130)
60 PRK00499 rnpA ribonuclease P; 86.1 4.2 9.1E-05 37.6 8.3 54 333-386 42-105 (114)
61 PRK12269 bifunctional cytidyla 86.1 2.5 5.5E-05 51.7 8.8 38 108-147 574-611 (863)
62 TIGR00717 rpsA ribosomal prote 86.0 1.7 3.7E-05 49.5 7.0 36 110-147 357-392 (516)
63 cd04473 S1_RecJ_like S1_RecJ_l 85.9 1.1 2.3E-05 38.3 4.1 35 110-146 14-48 (77)
64 PRK04390 rnpA ribonuclease P; 85.6 4.6 0.0001 37.8 8.4 53 333-385 48-110 (120)
65 PRK09202 nusA transcription el 85.4 1.7 3.7E-05 49.6 6.6 123 290-461 171-296 (470)
66 COG0539 RpsA Ribosomal protein 85.0 1.4 3.1E-05 51.0 5.7 68 76-147 243-310 (541)
67 PRK12269 bifunctional cytidyla 83.9 2.5 5.4E-05 51.7 7.3 35 110-147 491-525 (863)
68 PRK01313 rnpA ribonuclease P; 83.6 5.6 0.00012 37.9 8.1 52 333-384 51-113 (129)
69 COG2183 Tex Transcriptional ac 83.1 1.7 3.8E-05 52.0 5.4 37 109-147 655-691 (780)
70 PRK06299 rpsA 30S ribosomal pr 82.7 2.9 6.3E-05 48.3 7.0 36 110-147 371-406 (565)
71 PRK06676 rpsA 30S ribosomal pr 82.4 3.1 6.7E-05 45.8 6.8 35 110-147 190-224 (390)
72 PRK07899 rpsA 30S ribosomal pr 82.3 3.1 6.8E-05 47.8 7.0 35 110-146 291-325 (486)
73 PRK13806 rpsA 30S ribosomal pr 80.4 1.6 3.4E-05 50.0 3.8 38 108-147 288-325 (491)
74 PRK01903 rnpA ribonuclease P; 80.4 9.3 0.0002 36.6 8.4 53 333-385 54-129 (133)
75 COG1185 Pnp Polyribonucleotide 80.3 1.4 3.1E-05 51.9 3.4 39 107-147 614-652 (692)
76 PRK00038 rnpA ribonuclease P; 79.8 10 0.00023 35.8 8.4 51 333-383 54-118 (123)
77 cd05693 S1_Rrp5_repeat_hs1_sc1 79.5 2 4.4E-05 38.9 3.4 35 111-147 2-36 (100)
78 TIGR00188 rnpA ribonuclease P 79.2 6 0.00013 36.0 6.4 51 333-383 45-104 (105)
79 PRK06676 rpsA 30S ribosomal pr 79.0 5.5 0.00012 43.8 7.4 36 110-147 15-51 (390)
80 PRK04820 rnpA ribonuclease P; 78.6 10 0.00022 36.9 8.2 54 333-386 52-115 (145)
81 PRK01492 rnpA ribonuclease P; 78.1 9.5 0.00021 35.7 7.6 53 332-384 49-115 (118)
82 PRK01732 rnpA ribonuclease P; 77.6 7.7 0.00017 36.1 6.7 53 333-385 49-111 (114)
83 PRK12327 nusA transcription el 77.6 4.6 9.9E-05 44.8 6.1 32 111-145 133-164 (362)
84 TIGR01953 NusA transcription t 77.4 5.2 0.00011 44.0 6.5 34 111-146 130-163 (341)
85 cd05703 S1_Rrp5_repeat_hs12_sc 74.4 3.7 8.1E-05 34.7 3.5 33 113-147 1-33 (73)
86 TIGR00717 rpsA ribosomal prote 74.2 2.7 5.9E-05 47.9 3.4 36 110-147 270-305 (516)
87 PF00684 DnaJ_CXXCXGXG: DnaJ c 73.5 2.6 5.5E-05 35.3 2.2 31 588-620 24-54 (66)
88 PRK00087 4-hydroxy-3-methylbut 72.5 7.2 0.00016 46.2 6.4 35 110-147 475-509 (647)
89 PF07092 DUF1356: Protein of u 71.9 1.5 3.3E-05 45.8 0.7 29 584-621 24-52 (238)
90 COG0594 RnpA RNase P protein c 71.0 23 0.0005 33.1 8.2 54 333-386 45-108 (117)
91 PRK00730 rnpA ribonuclease P; 71.0 12 0.00026 36.3 6.4 53 332-385 49-110 (138)
92 PF00825 Ribonuclease_P: Ribon 70.1 12 0.00026 34.2 6.0 54 333-386 46-110 (111)
93 COG2996 Predicted RNA-bindinin 69.6 9.4 0.0002 40.9 5.8 37 110-147 71-107 (287)
94 PRK00087 4-hydroxy-3-methylbut 65.1 16 0.00034 43.4 7.2 35 110-146 560-594 (647)
95 PRK03031 rnpA ribonuclease P; 64.9 36 0.00078 31.9 8.2 54 333-386 51-115 (122)
96 cd05791 S1_CSL4 S1_CSL4: CSL4, 59.9 11 0.00024 33.6 3.7 35 111-147 5-47 (92)
97 PRK12328 nusA transcription el 58.1 24 0.00052 39.5 6.6 33 110-144 136-168 (374)
98 TIGR02063 RNase_R ribonuclease 57.5 20 0.00044 42.9 6.4 35 111-147 626-661 (709)
99 TIGR02642 phage_xxxx uncharact 51.8 7.7 0.00017 39.3 1.4 17 608-624 116-132 (186)
100 PRK11642 exoribonuclease R; Pr 50.6 34 0.00075 41.9 6.9 35 111-147 642-677 (813)
101 cd04460 S1_RpoE S1_RpoE: RpoE, 48.9 19 0.00041 32.0 3.3 30 115-147 2-31 (99)
102 PTZ00162 DNA-directed RNA poly 46.3 68 0.0015 32.1 7.1 37 108-147 77-113 (176)
103 TIGR00358 3_prime_RNase VacB a 44.4 45 0.00098 39.8 6.5 35 111-147 571-606 (654)
104 COG1093 SUI2 Translation initi 44.1 45 0.00097 35.7 5.6 35 110-146 9-45 (269)
105 TIGR03147 cyt_nit_nrfF cytochr 43.1 19 0.0004 34.5 2.4 35 609-643 42-76 (126)
106 TIGR02642 phage_xxxx uncharact 42.9 14 0.0003 37.5 1.7 16 607-622 99-114 (186)
107 TIGR00448 rpoE DNA-directed RN 40.0 31 0.00068 34.2 3.6 35 110-147 79-113 (179)
108 cd05695 S1_Rrp5_repeat_hs3 S1_ 39.0 36 0.00077 28.1 3.3 32 113-146 1-32 (66)
109 PRK10144 formate-dependent nit 38.9 24 0.00052 33.8 2.5 36 608-643 41-76 (126)
110 COG1568 Predicted methyltransf 37.6 30 0.00064 37.6 3.2 32 606-640 90-121 (354)
111 PRK08563 DNA-directed RNA poly 34.2 43 0.00093 33.3 3.6 35 110-147 79-113 (187)
112 COG0484 DnaJ DnaJ-class molecu 33.9 15 0.00033 40.9 0.4 53 333-393 10-64 (371)
113 PRK12329 nusA transcription el 32.9 1.1E+02 0.0023 35.3 6.7 32 110-143 150-186 (449)
114 cd05790 S1_Rrp40 S1_Rrp40: Rrp 32.2 68 0.0015 28.7 4.1 34 110-145 4-37 (86)
115 COG0484 DnaJ DnaJ-class molecu 31.0 29 0.00062 38.8 1.9 22 366-387 12-33 (371)
116 PF03918 CcmH: Cytochrome C bi 30.8 21 0.00045 34.9 0.7 36 608-643 41-76 (148)
117 KOG2925 Predicted translation 30.3 27 0.00059 34.4 1.4 24 481-504 53-76 (167)
118 COG3088 CcmH Uncharacterized p 28.4 39 0.00085 33.3 2.1 35 609-643 46-80 (153)
119 PF08800 VirE_N: VirE N-termin 26.9 1.5E+02 0.0032 28.3 5.8 51 541-596 26-77 (136)
120 PHA02945 interferon resistance 26.5 1.8E+02 0.004 26.3 5.8 33 111-146 10-44 (88)
121 PF11314 DUF3117: Protein of u 26.5 47 0.001 26.9 1.9 15 486-500 22-36 (51)
122 PRK14296 chaperone protein Dna 26.5 41 0.00088 37.4 2.1 26 333-358 10-36 (372)
123 smart00778 Prim_Zn_Ribbon Zinc 26.5 28 0.00062 26.5 0.6 12 607-618 3-14 (37)
124 cd05792 S1_eIF1AD_like S1_eIF1 25.7 44 0.00095 29.5 1.7 23 479-501 29-51 (78)
125 COG3585 MopI Molybdopterin-bin 25.6 44 0.00096 28.7 1.7 26 112-137 5-30 (69)
126 PRK14298 chaperone protein Dna 24.7 40 0.00086 37.5 1.6 26 333-358 11-37 (377)
127 PF04472 DUF552: Protein of un 24.3 1.4E+02 0.0031 25.3 4.6 41 531-575 10-50 (73)
128 PRK06921 hypothetical protein; 23.7 40 0.00087 35.6 1.4 13 608-620 33-45 (266)
129 PRK14290 chaperone protein Dna 23.2 61 0.0013 35.8 2.7 26 333-358 9-35 (365)
130 TIGR03655 anti_R_Lar restricti 23.1 40 0.00086 27.0 0.9 11 608-618 2-12 (53)
131 PRK14277 chaperone protein Dna 22.4 53 0.0012 36.6 2.1 26 333-358 11-37 (386)
132 PF08273 Prim_Zn_Ribbon: Zinc- 21.8 24 0.00053 27.3 -0.5 13 607-619 3-15 (40)
133 PLN03165 chaperone protein dna 21.7 63 0.0014 30.3 2.1 16 604-619 72-87 (111)
134 PF08508 DUF1746: Fungal domai 21.5 63 0.0014 30.5 2.0 20 546-566 84-103 (116)
135 TIGR00630 uvra excinuclease AB 21.4 1.2E+02 0.0027 37.8 5.0 35 548-583 199-233 (924)
136 cd06836 PLPDE_III_ODC_DapDC_li 21.0 7.7E+02 0.017 27.2 10.7 150 409-574 72-242 (379)
137 KOG1070 rRNA processing protei 20.9 1.4E+02 0.003 38.9 5.2 78 68-151 557-636 (1710)
138 PRK00349 uvrA excinuclease ABC 20.8 1.3E+02 0.0028 37.8 5.0 34 548-582 203-236 (943)
139 PF07013 DUF1314: Protein of u 20.3 76 0.0017 31.9 2.4 33 479-515 5-37 (177)
140 PTZ00037 DnaJ_C chaperone prot 20.2 59 0.0013 36.9 1.8 26 333-358 34-60 (421)
141 PRK14282 chaperone protein Dna 20.1 67 0.0014 35.6 2.2 26 333-358 10-36 (369)
No 1
>PRK11712 ribonuclease G; Provisional
Probab=100.00 E-value=5.6e-126 Score=1045.47 Aligned_cols=446 Identities=33% Similarity=0.585 Sum_probs=408.3
Q ss_pred CceEEEEEecCCCeEEEEEEECCEEeEEEEeeCCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcC
Q 006020 74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF 153 (664)
Q Consensus 74 ~~~~ilIn~~~~~e~RvAvlEdg~L~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~~~~~~ 153 (664)
|+++|+||..+ .++|+|++|||+|+||++|+.+...++||||+|+|+||+|||||||||||.+||||||++|. +
T Consensus 1 M~~~i~i~~~~-~e~r~Alledg~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~-----~ 74 (489)
T PRK11712 1 MTAELLVNVTP-SETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI-----V 74 (489)
T ss_pred CceEEEEecCC-CeEEEEEEECCEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc-----c
Confidence 78999999987 79999999999999999999999999999999999999999999999999999999999986 2
Q ss_pred CcccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 006020 154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD 233 (664)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (664)
|++..... ++
T Consensus 75 ~~~~~~~~------------------------------------------------~~---------------------- 84 (489)
T PRK11712 75 PHTECVAG------------------------------------------------EE---------------------- 84 (489)
T ss_pred chhhhccc------------------------------------------------cc----------------------
Confidence 22100000 00
Q ss_pred CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCcee
Q 006020 234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL 313 (664)
Q Consensus 234 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQVvKE~igtKGprL 313 (664)
+.. . . ..++...+++||+|||||+|||+++|||+|
T Consensus 85 -------------------~~~------------~-----------~---~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~l 119 (489)
T PRK11712 85 -------------------QKQ------------F-----------V---VRDISELVRQGQDIMVQVVKDPLGTKGARL 119 (489)
T ss_pred -------------------ccc------------c-----------c---cccHHHhccCCCEEEEEEEeCCcCCCCCeE
Confidence 000 0 0 002345799999999999999999999999
Q ss_pred eecceeeceeEEEeeCCCceeeecccChh-HHHHHHHHHHhcCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 006020 314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH 392 (664)
Q Consensus 314 T~~ISL~GRYlVL~P~~~~IgVSrKI~de-eR~rLk~i~~~l~~eg~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~ 392 (664)
|++|||||||+||+|++++|||||||.++ +|+||+.++..+.++++|+||||+|+++++++|.+|+++|.+.|+.|.++
T Consensus 120 T~~Isl~GrylVl~P~~~~vgiSrKI~de~~R~rLk~i~~~~~~~~~GvIiRT~A~~a~~eel~~dl~~L~~~w~~i~~~ 199 (489)
T PRK11712 120 TTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQGGFIIRTAAEGVGEEELAQDAAFLKRLWTKVMER 199 (489)
T ss_pred EEEEEeccceEEEECCCCCeeEecCCCChHHHHHHHHHHHhhCCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999876 69999999999988889999999999999999999999999999999999
Q ss_pred HHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCccCceeeccCCcCcccc
Q 006020 393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472 (664)
Q Consensus 393 ak~~~~~~~~g~~~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~pLF~~ 472 (664)
++.+ ++|+|||++.+++.+++||++++++++|+||+++.|+++++|+..+.|++..++++|.+..|||+.
T Consensus 200 ~~~~----------~~p~ll~~e~~~~~~~lrD~~~~~~~~IivD~~~~~~~i~~~~~~~~p~~~~~v~~y~~~~plF~~ 269 (489)
T PRK11712 200 KKRY----------QTRYQLYGELALAQRVLRDFVGAELDRIRVDSRLTYEELKEFTSEYIPEMTDKLEHYSGRQPIFDL 269 (489)
T ss_pred HhcC----------CCCeEEEcCCcHHHHHHHHhccCCCCEEEECCHHHHHHHHHHHHHhCccccceeEEecCCCChhHh
Confidence 9876 589999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 006020 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (664)
Q Consensus 473 y~Ie~~I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVID 552 (664)
|||+++|+++++++||||||||||||+||||||||||||+ +++++++++|+++||+|||+||||||||||||||||||
T Consensus 270 y~ie~~i~~~l~~~V~L~sGg~lvIe~TeAlt~IDVnsGk--~~~~~~~eet~~~tN~eAa~eiarqlrLR~igGiIviD 347 (489)
T PRK11712 270 YDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGA--FVGHRNLEETIFNTNIEATQAIARQLRLRNLGGIIIID 347 (489)
T ss_pred cCHHHHHHHHhcCcEEcCCCcEEEEeccccEEEEEecCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEE
Confidence 9999999999999999999999999999999999999999 46778999999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCcchhccccCCCCCceeEEechhhHHHHHHHH
Q 006020 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (664)
Q Consensus 553 FIdM~~~~~r~~V~~~Lk~~lk~D~~kt~V~giT~LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~s~et~~~~i~re 632 (664)
||||+++++|++|++.|+++|++|+++|+|+|||+||||||||||.|+||.++++++||+|+|+|+|+|+++++.+|+|+
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 HHHHHhhcCCCCceEEEEeechh
Q 006020 633 ISRLLVSKSYNQSTFYFIRHIPK 655 (664)
Q Consensus 633 i~~~~~~~~~~~~~~~~~~~~~~ 655 (664)
|.+... +.+...+. +..+|.
T Consensus 428 i~~~~~--~~~~~~~~-~~~~p~ 447 (489)
T PRK11712 428 IVRVHH--AYDSDRFL-VYASPA 447 (489)
T ss_pred HHHHHh--hCCCceEE-EEECHH
Confidence 998864 33344554 444443
No 2
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=100.00 E-value=8.7e-122 Score=997.42 Aligned_cols=412 Identities=40% Similarity=0.682 Sum_probs=382.1
Q ss_pred EEEEEEECCEEeEEEEeeCCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCCcccccchhhhccc
Q 006020 88 QRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNG 167 (664)
Q Consensus 88 ~RvAvlEdg~L~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~~~~~~~~~~~~~~~~~~~~ 167 (664)
+|+|++|||+|+||++|+.....++||||+|+|++|+|||||||||||.+++||||++|.. |.+.....
T Consensus 1 ~r~Alledg~l~e~~ie~~~~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-----~~~~~~~~------ 69 (414)
T TIGR00757 1 TRVALVEGGRLFDLIIERPKSRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-----PNYECLAP------ 69 (414)
T ss_pred CEEEEEECCEEEEEEEecCcCcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-----chhhcccc------
Confidence 5999999999999999999999999999999999999999999999999999999999852 21100000
Q ss_pred chhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCCCCccccccccCC
Q 006020 168 SASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGD 247 (664)
Q Consensus 168 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 247 (664)
++
T Consensus 70 ------------------------------------------~~------------------------------------ 71 (414)
T TIGR00757 70 ------------------------------------------AE------------------------------------ 71 (414)
T ss_pred ------------------------------------------cc------------------------------------
Confidence 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceeeecceeeceeEEEe
Q 006020 248 HHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILI 327 (664)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQVvKE~igtKGprLT~~ISL~GRYlVL~ 327 (664)
.. . . . ..++...+++||+|+|||+|||+++|||+||++|||||||+||+
T Consensus 72 ----~~-~------------~-----------~---~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~lT~~Isl~GrylVl~ 120 (414)
T TIGR00757 72 ----AK-R------------E-----------A---GPSISELLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLM 120 (414)
T ss_pred ----cc-c------------c-----------c---cCCHHHhCcCCCEEEEEEeeCCcCCCCCeEEEEEEeccceEEEe
Confidence 00 0 0 0 00233569999999999999999999999999999999999999
Q ss_pred eCCCceeeecccChh-HHHHHHHHHHh-cCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCcc
Q 006020 328 TSCDRIGVSRKITGV-ERTRLKVIAKT-LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVE 405 (664)
Q Consensus 328 P~~~~IgVSrKI~de-eR~rLk~i~~~-l~~eg~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~ak~~~~~~~~g~~ 405 (664)
|+++++||||||.++ +|++|+.++.. +.++++|+||||+|+++++++|.+|+++|.+.|+.|+++++.+
T Consensus 121 P~~~~v~ISrkI~d~~eR~rL~~i~~~~~~~~~~GvIiRT~A~~a~~eel~~el~~L~~~w~~I~~~~~~~--------- 191 (414)
T TIGR00757 121 PNNSHVGVSRRIESGEERERLKKLLRSEELPEGMGLIIRTAAEGASEEALIKDLEFLLRKWEKIKEKAQKR--------- 191 (414)
T ss_pred cCCCCceeecccCCHHHHHHHHHHHHhhccCCCceEEEEeccCCCCHHHHHHHHHHHHHHHHHHHHHHhcC---------
Confidence 999999999999875 79999999995 8888999999999999999999999999999999999999865
Q ss_pred CCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCccCceeeccCCcCcccccCHHHHHHhHhCC
Q 006020 406 GAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSK 485 (664)
Q Consensus 406 ~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~pLF~~y~Ie~~I~~~l~r 485 (664)
++|.|||++++++.+++||++++++++|+||+++.|+++++|++.+.|.+..+|++|.+..|||+.|+|+++|++++++
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 5899999999999999999999999999999999999999999999999999999999989999999999999999999
Q ss_pred ceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHH
Q 006020 486 RVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLV 565 (664)
Q Consensus 486 rV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVIDFIdM~~~~~r~~V 565 (664)
+||||||||||||+||||||||||||+ ++++.++++|+++||+|||+||||||||||||||||||||||+++++|++|
T Consensus 271 ~V~L~~Gg~lvIe~TEALtvIDVNsG~--~~~~~~~eet~~~~NleAa~EIaRQlRLRnigGiIvIDFIdM~~~~~~~~v 348 (414)
T TIGR00757 271 KVWLPSGGYIVIDQTEALTTIDVNSGR--FTGGGNLEETALNTNLEAAKEIARQLRLRNLGGIIIIDFIDMKSEKNQRRV 348 (414)
T ss_pred cEECCCCeEEEEecCccEEEEEecCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEEECCCCCCHHHHHHH
Confidence 999999999999999999999999999 467789999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCcchhccccCCCCCceeEEechhhHHHHHHH
Q 006020 566 YEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (664)
Q Consensus 566 ~~~Lk~~lk~D~~kt~V~giT~LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~s~et~~~~i~r 631 (664)
++.|+++|++|+++++|+|||+||||||||||.|+||.++++++||+|+|+|+|+|+++++++|+|
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 999999999999999999999999999999999999999999999999999999999999999875
No 3
>PRK10811 rne ribonuclease E; Reviewed
Probab=100.00 E-value=1e-116 Score=1003.42 Aligned_cols=442 Identities=34% Similarity=0.593 Sum_probs=406.0
Q ss_pred eEEEEEecCCCeEEEEEEECCEEeEEEEeeCCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCCc
Q 006020 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP 155 (664)
Q Consensus 76 ~~ilIn~~~~~e~RvAvlEdg~L~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~~~~~~~~ 155 (664)
++||||.....+.|+||++||+|.||+||+.++...+||||+|+|+||+|||+|||||||.+++|||+++|...++ |+.
T Consensus 2 kkIiIn~~~~~e~RvALvEdgrL~EL~IEr~~~e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~-f~~ 80 (1068)
T PRK10811 2 KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREY-FPA 80 (1068)
T ss_pred cEEEEeccCCceEEEEEEcCCEEEEEEeccCccccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccc-ccc
Confidence 7899999843689999999999999999998888899999999999999999999999999999999999975443 110
Q ss_pred ccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCCC
Q 006020 156 FRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGE 235 (664)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (664)
-+.
T Consensus 81 ~~~----------------------------------------------------------------------------- 83 (1068)
T PRK10811 81 NYS----------------------------------------------------------------------------- 83 (1068)
T ss_pred ccc-----------------------------------------------------------------------------
Confidence 000
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceeee
Q 006020 236 PEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTA 315 (664)
Q Consensus 236 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQVvKE~igtKGprLT~ 315 (664)
.+ . .+++...|++||+|||||+||++++|||+||+
T Consensus 84 ------------~~-----~----------------------------~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LTt 118 (1068)
T PRK10811 84 ------------AH-----G----------------------------RPNIKDVLREGQEVIVQIDKEERGNKGAALTT 118 (1068)
T ss_pred ------------cc-----c----------------------------ccccccccCCCCEEEEEEeecccCCCCCceee
Confidence 00 0 00223468999999999999999999999999
Q ss_pred cceeeceeEEEeeCCCc-eeeecccChhHHHHHHHHHHhc-CCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 006020 316 YPKLRSRFWILITSCDR-IGVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (664)
Q Consensus 316 ~ISL~GRYlVL~P~~~~-IgVSrKI~deeR~rLk~i~~~l-~~eg~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~a 393 (664)
+|||+|||+||||++++ +||||||.+++|.+|+.++..+ .++++|+||||+|+|+++++|..||++|+..|+.|++++
T Consensus 119 ~ISLpGRYLVLtP~~~~~IgISRKI~deeR~rLkeil~~l~lpe~~GIIVRTaAegAseE~L~~ELe~L~~~w~~I~k~a 198 (1068)
T PRK10811 119 FISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAA 198 (1068)
T ss_pred eEEecceeEEEeCCCCCcceecCCCchHHHHHHHHHHHhhccCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999988 7999999988899999999876 788999999999999999999999999999999999998
Q ss_pred HHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhh-CCCccCceeeccCCcCcccc
Q 006020 394 KSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLFDK 472 (664)
Q Consensus 394 k~~~~~~~~g~~~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~~-~p~~~~~v~ly~~~~pLF~~ 472 (664)
+++ ++|.|||++.+++.+++|||+..++++|+||+++.|+.++.|+..+ .|++..+|++|.+..|||+.
T Consensus 199 ~~~----------~aP~LLy~e~~~~~ralRD~l~~dv~eIvVDd~e~~e~ik~yl~~~~~pd~~~kI~lY~~~~pLFe~ 268 (1068)
T PRK10811 199 ESR----------PAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSH 268 (1068)
T ss_pred hcC----------CCceEeecCCchHHHHHHHhcccCccEEEECCHHHHHHHHHHHHHhcccccccceeeecCCCChHHh
Confidence 876 5899999999999999999999999999999999999999999988 58877899999999999999
Q ss_pred cCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 006020 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD 552 (664)
Q Consensus 473 y~Ie~~I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVID 552 (664)
|+|+.+|++||+++||||||||||||+||||||||||||++ +++.+.++|+|+||++||+||||||||||||||||||
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 99999999999999999999999999999999999999994 5677999999999999999999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCcchhccccCCCCCceeEEechhhHHHHHHHH
Q 006020 553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQE 632 (664)
Q Consensus 553 FIdM~~~~~r~~V~~~Lk~~lk~D~~kt~V~giT~LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~s~et~~~~i~re 632 (664)
||||+.++|+++|++.|+++|++|+.+++|+|||+||||||||||.|+||.++++++||+|+|+|+|+|.+++++.|.|+
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 HHHHHhhcCCCCceEEEEeech
Q 006020 633 ISRLLVSKSYNQSTFYFIRHIP 654 (664)
Q Consensus 633 i~~~~~~~~~~~~~~~~~~~~~ 654 (664)
|.+... ..+...|++..+.+
T Consensus 427 I~re~~--~~~~~~~~i~~~~~ 446 (1068)
T PRK10811 427 IEEEAL--KENTQEVHAIVPVP 446 (1068)
T ss_pred HHHHHh--hcccccEEEEECHH
Confidence 999864 34556677766654
No 4
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-100 Score=844.92 Aligned_cols=437 Identities=37% Similarity=0.617 Sum_probs=402.8
Q ss_pred ceEEEEEecCCCeEEEEEEECCEEeEEEEeeCCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeeccccCCCCcCC
Q 006020 75 STVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFP 154 (664)
Q Consensus 75 ~~~ilIn~~~~~e~RvAvlEdg~L~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~~~~~~~ 154 (664)
++.||||.++ .|+|||++++|.|.|+++|+..+.+++||||+|||+||+|||||||||||.+||||||+++. .+
T Consensus 1 ~k~~~i~~~~-~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~-----~~ 74 (487)
T COG1530 1 MKKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEI-----VP 74 (487)
T ss_pred CceEEEeccc-ceeEEEEEeCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEeccc-----ch
Confidence 4689999998 89999999999999999999999999999999999999999999999999999999999985 22
Q ss_pred cccccchhhhcccchhhHHHHhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCCC
Q 006020 155 PFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDG 234 (664)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (664)
+.....
T Consensus 75 -~~~~~~------------------------------------------------------------------------- 80 (487)
T COG1530 75 -YFRAVL------------------------------------------------------------------------- 80 (487)
T ss_pred -hhhhcc-------------------------------------------------------------------------
Confidence 111000
Q ss_pred CCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEeecCCCCCCceee
Q 006020 235 EPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLT 314 (664)
Q Consensus 235 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQVvKE~igtKGprLT 314 (664)
.+++...++.||.++|||+|+|.|+|||++|
T Consensus 81 -------------------------------------------------~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 81 -------------------------------------------------EEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred -------------------------------------------------cccceeeecCCceEEEEEEeecCccccccce
Confidence 0012346899999999999999999999999
Q ss_pred ecceeeceeEEEeeCCCcee-eecccChh-HHHHHHHHHHhcCCC-CeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 006020 315 AYPKLRSRFWILITSCDRIG-VSRKITGV-ERTRLKVIAKTLQPE-GFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME 391 (664)
Q Consensus 315 ~~ISL~GRYlVL~P~~~~Ig-VSrKI~de-eR~rLk~i~~~l~~e-g~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~ 391 (664)
++||++|||+||||+.+.++ +|+||+++ +|++|+.++..+.+. ++|+|+||+|++++.++|.+|+++|...|+.|+.
T Consensus 112 ~~Is~~grylVl~p~~~~~g~is~ri~~~~er~~Lk~~~~~l~~~~~~g~iiRTa~~g~~~eel~~d~~~l~~~w~~i~~ 191 (487)
T COG1530 112 TDISLAGRYLVLMPNAPDVGGISRRIEGEIERERLKEIVRELVDPGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILE 191 (487)
T ss_pred eEEeeceeEEEEcCCCCcccceeeEeCCHHHHHhHHHHHhhccCcCCceEEEeecccCccHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999988 99999985 899999999998865 4799999999999999999999999999999999
Q ss_pred HHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCccCceeeccCCcCccc
Q 006020 392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFD 471 (664)
Q Consensus 392 ~ak~~~~~~~~g~~~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~pLF~ 471 (664)
++... ++|.+||++.+++.+++|||++.++.+|+||+...|..+++|+..+.|+...++++|.+..|+|+
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 98765 58999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCHHHHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEE
Q 006020 472 KFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVV 551 (664)
Q Consensus 472 ~y~Ie~~I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVI 551 (664)
.|+++.+|+++++|+|||||||||||++|||||+||||||++ ++..+.++|+++||+|||.||||||||||+||||+|
T Consensus 262 ~~~ie~~i~~al~r~V~L~sGG~~vId~tEAlt~IDVnsg~~--~~~~~~eeta~~tNleAa~eiarqlrlR~lgGiIiI 339 (487)
T COG1530 262 LFGIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRF--TGAGDLEETAVNTNLEAAEEIARQLRLRNLGGIIII 339 (487)
T ss_pred hhhHHHHHHHhhhheEecCCCCceeEeccceeEEEEccCccc--cccCchHHhhhhhhHHHHHHHHHHHhhcccCCeEEE
Confidence 999999999999999999999999999999999999999995 455669999999999999999999999999999999
Q ss_pred EcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCCCCcchhccccCCCCCceeEEechhhHHHHHHH
Q 006020 552 DFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEALETSFSKIEQ 631 (664)
Q Consensus 552 DFIdM~~~~~r~~V~~~Lk~~lk~D~~kt~V~giT~LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~s~et~~~~i~r 631 (664)
|||||..+++++.|+..|+++|+.|++++++.+||+|||+||||||.++||.+.++++||.|+|+|++.+.+++++.+.|
T Consensus 340 DfIdm~~~~~~~~v~~~l~~~l~~dr~r~~i~~~s~~Gl~emtR~R~~~sl~~~~~~~cp~c~G~g~v~~~~~~~~~i~R 419 (487)
T COG1530 340 DFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTRKRTRESLLEVLSERCPGCKGTGHVRSTESELLHILR 419 (487)
T ss_pred EeeeccchhhhHHHHHHHHHHhccCCcccccccccccCceEEEEEecCCCCceeeeeECCCceeeEEEecCchhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCceEEEEee
Q 006020 632 EISRLLVSKSYNQSTFYFIRH 652 (664)
Q Consensus 632 ei~~~~~~~~~~~~~~~~~~~ 652 (664)
.|.......+....-+.+..+
T Consensus 420 ~i~~~~~~~~~~~~~~~~~~~ 440 (487)
T COG1530 420 YIEEEADINKTPEVGVEVPPA 440 (487)
T ss_pred cchhhhccccCccceEEechh
Confidence 998875444444444444444
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=5.2e-81 Score=646.51 Aligned_cols=270 Identities=48% Similarity=0.754 Sum_probs=222.0
Q ss_pred eeeceeEEEeeCCCceeeecccChh-HHHHHHHHHHhcCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 006020 318 KLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSA 396 (664)
Q Consensus 318 SL~GRYlVL~P~~~~IgVSrKI~de-eR~rLk~i~~~l~~eg~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~ak~~ 396 (664)
||||||+||+|++++|+|||||+++ +|++|+++++.+.++++|+||||+|+++++++|.+|+++|.++|+.|+++++..
T Consensus 1 sl~GRYlVl~P~~~~i~vSrKI~d~~~R~~Lk~i~~~~~~~~~GvIiRT~A~~a~~e~L~~El~~L~~~w~~I~~~~~~~ 80 (271)
T PF10150_consen 1 SLPGRYLVLTPGGNGIGVSRKISDEEERERLKKILESLLPEGEGVIIRTAAAGASEEELEKELEELREKWEEIQKKAKSR 80 (271)
T ss_dssp SEETSSEEEETT-TT-EE-TTS-TH-HHHHHHHHHHTS--TT-EEEE-GGGGGS-HHHHHHHHHHHHHHHHHHHHHHCTS
T ss_pred CCCCceEEEecCCCCceecCCCCCchhHHHHHHHHHHhCCCCCeEEEecCcCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7999999999999999999999987 799999999999999999999999999999999999999999999999998765
Q ss_pred hhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHhhCCCccCceeeccCCcCcccccCHH
Q 006020 397 ALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIE 476 (664)
Q Consensus 397 ~~~~~~g~~~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~~~p~~~~~v~ly~~~~pLF~~y~Ie 476 (664)
++|+|||++++++.+++||++++++++|+||+++.|+++++|++.+.|++..++++|.+..|+|+.|+|+
T Consensus 81 ----------~~P~LLy~~~~~~~~~lrd~~~~~~~~Iivd~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~lf~~~~i~ 150 (271)
T PF10150_consen 81 ----------KAPSLLYREPDLYERVLRDYLDEDVDEIIVDDKEIYEEIKEYLKEFSPDLKDKIELYKDEEPLFELYGIE 150 (271)
T ss_dssp -----------STEEEE-STSHHHHHHHHH--TTEEEEEES-HHHHHHHHHHHHTT-GGGTTTEEE--SSS-HHHHTT-H
T ss_pred ----------CCCeEEEeCCChhhHHHhhcCcCCCCEEEECCcHHHHHHHHHHHHhCccccceEEEecCCCChHHhCCHH
Confidence 4799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhCCceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEEcCCC
Q 006020 477 EEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDM 556 (664)
Q Consensus 477 ~~I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~t~l~tNlEAA~EIARQLRLRnIgGIIVIDFIdM 556 (664)
.+|+++++++||||||||||||+||||||||||||++ +++.+.++++++||++||+||||||||||||||||||||||
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 9999999999999999999999999999999999994 56778999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHhcCCCCcEEeccCCCeeEEEeecCCC
Q 006020 557 ADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRVR 599 (664)
Q Consensus 557 ~~~~~r~~V~~~Lk~~lk~D~~kt~V~giT~LGLvEiTRkR~r 599 (664)
++++++++|++.|+++|++|+.+++|+|||+||||||||||.|
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=1.1e-15 Score=134.18 Aligned_cols=40 Identities=30% Similarity=0.615 Sum_probs=37.0
Q ss_pred CCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+..+|+||.|+|++|.|.|.|||||+|.+++||||+++.
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~sei 42 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDI 42 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHc
Confidence 4567999999999999999999999999999999999874
No 7
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=97.60 E-value=0.00026 Score=59.08 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=33.0
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
...|.||.|+|.+|.| .++|||+|.+..||+++.+.
T Consensus 2 ~~~G~iv~g~V~~v~~--~g~~V~l~~~~~g~ip~~~l 37 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVED--FGVFVDLGNGIEGFIPISEL 37 (74)
T ss_dssp SSTTSEEEEEEEEEET--TEEEEEESTSSEEEEEGGGS
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCcEEEEEEeehh
Confidence 3589999999999999 99999999999999988763
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=97.15 E-value=0.0014 Score=53.18 Aligned_cols=32 Identities=34% Similarity=0.494 Sum_probs=30.0
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|++|.|+|++|.| .++||+|+.+.+|||++.+
T Consensus 1 g~~~~g~V~~v~~--~G~~v~l~~~~~g~l~~~~ 32 (68)
T cd04472 1 GKIYEGKVVKIKD--FGAFVEILPGKDGLVHISE 32 (68)
T ss_pred CCEEEEEEEEEEE--eEEEEEeCCCCEEEEEhHH
Confidence 7899999999999 9999999999999998765
No 9
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=96.90 E-value=0.00095 Score=62.64 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=33.0
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeeccccC
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~ 148 (664)
-+|+++.|+|+.|.|- +|||++-.+..|+.||+++.
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 4899999999999995 89999999999999998863
No 10
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=96.80 E-value=0.0051 Score=49.62 Aligned_cols=32 Identities=44% Similarity=0.645 Sum_probs=29.7
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|++|.|+|+++.+ .++||+|+.+..||||..+
T Consensus 1 G~~~~g~V~~i~~--~g~~v~i~~~~~g~l~~~~ 32 (69)
T cd05692 1 GSVVEGTVTRLKP--FGAFVELGGGISGLVHISQ 32 (69)
T ss_pred CCEEEEEEEEEEe--eeEEEEECCCCEEEEEhHH
Confidence 7899999999998 6999999999999998765
No 11
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.78 E-value=0.0051 Score=49.36 Aligned_cols=34 Identities=38% Similarity=0.612 Sum_probs=31.1
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.|.+|.|+|.++.+ +++||++|.+..|||+..+.
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 79999999999999988763
No 12
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=96.66 E-value=0.04 Score=59.59 Aligned_cols=35 Identities=14% Similarity=0.274 Sum_probs=31.1
Q ss_pred ccCCEEEEEEeeecCCcceEEeccc--CCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG--~~k~aFL~~~d~ 147 (664)
-+|++..|+|++|.+ .+|||+++ .+..||+|+++.
T Consensus 16 ~~GdvV~g~V~~I~d--~GafV~L~EY~gvEGlIhiSEl 52 (319)
T PTZ00248 16 EEDDLVMVKVVRITE--MGAYVSLLEYDDIEGMILMSEL 52 (319)
T ss_pred CCCCEEEEEEEEEeC--CeEEEEecCCCCcEEEEEHHHh
Confidence 489999999999998 69999996 589999998773
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=96.42 E-value=0.01 Score=48.98 Aligned_cols=32 Identities=19% Similarity=0.292 Sum_probs=29.7
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.+|.|+|++|.+ .++||+++.+..||+|+++
T Consensus 1 g~~~~g~V~~v~~--~G~~V~l~~~~~gli~~s~ 32 (70)
T cd05698 1 GLKTHGTIVKVKP--NGCIVSFYNNVKGFLPKSE 32 (70)
T ss_pred CCEEEEEEEEEec--CcEEEEECCCCEEEEEHHH
Confidence 7899999999988 7999999999999998876
No 14
>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=96.35 E-value=0.004 Score=52.55 Aligned_cols=36 Identities=33% Similarity=0.526 Sum_probs=32.2
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeeccccC
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR 148 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~~ 148 (664)
+|.||.|+|++|.+. -+|||+++.+..||+|+.+..
T Consensus 3 ~G~iv~G~V~~i~~~-~g~~v~l~~~~~Glvhis~~s 38 (72)
T cd05704 3 EGAVTLGMVTKVIPH-SGLTVQLPFGKTGLVSIFHLS 38 (72)
T ss_pred CCCEEEEEEEEeeCC-cEEEEECCCCCEEEEEHHHhc
Confidence 799999999999876 457999999999999999863
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=96.25 E-value=0.013 Score=50.31 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=32.5
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.||.|+|++|.+ .++||+++.+..||+|+.+.
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 89999999999999988763
No 16
>PRK07252 hypothetical protein; Provisional
Probab=96.23 E-value=0.015 Score=54.44 Aligned_cols=33 Identities=30% Similarity=0.491 Sum_probs=30.8
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
+|++|.|+|++|.+ .+|||+|+.+..||+|+.+
T Consensus 3 vG~iv~G~V~~V~~--~G~fVei~~~~~Gllhise 35 (120)
T PRK07252 3 IGDKLKGTITGIKP--YGAFVALENGTTGLIHISE 35 (120)
T ss_pred CCCEEEEEEEEEeC--cEEEEEECCCCEEEEEHHH
Confidence 69999999999998 8999999999999998876
No 17
>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=96.20 E-value=0.012 Score=47.36 Aligned_cols=32 Identities=41% Similarity=0.571 Sum_probs=29.4
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|++|.|+|.+|.| .++||+++....||+|..+
T Consensus 1 g~~~~g~V~~i~~--~G~fv~l~~~~~g~~~~~~ 32 (68)
T cd05685 1 GMVLEGVVTNVTD--FGAFVDIGVKQDGLIHISK 32 (68)
T ss_pred CCEEEEEEEEEec--ccEEEEcCCCCEEEEEHHH
Confidence 7899999999998 6999999999999998765
No 18
>PRK08059 general stress protein 13; Validated
Probab=96.04 E-value=0.018 Score=53.79 Aligned_cols=35 Identities=34% Similarity=0.497 Sum_probs=32.0
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
-.+|++|.|+|.+|.+ .++||+|+.+..||+|+.+
T Consensus 5 ~k~G~iv~G~V~~i~~--~G~fV~i~~~~~Gli~~se 39 (123)
T PRK08059 5 YEVGSVVTGKVTGIQP--YGAFVALDEETQGLVHISE 39 (123)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEECCCCEEEEEHHH
Confidence 3479999999999999 8999999999999998876
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=96.03 E-value=0.024 Score=46.89 Aligned_cols=33 Identities=18% Similarity=0.416 Sum_probs=29.8
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
|+||.|+|.+|.+. +||||+|....|||+..+.
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 9999999999999987763
No 20
>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=95.91 E-value=0.021 Score=47.05 Aligned_cols=32 Identities=22% Similarity=0.448 Sum_probs=29.3
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.+|.|+|++|.+ .++||+++.+..||+|+.+
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~~~G~v~~s~ 32 (68)
T cd05707 1 GDVVRGFVKNIAN--NGVFVTLGRGVDARVRVSE 32 (68)
T ss_pred CCEEEEEEEEEEC--ccEEEEeCCCCEEEEEHHH
Confidence 7899999999997 6799999999999998876
No 21
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.62 E-value=0.056 Score=45.01 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=30.5
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
+|.||.|+|++|.+ .++||+++.+..||+|+.+
T Consensus 3 ~G~iv~g~V~~v~~--~gi~v~l~~~~~g~v~~s~ 35 (73)
T cd05706 3 VGDILPGRVTKVND--RYVLVQLGNKVTGPSFITD 35 (73)
T ss_pred CCCEEEEEEEEEeC--CeEEEEeCCCcEEEEEhhh
Confidence 79999999999988 5899999999999998876
No 22
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.52 E-value=0.043 Score=45.37 Aligned_cols=32 Identities=31% Similarity=0.518 Sum_probs=29.0
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.+|.|+|++|.+ .++||+++.+..||+|+.+
T Consensus 1 G~~v~g~V~~v~~--~Gv~V~l~~~v~g~i~~~~ 32 (69)
T cd05697 1 GQVVKGTIRKLRP--SGIFVKLSDHIKGLVPPMH 32 (69)
T ss_pred CCEEEEEEEEEec--cEEEEEecCCcEEEEEHHH
Confidence 7899999999988 5999999999999998765
No 23
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=95.42 E-value=0.03 Score=64.31 Aligned_cols=36 Identities=33% Similarity=0.536 Sum_probs=33.3
Q ss_pred CcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.-.+|.+..|+|++|-| .+||||||. -+|+||+.++
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 24
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=95.38 E-value=0.069 Score=44.99 Aligned_cols=33 Identities=30% Similarity=0.504 Sum_probs=29.0
Q ss_pred cCCEEEEEEeeecCCcceEEecc-cCCcceeeeccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKH 146 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDI-G~~k~aFL~~~d 146 (664)
+|.+|.|+|++|.+ .++||++ |....||+|+.+
T Consensus 3 ~g~~~~g~V~~i~~--fG~fv~l~~~~~eGlvh~se 36 (73)
T cd05686 3 LYQIFKGEVASVTE--YGAFVKIPGCRKQGLVHKSH 36 (73)
T ss_pred CCCEEEEEEEEEEe--eeEEEEECCCCeEEEEEchh
Confidence 79999999999998 7999999 334789998876
No 25
>PRK08582 hypothetical protein; Provisional
Probab=95.27 E-value=0.052 Score=52.03 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=31.9
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+|.+|.|+|++|.+. +|||+|+.+..||+|+.+.
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 4899999999999994 8999999999999998774
No 26
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=95.17 E-value=0.068 Score=44.07 Aligned_cols=32 Identities=25% Similarity=0.394 Sum_probs=29.3
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.+|.|+|++|.+ .++||+++.+..||+|+.+
T Consensus 1 G~~v~g~V~~v~~--~g~~v~l~~~~~g~i~~~~ 32 (73)
T cd05691 1 GSIVTGKVTEVDA--KGATVKLGDGVEGFLRAAE 32 (73)
T ss_pred CCEEEEEEEEEEC--CeEEEEeCCCCEEEEEHHH
Confidence 7899999999986 8999999999999998876
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=95.08 E-value=0.076 Score=44.70 Aligned_cols=33 Identities=27% Similarity=0.285 Sum_probs=28.6
Q ss_pred CCEEE-EEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~-GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.||. |+|++|+. =-+|||+++.+.+||+|+++
T Consensus 1 G~v~~~g~V~~v~~-~~G~~V~l~~gv~G~i~~s~ 34 (71)
T cd05696 1 GAVVDSVKVTKVEP-DLGAVFELKDGLLGFVHISH 34 (71)
T ss_pred CcEeeeeEEEEEcc-CceEEEEeCCCCEEEEEHHH
Confidence 78999 99999962 26899999999999998876
No 28
>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=95.07 E-value=0.083 Score=44.08 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=29.4
Q ss_pred cCCEEEEEEeeecCCcceEEecccC--Ccceeeecccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~--~k~aFL~~~d~ 147 (664)
.|.+|.|+|+++.+ .++||++.. +..||+|+.+.
T Consensus 3 ~G~~~~g~V~~v~~--~g~~v~l~~~~~~~gll~~s~l 38 (76)
T cd04452 3 EGELVVVTVKSIAD--MGAYVSLLEYGNIEGMILLSEL 38 (76)
T ss_pred CCCEEEEEEEEEEc--cEEEEEEcCCCCeEEEEEhHHc
Confidence 69999999999987 899999963 58999988763
No 29
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.71 E-value=0.11 Score=44.48 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=28.9
Q ss_pred ccCCEEEEEEeeecCCcceEEecccC-Ccceeeeccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKH 146 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~-~k~aFL~~~d 146 (664)
..|.++.|.|++|.+ .+||||+|. +-.|||+.++
T Consensus 3 ~~G~~v~g~V~si~d--~G~~v~~g~~gv~Gfl~~~~ 37 (74)
T cd05694 3 VEGMVLSGCVSSVED--HGYILDIGIPGTTGFLPKKD 37 (74)
T ss_pred CCCCEEEEEEEEEeC--CEEEEEeCCCCcEEEEEHHH
Confidence 469999999999996 599999994 6799997654
No 30
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=94.68 E-value=0.12 Score=42.99 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=28.6
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
+.|.|..|+|.++-+ +.+|||||. -.|||+.++
T Consensus 2 ~~g~iV~G~V~~~~~--~~~~vdig~-~eg~lp~~e 34 (67)
T cd04455 2 REGEIVTGIVKRVDR--GNVIVDLGK-VEAILPKKE 34 (67)
T ss_pred CCCCEEEEEEEEEcC--CCEEEEcCC-eEEEeeHHH
Confidence 479999999999999 579999997 899997554
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=94.66 E-value=0.086 Score=42.56 Aligned_cols=32 Identities=31% Similarity=0.492 Sum_probs=28.3
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
.|.+|.|+|.++.+. ++||++| +-.||||..+
T Consensus 1 ~g~~~~g~V~~v~~~--g~~v~l~-~~~g~l~~~e 32 (68)
T cd05688 1 EGDVVEGTVKSITDF--GAFVDLG-GVDGLLHISD 32 (68)
T ss_pred CCCEEEEEEEEEEee--eEEEEEC-CeEEEEEhHH
Confidence 489999999999985 8999998 6899998766
No 32
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=94.62 E-value=0.062 Score=63.68 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=33.0
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.||.|+|++|.+ -+|||+|+.+..||+|+++.
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 79999999999999999863
No 33
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=94.60 E-value=0.15 Score=44.03 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=31.5
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..|+|+.|+|.++.+ .++||+||.+..||||+.+.
T Consensus 5 ~~GdiV~g~V~~i~~--~g~~v~i~~~~~G~l~~se~ 39 (86)
T cd05789 5 EVGDVVIGRVTEVGF--KRWKVDINSPYDAVLPLSEV 39 (86)
T ss_pred CCCCEEEEEEEEECC--CEEEEECCCCeEEEEEHHHc
Confidence 589999999999987 56999999999999998763
No 34
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=94.49 E-value=0.21 Score=52.70 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=31.0
Q ss_pred cccCCEEEEEEeeecCCcceEEecccC--Ccceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~--~k~aFL~~~d~ 147 (664)
..+|+++.|+|++|.+ .+|||++.. +..||+|+.+.
T Consensus 6 P~~GdiV~G~V~~I~~--~G~fV~L~e~~gieGlI~iSEl 43 (262)
T PRK03987 6 PEEGELVVGTVKEVKD--FGAFVTLDEYPGKEGFIHISEV 43 (262)
T ss_pred CCCCCEEEEEEEEEEC--CEEEEEECCCCCcEEEEEHHHc
Confidence 3589999999999976 899999975 78999988763
No 35
>PRK05807 hypothetical protein; Provisional
Probab=94.38 E-value=0.16 Score=48.55 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=30.1
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+|.+|.|+|+.|.| .+|||++ .+..||+|+.+.
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 578999998764
No 36
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.36 E-value=0.12 Score=44.06 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=30.8
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+|++..|+|+++.+ .+|||++|.+-.||+|+.+.
T Consensus 2 k~G~~V~g~V~~i~~--~G~fV~l~~~v~G~v~~~~l 36 (74)
T cd05705 2 KEGQLLRGYVSSVTK--QGVFFRLSSSIVGRVLFQNV 36 (74)
T ss_pred CCCCEEEEEEEEEeC--CcEEEEeCCCCEEEEEHHHc
Confidence 479999999999974 57999999999999998763
No 37
>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=94.18 E-value=0.048 Score=46.35 Aligned_cols=33 Identities=27% Similarity=0.554 Sum_probs=29.7
Q ss_pred CCEEEEEEeeecCCcceEEeccc---CCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIG---NSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG---~~k~aFL~~~d~ 147 (664)
|.+|.|+|++|.|. ++||+|+ .+.+||+|+.+.
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 9999999 469999998774
No 38
>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=94.13 E-value=0.098 Score=62.04 Aligned_cols=37 Identities=27% Similarity=0.453 Sum_probs=33.4
Q ss_pred CcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
...+|.||.|+|++|.+ .+|||+|..+..||||+++.
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 89999999999999998764
No 39
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=93.84 E-value=0.15 Score=60.48 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=33.0
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.+|.|+|++|.+ .+|||+|+.+..||+|+.+.
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 89999999999999998763
No 40
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=93.78 E-value=0.3 Score=41.82 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=30.9
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
..+|+|=.|+|++| .-+.+|||||..-.|||++.+
T Consensus 4 p~~GdiV~G~V~~v--~~~~~~V~i~~~~~g~l~~~~ 38 (82)
T cd04454 4 PDVGDIVIGIVTEV--NSRFWKVDILSRGTARLEDSS 38 (82)
T ss_pred CCCCCEEEEEEEEE--cCCEEEEEeCCCceEEeechh
Confidence 35899999999999 567899999999999998765
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=93.69 E-value=0.24 Score=41.09 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=29.4
Q ss_pred cCCEEEEEEeeecCCcceEEecccC-Ccceeeeccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKH 146 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~-~k~aFL~~~d 146 (664)
+|.+|.|+|++|.+ .++||+++. +..||+|+.+
T Consensus 2 ~g~~v~g~V~~i~~--~g~~v~l~~~~~~g~i~~~~ 35 (77)
T cd05708 2 VGQKIDGTVRRVED--YGVFIDIDGTNVSGLCHKSE 35 (77)
T ss_pred CCCEEEEEEEEEEc--ceEEEEECCCCeEEEEEHHH
Confidence 59999999999987 899999984 7899998866
No 42
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=93.40 E-value=0.48 Score=47.39 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=28.7
Q ss_pred CcccCCEEEEEEeeecCCcceEEecccC----------Ccceeeeccc
Q 006020 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGN----------SRPSLMDIKH 146 (664)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVDIG~----------~k~aFL~~~d 146 (664)
...+|+|+.|+|++|.+ ..+||||+. +..||||+.+
T Consensus 61 ~~~~GdiV~GkV~~i~~--~g~~V~I~~~~~~~~~l~~~~~G~l~~s~ 106 (189)
T PRK09521 61 LLKKGDIVYGRVVDVKE--QRALVRIVSIEGSERELATSKLAYIHISQ 106 (189)
T ss_pred CCCCCCEEEEEEEEEcC--CeEEEEEEEecccccccCCCceeeEEhhH
Confidence 44689999999999977 899999974 4557776654
No 43
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=93.07 E-value=0.22 Score=38.99 Aligned_cols=29 Identities=24% Similarity=0.392 Sum_probs=25.2
Q ss_pred EEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 116 YLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 116 Y~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|.|+|+++.+ .++||+++.+..||++..+
T Consensus 1 v~g~V~~v~~--~g~~v~l~~~~~g~~~~~~ 29 (65)
T cd00164 1 VTGKVVSITK--FGVFVELEDGVEGLVHISE 29 (65)
T ss_pred CEEEEEEEEe--eeEEEEecCCCEEEEEHHH
Confidence 5799999996 5899999999999998765
No 44
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=92.64 E-value=0.85 Score=47.33 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.2
Q ss_pred EEEeeCCCCc--ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 101 LLLEPVKSNV--QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 101 l~iE~~~~~~--~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
+.+.+..... .+|+|-.|+|+++.+. .+||||+..-.||||+.+.
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 5555554443 5799999999999885 5999999999999998763
No 45
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=91.64 E-value=0.35 Score=58.80 Aligned_cols=35 Identities=29% Similarity=0.497 Sum_probs=31.6
Q ss_pred ccCCEEE-EEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYL-GVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~-GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+|.||. |+|++|.+ -+|||+|+.+..||+|+++.
T Consensus 752 ~vG~iy~~g~V~~I~~--FGaFVeL~~g~EGLVHISeL 787 (891)
T PLN00207 752 TVGDIYRNCEIKSIAP--YGAFVEIAPGREGLCHISEL 787 (891)
T ss_pred CCCcEEECcEEEEEec--cEEEEEeCCCCEEEEEhhhc
Confidence 4999995 69999998 69999999999999999874
No 46
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=91.40 E-value=0.19 Score=41.04 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=30.1
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
|.+|.|+|++|.| .++||+++.+.+||+|+.+.
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 68999999999999998874
No 47
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=90.95 E-value=0.29 Score=40.61 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=31.2
Q ss_pred cCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
+|.+|.|+|.+|.+ -++||+++.+.+||+|+.+.
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 69999999999999998773
No 48
>PRK14865 rnpA ribonuclease P; Provisional
Probab=90.32 E-value=1.3 Score=41.05 Aligned_cols=53 Identities=21% Similarity=0.383 Sum_probs=38.5
Q ss_pred eeeecccChh-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~~~l-------~~-eg~GvIIRTaA~~aseeeL~~El~~L~~~ 385 (664)
+.||||+... .|+|+|.++... .+ .++=+|.|..+.+++.++|++++..|.+.
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 6689999765 677766554331 12 24457889999999999999999877554
No 49
>PRK00588 rnpA ribonuclease P; Reviewed
Probab=90.15 E-value=1.5 Score=41.10 Aligned_cols=52 Identities=13% Similarity=0.121 Sum_probs=35.6
Q ss_pred eeeecccChh-HHHHHHHHHHh----c---CCCCeeEE--EeecCCCCCHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKVIAKT----L---QPEGFGLT--IRTVAAGHSLEELQKDLEGLLS 384 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~~~----l---~~eg~GvI--IRTaA~~aseeeL~~El~~L~~ 384 (664)
+.||||+... .|+|+|.++.. . .+.+.=+| .|..|..++..+|++++..|..
T Consensus 47 ~~VsKKvG~AV~RNRiKR~lRE~~R~~~~~l~~~~~vVviaR~~~~~~~~~~l~~~l~~ll~ 108 (118)
T PRK00588 47 LIIAKSVGSAVERHRVARRLRHVARPILKELHPSDRVVIRALPSSRHVSSARLEQQLRCGLR 108 (118)
T ss_pred EEEeeecCchhHHHHHHHHHHHHHHHhhhccCCCCEEEEecCcccccCCHHHHHHHHHHHHH
Confidence 5689999765 67766654433 2 22333333 6888999999999999887644
No 50
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.72 E-value=0.7 Score=52.92 Aligned_cols=35 Identities=34% Similarity=0.547 Sum_probs=30.8
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.|+.|+|++|.|. +|||||| +..||+|+++.
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 59999998763
No 51
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=89.28 E-value=0.82 Score=49.54 Aligned_cols=36 Identities=28% Similarity=0.512 Sum_probs=32.1
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
...|.|-.|+|.+|.++ +||||||....|||++.+.
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 46899999999999765 8999999999999988764
No 52
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=89.15 E-value=2.1 Score=40.25 Aligned_cols=54 Identities=24% Similarity=0.250 Sum_probs=37.5
Q ss_pred eeeecccChh-HHHHHHHHH----HhcC---CCCee--EEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKVIA----KTLQ---PEGFG--LTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~----~~l~---~eg~G--vIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||||+... +|+|+|.++ ..+. +.|+- +|.|..+.+++..+|.+|+..|....
T Consensus 52 ~~VsKKvG~AV~RNRiKR~lRe~~R~~~~~l~~g~D~Viiar~~~~~~~~~~l~~~l~~ll~k~ 115 (122)
T PRK03459 52 LVVSKAVGNAVIRHRVSRRLRHICADIVDQVPETHHVVIRALPGAATASSAELERDVRAGLGKL 115 (122)
T ss_pred EEEeeeccchhHHHHHHHHHHHHHHHhhhccCCCcEEEEEECcccccCCHHHHHHHHHHHHHHh
Confidence 5689999765 677665444 3322 34444 45677888999999999998876653
No 53
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=88.96 E-value=0.99 Score=48.93 Aligned_cols=39 Identities=28% Similarity=0.526 Sum_probs=32.8
Q ss_pred CCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 106 VKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 106 ~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.....-+|.||.|+|++|.+ -++||++| +..||+|+.+.
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 34456689999999999998 89999997 67899988763
No 54
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=88.96 E-value=0.93 Score=51.84 Aligned_cols=36 Identities=33% Similarity=0.501 Sum_probs=32.3
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
...|.||.|+|++|.+ .+||||||.+..||+|+.+.
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 58999999899999998774
No 55
>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=88.48 E-value=0.46 Score=39.03 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=28.2
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
|.||.|+|+++.+ .++||++ .+-.|||+..+.
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 579999988763
No 56
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=88.43 E-value=0.54 Score=39.11 Aligned_cols=33 Identities=9% Similarity=0.159 Sum_probs=30.2
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
|.|+.|+|++|.+. .+||+++.+..||+++.+.
T Consensus 1 G~iV~g~V~~i~~~--gi~v~l~~~i~g~i~~~~i 33 (70)
T cd05702 1 GDLVKAKVKSVKPT--QLNVQLADNVHGRIHVSEV 33 (70)
T ss_pred CCEEEEEEEEEECC--cEEEEeCCCcEEEEEHHHh
Confidence 78999999999884 7999999999999999874
No 57
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=87.71 E-value=1.2 Score=51.48 Aligned_cols=35 Identities=31% Similarity=0.528 Sum_probs=31.7
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
...|.|+.|+|++|.+. +||||+| +..||+|+.+.
T Consensus 199 l~~G~iv~g~V~~v~~~--G~~V~i~-g~~glv~~se~ 233 (565)
T PRK06299 199 LEEGQVVEGVVKNITDY--GAFVDLG-GVDGLLHITDI 233 (565)
T ss_pred CCCCCEEEEEEEEEeCC--eEEEEEC-CEEEEEEHHHh
Confidence 46899999999999994 8999999 89999999874
No 58
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=87.64 E-value=0.61 Score=39.32 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=30.6
Q ss_pred cCCEEEEEEeeecCCcceEEecccC-Ccceeeecccc
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~-~k~aFL~~~d~ 147 (664)
+|.+|.|+|++|.+ .++||+++. +..||+|+.+.
T Consensus 1 ~g~~~~g~V~~v~~--~G~fv~l~~~~~~G~v~~~~l 35 (83)
T cd04471 1 VGEEFDGVISGVTS--FGLFVELDNLTVEGLVHVSTL 35 (83)
T ss_pred CCCEEEEEEEeEEe--eeEEEEecCCCEEEEEEEEec
Confidence 48899999999998 599999998 89999999874
No 59
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=87.38 E-value=2.9 Score=39.83 Aligned_cols=58 Identities=19% Similarity=0.302 Sum_probs=39.7
Q ss_pred eeeecc-cChh-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 006020 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (664)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~l-------~~-eg~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~a 393 (664)
+.|||| +... .|+|+|.++... .+ -++=||.|..+.+++..+|.+++..| |+.+...+
T Consensus 50 ~~VsKK~~g~AV~RNRiKR~lRE~fR~~~~~l~g~DiVviaR~~~~~~~~~~l~~~l~~l---l~kl~~~~ 117 (130)
T PRK00396 50 LVIGKKSVKLAVDRNRLKRLIRESFRLNQHSLAGWDIVVVARKGLGELENPELHQQFGKL---WKRLARNR 117 (130)
T ss_pred EEEecccCccHhHHHHHHHHHHHHHHHhhccCCCeeEEEEeCCCcccCCHHHHHHHHHHH---HHHHHHhc
Confidence 556899 6655 688777665432 12 23456788899999999999999876 44554443
No 60
>PRK00499 rnpA ribonuclease P; Reviewed
Probab=86.10 E-value=4.2 Score=37.55 Aligned_cols=54 Identities=30% Similarity=0.379 Sum_probs=38.9
Q ss_pred eeeecccChh-HHHHHHHHHHh----c---CCC--CeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKVIAKT----L---QPE--GFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~~~----l---~~e--g~GvIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||||+... .|+++|.++.. . .+. ++-+|+|-.+..++..+|.+|+..|....
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 6789999765 57766554432 2 122 45678888999999999999998887754
No 61
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=86.09 E-value=2.5 Score=51.67 Aligned_cols=38 Identities=26% Similarity=0.438 Sum_probs=33.8
Q ss_pred CCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
++..+|+|+.|+|++|.| -+|||+++.+-.||+|+++.
T Consensus 574 ~~~~vG~iV~G~V~~I~~--fG~fVeL~~gveGLvhiSEl 611 (863)
T PRK12269 574 NKFGVNDVVKGRVTKIAD--FGAFIELAEGIEGLAHISEF 611 (863)
T ss_pred ccCCCCCEEEEEEEEEeC--CeEEEEecCCceeeeEHHHh
Confidence 445689999999999998 68999999999999999875
No 62
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=86.00 E-value=1.7 Score=49.48 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=32.2
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|+++.|+|+++.+. ++||++|.+..||+|+.+.
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 35899999999999776 8999999999999998874
No 63
>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=85.91 E-value=1.1 Score=38.26 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=31.7
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
..+|.+|.|+|.++.+ .++||++..+..||+|..+
T Consensus 14 ~~~G~~~~g~V~~i~~--~G~fV~l~~~~~Glv~~se 48 (77)
T cd04473 14 LEVGKLYKGKVNGVAK--YGVFVDLNDHVRGLIHRSN 48 (77)
T ss_pred CCCCCEEEEEEEeEec--ceEEEEECCCcEEEEEchh
Confidence 4589999999999987 8999999999999998876
No 64
>PRK04390 rnpA ribonuclease P; Reviewed
Probab=85.61 E-value=4.6 Score=37.78 Aligned_cols=53 Identities=17% Similarity=0.282 Sum_probs=36.9
Q ss_pred eeeeccc-Chh-HHHHHHHHHHhc-------CC-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 006020 333 IGVSRKI-TGV-ERTRLKVIAKTL-------QP-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (664)
Q Consensus 333 IgVSrKI-~de-eR~rLk~i~~~l-------~~-eg~GvIIRTaA~~aseeeL~~El~~L~~~ 385 (664)
+.||||. ... +|+|+|.++... .+ -++=+|.|..+.+.+..+|.+|+..|...
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 444 687777655432 12 23446778888899999999998876554
No 65
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=85.44 E-value=1.7 Score=49.63 Aligned_cols=123 Identities=21% Similarity=0.286 Sum_probs=69.6
Q ss_pred cccCCCEEEEEEeecCCCCCCceeeecceeeceeEEEeeCCCceeeecccChhHHHHHHHHHHhcCCC-Cee-EEEeecC
Q 006020 290 QVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPE-GFG-LTIRTVA 367 (664)
Q Consensus 290 ~lk~Gq~ILVQVvKE~igtKGprLT~~ISL~GRYlVL~P~~~~IgVSrKI~deeR~rLk~i~~~l~~e-g~G-vIIRTaA 367 (664)
.+++||.|-|-|.+-...+||| .|-+||+-. .-|+.+++.=.|+ ..| +.|+..|
T Consensus 171 ~~~~GdrIka~I~~Vd~~~kg~--------------------qIilSRt~p----~~l~~Lf~~EVPEI~~G~ieIk~ia 226 (470)
T PRK09202 171 NFRPGDRVRAYVYEVRKEARGP--------------------QIILSRTHP----EFLKKLFEQEVPEIADGLIEIKAIA 226 (470)
T ss_pred cCCCCCEEEEEEEEEecCCCCC--------------------eEEEEeCcH----HHHHHHHHHhCcccccCeEEEEEEe
Confidence 3677999999998877666665 355777654 3455555555564 234 5677777
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCccCCcceeeeccCCchhhhhhhhcCCCccEEEEc-ChhHHHHHH
Q 006020 368 AGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVD-SPRTYHEVT 446 (664)
Q Consensus 368 ~~aseeeL~~El~~L~~~W~~I~~~ak~~~~~~~~g~~~~~P~lLy~~~~~~~~~lrD~~~~~v~~IvvD-~~~~y~~i~ 446 (664)
..+.. ++|-+-...+..+.+ ...++-....-+..+.+.+-+++++-|..+ |+..| +.
T Consensus 227 R~pG~-------------------RaKvAV~s~d~~iDp-vga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f--i~ 284 (470)
T PRK09202 227 RDPGS-------------------RAKIAVKSNDPRIDP-VGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQF--II 284 (470)
T ss_pred ecCcc-------------------eeEEEEEcCCCCCCh-hHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHHH--HH
Confidence 66541 122111122333322 345666666667777777778888866543 44432 22
Q ss_pred HHHHhhCCCccCcee
Q 006020 447 SYLQDIAPDLCDRVE 461 (664)
Q Consensus 447 ~~l~~~~p~~~~~v~ 461 (664)
+ .++|.....|.
T Consensus 285 n---al~pa~v~~v~ 296 (470)
T PRK09202 285 N---ALSPAEVSSVV 296 (470)
T ss_pred H---hCCCCEEEEEE
Confidence 2 24566555553
No 66
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=84.98 E-value=1.4 Score=50.97 Aligned_cols=68 Identities=24% Similarity=0.249 Sum_probs=49.0
Q ss_pred eEEEEEecCCCeEEEEEEECCEEeEEEEeeCCCCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 76 TVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 76 ~~ilIn~~~~~e~RvAvlEdg~L~El~iE~~~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
+..+|.... ...||.+= =-+|.+-=++...+..-+|..+.|+|+|+.| .+|||+|+.+-.||+|++++
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-LKQLEEDPWEGIEKKYPVGDKVEGKVTNLTD--YGAFVEIEEGVEGLVHVSEI 310 (541)
T ss_pred EEEEEEEcc-CCCeEEEE-ehhcccCcHHHHhhhcCCCCEEEEEEEEeec--CcEEEEecCCccceeechhh
Confidence 345556554 34566542 2233333444556667899999999999999 48999999999999999885
No 67
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=83.90 E-value=2.5 Score=51.74 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=30.7
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|++|.|+|+++.+ .+||||+| +-.||+|+++.
T Consensus 491 l~~G~~V~G~Vk~i~~--~G~fVdl~-Gv~Gfvp~Sei 525 (863)
T PRK12269 491 VHIEDSVSGVVKSFTS--FGAFIDLG-GFDGLLHVNDM 525 (863)
T ss_pred CCCCCEEEEEEEEEeC--CcEEEEEC-CEEEEEEchhc
Confidence 3579999999999998 49999996 68999998875
No 68
>PRK01313 rnpA ribonuclease P; Reviewed
Probab=83.56 E-value=5.6 Score=37.92 Aligned_cols=52 Identities=17% Similarity=0.279 Sum_probs=38.1
Q ss_pred eeeecccChh-HHHHHHH----HHHhcCC----C--CeeEEEeecCCCCCHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKV----IAKTLQP----E--GFGLTIRTVAAGHSLEELQKDLEGLLS 384 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~----i~~~l~~----e--g~GvIIRTaA~~aseeeL~~El~~L~~ 384 (664)
+.||||+... .|+|+|. ++....+ . ++=+|.|..+.+++..+|.++|..+..
T Consensus 51 ~~VSKKvG~AV~RNRiKR~lRE~fR~~~~~~~~~g~DiVivar~~~~~~~~~~l~~~L~~~l~ 113 (129)
T PRK01313 51 FTVTKKNGNAVERNRIRRRLKEAVRLHAGFDMAPGTDYVIVARRDALNAPFSQLTEELSRRIE 113 (129)
T ss_pred EEEecccCcchHHHHHHHHHHHHHHHhchhccCCCceEEEEECcccccCCHHHHHHHHHHHHH
Confidence 5679999765 5766554 4433221 2 456888999999999999999998777
No 69
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=83.10 E-value=1.7 Score=51.95 Aligned_cols=37 Identities=30% Similarity=0.484 Sum_probs=32.9
Q ss_pred CcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 109 NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 109 ~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.-..|.|--|.|+||.- -+||||||....|++|++..
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 45689999999999986 58999999999999999864
No 70
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.68 E-value=2.9 Score=48.34 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=32.1
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|+++.|+|++|.+ .+|||++|.+..||+|+.+.
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 59999999999999999874
No 71
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.38 E-value=3.1 Score=45.79 Aligned_cols=35 Identities=34% Similarity=0.502 Sum_probs=31.1
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.++.|+|+++.+ .++||++| +..||+|+.+.
T Consensus 190 ~~~G~~v~g~V~~v~~--~G~fV~l~-~v~g~v~~sel 224 (390)
T PRK06676 190 LKEGDVVEGTVARLTD--FGAFVDIG-GVDGLVHISEL 224 (390)
T ss_pred CCCCCEEEEEEEEEec--ceEEEEeC-CeEEEEEHHHc
Confidence 4689999999999998 67999997 59999998875
No 72
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=82.35 E-value=3.1 Score=47.76 Aligned_cols=35 Identities=37% Similarity=0.494 Sum_probs=31.5
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
..+|.+|.|+|++|.| -++||++..+-.||+|+.+
T Consensus 291 ~~vG~vv~G~V~~I~~--fGvFVeL~~gieGLvh~Se 325 (486)
T PRK07899 291 HAIGQIVPGKVTKLVP--FGAFVRVEEGIEGLVHISE 325 (486)
T ss_pred cCCCCEEEEEEEEEec--cEEEEEeCCCcEEEEEHHH
Confidence 3479999999999999 7999999888999998866
No 73
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=80.43 E-value=1.6 Score=50.01 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=34.0
Q ss_pred CCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+..+|.+|.|+|++|.| .+|||+++.+-.||+|+++.
T Consensus 288 ~~~~~G~~v~G~V~~v~~--~G~fV~l~~gv~Glvh~sel 325 (491)
T PRK13806 288 DRLKAGDKVTGKVVRLAP--FGAFVEILPGIEGLVHVSEM 325 (491)
T ss_pred ccCCCCCEEEEEEEEEeC--ceEEEEeCCCcEEEEEHHHc
Confidence 345689999999999988 79999999999999999875
No 74
>PRK01903 rnpA ribonuclease P; Reviewed
Probab=80.35 E-value=9.3 Score=36.58 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=34.5
Q ss_pred eeeecc-cChh-HHHHHHHHHHhc-------CCC-------------CeeEEEeec-CCCCCHHHHHHHHHHHHHH
Q 006020 333 IGVSRK-ITGV-ERTRLKVIAKTL-------QPE-------------GFGLTIRTV-AAGHSLEELQKDLEGLLST 385 (664)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~l-------~~e-------------g~GvIIRTa-A~~aseeeL~~El~~L~~~ 385 (664)
+.|||| +... .|+|+|.++... .+. ..-+++|.. +...+.+++.+++..|...
T Consensus 54 ~sVsKK~~g~AV~RNRiKR~lREa~R~~~~~l~~~~~~~~~~~~~~~~iv~i~~~~~~~~~~~~~l~~~l~~ll~r 129 (133)
T PRK01903 54 FSVSKKRVPRAVKRNRIKRLMREAYRLEKHVLLDRLETDAGAKNRQLAIAFLYTGRSDEIPSLAEFRREMRKLLQR 129 (133)
T ss_pred EEEecccCCchhhhhHHHHHHHHHHHHhHhhhcccccccccccCcceEEEEEEeccccccCCHHHHHHHHHHHHHH
Confidence 455799 6665 688777655331 222 234577773 4447899999999877664
No 75
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=80.29 E-value=1.4 Score=51.93 Aligned_cols=39 Identities=31% Similarity=0.509 Sum_probs=35.5
Q ss_pred CCCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 107 KSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 107 ~~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
....-||-||.|+|+++.+ =+|||++..++.|++|+...
T Consensus 614 ~~e~evg~iy~G~V~ri~~--fGaFv~l~~gkdgl~hiS~~ 652 (692)
T COG1185 614 TREVEVGEVYEGTVVRIVD--FGAFVELLPGKDGLVHISQL 652 (692)
T ss_pred HhhcccccEEEEEEEEEee--cceEEEecCCcceeEEehhh
Confidence 3566899999999999999 89999999999999999874
No 76
>PRK00038 rnpA ribonuclease P; Reviewed
Probab=79.82 E-value=10 Score=35.85 Aligned_cols=51 Identities=14% Similarity=0.350 Sum_probs=34.1
Q ss_pred eeeeccc-Chh-HHHHHHHHHHh--------cCCCCeeEEEeecCCCCCHHHH----HHHHHHHH
Q 006020 333 IGVSRKI-TGV-ERTRLKVIAKT--------LQPEGFGLTIRTVAAGHSLEEL----QKDLEGLL 383 (664)
Q Consensus 333 IgVSrKI-~de-eR~rLk~i~~~--------l~~eg~GvIIRTaA~~aseeeL----~~El~~L~ 383 (664)
+.||||. ... .|+|+|..+.. +.+.++=||.|..+.+++.++| ..|+..|.
T Consensus 54 i~VsKKv~g~AV~RNRiKR~lRE~~R~~~~~l~~~D~VviaR~~~~~~~~~~l~~~~~~~~~~l~ 118 (123)
T PRK00038 54 LVIAKRFAARAVTRNTLKRVIREAFRARRLALPAQDYVVRLHSKLTPASLTALKRSARAEVDAHF 118 (123)
T ss_pred EEEecccCCCchhHHHHHHHHHHHHHHhhccCCCCCEEEEECCCCCcCCHHHHHHHHHHHHHHHH
Confidence 6689995 444 67777654433 2223566788999999999999 55555443
No 77
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=79.47 E-value=2 Score=38.86 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=31.5
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.+|.+-.|+|++|-+. ++||+++.+..||+++.+.
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 4799999999999765 9999999999999999885
No 78
>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=79.22 E-value=6 Score=36.01 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=37.3
Q ss_pred eeeecccChh-HHHHHHHHHHh----cC---C-CCeeEEEeecCCCCCHHHHHHHHHHHH
Q 006020 333 IGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLL 383 (664)
Q Consensus 333 IgVSrKI~de-eR~rLk~i~~~----l~---~-eg~GvIIRTaA~~aseeeL~~El~~L~ 383 (664)
+.||||+... .|+++|.++.. .. + -++=+|+|..+..++.++|.+++..|.
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 5679998765 67776655433 22 2 244678899999999999999998774
No 79
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=78.99 E-value=5.5 Score=43.84 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=31.8
Q ss_pred cccCCEEEEEEeeecCCcceEEecc-cCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNI-GNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDI-G~~k~aFL~~~d~ 147 (664)
...|.|..|+|+++.++ ++|||| |.+-.|||+..+.
T Consensus 15 ~~~G~iv~G~V~~i~~~--g~~V~i~~~~~~g~lp~~e~ 51 (390)
T PRK06676 15 VEVGDVVTGEVLKVEDK--QVFVNIEGYKVEGVIPISEL 51 (390)
T ss_pred ccCCCEEEEEEEEEECC--eEEEEEecCCcEEEEEHHHh
Confidence 46899999999999984 799999 8899999988764
No 80
>PRK04820 rnpA ribonuclease P; Reviewed
Probab=78.61 E-value=10 Score=36.89 Aligned_cols=54 Identities=30% Similarity=0.418 Sum_probs=38.8
Q ss_pred eeeecccC-hh-HHHHHHHHHHh--------cCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKIT-GV-ERTRLKVIAKT--------LQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSrKI~-de-eR~rLk~i~~~--------l~~eg~GvIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||||+. .. .|+|+|.++.. +.+.++=+|.|-.+..++.++|++++..|....
T Consensus 52 ~sVSKKvg~~AV~RNRiKR~lRE~fR~~~~~l~~~DiVviar~~~~~~~~~~l~~~l~~LL~k~ 115 (145)
T PRK04820 52 LAVSRKVDTRAVGRNRIKRVLREAMRQLLPELAPGDYVVVARSAAAKASNPQLRDAFLRLLRRA 115 (145)
T ss_pred EEEeccccCcchhHHHHHHHHHHHHHHhhhccCCCCEEEEEeCCcccCCHHHHHHHHHHHHHHh
Confidence 66899984 44 57776655433 222355678888999999999999988777654
No 81
>PRK01492 rnpA ribonuclease P; Reviewed
Probab=78.13 E-value=9.5 Score=35.73 Aligned_cols=53 Identities=19% Similarity=0.233 Sum_probs=37.6
Q ss_pred ceeeecccC-hh-HHHHHHHHH----HhcCC----C--C--eeEEEeecCCCCCHHHHHHHHHHHHH
Q 006020 332 RIGVSRKIT-GV-ERTRLKVIA----KTLQP----E--G--FGLTIRTVAAGHSLEELQKDLEGLLS 384 (664)
Q Consensus 332 ~IgVSrKI~-de-eR~rLk~i~----~~l~~----e--g--~GvIIRTaA~~aseeeL~~El~~L~~ 384 (664)
++.||||+. .. .|+|+|.++ ....+ . | +=+|.|..+.+.+..+|.+|+..|.-
T Consensus 49 G~sVSKKv~~kAV~RNRiKR~lRE~fR~~~~~~~l~~~g~DiVviaR~~~~~~~~~~l~~~l~~l~~ 115 (118)
T PRK01492 49 GIKVSRKLNKKAVVRNKIKRRIRHLIRIIVSDSSFKAIKFAMIIIPRKGFEEINFSHLNYELSKIIL 115 (118)
T ss_pred EEEEecccCCchhhHHHHHHHHHHHHHHhCcccccCCCCceEEEEECCCcccCCHHHHHHHHHHHHH
Confidence 467899954 44 577766544 33322 1 3 34788999999999999999988764
No 82
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=77.63 E-value=7.7 Score=36.07 Aligned_cols=53 Identities=28% Similarity=0.366 Sum_probs=37.3
Q ss_pred eeeecc-cChh-HHHHHHHHHHhc----C---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 006020 333 IGVSRK-ITGV-ERTRLKVIAKTL----Q---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (664)
Q Consensus 333 IgVSrK-I~de-eR~rLk~i~~~l----~---~-eg~GvIIRTaA~~aseeeL~~El~~L~~~ 385 (664)
+.|||| +... .|+++|.++... . + -++=+|.|-.+.+++..+|.+|+..|.+.
T Consensus 49 ~~VsKK~~g~AV~RNriKR~lRe~~R~~~~~l~~~diVviar~~~~~~~~~~l~~~l~~ll~k 111 (114)
T PRK01732 49 LTVAKKNVKRAHERNRIKRLTRESFRLHQHELPAMDFVVIAKKGVADLDNRELFELLEKLWRR 111 (114)
T ss_pred EEEEcccCcchhHHHHHHHHHHHHHHHhhhcCCCCeEEEEeCCCcccCCHHHHHHHHHHHHHH
Confidence 567899 6654 577666554332 1 2 23445889999999999999999887654
No 83
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=77.57 E-value=4.6 Score=44.80 Aligned_cols=32 Identities=19% Similarity=0.266 Sum_probs=27.9
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeecc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~ 145 (664)
..|+|-.|+|.++.+ +++|||+|. -.|||+.+
T Consensus 133 k~GeiV~G~V~~~~~--~~~~Vdlg~-vEa~LP~~ 164 (362)
T PRK12327 133 REGDIVTGVVQRRDN--RFVYVNLGK-IEAVLPPA 164 (362)
T ss_pred hcCCEEEEEEEEEeC--CcEEEEeCC-eEEEecHH
Confidence 789999999999988 589999987 68899653
No 84
>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=77.39 E-value=5.2 Score=44.00 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=27.5
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
..|.|..|+|.++.++ +..||||| +-.|||+.++
T Consensus 130 k~GeiV~G~V~~v~~~-g~v~VdiG-~~ea~LP~~E 163 (341)
T TIGR01953 130 KEGEIISGTVKRVNRR-GNLYVELG-KTEGILPKKE 163 (341)
T ss_pred hcCCEEEEEEEEEecC-CcEEEEEC-CeEEEecHHH
Confidence 4899999999999874 24899998 6789996543
No 85
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=74.38 E-value=3.7 Score=34.75 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=29.6
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
|++..|+|+++.+ .++||.++.+-.||+++.+.
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 59999999999999998874
No 86
>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=74.23 E-value=2.7 Score=47.90 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=32.3
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.||.|+|+++.+ .+|||++|.+..||+|+.+.
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 48999999999999998874
No 87
>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=73.50 E-value=2.6 Score=35.30 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=22.3
Q ss_pred CeeEEEeecCCCCCcchhccccCCCCCceeEEe
Q 006020 588 HGLMEITRKRVRPSVTFMISEPCTCCQGTGRVE 620 (664)
Q Consensus 588 LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~ 620 (664)
-|.+.++++ ..........+|+.|+|+|++.
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 455666555 6667777888999999999985
No 88
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=72.45 E-value=7.2 Score=46.22 Aligned_cols=35 Identities=29% Similarity=0.418 Sum_probs=30.1
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|++|.|+|+++.+ .++||++ .+-.||||+++.
T Consensus 475 l~~G~iV~g~V~~v~~--~G~fV~l-~gv~Gll~~sel 509 (647)
T PRK00087 475 LEEGDVVEGEVKRLTD--FGAFVDI-GGVDGLLHVSEI 509 (647)
T ss_pred CCCCCEEEEEEEEEeC--CcEEEEE-CCEEEEEEHHHc
Confidence 3479999999999987 4899999 578899988764
No 89
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=71.92 E-value=1.5 Score=45.80 Aligned_cols=29 Identities=38% Similarity=0.696 Sum_probs=19.8
Q ss_pred ccCCCeeEEEeecCCCCCcchhccccCCCCCceeEEec
Q 006020 584 ELSRHGLMEITRKRVRPSVTFMISEPCTCCQGTGRVEA 621 (664)
Q Consensus 584 giT~LGLvEiTRkR~r~sL~~~l~~~Cp~C~G~G~V~s 621 (664)
.++.+.-+|.+-+ -+.+||.|+|+|||-+
T Consensus 24 ~~~~~py~e~~g~---------~~vtCPTCqGtGrIP~ 52 (238)
T PF07092_consen 24 DISSFPYVEFTGR---------DSVTCPTCQGTGRIPR 52 (238)
T ss_pred ccccCccccccCC---------CCCcCCCCcCCccCCc
Confidence 4455555555541 3458999999999865
No 90
>COG0594 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]
Probab=71.05 E-value=23 Score=33.14 Aligned_cols=54 Identities=30% Similarity=0.395 Sum_probs=38.0
Q ss_pred eeeec-ccChh-HHHHHHHHHHh-------cCC-CCeeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSR-KITGV-ERTRLKVIAKT-------LQP-EGFGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSr-KI~de-eR~rLk~i~~~-------l~~-eg~GvIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||| |+... +|.|+|.++.. +.| .++=||+|..+.+++..++++++..+....
T Consensus 45 lsVsKkk~g~AV~RNRiKR~iRe~~r~~~~~~~~~d~Viiar~~~~~~~~~~l~~~L~~~l~~~ 108 (117)
T COG0594 45 LTVSKKKVGNAVERNRIKRLIREAFRLLQHLLPGFDIVIIARKGFLELDFSELEKELSQLLKRA 108 (117)
T ss_pred EEEEchhccchhhHHHHHHHHHHHHHhhhhhCCCceEEEEECCCCCCCCHHHHHHHHHHHHHHh
Confidence 66899 77765 67666544322 222 356789999999999999988877665543
No 91
>PRK00730 rnpA ribonuclease P; Reviewed
Probab=70.99 E-value=12 Score=36.26 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=37.1
Q ss_pred ceeeecccChh-HHHHHHHHHHh----cC---C-CCeeEEEeecCCCCCHHHHHHHHHHHHHH
Q 006020 332 RIGVSRKITGV-ERTRLKVIAKT----LQ---P-EGFGLTIRTVAAGHSLEELQKDLEGLLST 385 (664)
Q Consensus 332 ~IgVSrKI~de-eR~rLk~i~~~----l~---~-eg~GvIIRTaA~~aseeeL~~El~~L~~~ 385 (664)
++.||||+... .|+|+|.++.. .. + -++=||.|..+. ++.++|.+|+..+...
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 36789999765 68777655533 22 2 234567888887 9999999998877653
No 92
>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=70.14 E-value=12 Score=34.19 Aligned_cols=54 Identities=33% Similarity=0.446 Sum_probs=36.5
Q ss_pred eeeecccCh-h-HHHHHHHHHHhc----C---CCC--eeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKITG-V-ERTRLKVIAKTL----Q---PEG--FGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSrKI~d-e-eR~rLk~i~~~l----~---~eg--~GvIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||||+.. . .|+++|.++..+ . +.+ +=++.|..+..++.++|.+++..|....
T Consensus 46 ~~vsKK~gk~AV~RNriKR~lRe~~R~~~~~l~~~~d~v~~~r~~~~~~~~~~l~~~l~~ll~k~ 110 (111)
T PF00825_consen 46 FSVSKKVGKRAVKRNRIKRRLREAFRLNKPELPPGYDIVFIARPGALELSFEELEKELKKLLKKA 110 (111)
T ss_dssp EEE-STTSS-HHHHHHHHHHHHHHHHHCTTTS-SSSEEEEEE-CGGGGS-HHHHHHHHHHHHHHH
T ss_pred EEecCccccchhHHHHHHHHHHHHHHHHHhhccCCcEEEEEEcCCcCcCCHHHHHHHHHHHHHhh
Confidence 568999977 5 688777665442 2 223 3567788889999999999998887653
No 93
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=69.62 E-value=9.4 Score=40.87 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=33.4
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
.++|.-=+|+|+.|-+.++ ||||.|..|.-|+++++.
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 3689999999999999985 799999999999999873
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=65.11 E-value=16 Score=43.45 Aligned_cols=35 Identities=31% Similarity=0.516 Sum_probs=31.6
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
..+|.+|.|+|++|.+ .++||+++.+-.||+|+.+
T Consensus 560 ~~~G~~v~g~V~~i~~--~G~fV~l~~~i~Gli~~se 594 (647)
T PRK00087 560 YPVGSIVLGKVVRIAP--FGAFVELEPGVDGLVHISQ 594 (647)
T ss_pred ccCCeEEEEEEEEEEC--CeEEEEECCCCEEEEEhhh
Confidence 3589999999999999 5999999999999998866
No 95
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=64.87 E-value=36 Score=31.87 Aligned_cols=54 Identities=28% Similarity=0.427 Sum_probs=36.6
Q ss_pred eeeecccC-hh-HHHHHHH----HHHhcC---CCC--eeEEEeecCCCCCHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKIT-GV-ERTRLKV----IAKTLQ---PEG--FGLTIRTVAAGHSLEELQKDLEGLLSTW 386 (664)
Q Consensus 333 IgVSrKI~-de-eR~rLk~----i~~~l~---~eg--~GvIIRTaA~~aseeeL~~El~~L~~~W 386 (664)
+.||||.. .. .|+++|. ++..+. +.+ +=+|.|..+.+++..+|.+|+..|....
T Consensus 51 ~~VsKK~~~~AV~RNriKR~lRe~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k~ 115 (122)
T PRK03031 51 ISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQA 115 (122)
T ss_pred EEEecccccchhhhhHHHHHHHHHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHHc
Confidence 56799964 34 5665554 443322 233 3467788999999999999998877653
No 96
>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=59.89 E-value=11 Score=33.56 Aligned_cols=35 Identities=23% Similarity=0.340 Sum_probs=30.7
Q ss_pred ccCCEEEEEEeeecCCcceEEecc--------cCCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNI--------GNSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDI--------G~~k~aFL~~~d~ 147 (664)
.+|+|=.|+|++|-+.+ |+||| ...-.|+||+.+.
T Consensus 5 ~~GDiVig~V~~v~~~~--~~v~I~~v~~~~l~~~~~g~l~~~dv 47 (92)
T cd05791 5 KVGSIVIARVTRINPRF--AKVDILCVGGRPLKESFRGVIRKEDI 47 (92)
T ss_pred CCCCEEEEEEEEEcCCE--EEEEEEEecCeecCCCcccEEEHHHc
Confidence 58999999999997554 99999 8888899998885
No 97
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=58.13 E-value=24 Score=39.48 Aligned_cols=33 Identities=12% Similarity=0.358 Sum_probs=26.3
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeec
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDI 144 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~ 144 (664)
..+|+|..|.|.++..+ +..|||+| +-.|||+-
T Consensus 136 ~~~Geiv~g~V~r~~~~-~~i~vdlg-~~ea~LP~ 168 (374)
T PRK12328 136 KKVGKIVFGTVVRVDNE-ENTFIEID-EIRAVLPM 168 (374)
T ss_pred HhcCcEEEEEEEEEecC-CCEEEEcC-CeEEEeCH
Confidence 36899999999999864 35899998 56788843
No 98
>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=57.51 E-value=20 Score=42.91 Aligned_cols=35 Identities=23% Similarity=0.410 Sum_probs=31.0
Q ss_pred ccCCEEEEEEeeecCCcceEEecccC-Ccceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGN-SRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~-~k~aFL~~~d~ 147 (664)
.+|.+|.|+|++|.+ -++||++.. +..||+|+.+.
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 689999987 79999998763
No 99
>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=51.83 E-value=7.7 Score=39.34 Aligned_cols=17 Identities=35% Similarity=0.786 Sum_probs=13.4
Q ss_pred ccCCCCCceeEEechhh
Q 006020 608 EPCTCCQGTGRVEALET 624 (664)
Q Consensus 608 ~~Cp~C~G~G~V~s~et 624 (664)
.+|+.|+|+|+|.....
T Consensus 116 ~~C~~C~G~G~v~~~~~ 132 (186)
T TIGR02642 116 RECDTCAGTGRFRPTVE 132 (186)
T ss_pred CCCCCCCCccEEeeeEE
Confidence 68999999998877554
No 100
>PRK11642 exoribonuclease R; Provisional
Probab=50.65 E-value=34 Score=41.91 Aligned_cols=35 Identities=23% Similarity=0.441 Sum_probs=30.7
Q ss_pred ccCCEEEEEEeeecCCcceEEecccCC-cceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGNS-RPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~~-k~aFL~~~d~ 147 (664)
.+|.+|.|+|+.|.+. ++||.+... -.||+|+.+.
T Consensus 642 ~iGe~f~G~Is~V~~f--GifVeL~~~~vEGlV~vs~L 677 (813)
T PRK11642 642 QVGNVFKGVISSVTGF--GFFVRLDDLFIDGLVHVSSL 677 (813)
T ss_pred cCCcEEEEEEEEeecC--ceEEEECCCCeeeeEEEeec
Confidence 4899999999999884 999999864 9999998764
No 101
>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=48.87 E-value=19 Score=32.02 Aligned_cols=30 Identities=40% Similarity=0.537 Sum_probs=26.5
Q ss_pred EEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 115 IY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
+|.|+|+.|.+ .++||+++ .-.||+++.+.
T Consensus 2 vv~g~V~~i~~--~GifV~l~-~v~G~v~~~~l 31 (99)
T cd04460 2 VVEGEVVEVVD--FGAFVRIG-PVDGLLHISQI 31 (99)
T ss_pred EEEEEEEEEEe--ccEEEEEc-CeEEEEEEEEc
Confidence 79999999988 59999998 48999998875
No 102
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=46.27 E-value=68 Score=32.08 Aligned_cols=37 Identities=19% Similarity=0.170 Sum_probs=31.3
Q ss_pred CCcccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 108 SNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 108 ~~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
=+...|-|--|+|+++.+ .++||.+|.=. +|+|....
T Consensus 77 FrPf~gEVv~g~V~~v~~--~G~~v~~Gp~~-ifI~~~~l 113 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNK--LGFFAQAGPLK-AFVSRSAI 113 (176)
T ss_pred EecCCCCEEEEEEEEEec--ceEEEEeeCeE-EEEcHHHC
Confidence 345689999999999999 59999999888 99977653
No 103
>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=44.39 E-value=45 Score=39.76 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=30.9
Q ss_pred ccCCEEEEEEeeecCCcceEEeccc-CCcceeeecccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIG-NSRPSLMDIKHY 147 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG-~~k~aFL~~~d~ 147 (664)
.+|.+|-|+|+.|.+ .++||++. .+-.||+|+.+.
T Consensus 571 ~iG~~~~g~I~~v~~--~GifV~L~~~~veGlV~~s~l 606 (654)
T TIGR00358 571 KVGTEFSGEISSVTR--FGMFVRLDDNGIDGLIHISTL 606 (654)
T ss_pred CCCcEEEEEEEeEEc--CcEEEEecCCceEEEEEeEeC
Confidence 469999999999998 46999998 789999999864
No 104
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=44.13 E-value=45 Score=35.69 Aligned_cols=35 Identities=17% Similarity=0.432 Sum_probs=27.2
Q ss_pred cccCCEEEEEEeeecCCcceEEeccc--CCcceeeeccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIG--NSRPSLMDIKH 146 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG--~~k~aFL~~~d 146 (664)
.-.|.|-.|+|++|... +|||..- .++.||+|+++
T Consensus 9 PeeGEiVv~tV~~V~~~--GAyv~L~EY~g~Eg~ihiSE 45 (269)
T COG1093 9 PEEGEIVVGTVKQVADY--GAYVELDEYPGKEGFIHISE 45 (269)
T ss_pred CCCCcEEEEEEEEeecc--ccEEEeeccCCeeeeEEHHH
Confidence 34799999999999874 7888764 35778887765
No 105
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=43.13 E-value=19 Score=34.52 Aligned_cols=35 Identities=20% Similarity=0.320 Sum_probs=30.8
Q ss_pred cCCCCCceeEEechhhHHHHHHHHHHHHHhhcCCC
Q 006020 609 PCTCCQGTGRVEALETSFSKIEQEISRLLVSKSYN 643 (664)
Q Consensus 609 ~Cp~C~G~G~V~s~et~~~~i~rei~~~~~~~~~~ 643 (664)
-||+|+|.-.-.|...++..++++|++.+.....+
T Consensus 42 RC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd 76 (126)
T TIGR03147 42 RCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSN 76 (126)
T ss_pred CCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCH
Confidence 59999999999999999999999999988666554
No 106
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=42.87 E-value=14 Score=37.52 Aligned_cols=16 Identities=38% Similarity=0.760 Sum_probs=13.8
Q ss_pred cccCCCCCceeEEech
Q 006020 607 SEPCTCCQGTGRVEAL 622 (664)
Q Consensus 607 ~~~Cp~C~G~G~V~s~ 622 (664)
...||.|+|+|.+...
T Consensus 99 ~~~C~~C~G~G~~i~~ 114 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRR 114 (186)
T ss_pred CCcCCCCCCeeEEecC
Confidence 7899999999998653
No 107
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=39.95 E-value=31 Score=34.18 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=30.1
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.++-|+|+++.+ .++||++|. -+|+++..+.
T Consensus 79 p~~gEvv~G~V~~v~~--~GifV~lg~-~~gi~~~~~l 113 (179)
T TIGR00448 79 PELGEIVEGEVIEIVE--FGAFVSLGP-FDGLFHVSQV 113 (179)
T ss_pred ccCCCEEEEEEEEEEe--eEEEEEeCC-ceEEEEcHHh
Confidence 4579999999999999 599999985 7888887764
No 108
>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=39.00 E-value=36 Score=28.15 Aligned_cols=32 Identities=19% Similarity=0.244 Sum_probs=27.2
Q ss_pred CCEEEEEEeeecCCcceEEecccCCcceeeeccc
Q 006020 113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKH 146 (664)
Q Consensus 113 GnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d 146 (664)
|++--|+|++|.+ .+|||++..+-.||++..+
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 5799999667899998765
No 109
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=38.93 E-value=24 Score=33.80 Aligned_cols=36 Identities=11% Similarity=0.255 Sum_probs=31.2
Q ss_pred ccCCCCCceeEEechhhHHHHHHHHHHHHHhhcCCC
Q 006020 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLVSKSYN 643 (664)
Q Consensus 608 ~~Cp~C~G~G~V~s~et~~~~i~rei~~~~~~~~~~ 643 (664)
--||.|+|.-.-.|...++..+.+++++.+.....+
T Consensus 41 LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd 76 (126)
T PRK10144 41 LRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSE 76 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCH
Confidence 359999999999999999999999999988666554
No 110
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=37.63 E-value=30 Score=37.63 Aligned_cols=32 Identities=19% Similarity=0.558 Sum_probs=21.1
Q ss_pred ccccCCCCCceeEEechhhHHHHHHHHHHHHHhhc
Q 006020 606 ISEPCTCCQGTGRVEALETSFSKIEQEISRLLVSK 640 (664)
Q Consensus 606 l~~~Cp~C~G~G~V~s~et~~~~i~rei~~~~~~~ 640 (664)
....|+||+|+|..+.. ...|.+..+...+.+
T Consensus 90 ~~~~C~~CeGrgi~l~~---f~dll~kf~eiaK~R 121 (354)
T COG1568 90 YDYTCECCEGRGISLQA---FKDLLEKFREIAKDR 121 (354)
T ss_pred ccccccCcCCccccchh---HHHHHHHHHHHHhcC
Confidence 45679999999997776 445555554443333
No 111
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=34.25 E-value=43 Score=33.27 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=29.9
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecccc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHY 147 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~d~ 147 (664)
..+|.++.|+|+++.+ .++||++|. -+||++..+.
T Consensus 79 P~~GEVv~g~V~~v~~--~Gi~V~lg~-~~g~v~~~~l 113 (187)
T PRK08563 79 PELQEVVEGEVVEVVE--FGAFVRIGP-VDGLLHISQI 113 (187)
T ss_pred ccCCCEEEEEEEEEEc--cEEEEEEeC-ceEEEEcHHc
Confidence 4579999999999987 699999994 8899887653
No 112
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=33.86 E-value=15 Score=40.91 Aligned_cols=53 Identities=23% Similarity=0.362 Sum_probs=34.2
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCC-CeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPE-GFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHA 393 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~e-g~GvIIRTaA~~aseeeL~~El~~L~~~W~~I~~~a 393 (664)
+||||--+.+| ++..|+++..+.|+ +-| ....++--+|+...++...+=++++
T Consensus 10 LGV~k~As~~EIKkAYRkLA~kyHPD~n~g--------~~~AeeKFKEI~eAYEVLsD~eKRa 64 (371)
T COG0484 10 LGVSKDASEEEIKKAYRKLAKKYHPDRNPG--------DKEAEEKFKEINEAYEVLSDPEKRA 64 (371)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHhCCCCCCC--------CHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 68999998776 88999999999885 333 3344555555555554444444433
No 113
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=32.93 E-value=1.1e+02 Score=35.29 Aligned_cols=32 Identities=9% Similarity=0.101 Sum_probs=24.8
Q ss_pred cccCCEEEEEEeeecCCcceEEecccC--C---cceeee
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGN--S---RPSLMD 143 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~--~---k~aFL~ 143 (664)
..+|.|-.|+|.++..+ ..+||+|. + -.|+|+
T Consensus 150 ~~~GeIV~G~V~r~e~~--~viv~l~~~~g~~~~EaiLP 186 (449)
T PRK12329 150 DLEDTVLTARVLRFERQ--SVIMAVSSGFGQPEVEAELP 186 (449)
T ss_pred HhcCcEEEEEEEEEcCC--CEEEEecccCCCcceEEEec
Confidence 36899999999999886 69999842 3 456664
No 114
>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=32.22 E-value=68 Score=28.68 Aligned_cols=34 Identities=21% Similarity=0.181 Sum_probs=29.8
Q ss_pred cccCCEEEEEEeeecCCcceEEecccCCcceeeecc
Q 006020 110 VQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (664)
Q Consensus 110 ~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~ 145 (664)
..+|++=+|+|+.+. -..-+||||..-+|+|++.
T Consensus 4 P~~gD~VIG~V~~~~--~~~~~VdI~s~~~a~L~~~ 37 (86)
T cd05790 4 PAKGDHVIGIVVAKA--GDFFKVDIGGSEPASLSYL 37 (86)
T ss_pred CCCCCEEEEEEEEEc--CCeEEEEcCCCcceEechH
Confidence 458999999999995 4889999999999999763
No 115
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=30.96 E-value=29 Score=38.83 Aligned_cols=22 Identities=27% Similarity=0.368 Sum_probs=19.1
Q ss_pred cCCCCCHHHHHHHHHHHHHHHH
Q 006020 366 VAAGHSLEELQKDLEGLLSTWK 387 (664)
Q Consensus 366 aA~~aseeeL~~El~~L~~~W~ 387 (664)
...+|+++||.+-+..|..+|.
T Consensus 12 V~k~As~~EIKkAYRkLA~kyH 33 (371)
T COG0484 12 VSKDASEEEIKKAYRKLAKKYH 33 (371)
T ss_pred CCCCCCHHHHHHHHHHHHHHhC
Confidence 4568999999999999999884
No 116
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=30.82 E-value=21 Score=34.88 Aligned_cols=36 Identities=17% Similarity=0.338 Sum_probs=24.4
Q ss_pred ccCCCCCceeEEechhhHHHHHHHHHHHHHhhcCCC
Q 006020 608 EPCTCCQGTGRVEALETSFSKIEQEISRLLVSKSYN 643 (664)
Q Consensus 608 ~~Cp~C~G~G~V~s~et~~~~i~rei~~~~~~~~~~ 643 (664)
-.||+|.|.-.-.|...++..++++|++.++....+
T Consensus 41 LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~ 76 (148)
T PF03918_consen 41 LRCPVCQNQSIADSNAPIARDMRREIREMLAEGKSD 76 (148)
T ss_dssp CE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT--H
T ss_pred ccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcCCCH
Confidence 359999997666677789999999999988665543
No 117
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=30.29 E-value=27 Score=34.42 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=20.8
Q ss_pred hHhCCceecCCCcEEEEecccceE
Q 006020 481 NMLSKRVPLPNGGSLVIEQTEALV 504 (664)
Q Consensus 481 ~~l~rrV~L~sGGyLVIE~TEALt 504 (664)
.-+.+.||++-|+++||+++|-+-
T Consensus 53 ~KfRksiWiRRg~FvvVdpiee~~ 76 (167)
T KOG2925|consen 53 AKFRKSIWIRRGSFVVVDPIEEEK 76 (167)
T ss_pred HhhhhceEEeeCCEEEEccccccc
Confidence 346788999999999999999876
No 118
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=28.37 E-value=39 Score=33.33 Aligned_cols=35 Identities=14% Similarity=0.304 Sum_probs=31.7
Q ss_pred cCCCCCceeEEechhhHHHHHHHHHHHHHhhcCCC
Q 006020 609 PCTCCQGTGRVEALETSFSKIEQEISRLLVSKSYN 643 (664)
Q Consensus 609 ~Cp~C~G~G~V~s~et~~~~i~rei~~~~~~~~~~ 643 (664)
-||.|++.-...|-..++..+..++..++...+.+
T Consensus 46 RCp~CQNqsIadSnA~IA~DlR~~V~e~l~eGkS~ 80 (153)
T COG3088 46 RCPQCQNQSIADSNAPIARDLRHQVYELLQEGKSD 80 (153)
T ss_pred CCCcCCCCChhhhccHHHHHHHHHHHHHHHcCCcH
Confidence 59999999999999999999999999998777655
No 119
>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=26.92 E-value=1.5e+02 Score=28.27 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=36.3
Q ss_pred hcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhcCCC-CcEEeccCCCeeEEEeec
Q 006020 541 RLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRS-MVKVSELSRHGLMEITRK 596 (664)
Q Consensus 541 RLRnIgGIIVIDFIdM~~~~~r~~V~~~Lk~~lk~D~~-kt~V~giT~LGLvEiTRk 596 (664)
.|..-+|+|+|||=++. .+ + ++.+++.+..|+- -.-+++.|.-||==+.|=
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 45778999999998887 32 2 4677778888875 335667777777666654
No 120
>PHA02945 interferon resistance protein; Provisional
Probab=26.52 E-value=1.8e+02 Score=26.34 Aligned_cols=33 Identities=12% Similarity=0.173 Sum_probs=25.2
Q ss_pred ccCCEEEEEEeeecCCcceEEecccC--Ccceeeeccc
Q 006020 111 QCDSVYLGVVTKLVPNMGGAFVNIGN--SRPSLMDIKH 146 (664)
Q Consensus 111 ~vGnIY~GrV~kV~Pgm~AAFVDIG~--~k~aFL~~~d 146 (664)
-.|.|-+|+|+. .=.+|||+.-. ++.||+|+..
T Consensus 10 ~~GelvigtV~~---~d~ga~v~L~EY~g~eg~i~~se 44 (88)
T PHA02945 10 NVGDVLKGKVYE---NGYALYIDLFDYPHSEAILAESV 44 (88)
T ss_pred CCCcEEEEEEEe---cCceEEEEecccCCcEEEEEeeh
Confidence 378999999999 44688888743 6778887763
No 121
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.51 E-value=47 Score=26.88 Aligned_cols=15 Identities=60% Similarity=1.012 Sum_probs=13.0
Q ss_pred ceecCCCcEEEEecc
Q 006020 486 RVPLPNGGSLVIEQT 500 (664)
Q Consensus 486 rV~L~sGGyLVIE~T 500 (664)
||+|.+||.||+|-+
T Consensus 22 RvPleGGGRLVvEl~ 36 (51)
T PF11314_consen 22 RVPLEGGGRLVVELN 36 (51)
T ss_pred EEecCCCcEEEEEeC
Confidence 789999999999843
No 122
>PRK14296 chaperone protein DnaJ; Provisional
Probab=26.50 E-value=41 Score=37.39 Aligned_cols=26 Identities=31% Similarity=0.519 Sum_probs=20.0
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
+|||+..+.++ |+..|+++..+.|+-
T Consensus 10 Lgv~~~a~~~eik~ayrkla~~~HPD~ 36 (372)
T PRK14296 10 LGVSKTASEQEIRQAYRKLAKQYHPDL 36 (372)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCcCC
Confidence 57888877665 888888888888763
No 123
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=26.46 E-value=28 Score=26.48 Aligned_cols=12 Identities=42% Similarity=1.104 Sum_probs=10.4
Q ss_pred cccCCCCCceeE
Q 006020 607 SEPCTCCQGTGR 618 (664)
Q Consensus 607 ~~~Cp~C~G~G~ 618 (664)
..|||.|.|+.+
T Consensus 3 ~~pCP~CGG~Dr 14 (37)
T smart00778 3 HGPCPNCGGSDR 14 (37)
T ss_pred ccCCCCCCCccc
Confidence 469999999887
No 124
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=25.67 E-value=44 Score=29.46 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=19.2
Q ss_pred HHhHhCCceecCCCcEEEEeccc
Q 006020 479 INNMLSKRVPLPNGGSLVIEQTE 501 (664)
Q Consensus 479 I~~~l~rrV~L~sGGyLVIE~TE 501 (664)
|-.=|.++||.+-|+|+++++.+
T Consensus 29 iP~KfRk~iWIkrGd~VlV~p~~ 51 (78)
T cd05792 29 MPTKFRKNIWIKRGDFVLVEPIE 51 (78)
T ss_pred echhhcccEEEEeCCEEEEEecc
Confidence 34557889999999999998866
No 125
>COG3585 MopI Molybdopterin-binding protein [Coenzyme metabolism]
Probab=25.62 E-value=44 Score=28.73 Aligned_cols=26 Identities=19% Similarity=0.139 Sum_probs=21.5
Q ss_pred cCCEEEEEEeeecCCcceEEecccCC
Q 006020 112 CDSVYLGVVTKLVPNMGGAFVNIGNS 137 (664)
Q Consensus 112 vGnIY~GrV~kV~Pgm~AAFVDIG~~ 137 (664)
.-|+++|+|+.|++|+=-+=|+|-..
T Consensus 5 aRN~lKG~Vk~iv~G~Vnsev~iei~ 30 (69)
T COG3585 5 ARNQLKGKVKEIVKGSVNSEVTIEIG 30 (69)
T ss_pred hhheeccEEEEEEEcccceEEEEEeC
Confidence 45899999999999998887776444
No 126
>PRK14298 chaperone protein DnaJ; Provisional
Probab=24.72 E-value=40 Score=37.52 Aligned_cols=26 Identities=15% Similarity=0.415 Sum_probs=20.2
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
++|++..+.++ ++..++++..+.|+.
T Consensus 11 Lgv~~~a~~~eik~ayr~la~~~HPD~ 37 (377)
T PRK14298 11 LGLSKDASVEDIKKAYRKLAMKYHPDK 37 (377)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHhCccc
Confidence 57888777665 788888888888864
No 127
>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=24.26 E-value=1.4e+02 Score=25.30 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhcccCCCcEEEEcCCCCChhhHHHHHHHHHHHHhc
Q 006020 531 AAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVER 575 (664)
Q Consensus 531 EAA~EIARQLRLRnIgGIIVIDFIdM~~~~~r~~V~~~Lk~~lk~ 575 (664)
+-|.+|+.+||=. -++++||-+|..+. .+++++.|..+...
T Consensus 10 ~D~~~i~~~l~~g---~~Vivnl~~l~~~~-~~Ri~Dfl~G~~~a 50 (73)
T PF04472_consen 10 EDAREIVDALREG---KIVIVNLENLDDEE-AQRILDFLSGAVYA 50 (73)
T ss_dssp GGHHHHHHHHHTT-----EEEE-TTS-HHH-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcC---CEEEEECCCCCHHH-HHHHHHHHhchhee
Confidence 4578899999876 46999999998776 66788888877654
No 128
>PRK06921 hypothetical protein; Provisional
Probab=23.74 E-value=40 Score=35.60 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=11.4
Q ss_pred ccCCCCCceeEEe
Q 006020 608 EPCTCCQGTGRVE 620 (664)
Q Consensus 608 ~~Cp~C~G~G~V~ 620 (664)
..||.|++||.|.
T Consensus 33 ~~Cp~C~dtG~i~ 45 (266)
T PRK06921 33 YDCPKCKDRGIII 45 (266)
T ss_pred CCCCCCCCCEEEE
Confidence 4599999999994
No 129
>PRK14290 chaperone protein DnaJ; Provisional
Probab=23.21 E-value=61 Score=35.82 Aligned_cols=26 Identities=23% Similarity=0.503 Sum_probs=20.9
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
++|++..+.++ |++.++++..+.|+.
T Consensus 9 Lgv~~~a~~~eik~ayr~la~~~HPD~ 35 (365)
T PRK14290 9 LGVDRNASQEDIKKAFRELAKKWHPDL 35 (365)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCcCC
Confidence 57888877765 889999999888873
No 130
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.08 E-value=40 Score=27.04 Aligned_cols=11 Identities=36% Similarity=1.072 Sum_probs=9.8
Q ss_pred ccCCCCCceeE
Q 006020 608 EPCTCCQGTGR 618 (664)
Q Consensus 608 ~~Cp~C~G~G~ 618 (664)
.|||.|+|+.+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 58999999888
No 131
>PRK14277 chaperone protein DnaJ; Provisional
Probab=22.43 E-value=53 Score=36.60 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=21.0
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
++|++..+.++ |+..++++..+.|+.
T Consensus 11 Lgv~~~a~~~eik~ayr~la~~~HPD~ 37 (386)
T PRK14277 11 LGVDRNATEEEIKKAYRRLAKKYHPDL 37 (386)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCCCc
Confidence 67888887765 889999998888863
No 132
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.82 E-value=24 Score=27.27 Aligned_cols=13 Identities=38% Similarity=1.004 Sum_probs=7.4
Q ss_pred cccCCCCCceeEE
Q 006020 607 SEPCTCCQGTGRV 619 (664)
Q Consensus 607 ~~~Cp~C~G~G~V 619 (664)
..|||.|.|+.+-
T Consensus 3 h~pCP~CGG~DrF 15 (40)
T PF08273_consen 3 HGPCPICGGKDRF 15 (40)
T ss_dssp EE--TTTT-TTTE
T ss_pred CCCCCCCcCcccc
Confidence 3689999998763
No 133
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=21.71 E-value=63 Score=30.30 Aligned_cols=16 Identities=25% Similarity=0.573 Sum_probs=11.7
Q ss_pred hhccccCCCCCceeEE
Q 006020 604 FMISEPCTCCQGTGRV 619 (664)
Q Consensus 604 ~~l~~~Cp~C~G~G~V 619 (664)
...+.+|+.|+|+|++
T Consensus 72 ~q~~~~C~~C~G~Gk~ 87 (111)
T PLN03165 72 EKEVSKCINCDGAGSL 87 (111)
T ss_pred EEEEEECCCCCCccee
Confidence 3457788888888863
No 134
>PF08508 DUF1746: Fungal domain of unknown function (DUF1746); InterPro: IPR013715 This is a fungal domain of unknown function.
Probab=21.49 E-value=63 Score=30.52 Aligned_cols=20 Identities=25% Similarity=0.600 Sum_probs=15.9
Q ss_pred CCcEEEEcCCCCChhhHHHHH
Q 006020 546 GGIIVVDFIDMADDSNKRLVY 566 (664)
Q Consensus 546 gGIIVIDFIdM~~~~~r~~V~ 566 (664)
|| ++||||..+-+..|-+++
T Consensus 84 GG-l~IdFIGq~~p~srl~ll 103 (116)
T PF08508_consen 84 GG-LIIDFIGQKPPPSRLELL 103 (116)
T ss_pred Cc-eEEEeccCCCCcchHHHH
Confidence 55 899999999887776654
No 135
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.38 E-value=1.2e+02 Score=37.81 Aligned_cols=35 Identities=20% Similarity=0.367 Sum_probs=27.6
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCcEEe
Q 006020 548 IIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVS 583 (664)
Q Consensus 548 IIVIDFIdM~~~~~r~~V~~~Lk~~lk~D~~kt~V~ 583 (664)
-||||-+-.+. ..+..+.+.+..+|+.-...+.+.
T Consensus 199 ~vvvdr~~~~~-~~~~r~~~s~~~a~~~g~g~~~~~ 233 (924)
T TIGR00630 199 DVVIDRLKVKN-ENRSRLAESVETALRLGDGLLEVE 233 (924)
T ss_pred EEEEEEEEeCc-chHHHHHHHHHHHHHhCCCeEEEE
Confidence 48999877764 578899999999999877666553
No 136
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=20.99 E-value=7.7e+02 Score=27.16 Aligned_cols=150 Identities=15% Similarity=0.140 Sum_probs=83.7
Q ss_pred ceeeeccCCchhhhhhhhcCCCccEEEEcChhHHHHHHHHHHh-hCCC--ccCceee--ccC------CcCcccccCHHH
Q 006020 409 PILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQD-IAPD--LCDRVEL--YDK------RIPLFDKFNIEE 477 (664)
Q Consensus 409 P~lLy~~~~~~~~~lrD~~~~~v~~IvvD~~~~y~~i~~~l~~-~~p~--~~~~v~l--y~~------~~pLF~~y~Ie~ 477 (664)
-.++|..+.....-|+..+...+ .|++|+...++++.+.... ..+. ..-||.. ..+ ......+||+..
T Consensus 72 ~~Ii~~gp~K~~~~L~~ai~~gv-~i~iDS~~El~~i~~~a~~~~~~~~~v~lRvnp~~~~~~~~~~~~~~~~skFG~~~ 150 (379)
T cd06836 72 ERIVFDSPAKTRAELREALELGV-AINIDNFQELERIDALVAEFKEASSRIGLRVNPQVGAGKIGALSTATATSKFGVAL 150 (379)
T ss_pred hhEEEeCCCCCHHHHHHHHHCCC-EEEECCHHHHHHHHHHHHHhcCCCceEEEEECCCCCCCCccccccCCCCCCCCcCc
Confidence 35888887777777888788888 7999999999998887754 2222 2222221 100 112457888665
Q ss_pred H---HHhHhCCceecCCCcEEEEecccceEEEEecCCCCcCCCCCCHHH--HHHHHHHHHHHHHHH-----HHhcccCCC
Q 006020 478 E---INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEK--AILDVNLAAAKQIAR-----ELRLRDIGG 547 (664)
Q Consensus 478 ~---I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~~~~~~~e~--t~l~tNlEAA~EIAR-----QLRLRnIgG 547 (664)
+ +..++... ..+..| .-|-...|... .+.+. .+++.-+..|.++.+ +++.-||||
T Consensus 151 ~~~~~~~~~~~~---~~~~~l--------~GlH~H~GS~~----~~~~~~~~~~~~~~~l~~~l~~~~g~~~~~~IDiGG 215 (379)
T cd06836 151 EDGARDEIIDAF---ARRPWL--------NGLHVHVGSQG----CELSLLAEGIRRVVDLAEEINRRVGRRQITRIDIGG 215 (379)
T ss_pred chhHHHHHHHHH---hcCCCe--------EEEEEecccCC----CCHHHHHHHHHHHHHHHHHHHHHhCCCCCcEEEeCC
Confidence 4 55555421 111112 25566666421 12221 112223333455543 467789999
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHh
Q 006020 548 IIVVDFIDMADDSNKRLVYEEVKKAVE 574 (664)
Q Consensus 548 IIVIDFIdM~~~~~r~~V~~~Lk~~lk 574 (664)
=.-|++-+...+-+-++..+.+.+.+.
T Consensus 216 Gf~v~y~~~~~~~~~~~~~~~i~~~l~ 242 (379)
T cd06836 216 GLPVNFESEDITPTFADYAAALKAAVP 242 (379)
T ss_pred ccccCCCCCCCCCCHHHHHHHHHHHHH
Confidence 888888665433344455555555554
No 137
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=20.86 E-value=1.4e+02 Score=38.89 Aligned_cols=78 Identities=17% Similarity=0.261 Sum_probs=59.4
Q ss_pred cccccCCceEEEEEecCCCeEEEEEEECCEEeEEEEeeCCC--CcccCCEEEEEEeeecCCcceEEecccCCcceeeecc
Q 006020 68 ISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKS--NVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIK 145 (664)
Q Consensus 68 ~~~~~~~~~~ilIn~~~~~e~RvAvlEdg~L~El~iE~~~~--~~~vGnIY~GrV~kV~Pgm~AAFVDIG~~k~aFL~~~ 145 (664)
+-..... +.+.+|.. ..|+|+.-.+.|++...+-+.. +.+-|.+|+|.|.++-+ ++|||-+=.+-.||++..
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 3333344 77888874 4699999999999996553332 23459999999999998 699999999999999777
Q ss_pred ccCCCC
Q 006020 146 HYREPF 151 (664)
Q Consensus 146 d~~~~~ 151 (664)
.+...|
T Consensus 631 ~~sd~~ 636 (1710)
T KOG1070|consen 631 EMSDDF 636 (1710)
T ss_pred hhhhhh
Confidence 654433
No 138
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=20.77 E-value=1.3e+02 Score=37.76 Aligned_cols=34 Identities=18% Similarity=0.303 Sum_probs=25.0
Q ss_pred cEEEEcCCCCChhhHHHHHHHHHHHHhcCCCCcEE
Q 006020 548 IIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKV 582 (664)
Q Consensus 548 IIVIDFIdM~~~~~r~~V~~~Lk~~lk~D~~kt~V 582 (664)
-||||=+-... .++..+.+.+..+++.=...+.+
T Consensus 203 ~vvvdr~~~~~-~~~~r~~~s~~~a~~~g~g~~~~ 236 (943)
T PRK00349 203 EVVVDRLVVKE-DIRQRLADSIETALKLSDGLVVV 236 (943)
T ss_pred EEEEEEEEeCc-chHHHHHHHHHHHHHhcCceEEE
Confidence 48888777663 47788889999999875555544
No 139
>PF07013 DUF1314: Protein of unknown function (DUF1314); InterPro: IPR010741 This family consists of several alphaherpesvirus proteins of around 200 residues in length. They belong to the varicellovirus ORF2 family and their function is unknown.
Probab=20.29 E-value=76 Score=31.90 Aligned_cols=33 Identities=21% Similarity=0.363 Sum_probs=25.8
Q ss_pred HHhHhCCceecCCCcEEEEecccceEEEEecCCCCcC
Q 006020 479 INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMF 515 (664)
Q Consensus 479 I~~~l~rrV~L~sGGyLVIE~TEALtvIDVNSGk~~~ 515 (664)
++.+-.|.|.||+||++.|-.+-.-+ |+|++.+
T Consensus 5 l~~LaGR~iDLPgG~el~I~~~~g~~----~~~~f~~ 37 (177)
T PF07013_consen 5 LRSLAGRTIDLPGGDELRISANTGRP----NTGKFVR 37 (177)
T ss_pred hhhhcCcceecCCCCeEEEecCCCCc----eEEEEec
Confidence 56778899999999999998765555 6777543
No 140
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=20.20 E-value=59 Score=36.91 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=19.4
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
+|||+--+.++ |+..|+++..+.|+.
T Consensus 34 LGV~~~As~~eIKkAYrkla~k~HPDk 60 (421)
T PTZ00037 34 LNLSKDCTTSEIKKAYRKLAIKHHPDK 60 (421)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCCCC
Confidence 56777776665 788888888888764
No 141
>PRK14282 chaperone protein DnaJ; Provisional
Probab=20.13 E-value=67 Score=35.57 Aligned_cols=26 Identities=35% Similarity=0.537 Sum_probs=21.2
Q ss_pred eeeecccChhH-HHHHHHHHHhcCCCC
Q 006020 333 IGVSRKITGVE-RTRLKVIAKTLQPEG 358 (664)
Q Consensus 333 IgVSrKI~dee-R~rLk~i~~~l~~eg 358 (664)
++|++..+.++ |+..++++..+.|+.
T Consensus 10 lgv~~~a~~~eik~ayr~la~~~HPD~ 36 (369)
T PRK14282 10 LGVSRNATQEEIKRAYKRLVKEWHPDR 36 (369)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHCCCC
Confidence 67888888765 889999999888864
Done!